Drop support for retired Python 3.5

Upgrade syntax using `pyupgrade --py36-plus` .

Manually drop several `six` imports.

Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py

.circleci/config.yml

@@ -27,7 +27,7 @@ variables:
 jobs:
   get_code:
     docker:
-      - image: circleci/python:3.5
+      - image: circleci/python:3.6
     <<: *set_workdir
     steps:
       # Replace standard code checkout with shallow clone to speed things up.
@@ -83,34 +83,34 @@ jobs:
           key: v1-repo-{{ .Environment.CIRCLE_SHA1 }}
           paths:
             - ~/repo
-  py35_docstring:
+  py36_docstring:
     docker:
-      - image: circleci/python:3.5
+      - image: circleci/python:3.6
     <<: *set_workdir
     steps:
       - *restore_repo_cache
       - *install_tox
-      - run: tox -e py35-lint_docstring_include_list
-  py35_lint:
+      - run: tox -e py36-lint_docstring_include_list
+  py36_lint:
     docker:
-      - image: circleci/python:3.5
+      - image: circleci/python:3.6
     <<: *set_workdir
     steps:
       - *restore_repo_cache
       - *install_tox
-      - run: tox -e py35-lint
-  py35_unit:
+      - run: tox -e py36-lint
+  py36_unit:
     docker:
-      - image: circleci/python:3.5
+      - image: circleci/python:3.6
     <<: *set_workdir
     steps:
       - *restore_repo_cache
       - *install_tox
       - *install_ffprobe
-      - run: tox -e py35-unit
-  py35_first_startup:
+      - run: tox -e py36-unit
+  py36_first_startup:
     docker:
-      - image: circleci/python:3.5
+      - image: circleci/python:3.6
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -118,10 +118,10 @@ jobs:
       - run: wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0141.sqlite
       - run: mv db_gx_rev_0141.sqlite database/universe.sqlite
       - *install_tox
-      - run: tox -e py35-first_startup
+      - run: tox -e py36-first_startup
   validate_test_tools:
     docker:
-      - image: circleci/python:3.5
+      - image: circleci/python:3.6
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -131,7 +131,7 @@ jobs:
       - run: tox -e validate_test_tools
   test_galaxy_packages:
     docker:
-      - image: circleci/python:3.5
+      - image: circleci/python:3.6
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -167,13 +167,13 @@ workflows:
   get_code_and_test:
     jobs:
       - get_code
-      - py35_docstring:
+      - py36_docstring:
           <<: *requires_get_code
-      - py35_lint:
+      - py36_lint:
           <<: *requires_get_code
-      - py35_unit:
+      - py36_unit:
           <<: *requires_get_code
-      - py35_first_startup:
+      - py36_first_startup:
           <<: *requires_get_code
       - test_galaxy_packages:
           <<: *requires_get_code

README.rst

@@ -24,7 +24,7 @@ Community support is available at `Galaxy Help <https://help.galaxyproject.org/>
 Galaxy Quickstart
 =================
 
-Galaxy requires Python 3.5 or 3.6 . To check your Python version, run:
+Galaxy requires Python 3.6 . To check your Python version, run:
 
 .. code:: console
 

client/src/assets/images/circle.py

@@ -2,7 +2,6 @@
 """
 usage: %prog width height bg_color hatch_color [color alpha stop_pos] +
 """
-from __future__ import division
 
 import sys
 from math import pi

config/plugins/webhooks/demo/tour_generator/__init__.py

@@ -8,7 +8,7 @@ from galaxy.util import Params
 log = logging.getLogger(__name__)
 
 
-class TourGenerator(object):
+class TourGenerator:
     def __init__(self, trans, tool_id, tool_version):
         self._trans = trans
         self._tool = self._trans.app.toolbox.get_tool(tool_id, tool_version)
@@ -177,14 +177,14 @@ class TourGenerator(object):
                 if name in test_inputs:
                     hid = self._hids[name]
                     dataset = self._test.inputs[name][0]
-                    step['content'] = 'Select dataset: <b>%s: %s</b>' % (
+                    step['content'] = 'Select dataset: <b>{}: {}</b>'.format(
                         hid, dataset
                     )
                 else:
                     step['content'] = 'Select a dataset'
 
             elif input.type == 'conditional':
-                param_id = '%s|%s' % (input.name, input.test_param.name)
+                param_id = f'{input.name}|{input.test_param.name}'
                 step['title'] = input.test_param.label
                 step['element'] = '[tour_id="%s"]' % param_id
                 params = []
@@ -203,7 +203,7 @@ class TourGenerator(object):
                                 cases[key] = value.label
 
                     for case_id, case_title in cases.items():
-                        tour_id = '%s|%s' % (input.name, case_id)
+                        tour_id = f'{input.name}|{case_id}'
                         if tour_id in self._test.inputs.keys():
                             if case_id in self._data_inputs.keys():
                                 hid = self._hids[case_id]

contrib/galaxy_config_merger.py

@@ -23,14 +23,12 @@ THE ORIGINAL WORK IS WITH YOU.
 
 Script for merging specific local Galaxy config galaxy.ini.cri with default Galaxy galaxy.ini.sample
 '''
-from __future__ import print_function
 
+import configparser
 import logging
 import optparse
 import sys
 
-from six.moves import configparser
-
 
 def main():
     # logging configuration
@@ -51,12 +49,12 @@ def main():
 
     config_sample = configparser.RawConfigParser()
     config_sample.read(options.sample)
-    config_sample_content = open(options.sample, 'r').read()
+    config_sample_content = open(options.sample).read()
 
     config = configparser.RawConfigParser()
     config.read(options.config)
 
-    logging.info("Merging your own config file %s into the sample one %s." % (options.config, options.sample))
+    logging.info(f"Merging your own config file {options.config} into the sample one {options.sample}.")
     logging.info("---------- DIFFERENCE ANALYSIS BEGIN ----------")
     for section in config.sections():
         if not config_sample.has_section(section):
@@ -65,13 +63,13 @@ def main():
             for (name, value) in config.items(section):
                 if not config_sample.has_option(section, name):
                     if not "#%s" % name in config_sample_content:
-                        logging.warning("-MISSING- section [%s] option '%s' not found in sample file. It will be ignored." % (section, name))
+                        logging.warning(f"-MISSING- section [{section}] option '{name}' not found in sample file. It will be ignored.")
                     else:
-                        logging.info("-notset- section [%s] option '%s' not set in sample file. It will be added." % (section, name))
+                        logging.info(f"-notset- section [{section}] option '{name}' not set in sample file. It will be added.")
                         config_sample.set(section, name, value)
                 else:
                     if not config_sample.get(section, name) == value:
-                        logging.info("- diff - section [%s] option '%s' has different value ('%s':'%s'). It will be modified." % (section, name, 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))
                         config_sample.set(section, name, value)
     logging.info("---------- DIFFERENCE ANALYSIS END   ----------")
 

contrib/nagios/check_galaxy.py

@@ -3,7 +3,6 @@
 check_galaxy can be run by hand, although it is meant to run from cron
 via the check_galaxy.sh script in Galaxy's cron/ directory.
 """
-from __future__ import print_function
 
 import formatter
 import getopt
@@ -14,13 +13,12 @@ import socket
 import sys
 import time
 import warnings
-from user import home
-
-from six.moves.urllib.request import (
+from urllib.request import (
     build_opener,
     HTTPCookieProcessor,
-    Request
+    Request,
 )
+from user import home
 
 with warnings.catch_warnings():
     warnings.simplefilter('ignore')
@@ -52,7 +50,7 @@ handler = args[3]
 warntime = 240
 
 new_history = False
-for o, a in opts:
+for o, _ in opts:
     if o == "-n":
         if debug:
             print("Specified -n, will create a new history")
@@ -73,7 +71,7 @@ tc.agent("Mozilla/5.0 (compatible; check_galaxy/0.2)")
 tc.config('use_tidy', 0)
 
 
-class Browser(object):
+class Browser:
     def __init__(self):
         self.server = server
         self.handler = handler
@@ -93,7 +91,7 @@ class Browser(object):
         self.opener = build_opener(HTTPCookieProcessor(tc.get_browser().cj))
 
     def get(self, path):
-        tc.go("%s%s" % (self.server, path))
+        tc.go(f"{self.server}{path}")
         tc.code(200)
 
     def req(self, path, data=None, method=None):
@@ -105,7 +103,7 @@ class Browser(object):
         if method:
             req.get_method = lambda: method
         res = self.opener.open(req)
-        print('==> at %s (%s)' % (url, method or 'GET'))
+        print('==> at {} ({})'.format(url, method or 'GET'))
         assert res.getcode() == 200, url
         return res
 
@@ -226,7 +224,7 @@ class Browser(object):
         if self.hda_state != "ok":
             self.get("/datasets/%s/stderr" % self.hda_id)
             print(tc.browser.get_html())
-            raise Exception("HDA %s NOT OK: %s" % (self.hda_id, self.hda_state))
+            raise Exception(f"HDA {self.hda_id} NOT OK: {self.hda_state}")
 
     def check_hda_content(self):
         self.get("/datasets/%s/display?to_ext=txt" % self.hda_id)
@@ -240,7 +238,7 @@ class Browser(object):
 
     def delete_datasets(self):
         for hda in self.undeleted_hdas:
-            path = '/api/histories/%s/contents/%s' % (self.history_id, hda['id'])
+            path = '/api/histories/{}/contents/{}'.format(self.history_id, hda['id'])
             self.req(path, method='DELETE')
         hdas = [hda['id'] for hda in self.undeleted_hdas]
         if hdas:

cron/add_manual_builds.py

@@ -6,7 +6,6 @@ Adds Manually created builds and chrom info to Galaxy's info tables
 Usage:
 python add_manual_builds.py input_file builds.txt chrom_length_dir
 """
-from __future__ import print_function
 
 import os
 import sys

cron/build_chrom_db.py

@@ -11,14 +11,13 @@ All chromInfo is placed in a path with the convention
 Usage:
 python build_chrom_db.py dbpath/ [builds_file]
 """
-from __future__ import print_function
 
 import fileinput
 import os
 import sys
+from urllib.parse import urlencode
 
 import requests
-from six.moves.urllib.parse import urlencode
 
 import parse_builds  # noqa: I100,I202
 
@@ -78,5 +77,5 @@ if __name__ == "__main__":
                 for chrominfo in getchrominfo("http://genome-test.gi.ucsc.edu/cgi-bin/hgTables?", build):
                     print("\t".join(chrominfo), file=outfile)
         except Exception as e:
-            print("Failed to retrieve %s: %s" % (build, e))
+            print(f"Failed to retrieve {build}: {e}")
             os.remove(outfile_name)

cron/parse_builds.py

@@ -4,7 +4,6 @@ Connects to the URL specified and outputs builds available at that
 DSN in tabular format.  UCSC Main gateway is used as default.
 build   description
 """
-from __future__ import print_function
 
 import sys
 import xml.etree.ElementTree as ElementTree

cron/parse_builds_3_sites.py

@@ -2,7 +2,6 @@
 """
 Connects to sites and determines which builds are available at each.
 """
-from __future__ import print_function
 
 import xml.etree.ElementTree as ElementTree
 

doc/parse_gx_xsd.py

@@ -1,17 +1,15 @@
-# coding: utf-8
 # TODO: Add examples, tables and best practice links to command
 # TODO: Examples of truevalue, falsevalue
 # TODO: Test param extra_file
 # Things dropped from schema_template.md (still documented inside schema).
 #  - request_parameter_translation
-from __future__ import print_function
 
 import sys
+from io import StringIO
 
 from lxml import etree
-from six import StringIO
 
-with open(sys.argv[2], "r") as f:
+with open(sys.argv[2]) as f:
     xmlschema_doc = etree.parse(f)
 
 markdown_buffer = StringIO()
@@ -22,7 +20,7 @@ def main():
     toc_list = []
     content_list = []
     found_tag = False
-    with open(sys.argv[1], "r") as markdown_template:
+    with open(sys.argv[1]) as markdown_template:
         for line in markdown_template:
             if line.startswith("$tag:"):
                 found_tag = True
@@ -41,7 +39,7 @@ def main():
         print(el, end='')
 
 
-class Tag(object):
+class Tag:
 
     def __init__(self, line):
         assert line.startswith("$tag:")
@@ -71,7 +69,7 @@ class Tag(object):
         return " > ".join("``%s``" % p for p in self.title.split("|"))
 
     def build_toc_entry(self):
-        return "* [%s](%s)" % (self._pretty_title, self._anchor)
+        return f"* [{self._pretty_title}]({self._anchor})"
 
     def build_help(self):
         tag = xmlschema_doc.find(self.xpath)
@@ -113,7 +111,7 @@ def _build_tag(tag, hide_attributes):
                     doc = _doc_or_none(_type_el(element))
                 assert doc is not None, "Documentation for %s is empty" % element.attrib["name"]
                 doc = doc.strip()
-                assertions_buffer.write("``%s`` | %s\n" % (element.attrib["name"], doc))
+                assertions_buffer.write("``{}`` | {}\n".format(element.attrib["name"], doc))
             text = text.replace(line, assertions_buffer.getvalue())
     tag_help.write(text)
     best_practices = _get_bp_link(annotation_el)
@@ -165,7 +163,7 @@ def _build_attributes_table(tag, attributes, hide_attributes=False, attribute_na
             if best_practices:
                 details += """ Find the Intergalactic Utilities Commision suggested best practices for this element [here](%s).""" % best_practices
 
-            attribute_table.write("``%s`` | %s | %s\n" % (name, details, use))
+            attribute_table.write(f"``{name}`` | {details} | {use}\n")
     return attribute_table.getvalue()
 
 

doc/source/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Galaxy documentation build configuration file, created by
 # sphinx-quickstart on Tue Mar  6 10:44:44 2012.
@@ -80,8 +79,8 @@ source_suffix = ['.rst', '.md']
 master_doc = 'index'
 
 # General information about the project.
-project = u'Galaxy Project'
-copyright = str(datetime.datetime.now().year) + u', Galaxy Committers'
+project = 'Galaxy Project'
+copyright = str(datetime.datetime.now().year) + ', Galaxy Committers'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -233,8 +232,8 @@ latex_elements = {
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-    ('index', 'Galaxy.tex', u'Galaxy Code Documentation',
-     u'Galaxy Team', 'manual'),
+    ('index', 'Galaxy.tex', 'Galaxy Code Documentation',
+     'Galaxy Team', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -263,8 +262,8 @@ latex_documents = [
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'galaxy', u'Galaxy Documentation',
-     [u'Galaxy Team'], 1)
+    ('index', 'galaxy', 'Galaxy Documentation',
+     ['Galaxy Team'], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -277,8 +276,8 @@ man_pages = [
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    ('index', 'Galaxy', u'Galaxy Documentation',
-     u'Galaxy Team', 'Galaxy', 'Data intensive biology for everyone.',
+    ('index', 'Galaxy', 'Galaxy Documentation',
+     'Galaxy Team', 'Galaxy', 'Data intensive biology for everyone.',
      'Miscellaneous'),
 ]
 
