Merge pull request #12774 from nsoranzo/pyupgrade_fixes

New pyupgrade cleanups

contrib/galaxy_config_merger.py

@@ -69,7 +69,7 @@ def main():
                         config_sample.set(section, name, value)
                 else:
                     if not config_sample.get(section, name) == value:
-                        logging.info("- diff - section [{}] option '{}' has different value ('{}':'{}'). It will be modified.".format(section, name, config_sample.get(section, name), value))
+                        logging.info(f"- diff - section [{section}] option '{name}' has different value ('{config_sample.get(section, name)}':'{value}'). It will be modified.")
                         config_sample.set(section, name, value)
     logging.info("---------- DIFFERENCE ANALYSIS END   ----------")
 

lib/galaxy/config/__init__.py

@@ -975,7 +975,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
                 log.warning("Sanitize log file explicitly specified as '%s' but does not exist, continuing with no tools allowlisted.", self.sanitize_allowlist_file)
         else:
             with open(self.sanitize_allowlist_file) as f:
-                self.sanitize_allowlist = sorted([line.strip() for line in f.readlines() if not line.startswith('#')])
+                self.sanitize_allowlist = sorted(line.strip() for line in f.readlines() if not line.startswith('#'))
 
     def ensure_tempdir(self):
         self._ensure_directory(self.new_file_path)

lib/galaxy/containers/docker_model.py

@@ -44,7 +44,7 @@ class DockerAttributeContainer:
         return not self.__eq__(other)
 
     def __hash__(self):
-        return hash(tuple(sorted([repr(x) for x in self._members])))
+        return hash(tuple(sorted(repr(x) for x in self._members)))
 
     def __str__(self):
         return ', '.join(str(x) for x in self._members) or 'None'

lib/galaxy/datatypes/binary.py

@@ -1600,7 +1600,7 @@ class H5MLM(H5):
 
         repr_ = self.get_repr(dataset.file_name)
 
-        return "<pre>{}</pre><pre>{}</pre>".format(repr_, rval)
+        return f"<pre>{repr_}</pre><pre>{rval}</pre>"
 
 
 class HexrdMaterials(H5):

lib/galaxy/datatypes/images.py

@@ -359,7 +359,7 @@ class Gmaj(data.Data):
                     "nobutton": "false",
                     "urlpause": "100",
                     "debug": "false",
-                    "posturl": "history_add_to?%s" % "&".join("{}={}".format(x[0], quote_plus(str(x[1]))) for x in [('copy_access_from', dataset.id), ('history_id', dataset.history_id), ('ext', 'maf'), ('name', f'GMAJ Output on data {dataset.hid}'), ('info', 'Added by GMAJ'), ('dbkey', dataset.dbkey)])
+                    "posturl": "history_add_to?%s" % "&".join(f"{x[0]}={quote_plus(str(x[1]))}" for x in [('copy_access_from', dataset.id), ('history_id', dataset.history_id), ('ext', 'maf'), ('name', f'GMAJ Output on data {dataset.hid}'), ('info', 'Added by GMAJ'), ('dbkey', dataset.dbkey)])
                 }
                 class_name = "edu.psu.bx.gmaj.MajApplet.class"
                 archive = "/static/gmaj/gmaj.jar"

lib/galaxy/datatypes/tabular.py

@@ -103,7 +103,7 @@ class TabularData(data.Text):
             else:
                 trans.response.set_content_type("text/html")
                 return trans.stream_template_mako("/dataset/large_file.mako",
-                                                  truncated_data=open(dataset.file_name, mode='r').read(max_peek_size),
+                                                  truncated_data=open(dataset.file_name).read(max_peek_size),
                                                   data=dataset)
         else:
             column_names = 'null'

lib/galaxy/files/__init__.py

@@ -250,13 +250,13 @@ class ProvidesUserFileSourcesUserContext:
     def role_names(self) -> Set[str]:
         """The set of role names of this user."""
         user = self.trans.user
-        return set(ura.role.name for ura in user.roles) if user else set()
+        return {ura.role.name for ura in user.roles} if user else set()
 
     @property
     def group_names(self) -> Set[str]:
         """The set of group names to which this user belongs."""
         user = self.trans.user
-        return set(ugr.group.name for ugr in user.groups) if user else set()
+        return {ugr.group.name for ugr in user.groups} if user else set()
 
     @property
     def is_admin(self):

lib/galaxy/jobs/__init__.py

@@ -539,12 +539,12 @@ class JobConfiguration(ConfiguresHandlers):
                 self.limits.__dict__[limit_type] = types.get(limit_type, str)(limit_value)
 
         if self.limits.walltime is not None:
-            h, m, s = [int(v) for v in self.limits.walltime.split(':')]
+            h, m, s = (int(v) for v in self.limits.walltime.split(':'))
             self.limits.walltime_delta = datetime.timedelta(0, s, 0, 0, m, h)
 
         if "raw" in self.limits.total_walltime:
-            h, m, s = [int(v) for v in
-                       self.limits.total_walltime["raw"].split(':')]
+            h, m, s = (int(v) for v in
+                       self.limits.total_walltime["raw"].split(':'))
             self.limits.total_walltime["delta"] = datetime.timedelta(
                 0, s, 0, 0, m, h
             )