@@ -293,7 +292,7 @@ texinfo_documents = [
 
 
 # -- ReadTheDocs.org Settings ------------------------------------------------
-class Mock(object):
+class Mock:
     def __init__(self, *args, **kwargs):
         pass
 

doc/source/conf.versioning.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Galaxy sphinxcontrib-simpleversioning documentation build configuration file
 #

lib/galaxy/actions/admin.py

@@ -76,7 +76,7 @@ class AdminActions:
             quota.description = params.description
             self.sa_session.add(quota)
             self.sa_session.flush()
-            message = "Quota '{}' has been renamed to '{}'.".format(old_name, params.name)
+            message = f"Quota '{old_name}' has been renamed to '{params.name}'."
             return message
 
     def _manage_users_and_groups_for_quota(self, quota, params, decode_id=None):
@@ -122,7 +122,7 @@ class AdminActions:
         else:
             if params.default != 'no':
                 self.app.quota_agent.set_default_quota(params.default, quota)
-                message = "Quota '{}' is now the default for {} users.".format(quota.name, params.default)
+                message = f"Quota '{quota.name}' is now the default for {params.default} users."
             else:
                 if quota.default:
                     message = "Quota '{}' is no longer the default for {} users.".format(quota.name, quota.default[0].type)

lib/galaxy/auth/providers/pam_auth.py

@@ -109,23 +109,23 @@ class PAM(AuthProvider):
 
         pam_service = options.get('pam-service', 'galaxy')
         use_helper = string_as_bool(options.get('use-external-helper', False))
-        log.debug("PAM auth: will use external helper: {}".format(use_helper))
+        log.debug(f"PAM auth: will use external helper: {use_helper}")
         authenticated = False
         if use_helper:
             authentication_helper = options.get('authentication-helper-script', '/bin/false').strip()
-            log.debug("PAM auth: external helper script: {}".format(authentication_helper))
+            log.debug(f"PAM auth: external helper script: {authentication_helper}")
             if not authentication_helper.startswith('/'):
                 # don't accept relative path
                 authenticated = False
             else:
-                auth_cmd = shlex.split('/usr/bin/sudo -n {}'.format(authentication_helper))
-                log.debug("PAM auth: external helper cmd: {}".format(auth_cmd))
-                message = '{}\n{}\n{}\n'.format(pam_service, pam_username, password)
+                auth_cmd = shlex.split(f'/usr/bin/sudo -n {authentication_helper}')
+                log.debug(f"PAM auth: external helper cmd: {auth_cmd}")
+                message = f'{pam_service}\n{pam_username}\n{password}\n'
                 try:
                     output = commands.execute(auth_cmd, input=message)
                 except commands.CommandLineException as e:
                     if e.stderr != '':
-                        log.debug("PAM auth: external authentication script had errors: status {} error {}".format(e.returncode, e.stderr))
+                        log.debug(f"PAM auth: external authentication script had errors: status {e.returncode} error {e.stderr}")
                     output = e.stdout
                 if output.strip() == 'True':
                     authenticated = True

lib/galaxy/auth/util.py

@@ -86,7 +86,7 @@ def parse_auth_results(trans, auth_results, options):
             i += 1
         else:
             raise Conflict("Cannot make unique username")
-    log.debug("Email: {}, auto-register with username: {}".format(auto_email, auto_username))
+    log.debug(f"Email: {auto_email}, auto-register with username: {auto_username}")
     auth_return["auto_reg"] = string_as_bool(options.get('auto-register', False))
     auth_return["email"] = auto_email
     auth_return["username"] = auto_username

lib/galaxy/authnz/custos_authnz.py

@@ -3,12 +3,12 @@ import hashlib
 import logging
 import os
 from datetime import datetime, timedelta
+from urllib.parse import quote
 
 import jwt
 import requests
 from oauthlib.common import generate_nonce
 from requests_oauthlib import OAuth2Session
-from six.moves.urllib.parse import quote
 
 from galaxy import exceptions
 from galaxy import util
@@ -248,16 +248,16 @@ class CustosAuthnz(IdentityProvider):
             base_url = self.config["url"]
             # Remove potential trailing slash to avoid "//realms"
             base_url = base_url if base_url[-1] != "/" else base_url[:-1]
-            return "{}/.well-known/openid-configuration".format(base_url)
+            return f"{base_url}/.well-known/openid-configuration"
         else:
-            raise Exception("Unknown Custos provider name: {}".format(provider))
+            raise Exception(f"Unknown Custos provider name: {provider}")
 
     def _fetch_well_known_oidc_config(self, well_known_uri):
         try:
             return requests.get(well_known_uri,
                                 verify=self._get_verify_param()).json()
         except Exception:
-            log.error("Failed to load well-known OIDC config URI: {}".format(well_known_uri))
+            log.error(f"Failed to load well-known OIDC config URI: {well_known_uri}")
             raise
 
     def _load_well_known_oidc_config(self, well_known_oidc_config):

lib/galaxy/authnz/managers.py

@@ -1,3 +1,4 @@
+import builtins
 import copy
 import json
 import logging
@@ -10,7 +11,6 @@ from cloudauthz import CloudAuthz
 from cloudauthz.exceptions import (
     CloudAuthzBaseException
 )
-from six.moves import builtins
 
 from galaxy import exceptions
 from galaxy import model
@@ -89,7 +89,7 @@ class AuthnzManager:
         except ImportError:
             raise
         except etree.ParseError as e:
-            raise etree.ParseError("Invalid configuration at `{}`: {} -- unable to continue.".format(config_file, e))
+            raise etree.ParseError(f"Invalid configuration at `{config_file}`: {e} -- unable to continue.")
 
     def _get_idp_icon(self, idp):
         return self.oidc_backends_config[idp].get('icon') or DEFAULT_OIDC_IDP_ICONS.get(idp)
@@ -109,7 +109,7 @@ class AuthnzManager:
                               "skipping the node.".format(child.tag))
                     continue
                 if 'name' not in child.attrib:
-                    log.error("Could not find a node attribute 'name'; skipping the node '{}'.".format(child.tag))
+                    log.error(f"Could not find a node attribute 'name'; skipping the node '{child.tag}'.")
                     continue
                 idp = child.get('name').lower()
                 if idp in BACKENDS_NAME:
@@ -127,7 +127,7 @@ class AuthnzManager:
         except ImportError:
             raise
         except etree.ParseError as e:
-            raise etree.ParseError("Invalid configuration at `{}`: {} -- unable to continue.".format(config_file, e))
+            raise etree.ParseError(f"Invalid configuration at `{config_file}`: {e} -- unable to continue.")
 
     def _parse_idp_config(self, config_xml):
         rtv = {
@@ -188,10 +188,10 @@ class AuthnzManager:
                 else:
                     return True, "", identity_provider_class(unified_provider_name, self.oidc_config, self.oidc_backends_config[unified_provider_name])
             except Exception as e:
-                log.exception('An error occurred when loading {}'.format(identity_provider_class.__name__))
+                log.exception(f'An error occurred when loading {identity_provider_class.__name__}')
                 return False, unicodify(e), None
         else:
-            msg = 'The requested identity provider, `{}`, is not a recognized/expected provider.'.format(provider)
+            msg = f'The requested identity provider, `{provider}`, is not a recognized/expected provider.'
             log.debug(msg)
             return False, msg, None
 
@@ -281,13 +281,13 @@ class AuthnzManager:
                 return False, message, None
             elif provider in KEYCLOAK_BACKENDS:
                 if (self.allowed_idps and (idphint not in self.allowed_idps)):
-                    msg = 'An error occurred when authenticating a user. Invalid EntityID: `{}`'.format(idphint)
+                    msg = f'An error occurred when authenticating a user. Invalid EntityID: `{idphint}`'
                     log.exception(msg)
                     return False, msg, None
-                return True, "Redirecting to the `{}` identity provider for authentication".format(provider), backend.authenticate(trans, idphint)
-            return True, "Redirecting to the `{}` identity provider for authentication".format(provider), backend.authenticate(trans)
+                return True, f"Redirecting to the `{provider}` identity provider for authentication", backend.authenticate(trans, idphint)
+            return True, f"Redirecting to the `{provider}` identity provider for authentication", backend.authenticate(trans)
         except Exception:
-            msg = 'An error occurred when authenticating a user on `{}` identity provider'.format(provider)
+            msg = f'An error occurred when authenticating a user on `{provider}` identity provider'
             log.exception(msg)
             return False, msg, None
 
@@ -322,7 +322,7 @@ class AuthnzManager:
             # check if logout is enabled for this idp and return false if not
             unified_provider_name = self._unify_provider_name(provider)
             if self.oidc_backends_config[unified_provider_name]['enable_idp_logout'] is False:
-                return False, "IDP logout is not enabled for {}".format(provider), None
+                return False, f"IDP logout is not enabled for {provider}", None
 
             success, message, backend = self._get_authnz_backend(provider)
             if success is False:

lib/galaxy/authnz/psa_authnz.py

@@ -316,11 +316,11 @@ def contains_required_data(response=None, is_new=False, **kwargs):
         # sent back from the identity provider. PSA internally handles such
         # scenarios; however, this case is implemented to prevent uncaught
         # server-side errors.
-        raise MalformedContents(err_msg="`response` not found. {}".format(hint_msg))
+        raise MalformedContents(err_msg=f"`response` not found. {hint_msg}")
     if not response.get("id_token"):
         # This can happen if a non-OIDC compliant backend is used;
         # e.g., an OAuth2.0-based backend that only generates access token.
-        raise MalformedContents(err_msg="Missing identity token. {}".format(hint_msg))
+        raise MalformedContents(err_msg=f"Missing identity token. {hint_msg}")
     if is_new and not response.get("refresh_token"):
         # An identity provider (e.g., Google) sends a refresh token the first
         # time user consents Galaxy's access (i.e., the first time user logs in
@@ -331,7 +331,7 @@ def contains_required_data(response=None, is_new=False, **kwargs):
         # user has provided consent. This can also happen under dev efforts.
         # The solution is to revoke the consent by visiting the identity provider's
         # website, and then retry the login process.
-        raise MalformedContents(err_msg="Missing refresh token. {}".format(hint_msg))
+        raise MalformedContents(err_msg=f"Missing refresh token. {hint_msg}")
 
 
 def verify(strategy=None, response=None, details=None, **kwargs):
@@ -344,7 +344,7 @@ def verify(strategy=None, response=None, details=None, **kwargs):
 
     if provider.lower() == "gcp":
         result = requests.post(
-            "https://iam.googleapis.com/v1/projects/-/serviceAccounts/{}:getIamPolicy".format(endpoint),
+            f"https://iam.googleapis.com/v1/projects/-/serviceAccounts/{endpoint}:getIamPolicy",
             headers={
                 'Authorization': 'Bearer {}'.format(response.get("access_token")),
                 'Accept': 'application/json'})
@@ -364,7 +364,7 @@ def verify(strategy=None, response=None, details=None, **kwargs):
             # sensitive information that should not be exposed to users.
             raise Exception(res["error"]["message"])
     else:
-        raise Exception("`{}` is an unsupported secondary authorization provider, contact admin.".format(provider))
+        raise Exception(f"`{provider}` is an unsupported secondary authorization provider, contact admin.")
 
 
 def allowed_to_disconnect(name=None, user=None, user_storage=None, strategy=None,

lib/galaxy/config/__init__.py

@@ -4,6 +4,7 @@ Universe configuration builder.
 # absolute_import needed for tool_shed package.
 
 import collections
+import configparser
 import errno
 import ipaddress
 import logging
@@ -22,7 +23,6 @@ from datetime import timedelta
 import yaml
 from beaker.cache import CacheManager
 from beaker.util import parse_cache_config_options
-from six.moves import configparser
 
 from galaxy.config.schema import AppSchema
 from galaxy.containers import parse_containers_config

lib/galaxy/config/config_manage.py

@@ -8,12 +8,12 @@ from collections import (
     namedtuple,
     OrderedDict
 )
+from io import StringIO
 from textwrap import TextWrapper
 
 import requests
 import yaml
 from boltons.iterutils import remap
-from six import StringIO
 
 try:
     from pykwalify.core import Core
@@ -405,7 +405,7 @@ def _to_rst(args, app_desc, heading_level="~"):
 def _write_option_rst(args, rst, key, heading_level, option_value):
     title = "``%s``" % key
     heading = heading_level * len(title)
-    rst.write("{}\n{}\n{}\n\n".format(heading, title, heading))
+    rst.write(f"{heading}\n{title}\n{heading}\n\n")
     option, value = _parse_option_value(option_value)
     desc = option["desc"]
     rst.write(":Description:\n")
@@ -649,7 +649,7 @@ def _is_ini(path):
 def _replace_file(args, f, app_desc, from_path, to_path):
     _write_to_file(args, f, to_path)
     backup_path = "%s.backup" % from_path
-    print("Moving [{}] to [{}]".format(from_path, backup_path))
+    print(f"Moving [{from_path}] to [{backup_path}]")
     if args.dry_run:
         print("... skipping because --dry-run is enabled.")
     else:
@@ -661,7 +661,7 @@ def _build_sample_yaml(args, app_desc):
         UWSGI_OPTIONS.update(SHED_ONLY_UWSGI_OPTIONS)
     schema = app_desc.schema
     f = StringIO()
-    for key, value in UWSGI_OPTIONS.items():
+    for value in UWSGI_OPTIONS.values():
         for field in ["desc", "default"]:
             if field not in value:
                 continue
@@ -693,7 +693,7 @@ def _write_to_file(args, f, path):
         contents = f
     if args.dry_run:
         contents_indented = "\n".join(" |%s" % l for l in contents.splitlines())
-        print("Overwriting {} with the following contents:\n{}".format(path, contents_indented))
+        print(f"Overwriting {path} with the following contents:\n{contents_indented}")
         print("... skipping because --dry-run is enabled.")
     else:
         print("Overwriting %s" % path)
@@ -743,10 +743,10 @@ def _write_option(args, f, key, option_value, as_comment=False, uwsgi_hack=False
     if uwsgi_hack:
         if option.get("type", "str") == "bool":
             value = str(value).lower()
-        key_val_str = "{}: {}".format(key, value)
+        key_val_str = f"{key}: {value}"
     else:
         key_val_str = yaml.dump({key: value}, width=float("inf")).lstrip("{").rstrip("\n}")
-    lines = "{}{}{}".format(comment, as_comment_str, key_val_str)
+    lines = f"{comment}{as_comment_str}{key_val_str}"
     lines_idented = "\n".join("  %s" % l for l in lines.split("\n"))
     f.write("%s\n\n" % lines_idented)
 
@@ -774,7 +774,7 @@ def _server_paste_to_uwsgi(app_desc, server_config, applied_filters):
     if server_config.get("use", "egg:Paste#http") != "egg:Paste#http":
         raise Exception("Unhandled paste server 'use' value [%s], file must be manually migrate.")
 
-    uwsgi_dict["http"] = "{}:{}".format(host, port)
+    uwsgi_dict["http"] = f"{host}:{port}"
     # default changing from 10 to 8
     uwsgi_dict["threads"] = int(server_config.get("threadpool_workers", 8))
     # required for static...
@@ -791,7 +791,7 @@ def _server_paste_to_uwsgi(app_desc, server_config, applied_filters):
             uwsgi_dict["http-auto-gzip"] = True
 
     if prefix:
-        uwsgi_dict["mount"] = "{}={}".format(prefix, app_desc.uwsgi_module)
+        uwsgi_dict["mount"] = f"{prefix}={app_desc.uwsgi_module}"
         uwsgi_dict["manage-script-name"] = True
     else:
         uwsgi_dict["module"] = app_desc.uwsgi_module

lib/galaxy/config/schema.py

@@ -84,7 +84,7 @@ class AppSchema(Schema):
 
         def check_type_is_str_or_any(option, key):
             if option.get('type') not in ('str', 'any'):
-                message = "Invalid schema: property '{}' should have type 'str'".format(key)
+                message = f"Invalid schema: property '{key}' should have type 'str'"
                 raise_error(message)
 
         def check_is_dag():

lib/galaxy/containers/__init__.py

@@ -17,7 +17,6 @@ from abc import (
 from collections import namedtuple
 
 import yaml
-from six.moves import shlex_quote
 
 from galaxy.exceptions import ContainerCLIError
 from galaxy.util.submodules import import_submodules
@@ -234,14 +233,14 @@ class ContainerInterface(metaclass=ABCMeta):
     def _stringify_kwopt_string(self, flag, val):
         """
         """
-        return '{flag} {value}'.format(flag=flag, value=shlex_quote(str(val)))
+        return '{flag} {value}'.format(flag=flag, value=shlex.quote(str(val)))
 
     def _stringify_kwopt_list(self, flag, val):
         """
         """
         if isinstance(val, str):
             return self._stringify_kwopt_string(flag, val)
-        return ' '.join('{flag} {value}'.format(flag=flag, value=shlex_quote(str(v))) for v in val)
+        return ' '.join('{flag} {value}'.format(flag=flag, value=shlex.quote(str(v))) for v in val)
 
     def _stringify_kwopt_list_of_kvpairs(self, flag, val):
         """
@@ -253,7 +252,7 @@ class ContainerInterface(metaclass=ABCMeta):
         else:
             # {'foo': 'bar', 'baz': 'quux'}
             for k, v in dict(val).items():
-                l.append('{k}={v}'.format(k=k, v=v))
+                l.append(f'{k}={v}')
         return self._stringify_kwopt_list(flag, l)
 
     def _stringify_kwopt_list_of_kovtrips(self, flag, val):
@@ -263,7 +262,7 @@ class ContainerInterface(metaclass=ABCMeta):
             return self._stringify_kwopt_string(flag, val)
         l = []
         for k, o, v in val:
-            l.append('{k}{o}{v}'.format(k=k, o=o, v=v))
+            l.append(f'{k}{o}{v}')
         return self._stringify_kwopt_list(flag, l)
 
     def _run_command(self, command, verbose=False):
@@ -275,7 +274,7 @@ class ContainerInterface(metaclass=ABCMeta):
         if p.returncode == 0:
             return stdout.strip()
         else:
-            msg = "Command '{}' returned non-zero exit status {}".format(command, p.returncode)
+            msg = f"Command '{command}' returned non-zero exit status {p.returncode}"
             log.error(msg + ': ' + stderr.strip())
             raise ContainerCLIError(
                 msg,
@@ -324,7 +323,7 @@ class ContainerInterfaceConfig(dict):
         try:
             return self[name]
         except KeyError:
-            raise AttributeError("'{}' object has no attribute '{}'".format(self.__class__.__name__, name))
+            raise AttributeError(f"'{self.__class__.__name__}' object has no attribute '{name}'")
 
     def get(self, name, default=None):
         try:

lib/galaxy/containers/docker.py

@@ -4,6 +4,7 @@ Interface to Docker
 
 import logging
 import os
+import shlex
 from functools import partial
 from itertools import cycle, repeat
 from time import sleep
@@ -18,7 +19,6 @@ try:
 except ImportError:
     ConnectionError = None
     ReadTimeout = None
-from six.moves import shlex_quote
 
 from galaxy.containers import ContainerInterface
 from galaxy.containers.docker_decorators import (
@@ -130,7 +130,7 @@ class DockerCLIInterface(DockerInterface):
         global_kwopts = []
         if self._conf.host:
             global_kwopts.append('--host')
-            global_kwopts.append(shlex_quote(self._conf.host))
+            global_kwopts.append(shlex.quote(self._conf.host))
         if self._conf.force_tlsverify:
             global_kwopts.append('--tlsverify')
         self._docker_command = self._conf['command_template'].format(
@@ -142,9 +142,9 @@ class DockerCLIInterface(DockerInterface):
 
     def _filter_by_id_or_name(self, id, name):
         if id:
-            return '--filter id={}'.format(id)
+            return f'--filter id={id}'
         elif name:
-            return '--filter name={}'.format(name)
+            return f'--filter name={name}'
         return None
 
     def _stringify_kwopt_docker_volumes(self, flag, val):
@@ -159,7 +159,7 @@ class DockerCLIInterface(DockerInterface):
             for hostvol, guestopts in val.items():
                 if isinstance(guestopts, str):
                     # {'/host/vol': '/container/vol'}
-                    l.append('{}:{}'.format(hostvol, guestopts))
+                    l.append(f'{hostvol}:{guestopts}')
                 else:
                     # {'/host/vol': {'bind': '/container/vol'}}
                     # {'/host/vol': {'bind': '/container/vol', 'mode': 'rw'}}
@@ -198,7 +198,7 @@ class DockerCLIInterface(DockerInterface):
             return self._run_docker(subcommand='inspect', args=container_id)[0]
         except (IndexError, ContainerCLIError) as exc:
             msg = "Invalid container id: %s" % container_id
-            if exc.stdout == '[]' and exc.stderr == 'Error: no such object: {container_id}'.format(container_id=container_id):
+            if exc.stdout == '[]' and exc.stderr == f'Error: no such object: {container_id}':
                 log.warning(msg)
                 return []
             else:
@@ -210,7 +210,7 @@ class DockerCLIInterface(DockerInterface):
             return self._run_docker(subcommand='image inspect', args=image)[0]
         except (IndexError, ContainerCLIError) as exc:
             msg = "%s not pulled, cannot get digest" % image
-            if exc.stdout == '[]' and exc.stderr == 'Error: no such image: {image}'.format(image=image):
+            if exc.stdout == '[]' and exc.stderr == f'Error: no such image: {image}':
                 log.warning(msg, image)
                 return []
             else:

lib/galaxy/containers/docker_model.py

@@ -3,13 +3,13 @@ Model objects for docker objects
 """
 
 import logging
+import shlex
 
 try:
     import docker
 except ImportError:
     from galaxy.util.bunch import Bunch
     docker = Bunch(errors=Bunch(NotFound=None))
-from six.moves import shlex_quote
 
 from galaxy.containers import (
     Container,
@@ -106,7 +106,7 @@ class DockerVolume(ContainerVolume):
     def __str__(self):
         volume_str = ":".join(filter(lambda x: x is not None, (self.host_path, self.path, self.mode)))
         if "$" not in volume_str:
-            volume_for_cmd_line = shlex_quote(volume_str)
+            volume_for_cmd_line = shlex.quote(volume_str)
         else:
             # e.g. $_GALAXY_JOB_TMP_DIR:$_GALAXY_JOB_TMP_DIR:rw so don't single quote.
             volume_for_cmd_line = '"%s"' % volume_str
@@ -393,10 +393,10 @@ class DockerServiceConstraint:
         return hash((self._name, self._op, self._value))
 
     def __repr__(self):
-        return '{}({}{}{})'.format(self.__class__.__name__, self._name, self._op, self._value)
+        return f'{self.__class__.__name__}({self._name}{self._op}{self._value})'
 
     def __str__(self):
-        return '{}{}{}'.format(self._name, self._op, self._value)
+        return f'{self._name}{self._op}{self._value}'
 
     @staticmethod
     def split_constraint_string(constraint_str):
@@ -508,7 +508,7 @@ class DockerNode:
 
     @property
     def state(self):
-        return ('{}-{}'.format(self._status, self._availability)).lower()
+        return (f'{self._status}-{self._availability}').lower()
 
     @property
     def cpus(self):
@@ -597,10 +597,10 @@ class DockerNodeLabel:
         return hash((self._name, self._value))
 
     def __repr__(self):
-        return '{}({}: {})'.format(self.__class__.__name__, self._name, self._value)
+        return f'{self.__class__.__name__}({self._name}: {self._value})'
 
     def __str__(self):
-        return '{}: {}'.format(self._name, self._value)
+        return f'{self._name}: {self._value}'
 
     @property
     def name(self):
@@ -612,12 +612,12 @@ class DockerNodeLabel:
 
     @property
     def constraint_string(self):
-        return 'node.labels.{name}=={value}'.format(name=self.name, value=self.value)
+        return f'node.labels.{self.name}=={self.value}'
 
     @property
     def constraint(self):
         return DockerServiceConstraint(
-            name='node.labels.{name}'.format(name=self.name),
+            name=f'node.labels.{self.name}',
             op='==',
             value=self.value
         )
@@ -744,7 +744,7 @@ class DockerTask:
 
     @property
     def state(self):
-        return ('{}-{}'.format(self._desired_state, self._state)).lower()
+        return (f'{self._desired_state}-{self._state}').lower()
 
     @property
     def current_state(self):

lib/galaxy/containers/docker_swarm.py

@@ -331,7 +331,7 @@ class DockerSwarmCLIInterface(DockerSwarmInterface, DockerCLIInterface):
 
     @docker_columns
     def service_ps(self, service_id):
-        return self._run_docker(subcommand='service ps', args='--no-trunc {}'.format(service_id))
+        return self._run_docker(subcommand='service ps', args=f'--no-trunc {service_id}')
 
     def service_rm(self, service_ids):
         service_ids = ' '.join(service_ids)
@@ -347,7 +347,7 @@ class DockerSwarmCLIInterface(DockerSwarmInterface, DockerCLIInterface):
 
     @docker_columns
     def node_ps(self, node_id):
-        return self._run_docker(subcommand='node ps', args='--no-trunc {}'.format(node_id))
+        return self._run_docker(subcommand='node ps', args=f'--no-trunc {node_id}')
 
     def node_update(self, node_id, **kwopts):
         return self._run_docker(subcommand='node update', args='{kwopts} {node_id}'.format(

lib/galaxy/datatypes/anvio.py

@@ -37,7 +37,7 @@ class AnvioComposite(Html):
                 missing_text = ''
                 if not os.path.exists(os.path.join(dataset.extra_files_path, composite_name)):
                     missing_text = ' (missing)'
-                rval.append('<li><a href="{}">{}</a>{}{}</li>'.format(composite_name, composite_name, opt_text, missing_text))
+                rval.append(f'<li><a href="{composite_name}">{composite_name}</a>{opt_text}{missing_text}</li>')
             rval.append("</ul>")
         defined_files = map(lambda x: x[0], defined_files)
         extra_files = []
@@ -49,7 +49,7 @@ class AnvioComposite(Html):
         if extra_files:
             rval.append("<p/>This composite dataset contains these undefined files:<p/><ul>")
             for rel_path in extra_files:
-                rval.append('<li><a href="{}">{}</a></li>'.format(rel_path, rel_path))
+                rval.append(f'<li><a href="{rel_path}">{rel_path}</a></li>')
             rval.append('</ul>')
         if not (defined_files or extra_files):
             rval.append("<p/>This composite dataset does not contain any files!<p/><ul>")

lib/galaxy/datatypes/assembly.py

@@ -157,7 +157,7 @@ class Velvet(Html):
             if composite_file.get('description'):
                 rval.append('<li><a href="{}" type="text/plain">{} ({})</a>{}</li>'.format(fn, fn, composite_file.get('description'), opt_text))
             else:
-                rval.append('<li><a href="{}" type="text/plain">{}</a>{}</li>'.format(fn, fn, opt_text))
+                rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
         rval.append('</ul></div></html>')
         return "\n".join(rval)
 