lib/galaxy/jobs/runners/kubernetes.py

@@ -110,7 +110,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             volume_claims = dict(volume.split(":") for volume in self.runner_params['k8s_persistent_volume_claims'].split(','))
         else:
             volume_claims = {}
-        mountable_volumes = list(set([claim_name if "/" not in claim_name else claim_name.split("/")[0] for claim_name in volume_claims]))
+        mountable_volumes = list({claim_name if "/" not in claim_name else claim_name.split("/")[0] for claim_name in volume_claims})
         mountable_volumes = [{'name': claim_name, 'persistentVolumeClaim': {'claimName': claim_name}} for claim_name in mountable_volumes]
         self.runner_params['k8s_mountable_volumes'] = mountable_volumes
         volume_mounts = [{'name': claim_name, 'mountPath': mount_path} for claim_name, mount_path in volume_claims.items()]
@@ -366,7 +366,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
                 }
             },
             "spec": {
-                "ports": [{"name": "job-{}-{}".format(self.__force_label_conformity(ajs.job_wrapper.get_id_tag()), p),
+                "ports": [{"name": f"job-{self.__force_label_conformity(ajs.job_wrapper.get_id_tag())}-{p}",
                            "port": int(p),
                            "protocol": "TCP",
                            "targetPort": int(p)} for p in guest_ports],
@@ -426,7 +426,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             }
         }
         if self.runner_params.get("k8s_interactivetools_use_ssl"):
-            domains = list(set([e["domain"] for e in entry_points]))
+            domains = list({e["domain"] for e in entry_points})
             k8s_spec_template["spec"]["tls"] = [{"hosts": [domain],
                                                  "secretName": re.sub("[^a-z0-9-]", "-", domain)} for domain in domains]
         if self.runner_params.get("k8s_interactivetools_ingress_annotations"):
@@ -809,7 +809,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
 
     def __cleanup_k8s_guest_ports(self, job_wrapper, k8s_job):
         k8s_job_prefix = self.__produce_k8s_job_prefix()
-        k8s_job_name = "{}-{}".format(k8s_job_prefix, self.__force_label_conformity(job_wrapper.get_id_tag()))
+        k8s_job_name = f"{k8s_job_prefix}-{self.__force_label_conformity(job_wrapper.get_id_tag())}"
         log.debug(f'Deleting service/ingress for job with ID {job_wrapper.get_id_tag()}')
         job_failed = (k8s_job.obj['status']['failed'] > 0
                       if 'failed' in k8s_job.obj['status'] else False)

lib/galaxy/jobs/runners/pbs.py

@@ -385,7 +385,7 @@ class PBSJobRunner(AsynchronousJobRunner):
                 pbs_job_state.job_wrapper.change_state(model.Job.states.RUNNING)
             if status.job_state == "R" and status.get('resources_used', False):
                 # resources_used may not be in the status for new jobs
-                h, m, s = [int(i) for i in status.resources_used.walltime.split(':')]
+                h, m, s = (int(i) for i in status.resources_used.walltime.split(':'))
                 runtime = timedelta(0, s, 0, 0, m, h)
                 if pbs_job_state.check_limits(runtime=runtime):
                     self.work_queue.put((self.fail_job, pbs_job_state))

lib/galaxy/jobs/runners/pulsar.py

@@ -376,7 +376,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
             remote_pulsar_app_config = dest_params.get("pulsar_app_config", {}).copy()
             if "pulsar_app_config_path" in dest_params:
                 pulsar_app_config_path = dest_params["pulsar_app_config_path"]
-                with open(pulsar_app_config_path, "r") as fh:
+                with open(pulsar_app_config_path) as fh:
                     remote_pulsar_app_config.update(yaml.safe_load(fh))
             job_directory_files = []
             config_files = job_wrapper.extra_filenames

lib/galaxy/managers/collections.py

@@ -305,7 +305,7 @@ class DatasetCollectionManager:
                 try:
                     self.hda_manager.error_unless_owner(dataset, user=trans.get_user(), current_history=trans.history)
                 except HistoryDatasetAssociationNoHistoryException:
-                    log.info("Cannot delete HistoryDatasetAssociation {}, HistoryDatasetAssociation has no associated History, cannot verify owner".format(dataset.id))
+                    log.info(f"Cannot delete HistoryDatasetAssociation {dataset.id}, HistoryDatasetAssociation has no associated History, cannot verify owner")
                     continue
                 if not dataset.deleted:
                     dataset.deleted = True

lib/galaxy/managers/collections_util.py

@@ -262,7 +262,7 @@ def gen_rank_fuzzy_counts(collection_type, fuzzy_count=None):
         return [None for rt in rank_collection_types]
     else:
         # This is a list...
-        paired_count = sum([1 if rt == "paired" else 0 for rt in rank_collection_types])
+        paired_count = sum(1 if rt == "paired" else 0 for rt in rank_collection_types)
         list_count = len(rank_collection_types) - paired_count
         paired_fuzzy_count_mult = 1 if paired_count == 0 else 2 << (paired_count - 1)
         list_fuzzy_count_mult = math.floor((fuzzy_count * 1.0) / paired_fuzzy_count_mult)

lib/galaxy/managers/genomes.py

@@ -57,7 +57,7 @@ class GenomesManager:
         ext = index_extensions[index_type]
         index_filename = self._get_index_filename(id, tbl_entries, ext, index_type)
         try:
-            with open(index_filename, mode='r') as f:
+            with open(index_filename) as f:
                 return f.read()
         except OSError:
             raise ReferenceDataError(f'Failed to load index file for {id}')