@@ -204,7 +204,7 @@ class Velvet(Html):
                 if composite_file.get('description'):
                     rval.append('<li><a href="{}" type="text/plain">{} ({})</a>{}</li>'.format(fn, fn, composite_file.get('description'), opt_text))
                 else:
-                    rval.append('<li><a href="{}" type="text/plain">{}</a>{}</li>'.format(fn, fn, opt_text))
+                    rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
         rval.append('</ul></div></html>')
         with open(dataset.file_name, 'w') as f:
             f.write("\n".join(rval))

lib/galaxy/datatypes/binary.py

@@ -403,7 +403,7 @@ class BamNative(CompressedArchive):
                             # Galaxy display each tag as separate column because 'tostring()' funcition put tabs in between each tag of tags column.
                             # Below code will remove spaces between each tag.
                             bamline_modified = ('\t').join(bamline.split()[:11] + [(' ').join(bamline.split()[11:])])
-                            ck_data = "{}\n{}".format(ck_data, bamline_modified)
+                            ck_data = f"{ck_data}\n{bamline_modified}"
                     else:
                         # Nothing to enumerate; we've either offset to the end
                         # of the bamfile, or there is no data. (possible with
@@ -489,9 +489,9 @@ class Bam(BamNative):
             # we start another process and discard stderr.
             if index_flag == '-b':
                 # IOError: No such file or directory: '-b' if index_flag is set to -b (pysam 0.15.4)
-                cmd = ['python', '-c', "import pysam; pysam.set_verbosity(0); pysam.index('{}', '{}')".format(file_name, index_name)]
+                cmd = ['python', '-c', f"import pysam; pysam.set_verbosity(0); pysam.index('{file_name}', '{index_name}')"]
             else:
-                cmd = ['python', '-c', "import pysam; pysam.set_verbosity(0); pysam.index('{}', '{}', '{}')".format(index_flag, file_name, index_name)]
+                cmd = ['python', '-c', f"import pysam; pysam.set_verbosity(0); pysam.index('{index_flag}', '{file_name}', '{index_name}')"]
             with open(os.devnull, 'w') as devnull:
                 subprocess.check_call(cmd, stderr=devnull, shell=False)
             needs_sorting = False
@@ -1711,7 +1711,7 @@ class CuffDiffSQlite(SQlite):
             for gene_id, gene_name in result:
                 if gene_name is None:
                     continue
-                gene = '{}: {}'.format(gene_id, gene_name)
+                gene = f'{gene_id}: {gene_name}'
                 if gene not in genes:
                     genes.append(gene)
             samples_query = 'SELECT DISTINCT(sample_name) as sample_name FROM samples ORDER BY sample_name'
@@ -1859,7 +1859,7 @@ class BlibSQlite(SQlite):
             c = conn.cursor()
             tables_query = "SELECT majorVersion,minorVersion FROM LibInfo"
             (majorVersion, minorVersion) = c.execute(tables_query).fetchall()[0]
-            dataset.metadata.blib_version = '{}.{}'.format(majorVersion, minorVersion)
+            dataset.metadata.blib_version = f'{majorVersion}.{minorVersion}'
         except Exception as e:
             log.warning('%s, set_meta Exception: %s', self, e)
 

lib/galaxy/datatypes/blast.py

@@ -147,7 +147,7 @@ class BlastXml(GenericXml):
                         raise ValueError("The header in BLAST XML file %s is too long" % f)
                 if "<BlastOutput>" not in header:
                     h.close()
-                    raise ValueError("{} is not a BLAST XML file:\n{}\n...".format(f, header))
+                    raise ValueError(f"{f} is not a BLAST XML file:\n{header}\n...")
                 if f == split_files[0]:
                     out.write(header)
                     old_header = header
@@ -223,7 +223,7 @@ class _BlastDb(Data):
         if not msg:
             msg = title
         # Galaxy assumes HTML for the display of composite datatypes,
-        return smart_str("<html><head><title>{}</title></head><body><pre>{}</pre></body></html>".format(title, msg))
+        return smart_str(f"<html><head><title>{title}</title></head><body><pre>{msg}</pre></body></html>")
 
     def merge(split_files, output_file):
         """Merge BLAST databases (not implemented for now)."""

lib/galaxy/datatypes/converters/fastq_to_fqtoc.py

@@ -34,7 +34,7 @@ def main():
             current_line += 1
             if 0 == current_line % lines_per_chunk:
                 chunk_end = in_file.tell()
-                out_file.write('{{"start":"{}","end":"{}","sequences":"{}"}},'.format(chunk_begin, chunk_end, sequences))
+                out_file.write(f'{{"start":"{chunk_begin}","end":"{chunk_end}","sequences":"{sequences}"}},')
                 chunk_begin = chunk_end
             line = in_file.readline()
 

lib/galaxy/datatypes/converters/lped_to_fped_converter.py

@@ -41,7 +41,7 @@ def rgConv(inpedfilepath, outhtmlname, outfilepath):
     try:
         mf = open(inmap)
     except Exception:
-        sys.exit('{} cannot open inmap file {} - do you have permission?\n'.format(prog, inmap))
+        sys.exit(f'{prog} cannot open inmap file {inmap} - do you have permission?\n')
     try:
         rsl = [x.split()[1] for x in mf]
     except Exception:
@@ -94,8 +94,8 @@ def main():
     flist = os.listdir(outfilepath)
     with open(outhtmlname, 'w') as f:
         f.write(galhtmlprefix % prog)
-        print('## Rgenetics: http://rgenetics.org Galaxy Tools {} {}'.format(prog, timenow()))  # becomes info
-        f.write('<div>## Rgenetics: http://rgenetics.org Galaxy Tools {} {}\n<ol>'.format(prog, timenow()))
+        print(f'## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}')  # becomes info
+        f.write(f'<div>## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}\n<ol>')
         for i, data in enumerate(flist):
             f.write('<li><a href="{}">{}</a></li>\n'.format(os.path.split(data)[-1], os.path.split(data)[-1]))
         f.write("</div></body></html>")

lib/galaxy/datatypes/converters/lped_to_pbed_converter.py

@@ -99,7 +99,7 @@ def main():
     flist = os.listdir(outfilepath)
     with open(outhtmlname, 'w') as f:
         f.write(galhtmlprefix % prog)
-        s = '## Rgenetics: http://rgenetics.org Galaxy Tools {} {}'.format(prog, timenow())  # becomes info
+        s = f'## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}'  # becomes info
         print(s)
         f.write('<div>%s\n<ol>' % (s))
         for i, data in enumerate(flist):

lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py

@@ -60,8 +60,8 @@ def makeLDreduced(basename, infpath=None, outfpath=None, plinke='plink', forcere
     inbase = os.path.join(infpath)
     plinktasks = []
     vclbase = [plinke, '--noweb']
-    plinktasks += [['--bfile', inbase, '--indep-pairwise {} {} {}'.format(winsize, winmove, r2thresh), '--out %s' % outbase],
-                   ['--bfile', inbase, '--extract {}.prune.in --make-bed --out {}'.format(outbase, outbase)]]
+    plinktasks += [['--bfile', inbase, f'--indep-pairwise {winsize} {winmove} {r2thresh}', '--out %s' % outbase],
+                   ['--bfile', inbase, f'--extract {outbase}.prune.in --make-bed --out {outbase}']]
     vclbase = [plinke, '--noweb']
     pruneLD(plinktasks=plinktasks, cd=outfpath, vclbase=vclbase)
 
@@ -99,10 +99,10 @@ def main():
     flist = os.listdir(outfilepath)
     with open(outhtmlname, 'w') as f:
         f.write(galhtmlprefix % prog)
-        s1 = '## Rgenetics: http://rgenetics.org Galaxy Tools {} {}'.format(prog, timenow())  # becomes info
-        s2 = 'Input {}, winsize={}, winmove={}, r2thresh={}'.format(base_name, winsize, winmove, r2thresh)
-        print('{} {}'.format(s1, s2))
-        f.write('<div>{}\n{}\n<ol>'.format(s1, s2))
+        s1 = f'## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}'  # becomes info
+        s2 = f'Input {base_name}, winsize={winsize}, winmove={winmove}, r2thresh={r2thresh}'
+        print(f'{s1} {s2}')
+        f.write(f'<div>{s1}\n{s2}\n<ol>')
         for i, data in enumerate(flist):
             f.write('<li><a href="{}">{}</a></li>\n'.format(os.path.split(data)[-1], os.path.split(data)[-1]))
         f.write("</div></body></html>")

lib/galaxy/datatypes/converters/pbed_to_lped_converter.py

@@ -65,7 +65,7 @@ def main():
     flist = os.listdir(outfilepath)
     with open(outhtmlname, 'w') as f:
         f.write(galhtmlprefix % prog)
-        s = '## Rgenetics: http://bitbucket.org/rgalaxy Galaxy Tools {} {}'.format(prog, timenow())  # becomes info
+        s = f'## Rgenetics: http://bitbucket.org/rgalaxy Galaxy Tools {prog} {timenow()}'  # becomes info
         print(s)
         f.write('<div>%s\n<ol>' % (s))
         for i, data in enumerate(flist):

lib/galaxy/datatypes/data.py

@@ -65,7 +65,7 @@ class DatatypeValidation:
         return DatatypeValidation("unknown", "Dataset validation unimplemented for this datatype.")
 
     def __repr__(self):
-        return "DatatypeValidation[state={},message={}]".format(self.state, self.message)
+        return f"DatatypeValidation[state={self.state},message={self.message}]"
 
 
 def validate(dataset_instance):
@@ -313,7 +313,7 @@ class Data(metaclass=DataMeta):
 
             display_name = os.path.splitext(outfname)[0]
             if not display_name.endswith(ext):
-                display_name = '{}_{}'.format(display_name, ext)
+                display_name = f'{display_name}_{ext}'
 
             error, msg = self._archive_main_file(archive, display_name, path)[:2]
             if not error:
@@ -339,7 +339,7 @@ class Data(metaclass=DataMeta):
                     outext = 'tgz'
                     if do_action == 'tbz':
                         outext = 'tbz'
-                    trans.response.headers["Content-Disposition"] = 'attachment; filename="{}.{}"'.format(outfname, outext)
+                    trans.response.headers["Content-Disposition"] = f'attachment; filename="{outfname}.{outext}"'
                     archive.wsgi_status = trans.response.wsgi_status()
                     archive.wsgi_headeritems = trans.response.wsgi_headeritems()
                     return archive.stream
@@ -438,7 +438,7 @@ class Data(metaclass=DataMeta):
                 self._clean_and_set_mime_type(trans, mime)
                 return self._yield_user_file_content(trans, data, file_path)
             else:
-                return webob.exc.HTTPNotFound("Could not find '{}' on the extra files path {}.".format(filename, file_path))
+                return webob.exc.HTTPNotFound(f"Could not find '{filename}' on the extra files path {file_path}.")
         self._clean_and_set_mime_type(trans, data.get_mime())
 
         trans.log_event("Display dataset id: %s" % str(data.id))
@@ -627,7 +627,7 @@ class Data(metaclass=DataMeta):
                 return getattr(self, self.supported_display_apps[type]['file_function'])(dataset, **kwd)
         except Exception:
             log.exception('Function %s is referred to in datatype %s for displaying as type %s, but is not accessible', self.supported_display_apps[type]['file_function'], self.__class__.__name__, type)
-        return "This display type ({}) is not implemented for this datatype ({}).".format(type, dataset.ext)
+        return f"This display type ({type}) is not implemented for this datatype ({dataset.ext})."
 
     def get_display_links(self, dataset, type, app, base_url, target_frame='_blank', **kwd):
         """
@@ -657,7 +657,7 @@ class Data(metaclass=DataMeta):
         converter = trans.app.datatypes_registry.get_converter_by_target_type(original_dataset.ext, target_type)
 
         if converter is None:
-            raise Exception("A converter does not exist for {} to {}.".format(original_dataset.ext, target_type))
+            raise Exception(f"A converter does not exist for {original_dataset.ext} to {target_type}.")
         # Generate parameter dictionary
         params = {}
         # determine input parameter name and add to params
@@ -683,7 +683,7 @@ class Data(metaclass=DataMeta):
                 value.visible = False
         if return_output:
             return converted_dataset
-        return "The file conversion of {} on data {} has been added to the Queue.".format(converter.name, original_dataset.hid)
+        return f"The file conversion of {converter.name} on data {original_dataset.hid} has been added to the Queue."
 
     # We need to clear associated files before we set metadata
     # so that as soon as metadata starts to be set, e.g. implicitly converted datasets are deleted and no longer available 'while' metadata is being set, not just after
@@ -856,7 +856,7 @@ class Text(Data):
             sample_lines = dataset_read.count('\n')
             est_lines = int(sample_lines * (float(dataset.get_size()) / float(sample_size)))
         except UnicodeDecodeError:
-            log.error('Unable to estimate lines in file {}'.format(dataset.file_name))
+            log.error(f'Unable to estimate lines in file {dataset.file_name}')
             est_lines = None
         return est_lines
 
@@ -880,7 +880,7 @@ class Text(Data):
                     if line and not line.startswith('#'):
                         data_lines += 1
             except UnicodeDecodeError:
-                log.error('Unable to count lines in file {}'.format(dataset.file_name))
+                log.error(f'Unable to count lines in file {dataset.file_name}')
                 data_lines = None
         return data_lines
 

lib/galaxy/datatypes/dataproviders/column.py

@@ -4,8 +4,7 @@ is further subdivided into multiple data (e.g. columns from a line).
 """
 import logging
 import re
-
-from six.moves.urllib.parse import unquote_plus
+from urllib.parse import unquote_plus
 
 from . import line
 

lib/galaxy/datatypes/dataproviders/decorators.py

@@ -17,8 +17,7 @@ DataProvider related decorators.
 import copy
 import logging
 from functools import wraps
-
-from six.moves.urllib.parse import unquote
+from urllib.parse import unquote
 
 log = logging.getLogger(__name__)
 
@@ -104,8 +103,8 @@ def dataprovider_factory(name, settings=None):
     def named_dataprovider_factory(func):
         setattr(func, _DATAPROVIDER_METHOD_NAME_KEY, name)
 
-        setattr(func, 'parse_query_string_settings', parse_query_string_settings)
-        setattr(func, 'settings', settings)
+        func.parse_query_string_settings = parse_query_string_settings
+        func.settings = settings
         # TODO: I want a way to inherit settings from the previous provider( this_name ) instead of defining over and over
 
         @wraps(func)

lib/galaxy/datatypes/dataproviders/external.py

@@ -6,9 +6,11 @@ import gzip
 import logging
 import subprocess
 import tempfile
-
-from six.moves.urllib.parse import urlencode, urlparse
-from six.moves.urllib.request import urlopen
+from urllib.parse import (
+    urlencode,
+    urlparse,
+)
+from urllib.request import urlopen
 
 from . import (
     base,

lib/galaxy/datatypes/display_applications/application.py

@@ -2,8 +2,7 @@
 import logging
 from collections import OrderedDict
 from copy import deepcopy
-
-from six.moves.urllib.parse import quote_plus
+from urllib.parse import quote_plus
 
 from galaxy.util import (
     parse_xml,
@@ -192,7 +191,7 @@ class DynamicDisplayApplicationBuilder:
                 # now populate
                 links.append(DisplayApplicationLink.from_elem(new_elem, display_application, other_values=dynamic_values))
             else:
-                log.warning('Invalid dynamic display application link specified in {}: "{}"'.format(filename, line))
+                log.warning(f'Invalid dynamic display application link specified in {filename}: "{line}"')
         self.links = links
 
     def __iter__(self):

lib/galaxy/datatypes/display_applications/parameters.py

@@ -1,7 +1,6 @@
 # Contains parameters that are used in Display Applications
 import mimetypes
-
-from six.moves.urllib.parse import quote_plus
+from urllib.parse import quote_plus
 
 from galaxy.util import string_as_bool
 from galaxy.util.bunch import Bunch
@@ -83,7 +82,7 @@ class DisplayApplicationDataParameter(DisplayApplicationParameter):
             data = data.value
         if self.metadata:
             rval = getattr(data.metadata, self.metadata, None)
-            assert rval, 'Unknown metadata name ({}) provided for dataset type ({}).'.format(self.metadata, data.datatype.__class__.name)
+            assert rval, f'Unknown metadata name ({self.metadata}) provided for dataset type ({data.datatype.__class__.name}).'
             return Bunch(file_name=rval.file_name, state=data.state, states=data.states, extension='data')
         elif self.extensions and (self.force_conversion or not isinstance(data.datatype, self.formats)):
             for ext in self.extensions:

lib/galaxy/datatypes/genetics.py

@@ -15,9 +15,9 @@ import logging
 import os
 import re
 import sys
+from urllib.parse import quote_plus
 
 from markupsafe import escape
-from six.moves.urllib.parse import quote_plus
 
 from galaxy.datatypes import metadata
 from galaxy.datatypes.data import (
@@ -107,7 +107,7 @@ class GenomeGraphs(Tabular):
                     display_url = quote_plus(display_url)
                     # was display_url = quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) )
                     # redirect_url = quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) )
-                    sl = ["{}db={}".format(site_url, dataset.dbkey), ]
+                    sl = [f"{site_url}db={dataset.dbkey}", ]
                     # sl.append("&hgt.customText=%s")
                     sl.append("&hgGenome_dataSetName={}&hgGenome_dataSetDescription={}".format(dataset.name, 'GalaxyGG_data'))
                     sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess")
@@ -117,7 +117,7 @@ class GenomeGraphs(Tabular):
                     s = ''.join(sl)
                     s = quote_plus(s)
                     redirect_url = s
-                    link = '{}?redirect_url={}&display_url={}'.format(internal_url, redirect_url, display_url)
+                    link = f'{internal_url}?redirect_url={redirect_url}&display_url={display_url}'
                     ret_val.append((site_name, link))
         return ret_val
 
@@ -286,7 +286,7 @@ class Rgenetics(Html):
             if composite_file.get('description'):
                 rval.append('<li><a href="{}" type="application/binary">{} ({})</a>{}</li>'.format(fn, fn, composite_file.get('description'), opt_text))
             else:
-                rval.append('<li><a href="{}" type="application/binary">{}</a>{}</li>'.format(fn, fn, opt_text))
+                rval.append(f'<li><a href="{fn}" type="application/binary">{fn}</a>{opt_text}</li>')
         rval.append('</ul></div></html>')
         return "\n".join(rval)
 
@@ -296,11 +296,11 @@ class Rgenetics(Html):
         """
         efp = dataset.extra_files_path
         flist = os.listdir(efp)
-        rval = ['<html><head><title>Files for Composite Dataset {}</title></head><body><p/>Composite {} contains:<p/><ul>'.format(dataset.name, dataset.name)]
+        rval = [f'<html><head><title>Files for Composite Dataset {dataset.name}</title></head><body><p/>Composite {dataset.name} contains:<p/><ul>']
         for fname in flist:
             sfname = os.path.split(fname)[-1]
             f, e = os.path.splitext(fname)
-            rval.append('<li><a href="{}">{}</a></li>'.format(sfname, sfname))
+            rval.append(f'<li><a href="{sfname}">{sfname}</a></li>')
         rval.append('</ul></body></html>')
         with open(dataset.file_name, 'w') as f:
             f.write("\n".join(rval))
@@ -334,7 +334,7 @@ class Rgenetics(Html):
             return False
         if len(flist) == 0:
             if verbose:
-                gal_Log.debug('@@@rgenetics set_meta failed - {} efp {} is empty?'.format(dataset.name, efp))
+                gal_Log.debug(f'@@@rgenetics set_meta failed - {dataset.name} efp {efp} is empty?')
             return False
         self.regenerate_primary_file(dataset)
         if not dataset.info:
@@ -555,7 +555,7 @@ class IdeasPre(Html):
         rval.append('<ul>')
         for composite_name in self.get_composite_files(dataset=dataset).keys():
             fn = composite_name
-            rval.append('<li><a href="{}>{}</a></li>'.format(fn, fn))
+            rval.append(f'<li><a href="{fn}>{fn}</a></li>')
         rval.append('</ul></body></html>\n')
         return "\n".join(rval)
 
@@ -566,7 +566,7 @@ class IdeasPre(Html):
         rval.append('<ul>')
         for fname in os.listdir(dataset.extra_files_path):
             fn = os.path.split(fname)[-1]
-            rval.append('<li><a href="{}">{}</a></li>'.format(fn, fn))
+            rval.append(f'<li><a href="{fn}">{fn}</a></li>')
         rval.append('</ul></body></html>')
         with open(dataset.file_name, 'w') as f:
             f.write("\n".join(rval))
@@ -752,7 +752,7 @@ class RexpBase(Html):
         rval = ['<html><head><title>Files for Composite Dataset %s</title></head><p/>Comprises the following files:<p/><ul>' % (bn)]
         for fname in flist:
             sfname = os.path.split(fname)[-1]
-            rval.append('<li><a href="{}">{}</a>'.format(sfname, sfname))
+            rval.append(f'<li><a href="{sfname}">{sfname}</a>')
         rval.append('</ul></html>')
         with open(dataset.file_name, 'w') as f:
             f.write("\n".join(rval))

lib/galaxy/datatypes/gis.py

@@ -42,7 +42,7 @@ class Shapefile(Binary):
             if composite_file.get('description'):
                 rval.append('<li><a href="{}" type="application/binary">{} ({})</a>{}</li>'.format(fn, fn, composite_file.get('description'), opt_text))
             else:
-                rval.append('<li><a href="{}" type="application/binary">{}</a>{}</li>'.format(fn, fn, opt_text))
+                rval.append(f'<li><a href="{fn}" type="application/binary">{fn}</a>{opt_text}</li>')
         rval.append('</ul></div></html>\n')
         return "\n".join(rval)
 

lib/galaxy/datatypes/images.py

@@ -4,8 +4,7 @@ Image classes
 import base64
 import logging
 import zipfile
-
-from six.moves.urllib.parse import quote_plus
+from urllib.parse import quote_plus
 
 from galaxy.datatypes.text import Html as HtmlFromText
 from galaxy.util import nice_size
@@ -52,7 +51,7 @@ class Image(data.Data):
         name = hda.name or ''
         with open(dataset.file_name, "rb") as f:
             base64_image_data = base64.b64encode(f.read()).decode("utf-8")
-        return "![{}](data:image/{};base64,{})".format(name, self.file_ext, base64_image_data)
+        return f"![{name}](data:image/{self.file_ext};base64,{base64_image_data})"
 
 
 class Jpg(Image):
@@ -177,14 +176,14 @@ def create_applet_tag_peek(class_name, archive, params):
       height="30" width="200" align="center" >
       <param name="archive" value="{}"/>""".format(class_name, archive)
     for name, value in params.items():
-        text += """<param name="{}" value="{}"/>""".format(name, value)
+        text += f"""<param name="{name}" value="{value}"/>"""
     text += """
 <object classid="clsid:8AD9C840-044E-11D1-B3E9-00805F499D93"
         height="30" width="200" >
         <param name="code" value="{}" />
         <param name="archive" value="{}"/>""".format(class_name, archive)
     for name, value in params.items():
-        text += """<param name="{}" value="{}"/>""".format(name, value)
+        text += f"""<param name="{name}" value="{value}"/>"""
     text += """<div class="errormessage">You must install and enable Java in your browser in order to access this applet.<div></object>
 </object>
 """
@@ -265,7 +264,7 @@ class Laj(data.Text):
                     "alignfile1": "display?id=%s" % dataset.id,
                     "buttonlabel": "Launch LAJ",
                     "title": "LAJ in Galaxy",
-                    "posturl": quote_plus("history_add_to?%s" % "&".join("{}={}".format(key, value) for key, value in {'history_id': dataset.history_id, 'ext': 'lav', 'name': 'LAJ Output', 'info': 'Added by LAJ', 'dbkey': dataset.dbkey, 'copy_access_from': dataset.id}.items())),
+                    "posturl": quote_plus("history_add_to?%s" % "&".join(f"{key}={value}" for key, value in {'history_id': dataset.history_id, 'ext': 'lav', 'name': 'LAJ Output', 'info': 'Added by LAJ', 'dbkey': dataset.dbkey, 'copy_access_from': dataset.id}.items())),
                     "noseq": "true"
                 }
                 class_name = "edu.psu.cse.bio.laj.LajApplet.class"

lib/galaxy/datatypes/interval.py

@@ -5,9 +5,9 @@ import logging
 import math
 import sys
 import tempfile
+from urllib.parse import quote_plus
 
 from bx.intervals.io import GenomicIntervalReader, ParseError
-from six.moves.urllib.parse import quote_plus
 
 from galaxy import util
 from galaxy.datatypes import metadata
@@ -264,7 +264,7 @@ class Interval(Tabular):
                                      (base_url, app.url_for(controller='root'), dataset.id, type))
             redirect_url = quote_plus("%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" %
                                       (site_url, dataset.dbkey, chrom, start, stop))
-            link = '{}?redirect_url={}&display_url={}'.format(internal_url, redirect_url, display_url)
+            link = f'{internal_url}?redirect_url={redirect_url}&display_url={display_url}'
             ret_val.append((site_name, link))
         return ret_val
 
@@ -604,11 +604,11 @@ class _RemoteCallMixin:
         the data available, followed by redirecting to the remote site with a
         link back to the available information.
         """
-        internal_url = "%s" % app.url_for(controller='dataset', dataset_id=dataset.id, action='display_at', filename='{}_{}'.format(type, site_name))
+        internal_url = "%s" % app.url_for(controller='dataset', dataset_id=dataset.id, action='display_at', filename=f'{type}_{site_name}')
         base_url = app.config.get("display_at_callback", base_url)
         display_url = quote_plus("%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" %
                                  (base_url, app.url_for(controller='root'), dataset.id, type))
-        link = '{}?redirect_url={}&display_url={}'.format(internal_url, redirect_url, display_url)
+        link = f'{internal_url}?redirect_url={redirect_url}&display_url={display_url}'
         return link
 
 
@@ -794,7 +794,7 @@ class Gff(Tabular, _RemoteCallMixin):
                 if site_name in app.datatypes_registry.get_display_sites('gbrowse'):
                     if seqid.startswith('chr') and len(seqid) > 3:
                         seqid = seqid[3:]
-                    redirect_url = quote_plus("{}/?q={}:{}..{}&eurl=%s".format(site_url, seqid, start, stop))
+                    redirect_url = quote_plus(f"{site_url}/?q={seqid}:{start}..{stop}&eurl=%s")
                     link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
                     ret_val.append((site_name, link))
         return ret_val
@@ -1146,7 +1146,7 @@ class Wiggle(Tabular, _RemoteCallMixin):
                 if site_name in app.datatypes_registry.get_display_sites('gbrowse'):
                     if chrom.startswith('chr') and len(chrom) > 3:
                         chrom = chrom[3:]
-                    redirect_url = quote_plus("{}/?q={}:{}..{}&eurl=%s".format(site_url, chrom, start, stop))
+                    redirect_url = quote_plus(f"{site_url}/?q={chrom}:{start}..{stop}&eurl=%s")
                     link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
                     ret_val.append((site_name, link))
         return ret_val
@@ -1157,7 +1157,7 @@ class Wiggle(Tabular, _RemoteCallMixin):
         if chrom is not None:
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey):
                 if site_name in app.datatypes_registry.get_display_sites('ucsc'):
-                    redirect_url = quote_plus("{}db={}&position={}:{}-{}&hgt.customText=%s".format(site_url, dataset.dbkey, chrom, start, stop))
+                    redirect_url = quote_plus(f"{site_url}db={dataset.dbkey}&position={chrom}:{start}-{stop}&hgt.customText=%s")
                     link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
                     ret_val.append((site_name, link))
         return ret_val
@@ -1324,8 +1324,8 @@ class CustomTrack(Tabular):
                 if site_name in app.datatypes_registry.get_display_sites('ucsc'):
                     internal_url = "%s" % app.url_for(controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name)
                     display_url = quote_plus("%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, app.url_for(controller='root'), dataset.id, type))
-                    redirect_url = quote_plus("{}db={}&position={}:{}-{}&hgt.customText=%s".format(site_url, dataset.dbkey, chrom, start, stop))
-                    link = '{}?redirect_url={}&display_url={}'.format(internal_url, redirect_url, display_url)
+                    redirect_url = quote_plus(f"{site_url}db={dataset.dbkey}&position={chrom}:{start}-{stop}&hgt.customText=%s")
+                    link = f'{internal_url}?redirect_url={redirect_url}&display_url={display_url}'
                     ret_val.append((site_name, link))
         return ret_val
 

lib/galaxy/datatypes/isa.py

@@ -274,7 +274,7 @@ class _Isa(data.Data):
                    </body></html>"""
         else:
             html = '<html><body>'
-            html += '<h1>{} {}</h1>'.format(investigation.title, investigation.identifier)
+            html += f'<h1>{investigation.title} {investigation.identifier}</h1>'
 