lib/galaxy/managers/remote_files.py

@@ -1,4 +1,3 @@
-
 import hashlib
 import logging
 from operator import itemgetter

lib/galaxy/managers/tool_data.py

@@ -1,4 +1,3 @@
-
 from pathlib import Path
 from typing import (
     Dict,

lib/galaxy/model/__init__.py

@@ -2488,7 +2488,7 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         if optimize:
             self.__add_datasets_optimized(datasets, genome_build=genome_build)
             if quota and self.user:
-                disk_usage = sum([d.get_total_size() for d in datasets if is_hda(d)])
+                disk_usage = sum(d.get_total_size() for d in datasets if is_hda(d))
                 self.user.adjust_total_disk_usage(disk_usage)
             sa_session.add_all(datasets)
             if flush:
@@ -3305,7 +3305,7 @@ class Dataset(StorableObject, Serializable, _HasTable):
         if rel_path is not None:
             if self.object_store.exists(self, extra_dir=rel_path, dir_only=True):
                 for root, _, files in os.walk(self.extra_files_path):
-                    self.total_size += sum([os.path.getsize(os.path.join(root, file)) for file in files if os.path.exists(os.path.join(root, file))])
+                    self.total_size += sum(os.path.getsize(os.path.join(root, file)) for file in files if os.path.exists(os.path.join(root, file)))
         return self.total_size
 
     def has_data(self):

lib/galaxy/model/dataset_collections/structure.py

@@ -119,7 +119,7 @@ class Tree(BaseTree):
         return True
 
     def __len__(self):
-        return sum([len(c[1]) for c in self.children])
+        return sum(len(c[1]) for c in self.children)
 
     def multiply(self, other_structure):
         if other_structure.is_leaf:

lib/galaxy/model/migrate/versions/0173_add_job_id_to_dataset.py

@@ -1,7 +1,6 @@
 """
 Migration script for adding job_id column to dataset table.
 """
-from __future__ import print_function
 
 import logging
 

lib/galaxy/selenium/context.py

@@ -64,7 +64,7 @@ class GalaxySeleniumContextImpl(GalaxySeleniumContext):
 
 def init(config=None, clazz=GalaxySeleniumContextImpl) -> GalaxySeleniumContext:
     if os.path.exists("galaxy_selenium_context.yml"):
-        with open("galaxy_selenium_context.yml", "r") as f:
+        with open("galaxy_selenium_context.yml") as f:
             as_dict = yaml.safe_load(f)
         context = clazz(as_dict)
     else:

lib/galaxy/tool_util/biotools/source.py

@@ -26,7 +26,7 @@ class GitContentBiotoolsMetadataSource(BiotoolsMetadataSource):
         path = os.path.join(self._content_directory, "data", biotools_reference, f"{biotools_reference}.biotools.json")
         if not os.path.exists(path):
             return None
-        with open(path, "r") as f:
+        with open(path) as f:
             content_json = json.load(f)
             return BiotoolsEntry.from_json(content_json)
 

lib/galaxy/tool_util/deps/container_resolvers/mulled.py

@@ -88,7 +88,7 @@ class CacheDirectory(metaclass=ABCMeta):
         contents = os.listdir(self.path)
         sorted_images = version_sorted(contents)
         raw_images = map(lambda name: identifier_to_cached_target(name, self.hash_func), sorted_images)
-        return list([i for i in raw_images if i is not None])
+        return list(i for i in raw_images if i is not None)
 
     @abstractmethod
     def list_cached_mulled_images_from_path(self):

lib/galaxy/tool_util/deps/mulled/mulled_search.py

@@ -217,12 +217,12 @@ def singularity_search(search_string):
 def readable_output(json, organization='biocontainers', channel='bioconda'):
 
     # if json is empty:
-    if sum([len(json[destination][results]) for destination in json for results in json[destination]]) == 0:
+    if sum(len(json[destination][results]) for destination in json for results in json[destination]) == 0:
         sys.stdout.write('No results found for that query.\n')
         return
 
     # return results for quay, conda and singularity together
-    if sum([len(json[destination][results]) for destination in ['quay', 'conda', 'singularity', ] for results in json.get(destination, [])]) > 0:
+    if sum(len(json[destination][results]) for destination in ['quay', 'conda', 'singularity', ] for results in json.get(destination, [])) > 0:
         sys.stdout.write("The query returned the following result(s).\n")
         # put quay, conda etc results as lists in lines
         lines = [['LOCATION', 'NAME', 'VERSION', 'COMMAND\n']]
@@ -262,7 +262,7 @@ def readable_output(json, organization='biocontainers', channel='bioconda'):
             sys.stdout.write(
                 "".join((line[0].ljust(col_width0), line[1])))  # output
 
-    if sum([len(json['github'][results]) for results in json.get('github', [])]) > 0:
+    if sum(len(json['github'][results]) for results in json.get('github', [])) > 0:
         sys.stdout.write('\n' if 'lines' in locals() else '')
         sys.stdout.write(
             "Other result(s) on the bioconda-recipes GitHub repository:\n")

lib/galaxy/tool_util/deps/requirements.py

@@ -140,7 +140,7 @@ class ToolRequirements:
         return len(self.tool_requirements)
 
     def __hash__(self):
-        return sum([r.__hash__() for r in self.tool_requirements])
+        return sum(r.__hash__() for r in self.tool_requirements)
 
     def to_dict(self):
         return [r.to_dict() for r in self.tool_requirements]

lib/galaxy/tool_util/edam_util.py

@@ -1,4 +1,3 @@
-import io
 import os
 from typing import Dict, Optional, TextIO
 
@@ -16,7 +15,7 @@ ROOT_TOPIC = 'topic_0003'
 def load_edam_tree(path: Optional[str] = None):
     if path is not None:
         assert os.path.exists(path), f"Failed to load EDAM tabular data at [{path}] path does not exist."
-        handle = io.open(path, "r")
+        handle = open(path)
     else:
         assert tabular_stream is not None, "Failed to load optional import from edam-onotology package, install using [pip install edam-ontology]."
         handle = tabular_stream()

lib/galaxy/tool_util/linters/inputs.py

@@ -1,4 +1,3 @@
-
 """This module contains a linting functions for tool inputs."""
 from galaxy.util import string_as_bool
 from ._util import is_datasource, is_valid_cheetah_placeholder
@@ -132,9 +131,9 @@ def lint_inputs(tool_xml, lint_ctx):
             # lint statically defined options
             if any(['value' not in option.attrib for option in select_options]):
                 lint_ctx.error(f"Select parameter [{param_name}] has option without value")
-            if len(set([option.text.strip() for option in select_options if option.text is not None])) != len(select_options):
+            if len({option.text.strip() for option in select_options if option.text is not None}) != len(select_options):
                 lint_ctx.error(f"Select parameter [{param_name}] has multiple options with the same text content")
-            if len(set([option.attrib.get("value") for option in select_options])) != len(select_options):
+            if len({option.attrib.get("value") for option in select_options}) != len(select_options):
                 lint_ctx.error(f"Select parameter [{param_name}] has multiple options with the same value")
 
             if param_attrib.get("display") == "checkboxes":

lib/galaxy/tool_util/toolbox/views/edam.py

@@ -142,8 +142,7 @@ class EdamToolPanelView(ToolPanelView):
         if self.include_topics:
             edam.extend(tool.edam_topics)
         if len(edam) > 0:
-            for term in edam:
-                yield term
+            yield from edam
         else:
             yield 'uncategorized'
 

lib/galaxy/util/pastescript/serve.py

@@ -369,7 +369,7 @@ class NotFoundCommand(Command):
             print('(try running python setup.py develop)')
             return 2
         print('Known commands:')
-        longest = max([len(n) for n, c in commands])
+        longest = max(len(n) for n, c in commands)
         for name, command in commands:
             print(f'  {self.pad(name, length=longest)}  {command.load().summary}')
         return 2

lib/galaxy/visualization/data_providers/genome.py

@@ -987,7 +987,7 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
             seq = read.seq
             strand = decode_strand(read.flag, 0x0010)
             if read.cigar is not None:
-                read_len = sum([cig[1] for cig in read.cigar])  # Use cigar to determine length
+                read_len = sum(cig[1] for cig in read.cigar)  # Use cigar to determine length
             else:
                 read_len = len(seq)  # If no cigar, just use sequence length
 

lib/galaxy/web/framework/middleware/error.py

@@ -308,10 +308,11 @@ class Supplement:
                 wsgi_vars[name] = value
         if self.environ['wsgi.version'] != (1, 0):
             wsgi_vars['wsgi.version'] = self.environ['wsgi.version']
-        proc_desc = tuple([int(bool(self.environ[key]))
-                           for key in ('wsgi.multiprocess',
-                                       'wsgi.multithread',
-                                       'wsgi.run_once')])
+        proc_desc = tuple(int(bool(self.environ[key])) for key in (
+            'wsgi.multiprocess',
+            'wsgi.multithread',
+            'wsgi.run_once'
+        ))
         wsgi_vars['wsgi process'] = self.process_combos[proc_desc]
         wsgi_vars['application'] = self.middleware.application
         if 'paste.config' in self.environ:

lib/galaxy/webapps/base/controller.py

@@ -1471,7 +1471,7 @@ class UsesExtendedMetadataMixin(SharableItemSecurityMixin):
         else:
             # BUG: Everything is cast to string, which can lead to false positives
             # for cross type comparisions, ie "True" == True
-            yield prefix, (f"{meta}").encode("utf8", errors='replace')
+            yield prefix, (f"{meta}").encode()
 
 
 def sort_by_attr(seq, attr):

lib/galaxy/webapps/galaxy/api/library_contents.py

@@ -375,7 +375,7 @@ class LibraryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
         else:
             # BUG: Everything is cast to string, which can lead to false positives
             # for cross type comparisions, ie "True" == True
-            yield prefix, (f"{meta}").encode("utf8", errors='replace')
+            yield prefix, (f"{meta}").encode()
 