             # Loop on all studies
             for study in investigation.studies:

lib/galaxy/datatypes/microarrays.py

@@ -38,9 +38,9 @@ class GenericMicroarrayFile(data.Text):
     def set_peek(self, dataset, is_multi_byte=False):
         if not dataset.dataset.purged:
             if dataset.metadata.block_count == 1:
-                dataset.blurb = "{} {}: Format {}, 1 block, {} headers and {} columns".format(dataset.metadata.file_type, dataset.metadata.version_number, dataset.metadata.file_format, dataset.metadata.number_of_optional_header_records, dataset.metadata.number_of_data_columns)
+                dataset.blurb = f"{dataset.metadata.file_type} {dataset.metadata.version_number}: Format {dataset.metadata.file_format}, 1 block, {dataset.metadata.number_of_optional_header_records} headers and {dataset.metadata.number_of_data_columns} columns"
             else:
-                dataset.blurb = "{} {}: Format {}, {} blocks, {} headers and {} columns".format(dataset.metadata.file_type, dataset.metadata.version_number, dataset.metadata.file_format, dataset.metadata.block_count, dataset.metadata.number_of_optional_header_records, dataset.metadata.number_of_data_columns)
+                dataset.blurb = f"{dataset.metadata.file_type} {dataset.metadata.version_number}: Format {dataset.metadata.file_format}, {dataset.metadata.block_count} blocks, {dataset.metadata.number_of_optional_header_records} headers and {dataset.metadata.number_of_data_columns} columns"
             dataset.peek = get_file_peek(dataset.file_name)
         else:
             dataset.peek = 'file does not exist'

lib/galaxy/datatypes/molecules.py

@@ -514,7 +514,7 @@ class PDB(GenericMolFile):
             hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
             chain_ids = ','.join(dataset.metadata.chain_ids) if len(dataset.metadata.chain_ids) > 0 else 'None'
             dataset.peek = get_file_peek(dataset.file_name)
-            dataset.blurb = "{} atoms and {} HET-atoms\nchain_ids: {}".format(atom_numbers, hetatm_numbers, chain_ids)
+            dataset.blurb = f"{atom_numbers} atoms and {hetatm_numbers} HET-atoms\nchain_ids: {chain_ids}"
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -565,7 +565,7 @@ class PDBQT(GenericMolFile):
             root_numbers = count_special_lines("^ROOT", dataset.file_name)
             branch_numbers = count_special_lines("^BRANCH", dataset.file_name)
             dataset.peek = get_file_peek(dataset.file_name)
-            dataset.blurb = "{} roots and {} branches".format(root_numbers, branch_numbers)
+            dataset.blurb = f"{root_numbers} roots and {branch_numbers} branches"
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'

lib/galaxy/datatypes/ngsindex.py

@@ -36,7 +36,7 @@ class BowtieIndex(Html):
         rval = ['<html><head><title>Files for Composite Dataset %s</title></head><p/>Comprises the following files:<p/><ul>' % (bn)]
         for fname in flist:
             sfname = os.path.split(fname)[-1]
-            rval.append('<li><a href="{}">{}</a>'.format(sfname, sfname))
+            rval.append(f'<li><a href="{sfname}">{sfname}</a>')
         rval.append('</ul></html>')
         with open(dataset.file_name, 'w') as f:
             f.write("\n".join(rval))

lib/galaxy/datatypes/proteomics.py

@@ -48,7 +48,7 @@ class Wiff(Binary):
             if composite_file.get('description'):
                 rval.append('<li><a href="{}" type="text/plain">{} ({})</a>{}</li>'.format(fn, fn, composite_file.get('description'), opt_text))
             else:
-                rval.append('<li><a href="{}" type="text/plain">{}</a>{}</li>'.format(fn, fn, opt_text))
+                rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
         rval.append('</ul></div></html>')
         return "\n".join(rval)
 
@@ -900,7 +900,7 @@ class SPLib(Msp):
             if composite_file.get('description'):
                 rval.append('<li><a href="{}" type="text/plain">{} ({})</a>{}</li>'.format(fn, fn, composite_file.get('description'), opt_text))
             else:
-                rval.append('<li><a href="{}" type="text/plain">{}</a>{}</li>'.format(fn, fn, opt_text))
+                rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
         rval.append('</ul></div></html>')
         return "\n".join(rval)
 
@@ -995,7 +995,7 @@ class ImzML(Binary):
             if composite_file.get('description'):
                 rval.append('<li><a href="{}" type="text/plain">{} ({})</a>{}</li>'.format(fn, fn, composite_file.get('description'), opt_text))
             else:
-                rval.append('<li><a href="{}" type="text/plain">{}</a>{}</li>'.format(fn, fn, opt_text))
+                rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
         rval.append('</ul></div></html>')
         return "\n".join(rval)
 
@@ -1041,6 +1041,6 @@ class Analyze75(Binary):
             if composite_file.get('description'):
                 rval.append('<li><a href="{}" type="text/plain">{} ({})</a>{}</li>'.format(fn, fn, composite_file.get('description'), opt_text))
             else:
-                rval.append('<li><a href="{}" type="text/plain">{}</a>{}</li>'.format(fn, fn, opt_text))
+                rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
         rval.append('</ul></div></html>')
         return "\n".join(rval)

lib/galaxy/datatypes/registry.py

@@ -330,7 +330,7 @@ class Registry:
                                 self.datatype_info_dicts.append(datatype_info_dict)
 
                                 for auto_compressed_type in auto_compressed_types:
-                                    compressed_extension = "{}.{}".format(extension, auto_compressed_type)
+                                    compressed_extension = f"{extension}.{auto_compressed_type}"
                                     upper_compressed_type = auto_compressed_type[0].upper() + auto_compressed_type[1:]
                                     auto_compressed_type_name = datatype_class_name + upper_compressed_type
                                     attributes = {}
@@ -372,7 +372,7 @@ class Registry:
                                     if not override:
                                         # Do not load the datatype since it conflicts with an existing datatype which we are not supposed
                                         # to override.
-                                        self.log.debug("Ignoring conflicting datatype with extension '{}' from {}.".format(extension, config))
+                                        self.log.debug(f"Ignoring conflicting datatype with extension '{extension}' from {config}.")
             # Load datatype sniffers from the config - we'll do this even if one or more datatypes were not properly processed in the config
             # since sniffers are not tightly coupled with datatypes.
             self.load_datatype_sniffers(root,
@@ -413,7 +413,7 @@ class Registry:
             if not os.path.exists(path):
                 sample_path = "%s.sample" % path
                 if os.path.exists(sample_path):
-                    self.log.debug("Build site file [{}] not found using sample [{}].".format(path, sample_path))
+                    self.log.debug(f"Build site file [{path}] not found using sample [{sample_path}].")
                     path = sample_path
 
             self.build_sites[site_type] = path
@@ -703,13 +703,13 @@ class Registry:
                                     del self.datatypes_by_extension[extension].display_applications[display_app.id]
                             if inherit and (self.datatypes_by_extension[extension], display_app) in self.inherit_display_application_by_class:
                                 self.inherit_display_application_by_class.remove((self.datatypes_by_extension[extension], display_app))
-                            self.log.debug("Deactivated display application '{}' for datatype '{}'.".format(display_app.id, extension))
+                            self.log.debug(f"Deactivated display application '{display_app.id}' for datatype '{extension}'.")
                         else:
                             self.display_applications[display_app.id] = display_app
                             self.datatypes_by_extension[extension].add_display_application(display_app)
                             if inherit and (self.datatypes_by_extension[extension], display_app) not in self.inherit_display_application_by_class:
                                 self.inherit_display_application_by_class.append((self.datatypes_by_extension[extension], display_app))
-                            self.log.debug("Loaded display application '{}' for datatype '{}', inherit={}.".format(display_app.id, extension, inherit))
+                            self.log.debug(f"Loaded display application '{display_app.id}' for datatype '{extension}', inherit={inherit}.")
                 except Exception:
                     if deactivate:
                         self.log.exception("Error deactivating display application (%s)" % config_path)
@@ -720,7 +720,7 @@ class Registry:
             for d_type2, display_app in self.inherit_display_application_by_class:
                 current_app = d_type1.get_display_application(display_app.id, None)
                 if current_app is None and isinstance(d_type1, type(d_type2)):
-                    self.log.debug("Adding inherited display application '{}' to datatype '{}'".format(display_app.id, extension))
+                    self.log.debug(f"Adding inherited display application '{display_app.id}' to datatype '{extension}'")
                     d_type1.add_display_application(display_app)
 
     def reload_display_applications(self, display_application_ids=None):
@@ -894,7 +894,7 @@ class Registry:
         for convert_ext in self.get_converters_by_datatype(ext):
             convert_ext_datatype = self.get_datatype_by_extension(convert_ext)
             if convert_ext_datatype is None:
-                self.log.warning("Datatype class not found for extension '{}', which is used as target for conversion from datatype '{}'".format(convert_ext, dataset.ext))
+                self.log.warning(f"Datatype class not found for extension '{convert_ext}', which is used as target for conversion from datatype '{dataset.ext}'")
             elif convert_ext_datatype.matches_any(accepted_formats):
                 converted_dataset = dataset and dataset.get_converted_files_by_type(convert_ext)
                 if converted_dataset:
@@ -919,7 +919,7 @@ class Registry:
                     help_txt = meta_spec.desc
                     if not help_txt or help_txt == meta_name:
                         help_txt = ""
-                    inputs.append('<param type="text" name="{}" label="Set metadata value for &quot;{}&quot;" value="{}" help="{}"/>'.format(meta_name, meta_name, meta_spec.default, help_txt))
+                    inputs.append(f'<param type="text" name="{meta_name}" label="Set metadata value for &quot;{meta_name}&quot;" value="{meta_spec.default}" help="{help_txt}"/>')
             rval[ext] = "\n".join(inputs)
         if 'auto' not in rval and 'txt' in rval:  # need to manually add 'auto' datatype
             rval['auto'] = rval['txt']

lib/galaxy/datatypes/sequence.py

@@ -186,7 +186,7 @@ class Sequence(data.Text):
                 ds = input_datasets[ds_no]
                 base_name = os.path.basename(ds.file_name)
                 part_path = os.path.join(dir, base_name)
-                split_data = dict(class_name='{}.{}'.format(cls.__module__, cls.__name__),
+                split_data = dict(class_name=f'{cls.__module__}.{cls.__name__}',
                                   output_name=part_path,
                                   input_name=ds.file_name,
                                   args=dict(start_sequence=start_sequence, num_sequences=sequences_per_file[part_no]))
@@ -431,7 +431,7 @@ class Fasta(Sequence):
             part_dir = subdir_generator_function()
             part_path = os.path.join(part_dir, os.path.basename(input_file))
             part_file = open(part_path, 'w')
-            log.debug("Writing {} part to {}".format(input_file, part_path))
+            log.debug(f"Writing {input_file} part to {part_path}")
             start_offset = 0
             while True:
                 offset = f.tell()
@@ -444,7 +444,7 @@ class Fasta(Sequence):
                     part_dir = subdir_generator_function()
                     part_path = os.path.join(part_dir, os.path.basename(input_file))
                     part_file = open(part_path, 'w')
-                    log.debug("Writing {} part to {}".format(input_file, part_path))
+                    log.debug(f"Writing {input_file} part to {part_path}")
                     start_offset = f.tell()
                 part_file.write(line)
         except Exception as e:
@@ -467,7 +467,7 @@ class Fasta(Sequence):
             part_dir = subdir_generator_function()
             part_path = os.path.join(part_dir, os.path.basename(input_file))
             part_file = open(part_path, 'w')
-            log.debug("Writing {} part to {}".format(input_file, part_path))
+            log.debug(f"Writing {input_file} part to {part_path}")
             rec_count = 0
             while True:
                 line = f.readline()
@@ -481,7 +481,7 @@ class Fasta(Sequence):
                         part_dir = subdir_generator_function()
                         part_path = os.path.join(part_dir, os.path.basename(input_file))
                         part_file = open(part_path, 'w')
-                        log.debug("Writing {} part to {}".format(input_file, part_path))
+                        log.debug(f"Writing {input_file} part to {part_path}")
                         rec_count = 1
                 part_file.write(line)
         except Exception as e:
@@ -633,7 +633,7 @@ class Fastg(Sequence):
             dataset.blurb += '\nversion=%s' % dataset.metadata.version
             for k, v in dataset.metadata.properties.items():
                 if k != 'version':
-                    dataset.blurb += '\n{}={}'.format(k, v)
+                    dataset.blurb += f'\n{k}={v}'
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'

lib/galaxy/datatypes/spaln.py

@@ -88,7 +88,7 @@ class _SpalnDb(Data):
         for i, fname in enumerate(flist):
             sfname = os.path.split(fname)[-1]
             f, e = os.path.splitext(fname)
-            rval.append('<li><a href="{}">{}</a></li>'.format(sfname, sfname))
+            rval.append(f'<li><a href="{sfname}">{sfname}</a></li>')
         rval.append("</ul></body></html>")
         with open(dataset.file_name, "w") as f:
             f.write("\n".join(rval))

lib/galaxy/datatypes/speech.py

@@ -25,7 +25,7 @@ class TextGrid(Text):
 
     def sniff(self, filename):
 
-        with open(filename, 'r') as fd:
+        with open(filename) as fd:
             text = fd.read(len(self.header))
             return text == self.header
 
@@ -56,7 +56,7 @@ class BPF(Text):
     def set_meta(self, dataset, overwrite=True, **kwd):
         """Set the metadata for this dataset from the file contents"""
         types = set()
-        with open(dataset.dataset.file_name, 'r') as fd:
+        with open(dataset.dataset.file_name) as fd:
             for line in fd:
                 # Split the line on a colon rather than regexing it
                 parts = line.split(':')

lib/galaxy/datatypes/tabular.py

@@ -305,7 +305,7 @@ class Tabular(TabularData):
                 if column_type2 == column_type:
                     return False
             # neither column type was found in our ordered list, this cannot happen
-            raise ValueError("Tried to compare unknown column types: {} and {}".format(column_type1, column_type2))
+            raise ValueError(f"Tried to compare unknown column types: {column_type1} and {column_type2}")
 
         def is_int(column_text):
             # Don't allow underscores in numeric literals (PEP 515)

lib/galaxy/datatypes/text.py

@@ -6,11 +6,10 @@ import json
 import logging
 import os
 import re
+import shlex
 import subprocess
 import tempfile
 
-from six.moves import shlex_quote
-
 from galaxy.datatypes.data import get_file_peek, Text
 from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
 from galaxy.datatypes.sniff import build_sniff_from_prefix, iter_headers
@@ -181,7 +180,7 @@ class Ipynb(Json):
                 ofilename = '%s.html' % ofilename
             except subprocess.CalledProcessError:
                 ofilename = dataset.file_name
-                log.exception('Command "%s" failed. Could not convert the Jupyter Notebook to HTML, defaulting to plain text.', ' '.join(map(shlex_quote, cmd)))
+                log.exception('Command "%s" failed. Could not convert the Jupyter Notebook to HTML, defaulting to plain text.', ' '.join(map(shlex.quote, cmd)))
             return open(ofilename, mode='rb')
 
     def set_meta(self, dataset, **kwd):
@@ -465,7 +464,7 @@ class Arff(Text):
         if not dataset.dataset.purged:
             dataset.peek = get_file_peek(dataset.file_name)
             dataset.blurb = "Attribute-Relation File Format (ARFF)"
-            dataset.blurb += ", {} comments, {} attributes".format(dataset.metadata.comment_lines, dataset.metadata.columns)
+            dataset.blurb += f", {dataset.metadata.comment_lines} comments, {dataset.metadata.columns} attributes"
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disc'

lib/galaxy/datatypes/tracks.py

@@ -38,7 +38,7 @@ class UCSCTrackHub(Html):
             opt_text = ''
             if composite_file.optional:
                 opt_text = ' (optional)'
-            rval.append('<li><a href="{}">{}</a>{}'.format(composite_name, composite_name, opt_text))
+            rval.append(f'<li><a href="{composite_name}">{composite_name}</a>{opt_text}')
         rval.append('</ul></html>')
         return "\n".join(rval)
 

lib/galaxy/datatypes/util/maf_utilities.py

@@ -16,7 +16,6 @@ from errno import EMFILE
 import bx.align.maf
 import bx.interval_index_file
 import bx.intervals
-from six.moves import xrange
 
 try:
     maketrans = str.maketrans
@@ -132,7 +131,7 @@ class TempFileHandler:
             self.files[index].flush()
 
     def __del__(self):
-        for i in xrange(len(self.files)):
+        for i in range(len(self.files)):
             self.close(i, delete=True)
 