     @expose_api
     def update(self, trans, id, library_id, payload, **kwd):

lib/galaxy/webapps/galaxy/api/library_datasets.py

@@ -456,7 +456,7 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
             path = os.path.join(full_dir, path)
             if unsafe_walk(path, allowlist=[full_dir] + trans.app.config.user_library_import_symlink_allowlist, username=username):
                 # the path is a dir and contains files that symlink outside the user dir
-                error = 'User attempted to import a path that resolves to a path outside of their import dir: %s -> %s' % (
+                error = 'User attempted to import a path that resolves to a path outside of their import dir: {} -> {}'.format(
                     path, os.path.realpath(path)
                 )
                 if trans.app.config.user_library_import_check_permissions:

lib/galaxy/webapps/galaxy/services/base.py

@@ -1,4 +1,3 @@
-
 from typing import (
     List,
     Optional,

lib/galaxy/webapps/galaxy/services/history_contents.py

@@ -1,4 +1,3 @@
-
 import datetime
 import json
 import logging

lib/galaxy/webapps/galaxy/services/library_folder_contents.py

@@ -1,4 +1,3 @@
-
 import logging
 
 from galaxy import (

lib/galaxy/webapps/galaxy/services/pages.py

@@ -1,4 +1,3 @@
-
 import logging
 
 from galaxy import (

lib/galaxy/webapps/galaxy/services/quotas.py

@@ -1,4 +1,3 @@
-
 import logging
 from typing import (
     Optional,

lib/galaxy/webapps/galaxy/services/visualizations.py

@@ -1,4 +1,3 @@
-
 import logging
 
 from galaxy.managers.visualizations import (

lib/galaxy/webapps/reports/controllers/tools.py

@@ -52,7 +52,7 @@ class Tools(BaseUIController):
                 return f"<font color=\"red\">{returned}</font>"
             return returned
         else:
-            splited = tuple([float(_) for _ in str(date).split(':')])
+            splited = tuple(float(_) for _ in str(date).split(':'))
             if splited[0]:
                 returned = '%d h. %d min.' % splited[:2]
                 if colored:

lib/galaxy_test/selenium/test_history_panel.py

@@ -201,7 +201,7 @@ class HistoryPanelTestCase(SeleniumTestCase):
 
         current_tags_size = len(close_tag_buttons)
 
-        errmsg = "there are more tags than expected! current {}, expected {}".format(current_tags_size, expected_tags_size)
+        errmsg = f"there are more tags than expected! current {current_tags_size}, expected {expected_tags_size}"
         assert expected_tags_size == current_tags_size, errmsg
 
         for close_btn in reversed(close_tag_buttons):

lib/galaxy_test/selenium/test_published_histories_grid.py

@@ -121,7 +121,7 @@ class HistoryGridTestCase(SharedStateSeleniumTestCase):
     @retry_assertion_during_transitions
     def assert_grid_histories_sorted_by_owner(self):
         histories = self.get_histories()
-        index_1, index_2, index_3 = [histories.index(n) for n in self.all_histories]
+        index_1, index_2, index_3 = (histories.index(n) for n in self.all_histories)
         # 1 and 3 are owned by a owner whose username lexicographically
         # precedes 2. So verify 1 and 3 come before 2.
         assert index_1 < index_2

lib/tool_shed/metadata/repository_metadata_manager.py

@@ -162,14 +162,18 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
 
     def compare_data_manager(self, ancestor_metadata, current_metadata):
         """Determine if ancestor_metadata is the same as or a subset of current_metadata for data_managers."""
+
         def __data_manager_dict_to_tuple_list(metadata_dict):
             # we do not check tool_guid or tool conf file name
-            return set(sorted([(name,
-                                tuple(sorted(value.get('data_tables', []))),
-                                value.get('guid'),
-                                value.get('version'),
-                                value.get('name'),
-                                value.get('id')) for name, value in metadata_dict.items()]))
+            return set(sorted((
+                name,
+                tuple(sorted(value.get('data_tables', []))),
+                value.get('guid'),
+                value.get('version'),
+                value.get('name'),
+                value.get('id')
+            ) for name, value in metadata_dict.items()))
+
         # only compare valid entries, any invalid entries are ignored
         ancestor_metadata = __data_manager_dict_to_tuple_list(ancestor_metadata.get('data_managers', {}))
         current_metadata = __data_manager_dict_to_tuple_list(current_metadata.get('data_managers', {}))

scripts/api/common.py

@@ -97,7 +97,7 @@ def display(api_key, url, return_formatted=True):
                     print('  name: %s' % i.pop('name'))
                 try:
                     for k, v in i.items():
-                        print('  %s: %s' % (k, v))
+                        print(f'  {k}: {v}')
                 except AttributeError:
                     for item in i:
                         print(item)

scripts/api/library_upload_dir.py

@@ -131,7 +131,7 @@ class Uploader:
             # So that we can check if it really needs to be uploaded.
             already_uploaded = memo_key in self.memo_path.keys()
             fid = self.memoized_path(basepath, base_folder=self.folder_id)
-            print('[{}/{}] {}/{} uploaded={}'.format(idx + 1, len(all_files), fid, fname, already_uploaded))
+            print(f'[{idx + 1}/{len(all_files)}] {fid}/{fname} uploaded={already_uploaded}')
 
             if not already_uploaded:
                 if self.non_local:

scripts/check_model.py

@@ -19,7 +19,7 @@ IndexTuple = namedtuple('IndexTuple', 'table column_names')
 
 
 def tuple_from_index(index):
-    columns = tuple([index.columns[key].name for key in index.columns.keys()])
+    columns = tuple(index.columns[key].name for key in index.columns.keys())
     if len(columns) == 1:
         columns = columns[0]
     return IndexTuple(index.table.name, columns)

scripts/cleanup_datasets/pgcleanup.py

@@ -218,7 +218,7 @@ class Action:
             for causal, s in zip(self.causals, results[primary]):
                 for r in sorted(s):
                     secondaries = ', '.join('%s: %s' % x for x in zip(causal[1:], r[1:]))
-                    self.log.info('{} {} caused {}'.format(causal[0], r[0], secondaries))
+                    self.log.info(f'{causal[0]} {r[0]} caused {secondaries}')
 
     def handle_results(self, cur):
         results = {}

scripts/config_sample_to_kwalify.py

@@ -39,7 +39,7 @@ def _dump_option(option, current_section_desc):
         print((" " * 6) + line)
     if "=" not in option:
         print(option)
-    key, default = [s.strip() for s in option.split("=", 1)]
+    key, default = (s.strip() for s in option.split("=", 1))
     key = key[1:]  # strip #
     if default.strip().lower() in ["true", "false"]:
         default = default.lower()

scripts/docker_swarm_manager.py

@@ -358,16 +358,16 @@ class SwarmState:
             # there are no cpu constraints, so no calculation can be done
             return 0, 0
         for node in nodes:
-            used += sum([t.cpus for t in node.non_terminal_tasks]) / self._cpus
+            used += sum(t.cpus for t in node.non_terminal_tasks) / self._cpus
             total += node.cpus / self._cpus
         # need at least this many slots
         needed = used + self.get_limit(constraints, 'slots_min_spare')
         if (len(services) > self._conf.service_wait_count_limit
                 and time.time() - self._waiting_since.get(constraints, time.time()) > self._conf.service_wait_time_limit):
             # add slots for waiting services that have exceeded limits
-            needed += sum([s.cpus for s in services]) / self._cpus
+            needed += sum(s.cpus for s in services) / self._cpus
         # subtract slots for spawning nodes
-        needed -= sum([n.get('slots', 0) for n in self._spawning_nodes.get(constraints, {})])
+        needed -= sum(n.get('slots', 0) for n in self._spawning_nodes.get(constraints, {}))
         # ensure no less than slots_min_limit slots will exist (free or used)
         needed = max(needed, self.get_limit(constraints, 'slots_min_limit'))
         # ensure no more than slots_max_limit slots will exist

scripts/get_uwsgi_args.py

@@ -86,7 +86,7 @@ def _get_uwsgi_args(cliargs, kwargs):
         'pythonpath': 'lib',
         'threads': '4',
         'buffer-size': '16384',  # https://github.com/galaxyproject/galaxy/issues/1530
-        'http': 'localhost:{port}'.format(port=DEFAULT_PORTS[cliargs.app]),
+        'http': f'localhost:{DEFAULT_PORTS[cliargs.app]}',
         'static-map': (f'/static={os.getcwd()}/static',
                        f'/favicon.ico={os.getcwd()}/static/favicon.ico'),
         'die-on-term': True,

scripts/helper.py

@@ -29,10 +29,10 @@ helper = idencoding.IdEncodingHelper(id_secret=app_properties.get('id_secret'))
 model = galaxy.config.init_models_from_config(config)
 
 if args.encode_id:
-    print('Encoded "{}": {}'.format(args.encode_id, helper.encode_id(args.encode_id)))
+    print(f'Encoded "{args.encode_id}": {helper.encode_id(args.encode_id)}')
 
 if args.decode_id:
-    print('Decoded "{}": {}'.format(args.decode_id, helper.decode_id(args.decode_id)))
+    print(f'Decoded "{args.decode_id}": {helper.decode_id(args.decode_id)}')
 
 if args.hda_id:
     try:

scripts/microbes/harvest_bacteria.py

@@ -151,7 +151,7 @@ def process_FASTA(filename, org_num, refseq):
 
     # Create Chrom Info File:
     chrom_info_file = open(os.path.join(os.path.split(filename)[0], "%s.info" % refseq), 'wb+')
-    chrom_info_file.write("chromosome={}\nname={}\nlength={}\norganism={}\n".format(refseq, chr_name, len(fasta), org_num))
+    chrom_info_file.write(f"chromosome={refseq}\nname={chr_name}\nlength={len(fasta)}\norganism={org_num}\n")
     try:
         chrom_info_file.write("gi=%s\n" % accesions['gi'])
     except Exception:

scripts/microbes/util.py

@@ -116,7 +116,7 @@ def get_bed_from_genbank(gb_file, chrom, feature_list):
             if not name:
                 name = "unknown"
 
-            features[feature_type].append("{}\t{}\t{}\t{}\t{}\t{}".format(chrom, feature.start, feature.end, name, 0, feature.strand))  # append new bed field here
+            features[feature_type].append(f"{chrom}\t{feature.start}\t{feature.end}\t{name}\t{0}\t{feature.strand}")  # append new bed field here
     return features
 
 

scripts/objectstore/copy_files_to_irods.py

@@ -79,16 +79,16 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
         return
 
     # read object_store_info file
-    with open(object_store_info_file, mode="r") as osi:
+    with open(object_store_info_file) as osi:
         object_store_info = json.load(osi)
     osi_keys = tuple(object_store_info.keys())
 
     # read irods_info_file
-    with open(irods_info_file, mode="r") as ii:
+    with open(irods_info_file) as ii:
         irods_info = json.load(ii)
 