 
@@ -295,7 +294,7 @@ def maf_index_by_uid(maf_uid, index_location_file):
                     maf_files = fields[4].replace("\n", "").replace("\r", "").split(",")
                     return bx.align.maf.MultiIndexed(maf_files, keep_open=True, parse_e_rows=False)
                 except Exception as e:
-                    raise Exception('MAF UID ({}) found, but configuration appears to be malformed: {}'.format(maf_uid, e))
+                    raise Exception(f'MAF UID ({maf_uid}) found, but configuration appears to be malformed: {e}')
         except Exception:
             pass
     return None
@@ -347,7 +346,7 @@ def build_maf_index_species_chromosomes(filename, index_species=None):
                         indexes.add(c.src, forward_strand_start, forward_strand_end, pos, max=c.src_size)
     except Exception as e:
         # most likely a bad MAF
-        log.debug('Building MAF index on {} failed: {}'.format(filename, e))
+        log.debug(f'Building MAF index on {filename} failed: {e}')
         return (None, [], {}, 0)
     return (indexes, species, species_chromosomes, blocks)
 
@@ -427,7 +426,7 @@ def orient_block_by_region(block, src, region, force_strand=None):
 
 
 def get_oriented_chopped_blocks_for_region(index, src, region, species=None, mincols=0, force_strand=None):
-    for block, idx, offset in get_oriented_chopped_blocks_with_index_offset_for_region(index, src, region, species, mincols, force_strand):
+    for block, _, _ in get_oriented_chopped_blocks_with_index_offset_for_region(index, src, region, species, mincols, force_strand):
         yield block
 
 
@@ -488,7 +487,7 @@ def iter_blocks_split_by_species(block, species=None):
 
 # generator yielding only chopped and valid blocks for a specified region
 def get_chopped_blocks_for_region(index, src, region, species=None, mincols=0):
-    for block, idx, offset in get_chopped_blocks_with_index_offset_for_region(index, src, region, species, mincols):
+    for block, _, _ in get_chopped_blocks_with_index_offset_for_region(index, src, region, species, mincols):
         yield block
 
 
@@ -512,7 +511,7 @@ def get_region_alignment(index, primary_species, chrom, start, end, strand='+',
 def reduce_block_by_primary_genome(block, species, chromosome, region_start):
     # returns ( startIndex, {species:texts}
     # where texts' contents are reduced to only positions existing in the primary genome
-    src = "{}.{}".format(species, chromosome)
+    src = f"{species}.{chromosome}"
     ref = block.get_component_by_src(src)
     start_offset = ref.start - region_start
     species_texts = {}
@@ -533,7 +532,7 @@ def fill_region_alignment(alignment, index, primary_species, chrom, start, end,
     region = bx.intervals.Interval(start, end)
     region.chrom = chrom
     region.strand = strand
-    primary_src = "{}.{}".format(primary_species, chrom)
+    primary_src = f"{primary_species}.{chrom}"
 
     # Order blocks overlaping this position by score, lowest first
     blocks = []
@@ -684,9 +683,9 @@ def remove_temp_index_file(index_filename):
 def get_fasta_header(component, attributes={}, suffix=None):
     header = ">%s(%s):%i-%i|" % (component.src, component.strand, component.get_forward_strand_start(), component.get_forward_strand_end())
     for key, value in attributes.items():
-        header = "{}{}={}|".format(header, key, value)
+        header = f"{header}{key}={value}|"
     if suffix:
-        header = "{}{}".format(header, suffix)
+        header = f"{header}{suffix}"
     else:
         header = "{}{}".format(header, src_split(component.src)[0])
     return header

lib/galaxy/dependencies/pipfiles/default/Pipfile

@@ -11,7 +11,6 @@ name = "pypi"
 [dev-packages]
 gunicorn = "*"
 lxml = "!=4.2.2"
-mock = "*"
 NoseHTML = "*"
 pygithub = "*"
 pytest = "*"
@@ -61,7 +60,6 @@ Beaker = "*"
 dictobj = "*"
 nose = "*"
 Parsley = "*"
-six = "*"
 sortedcontainers = "*"
 Whoosh = "*"
 galaxy_sequence_utils = "*"
@@ -88,4 +86,4 @@ gxformat2 = "*"
 refgenconf = ">=0.7.0"
 
 [requires]
-python_version = "3.5"
+python_version = "3.6"

lib/galaxy/files/__init__.py

@@ -12,7 +12,7 @@ log = logging.getLogger(__name__)
 FileSourcePath = namedtuple('FileSourcePath', ['file_source', 'path'])
 
 
-class ConfiguredFileSources(object):
+class ConfiguredFileSources:
     """Load plugins and resolve Galaxy URIs to FileSource objects."""
 
     def __init__(self, file_sources_config, conf_file=None, conf_dict=None, load_stock_plugins=False):
@@ -161,7 +161,7 @@ class ConfiguredFileSources(object):
         return ConfiguredFileSources(file_sources_config, conf_dict=sources_as_dict)
 
 
-class ConfiguredFileSourcesConfig(object):
+class ConfiguredFileSourcesConfig:
 
     def __init__(self, symlink_allowlist=[], library_import_dir=None, user_library_import_dir=None, ftp_upload_dir=None, ftp_upload_purge=True):
         self.symlink_allowlist = symlink_allowlist
@@ -202,7 +202,7 @@ class ConfiguredFileSourcesConfig(object):
         )
 
 
-class ProvidesUserFileSourcesUserContext(object):
+class ProvidesUserFileSourcesUserContext:
     """Implement a FileSourcesUserContext from a Galaxy ProvidesUserContext (e.g. trans)."""
 
     def __init__(self, trans):
@@ -228,7 +228,7 @@ class ProvidesUserFileSourcesUserContext(object):
         return user and user.extra_preferences
 
 
-class DictFileSourcesUserContext(object):
+class DictFileSourcesUserContext:
 
     def __init__(self, **kwd):
         self._kwd = kwd

lib/galaxy/files/sources/__init__.py

@@ -2,16 +2,13 @@ import abc
 import os
 import time
 
-import six
-
 from galaxy.util.template import fill_template
 
 DEFAULT_SCHEME = "gxfiles"
 DEFAULT_WRITABLE = False
 
 
-@six.add_metaclass(abc.ABCMeta)
-class FilesSource(object):
+class FilesSource(metaclass=abc.ABCMeta):
     """
     """
 

lib/galaxy/files/sources/galaxy.py

@@ -18,7 +18,7 @@ class UserFtpFilesSource(PosixFilesSource):
         if "delete_on_realize" not in posix_kwds:
             file_sources_config = kwd.get("file_sources_config")
             posix_kwds["delete_on_realize"] = file_sources_config.ftp_upload_purge
-        super(UserFtpFilesSource, self).__init__(**posix_kwds)
+        super().__init__(**posix_kwds)
 
     def get_prefix(self):
         return None
@@ -38,7 +38,7 @@ class LibraryImportFilesSource(PosixFilesSource):
             doc=doc,
         )
         posix_kwds.update(kwd)
-        super(LibraryImportFilesSource, self).__init__(**posix_kwds)
+        super().__init__(**posix_kwds)
 
     def get_prefix(self):
         return None
@@ -58,7 +58,7 @@ class UserLibraryImportFilesSource(PosixFilesSource):
             doc=doc,
         )
         posix_kwds.update(kwd)
-        super(UserLibraryImportFilesSource, self).__init__(**posix_kwds)
+        super().__init__(**posix_kwds)
 
     def get_prefix(self):
         return None

lib/galaxy/forms/forms.py

@@ -21,7 +21,7 @@ class FormDefinitionFactory:
         """
         Return new FormDefinition.
         """
-        assert form_type in self.form_types, 'Invalid FormDefinition type ( {} not in {} )'.format(form_type, self.form_types.keys())
+        assert form_type in self.form_types, f'Invalid FormDefinition type ( {form_type} not in {self.form_types.keys()} )'
         assert name, 'FormDefinition requires a name'
         if description is None:
             description = ''
@@ -113,7 +113,7 @@ class FormDefinitionFieldFactory:
         visible = string_as_bool(elem.get('visible', 'true'))
         field_layout = elem.get('layout', None)
         if field_layout:
-            assert layout and field_layout in layout, 'Invalid layout specified: {} not in {}'.format(field_layout, layout)
+            assert layout and field_layout in layout, f'Invalid layout specified: {field_layout} not in {layout}'
             field_layout = str(layout.index(field_layout))  # existing behavior: integer indexes are stored as strings. why?
         return self.new(name=name, label=label, required=required, helptext=helptext, default=default, visible=visible, layout=field_layout)
 

lib/galaxy/job_execution/output_collect.py

@@ -386,7 +386,7 @@ def collect_primary_datasets(job_context, output, input_ext):
             if dbkey == INPUT_DBKEY_TOKEN:
                 dbkey = job_context.input_dbkey
             if filename_index == 0 and extra_file_collector.assign_primary_output and output_index == 0:
-                new_outdata_name = fields_match.name or "{} ({})".format(outdata.name, designation)
+                new_outdata_name = fields_match.name or f"{outdata.name} ({designation})"
                 outdata.change_datatype(ext)
                 outdata.dbkey = dbkey
                 outdata.designation = designation
@@ -399,7 +399,7 @@ def collect_primary_datasets(job_context, output, input_ext):
                 primary_datasets[name] = OrderedDict()
             visible = fields_match.visible
             # Create new primary dataset
-            new_primary_name = fields_match.name or "{} ({})".format(outdata.name, designation)
+            new_primary_name = fields_match.name or f"{outdata.name} ({designation})"
             info = outdata.info
 
             # TODO: should be able to disambiguate files in different directories...
@@ -418,7 +418,7 @@ def collect_primary_datasets(job_context, output, input_ext):
                 dataset_attributes=new_primary_datasets_attributes,
             )
             # Associate new dataset with job
-            job_context.add_output_dataset_association('__new_primary_file_{}|{}__'.format(name, designation), primary_data)
+            job_context.add_output_dataset_association(f'__new_primary_file_{name}|{designation}__', primary_data)
 
             if new_primary_datasets_attributes:
                 extra_files_path = new_primary_datasets_attributes.get('extra_files', None)
@@ -577,7 +577,7 @@ def read_exit_code_from(exit_code_file, id_tag):
         exit_code = int(exit_code_str)
     except ValueError:
         galaxy_id_tag = id_tag
-        log.warning("({}) Exit code '{}' invalid. Using 0.".format(galaxy_id_tag, exit_code_str))
+        log.warning(f"({galaxy_id_tag}) Exit code '{exit_code_str}' invalid. Using 0.")
         exit_code = 0
 
     return exit_code

lib/galaxy/job_metrics/collectl/cli.py

@@ -110,13 +110,13 @@ class CollectlCli:
         if not interval2:
             return interval_arg
         self.__validate_interval_arg(interval2, multiple_of=int(interval))
-        interval_arg = "{}:{}".format(interval_arg, interval2)
+        interval_arg = f"{interval_arg}:{interval2}"
 
         interval3 = kwargs.get("interval3", None)
         if not interval3:
             return interval_arg
         self.__validate_interval_arg(interval3, multiple_of=int(interval))
-        interval_arg = "{}:{}".format(interval_arg, interval3)
+        interval_arg = f"{interval_arg}:{interval3}"
         return interval_arg
 
     def __validate_interval_arg(self, value, multiple_of=None):

lib/galaxy/job_metrics/instrumenters/__init__.py

@@ -49,7 +49,7 @@ class InstrumentPlugin(metaclass=ABCMeta):
         """ Provide a common pattern for naming files used by instrumentation
         plugins - to ease their staging out of remote job directories.
         """
-        return "{}_{}_{}".format(INSTRUMENT_FILE_PREFIX, self.plugin_type, name)
+        return f"{INSTRUMENT_FILE_PREFIX}_{self.plugin_type}_{name}"
 
     def _instrument_file_path(self, job_directory, name):
         return os.path.join(job_directory, self._instrument_file_name(name))

lib/galaxy/job_metrics/instrumenters/collectl.py

@@ -48,7 +48,7 @@ class CollectlFormatter(formatting.JobMetricFormatter):
             else:
                 value_str = str(value)
             resource_title = FORMATTED_RESOURCE_TITLES.get(resource_type, resource_type)
-            return ("{} ({})".format(resource_title, stat_type), value_str)
+            return (f"{resource_title} ({stat_type})", value_str)
 
 
 class CollectlPlugin(InstrumentPlugin):
@@ -102,7 +102,7 @@ class CollectlPlugin(InstrumentPlugin):
             rel_path = filter(self._is_instrumented_collectl_log, contents)[0]
             path = os.path.join(job_directory, rel_path)
         except IndexError:
-            message = "Failed to find collectl log in directory {}, files were {}".format(job_directory, contents)
+            message = f"Failed to find collectl log in directory {job_directory}, files were {contents}"
             raise Exception(message)
 
         properties = dict(

lib/galaxy/job_metrics/instrumenters/cpuinfo.py

@@ -51,7 +51,7 @@ class CpuInfoPlugin(InstrumentPlugin):
                     # If verbose, dump information about each processor
                     # into database...
                     key, value = line.split(":", 1)
-                    key = "processor_{}_{}".format(current_processor, key.strip())
+                    key = f"processor_{current_processor}_{key.strip()}"
                     value = value
         properties["processor_count"] = processor_count
         return properties