     # read db_connectin_info file
-    with open(db_connection_info_file, mode="r") as dci:
+    with open(db_connection_info_file) as dci:
         db_connection_info = json.load(dci)
 
     try:

scripts/tests_markdown.py

@@ -127,7 +127,7 @@ def _merge_summarizes(raw_data_dicts):
 
 
 def _prepare_raw_data(path):
-    with open(path, "r") as f:
+    with open(path) as f:
         inp_dict = json.load(f)
     environment = dict(raw_data=inp_dict, label=os.path.basename(path))
     __inject_summary(environment)
@@ -261,12 +261,12 @@ def __inject_api_timing_summary_test(test):
 def __inject_statistics(from_dict):
     raw_values = from_dict['raw']
     from_dict['sum'] = sum(raw_values)
-    from_dict['median'] = "{:.2f}".format(statistics.median(raw_values))
+    from_dict['median'] = f"{statistics.median(raw_values):.2f}"
     if len(raw_values) > 1:
-        from_dict['stdev'] = "{:.4f}".format(statistics.stdev(raw_values))
+        from_dict['stdev'] = f"{statistics.stdev(raw_values):.4f}"
     else:
         from_dict['stdev'] = "n/a"
-    from_dict['mean'] = "{:.2f}".format(statistics.mean(raw_values))
+    from_dict['mean'] = f"{statistics.mean(raw_values):.2f}"
     from_dict['count'] = len(raw_values)
     return from_dict
 

scripts/tools/re_escape_output.py

@@ -21,7 +21,7 @@ def __main__():
             suffix = 're_match_multiline'
         else:
             suffix = 're_match'
-        output = open("{}.{}".format(args[0], suffix), 'wb')
+        output = open(f"{args[0]}.{suffix}", 'wb')
     if options.multiline:
         lines = [re.escape(input.read())]
     else:

test/functional/webhooks/phdcomics/__init__.py

@@ -24,10 +24,10 @@ def main(trans, webhook, params):
             content = urlopen(url).read()
             soap = BeautifulSoup(content, 'html.parser')
             pattern = r'(?:http://www\.phdcomics\.com/comics\.php\?f=)(\d+)'
-            webhook.config['latest_id'] = max([
+            webhook.config['latest_id'] = max(
                 int(re.search(pattern, link.text).group(1))
                 for link in soap.find_all('link', text=re.compile(pattern))
-            ])
+            )
 
         random_id = random.randint(1, webhook.config['latest_id'])
         url = 'http://www.phdcomics.com/comics/archive.php?comicid=%d' % \

test/integration/test_scripts.py

@@ -178,7 +178,7 @@ class ScriptsIntegrationTestCase(integration_util.IntegrationTestCase):
             return unicodify(subprocess.check_output(cmd, cwd=cwd, env=clean_env))
         except Exception as e:
             if isinstance(e, subprocess.CalledProcessError):
-                raise Exception("{}\nOutput was:\n{}".format(unicodify(e), unicodify(e.output)))
+                raise Exception(f"{unicodify(e)}\nOutput was:\n{unicodify(e.output)}")
             raise
 
     def write_config_file(self):

test/integration/test_tool_data_delete.py

@@ -54,7 +54,7 @@ class AdminToolDataIntegrationTestCase(integration_util.IntegrationTestCase):
         time.sleep(2)
         show_response = self._get("tool_data/testbeta")
         updated_fields = show_response.json()["fields"]
-        self.assertEquals(len(updated_fields), original_count + 1)
+        self.assertEqual(len(updated_fields), original_count + 1)
         new_field = updated_fields[-1]
         url = self._api_url(f"tool_data/testbeta?key={self.galaxy_interactor.api_key}")
 

test/integration/test_workflow_scheduling_options.py

@@ -124,5 +124,5 @@ input1:
   name: fasta1
 text_input: foo
 """, history_id=history_id)
-            invocation = self._get("/invocations/{}".format(invocation_response.invocation_id)).json()
+            invocation = self._get(f"/invocations/{invocation_response.invocation_id}").json()
             assert 'wf_output_1' in invocation['output_collections']

test/unit/app/jobs/test_command_factory.py

@@ -43,7 +43,7 @@ class TestCommandFactory(TestCase):
         self.include_work_dir_outputs = False
         dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"]
         self.job_wrapper.dependency_shell_commands = dep_commands
-        self.__assert_command_is(_surround_command("{}; {}; return_code=$?".format(dep_commands[0], MOCK_COMMAND_LINE)))
+        self.__assert_command_is(_surround_command(f"{dep_commands[0]}; {MOCK_COMMAND_LINE}; return_code=$?"))
 
     def test_shell_commands_external(self):
         self.job_wrapper.commands_in_new_shell = True
@@ -55,7 +55,7 @@ class TestCommandFactory(TestCase):
                 self.job_wrapper.shell,
                 self.job_wrapper.working_directory,
             )))
-        self.__assert_tool_script_is("#!/bin/sh\n{}; {}".format(dep_commands[0], MOCK_COMMAND_LINE))
+        self.__assert_tool_script_is(f"#!/bin/sh\n{dep_commands[0]}; {MOCK_COMMAND_LINE}")
 
     def test_remote_dependency_resolution(self):
         self.include_work_dir_outputs = False
@@ -67,7 +67,7 @@ class TestCommandFactory(TestCase):
         self.include_work_dir_outputs = False
         dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"]
         self.job_wrapper.dependency_shell_commands = dep_commands
-        self.__assert_command_is(_surround_command("{}; {}; return_code=$?".format(dep_commands[0], MOCK_COMMAND_LINE)),
+        self.__assert_command_is(_surround_command(f"{dep_commands[0]}; {MOCK_COMMAND_LINE}; return_code=$?"),
                                  remote_command_params=dict(dependency_resolution="local"))
 
     def test_task_prepare_inputs(self):

test/unit/app/jobs/test_job_configuration.py

@@ -327,7 +327,7 @@ class AdvancedJobConfXmlParserTestCase(BaseJobConfXmlParserTestCase):
 
     def test_destination_tags(self):
         self._with_advanced_config()
-        longjob_dests_ids = sorted([j.id for j in self.job_config.destinations["longjobs"]])
+        longjob_dests_ids = sorted(j.id for j in self.job_config.destinations["longjobs"])
         assert len(longjob_dests_ids) == 2
         assert longjob_dests_ids[0] == "pbs_longjobs"
         assert longjob_dests_ids[1] == "remote_cluster"

test/unit/app/jobs/test_mapper.py

@@ -127,7 +127,7 @@ def __assert_mapper_errors_with_message(mapper, message):
     except Exception as e:
         exception = e
     assert exception
-    assert str(exception) == message, "{} != {}".format(str(exception), message)
+    assert str(exception) == message, f"{str(exception)} != {message}"
 
 
 def __mapper(tool_job_destination=TOOL_JOB_DESTINATION):

test/unit/files/_util.py

@@ -67,7 +67,7 @@ def assert_realizes_as(file_sources, uri, expected, user_context=None):
     file_source_path = file_sources.get_file_source_path(uri)
     with tempfile.NamedTemporaryFile(mode='r') as temp:
         file_source_path.file_source.realize_to(file_source_path.path, temp.name, user_context=user_context)
-        with open(temp.name, "r") as f:
+        with open(temp.name) as f:
             realized_contents = f.read()
         if realized_contents != expected:
             message = "Expected to realize contents at [{}] as [{}], instead found [{}]".format(

test/unit/files/test_posix.py

@@ -257,7 +257,7 @@ def test_posix_user_access_requires_role():
     user_context = user_context_fixture()
     _assert_user_access_prohibited(file_sources, user_context)
 
-    user_context = user_context_fixture(role_names=set([allowed_role_name]))
+    user_context = user_context_fixture(role_names={allowed_role_name})
     _assert_user_access_granted(file_sources, user_context)
 
 
@@ -271,7 +271,7 @@ def test_posix_user_access_requires_group():
     user_context = user_context_fixture()
     _assert_user_access_prohibited(file_sources, user_context)
 
-    user_context = user_context_fixture(group_names=set([allowed_group_name]))
+    user_context = user_context_fixture(group_names={allowed_group_name})
     _assert_user_access_granted(file_sources, user_context)
 
 
@@ -298,13 +298,13 @@ def test_posix_user_access_requires_role_and_group():
     }
     file_sources = _configured_file_sources(writable=True, plugin_extra_config=plugin_extra_config)
 
-    user_context = user_context_fixture(group_names=set([allowed_group_name]))
+    user_context = user_context_fixture(group_names={allowed_group_name})
     _assert_user_access_prohibited(file_sources, user_context)
 
-    user_context = user_context_fixture(role_names=set([allowed_role_name]))
+    user_context = user_context_fixture(role_names={allowed_role_name})
     _assert_user_access_prohibited(file_sources, user_context)
 
-    user_context = user_context_fixture(role_names=set([allowed_role_name]), group_names=set([allowed_group_name]))
+    user_context = user_context_fixture(role_names={allowed_role_name}, group_names={allowed_group_name})
     _assert_user_access_granted(file_sources, user_context)
 
 
@@ -316,32 +316,32 @@ def test_posix_user_access_using_boolean_rules():
     file_sources = _configured_file_sources(writable=True, plugin_extra_config=plugin_extra_config)
 
     user_context = user_context_fixture(
-        role_names=set([]),
-        group_names=set([])
+        role_names=set(),
+        group_names=set()
     )
     _assert_user_access_prohibited(file_sources, user_context)
 
     user_context = user_context_fixture(
-        role_names=set(["role1"]),
-        group_names=set(["group1", "group2"])
+        role_names={"role1"},
+        group_names={"group1", "group2"}
     )
     _assert_user_access_prohibited(file_sources, user_context)
 
     user_context = user_context_fixture(
-        role_names=set(["role1", "role3"]),
-        group_names=set(["group1", "group2", "group3"])
+        role_names={"role1", "role3"},
+        group_names={"group1", "group2", "group3"}
     )
     _assert_user_access_prohibited(file_sources, user_context)
 
     user_context = user_context_fixture(
-        role_names=set(["role1", "role2"]),
-        group_names=set(["group3", "group5"])
+        role_names={"role1", "role2"},
+        group_names={"group3", "group5"}
     )
     _assert_user_access_prohibited(file_sources, user_context)
 
     user_context = user_context_fixture(
-        role_names=set(["role1", "role3"]),
-        group_names=set(["group1", "group2"])
+        role_names={"role1", "role3"},
+        group_names={"group1", "group2"}
     )
     _assert_user_access_granted(file_sources, user_context)
 

test/unit/objectstore/test_objectstore.py

@@ -796,4 +796,4 @@ def _assert_has_keys(the_dict, keys):
 
 def _assert_key_has_value(the_dict, key, value):
     assert key in the_dict, f"dict [{key}] doesn't container expected key [{the_dict}]"
-    assert the_dict[key] == value, "{} != {}".format(the_dict[key], value)
+    assert the_dict[key] == value, f"{the_dict[key]} != {value}"