lib/galaxy/jobs/__init__.py

@@ -803,7 +803,7 @@ class JobConfiguration(ConfiguresHandlers):
                     log.warning("A non-class name was found in __all__, ignoring: %s" % id)
                     continue
                 except AssertionError:
-                    log.warning("Job runner classes must be subclassed from BaseJobRunner, {} has bases: {}".format(id, runner_class.__bases__))
+                    log.warning(f"Job runner classes must be subclassed from BaseJobRunner, {id} has bases: {runner_class.__bases__}")
                     continue
                 try:
                     rval[id] = runner_class(self.app, runner.get('workers', JobConfiguration.DEFAULT_NWORKERS), **runner.get('kwds', {}))
@@ -811,7 +811,7 @@ class JobConfiguration(ConfiguresHandlers):
                     log.exception("Job runner '%s:%s' has not been converted to a new-style runner or encountered TypeError on load",
                                   module_name, class_name)
                     rval[id] = runner_class(self.app)
-                log.debug("Loaded job runner '{}:{}' as '{}'".format(module_name, class_name, id))
+                log.debug(f"Loaded job runner '{module_name}:{class_name}' as '{id}'")
         return rval
 
     def is_id(self, collection):
@@ -847,13 +847,13 @@ class JobConfiguration(ConfiguresHandlers):
                     destination.params = job_runners[destination.runner].url_to_destination(destination.url).params
                     destination.converted = True
                     if destination.params:
-                        log.debug("Legacy destination with id '{}', url '{}' converted, got params:".format(id, destination.url))
+                        log.debug(f"Legacy destination with id '{id}', url '{destination.url}' converted, got params:")
                         for k, v in destination.params.items():
-                            log.debug("    {}: {}".format(k, v))
+                            log.debug(f"    {k}: {v}")
                     else:
-                        log.debug("Legacy destination with id '{}', url '{}' converted, got params:".format(id, destination.url))
+                        log.debug(f"Legacy destination with id '{id}', url '{destination.url}' converted, got params:")
                 else:
-                    log.warning("Legacy destination with id '{}' could not be converted: Unknown runner plugin: {}".format(id, destination.runner))
+                    log.warning(f"Legacy destination with id '{id}' could not be converted: Unknown runner plugin: {destination.runner}")
 
 
 class HasResourceParameters:
@@ -1129,7 +1129,7 @@ class JobWrapper(HasResourceParameters):
         if version_string_cmd_raw:
             version_command_template = string.Template(version_string_cmd_raw)
             version_string_cmd = version_command_template.safe_substitute({"__tool_directory__": compute_environment.tool_directory()})
-            self.write_version_cmd = "{} > {} 2>&1".format(version_string_cmd, compute_environment.version_path())
+            self.write_version_cmd = f"{version_string_cmd} > {compute_environment.version_path()} 2>&1"
         else:
             self.write_version_cmd = None
         return self.extra_filenames
@@ -1412,7 +1412,7 @@ class JobWrapper(HasResourceParameters):
         """
         if job is None:
             job = self.get_job()
-        log.debug('({}) Persisting job destination (destination id: {})'.format(job.id, job_destination.id))
+        log.debug(f'({job.id}) Persisting job destination (destination id: {job_destination.id})')
         job.destination_id = job_destination.id
         job.destination_params = job_destination.params
         job.job_runner_name = job_destination.runner
@@ -1594,7 +1594,7 @@ class JobWrapper(HasResourceParameters):
         try:
             self.reclaim_ownership()
         except Exception:
-            log.exception('({}) Failed to change ownership of {}, failing'.format(job.id, self.working_directory))
+            log.exception(f'({job.id}) Failed to change ownership of {self.working_directory}, failing')
             return fail()
 
         # if the job was deleted, don't finish it
@@ -1641,7 +1641,7 @@ class JobWrapper(HasResourceParameters):
             for dataset_path in self.get_output_fnames():
                 try:
                     shutil.move(dataset_path.false_path, dataset_path.real_path)
-                    log.debug("finish(): Moved {} to {}".format(dataset_path.false_path, dataset_path.real_path))
+                    log.debug(f"finish(): Moved {dataset_path.false_path} to {dataset_path.real_path}")
                 except OSError:
                     # this can happen if Galaxy is restarted during the job's
                     # finish method - the false_path file has already moved,
@@ -1661,7 +1661,7 @@ class JobWrapper(HasResourceParameters):
                 import_model_store = store.get_import_model_store_for_directory(os.path.join(self.working_directory, 'metadata', 'outputs_populated'), app=self.app, import_options=import_options)
                 import_model_store.perform_import(history=job.history)
             except Exception:
-                log.exception("problem importing job outputs. stdout [{}] stderr [{}]".format(job.stdout, job.stderr))
+                log.exception(f"problem importing job outputs. stdout [{job.stdout}] stderr [{job.stderr}]")
                 raise
         output_dataset_associations = job.output_datasets + job.output_library_datasets
         for dataset_assoc in output_dataset_associations:
@@ -1883,14 +1883,14 @@ class JobWrapper(HasResourceParameters):
     def get_env_setup_clause(self):
         if self.app.config.environment_setup_file is None:
             return ''
-        return '[ -f "{}" ] && . {}'.format(self.app.config.environment_setup_file, self.app.config.environment_setup_file)
+        return f'[ -f "{self.app.config.environment_setup_file}" ] && . {self.app.config.environment_setup_file}'
 
     def get_input_dataset_fnames(self, ds):
         filenames = []
         filenames = [ds.file_name]
         # we will need to stage in metadata file names also
         # TODO: would be better to only stage in metadata files that are actually needed (found in command line, referenced in config files, etc.)
-        for key, value in ds.metadata.items():
+        for _, value in ds.metadata.items():
             if isinstance(value, model.MetadataFile):
                 filenames.append(value.file_name)
         return filenames
@@ -1938,7 +1938,7 @@ class JobWrapper(HasResourceParameters):
         for (hda, dataset_path) in self.output_hdas_and_paths.values():
             if hda == dataset:
                 return dataset_path
-        raise KeyError("Couldn't find job output for [{}] in [{}]".format(dataset, self.output_hdas_and_paths.values()))
+        raise KeyError(f"Couldn't find job output for [{dataset}] in [{self.output_hdas_and_paths.values()}]")
 
     def get_mutable_output_fnames(self):
         if self.output_paths is None:
@@ -2100,7 +2100,7 @@ class JobWrapper(HasResourceParameters):
                 dependency_shell_commands = metadata_tool.build_dependency_shell_commands(job_directory=self.working_directory, metadata=True)
                 if dependency_shell_commands:
                     dependency_shell_commands = "; ".join(dependency_shell_commands)
-                    command = "{}; {}".format(dependency_shell_commands, command)
+                    command = f"{dependency_shell_commands}; {command}"
         return command
 
     def check_for_entry_points(self, check_already_configured=True):

lib/galaxy/jobs/actions/post.py

@@ -364,14 +364,14 @@ class DeleteIntermediatesAction(DefaultJobAction):
                 if wfi_step_job:
                     jobs_to_check.append(wfi_step_job)
                 else:
-                    log.debug("No job found yet for wfi_step {}, (step {})".format(wfi_step, wfi_step.workflow_step))
+                    log.debug(f"No job found yet for wfi_step {wfi_step}, (step {wfi_step.workflow_step})")
             for j2c in jobs_to_check:
                 creating_jobs = []
                 for input_dataset in j2c.input_datasets:
                     if not input_dataset.dataset:
-                        log.debug("PJA Async Issue: No dataset attached to input_dataset {} during handling of workflow invocation {}".format(input_dataset.id, wfi))
+                        log.debug(f"PJA Async Issue: No dataset attached to input_dataset {input_dataset.id} during handling of workflow invocation {wfi}")
                     elif not input_dataset.dataset.creating_job:
-                        log.debug("PJA Async Issue: No creating job attached to dataset {} during handling of workflow invocation {}".format(input_dataset.dataset.id, wfi))
+                        log.debug(f"PJA Async Issue: No creating job attached to dataset {input_dataset.dataset.id} during handling of workflow invocation {wfi}")
                     else:
                         creating_jobs.append((input_dataset, input_dataset.dataset.creating_job))
                 for (input_dataset, creating_job) in creating_jobs:
@@ -383,7 +383,7 @@ class DeleteIntermediatesAction(DefaultJobAction):
                     safe_to_delete = True
                     for job_to_check in [d_j.job for d_j in input_dataset.dependent_jobs]:
                         if job_to_check != job and job_to_check.state not in [job.states.OK, job.states.DELETED]:
-                            log.trace("Workflow Intermediates cleanup attempted, but non-terminal state '{}' detected for job {}".format(job_to_check.state, job_to_check.id))
+                            log.trace(f"Workflow Intermediates cleanup attempted, but non-terminal state '{job_to_check.state}' detected for job {job_to_check.id}")
                             safe_to_delete = False
                     if safe_to_delete:
                         # Support purging here too.

lib/galaxy/jobs/command_factory.py

@@ -155,7 +155,7 @@ def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_
         tool_commands,
     )
     write_script(local_container_script, script_contents, config)
-    commands = "{} {}".format(shell, local_container_script)
+    commands = f"{shell} {local_container_script}"
     # TODO: Cleanup for_pulsar hack.
     # - Integrate Pulsar sending tool_stdout/tool_stderr back
     #   https://github.com/galaxyproject/pulsar/pull/202
@@ -170,7 +170,7 @@ def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_
         for_pulsar = True
     if not for_pulsar:
         commands += " > ../outputs/tool_stdout 2> ../outputs/tool_stderr"
-    log.info("Built script [{}] for tool command [{}]".format(local_container_script, tool_commands))
+    log.info(f"Built script [{local_container_script}] for tool command [{tool_commands}]")
     return commands
 
 
@@ -236,14 +236,14 @@ def __handle_metadata(commands_builder, job_wrapper, runner, remote_command_para
     metadata_command = metadata_command.strip()
     if metadata_command:
         # Place Galaxy and its dependencies in environment for metadata regardless of tool.
-        metadata_command = "{}{}".format(SETUP_GALAXY_FOR_METADATA, metadata_command)
+        metadata_command = f"{SETUP_GALAXY_FOR_METADATA}{metadata_command}"
         commands_builder.capture_return_code()
         commands_builder.append_command(metadata_command)
 
 
 def __copy_if_exists_command(work_dir_output):
     source_file, destination = work_dir_output
-    return "if [ -f {} ] ; then cp {} {} ; fi".format(source_file, source_file, destination)
+    return f"if [ -f {source_file} ] ; then cp {source_file} {destination} ; fi"
 
 
 class CommandsBuilder:

lib/galaxy/jobs/handler.py

@@ -5,11 +5,11 @@ import datetime
 import os
 import time
 from collections import defaultdict
-
-from six.moves.queue import (
+from queue import (
     Empty,
-    Queue
+    Queue,
 )
+
 from sqlalchemy.exc import OperationalError
 from sqlalchemy.sql.expression import (
     and_,
@@ -217,7 +217,7 @@ class JobHandlerQueue(Monitors):
 
         for job in jobs_at_startup:
             if not self.app.toolbox.has_tool(job.tool_id, job.tool_version, exact=True):
-                log.warning("({}) Tool '{}' removed from tool config, unable to recover job".format(job.id, job.tool_id))
+                log.warning(f"({job.id}) Tool '{job.tool_id}' removed from tool config, unable to recover job")
                 self.job_wrapper(job).fail('This tool was disabled before the job completed.  Please contact your Galaxy administrator.')
             elif job.job_runner_name is not None and job.job_runner_external_id is None:
                 # This could happen during certain revisions of Galaxy where a runner URL was persisted before the job was dispatched to a runner.
@@ -238,7 +238,7 @@ class JobHandlerQueue(Monitors):
                 log.info('(%s) Converted job from a URL to a destination and recovered' % (job.id))
             elif job.job_runner_name is None:
                 # Never (fully) dispatched
-                log.debug("({}) No job runner assigned and job still in '{}' state, adding to the job handler queue".format(job.id, job.state))
+                log.debug(f"({job.id}) No job runner assigned and job still in '{job.state}' state, adding to the job handler queue")
                 if self.track_jobs_in_database:
                     job.set_state(model.Job.states.NEW)
                 else:
@@ -486,7 +486,7 @@ class JobHandlerQueue(Monitors):
             elif dataset_state == model.Dataset.states.ERROR:
                 jobs_to_pause[job_id].append("Input dataset '%s' is in error state" % hda_name)
             elif dataset_state != model.Dataset.states.OK:
-                jobs_to_ignore[job_id].append("Input dataset '{}' is in {} state".format(hda_name, dataset_state))
+                jobs_to_ignore[job_id].append(f"Input dataset '{hda_name}' is in {dataset_state} state")
         for job_id in sorted(jobs_to_pause):
             pause_message = ", ".join(jobs_to_pause[job_id])
             pause_message = "%s. To resume this job fix the input dataset(s)." % pause_message
@@ -557,7 +557,7 @@ class JobHandlerQueue(Monitors):
             # Cause the job_destination to be set and cached by the mapper
             job_destination = job_wrapper.job_destination
         except AssertionError as e:
-            log.warning("({}) Tool '{}' removed from tool config, unable to run job".format(job.id, job.tool_id))
+            log.warning(f"({job.id}) Tool '{job.tool_id}' removed from tool config, unable to run job")
             job_wrapper.fail(e)
             return JOB_ERROR, job_destination
         except JobNotReadyException as e:
@@ -631,7 +631,7 @@ class JobHandlerQueue(Monitors):
                 continue
             # don't run jobs for which the input dataset was deleted
             if idata.deleted:
-                self.job_wrappers.pop(job.id, self.job_wrapper(job)).fail("input data {} (file: {}) was deleted before the job started".format(idata.hid, idata.file_name))
+                self.job_wrappers.pop(job.id, self.job_wrapper(job)).fail(f"input data {idata.hid} (file: {idata.file_name}) was deleted before the job started")
                 return JOB_INPUT_DELETED
             # an error in the input data causes us to bail immediately
             elif idata.state == idata.states.ERROR:
@@ -1000,12 +1000,12 @@ class DefaultJobDispatcher:
         try:
             if isinstance(job_wrapper, TaskWrapper):
                 # DBTODO Refactor
-                log.debug("({}) Dispatching task {} to {} runner".format(job_wrapper.job_id, job_wrapper.task_id, runner_name))
+                log.debug(f"({job_wrapper.job_id}) Dispatching task {job_wrapper.task_id} to {runner_name} runner")
             else:
-                log.debug("({}) Dispatching to {} runner".format(job_wrapper.job_id, runner_name))
+                log.debug(f"({job_wrapper.job_id}) Dispatching to {runner_name} runner")
             self.job_runners[runner_name].put(job_wrapper)
         except KeyError:
-            log.error('put(): ({}) Invalid job runner: {}'.format(job_wrapper.job_id, runner_name))
+            log.error(f'put(): ({job_wrapper.job_id}) Invalid job runner: {runner_name}')
             job_wrapper.fail(DEFAULT_JOB_PUT_FAILURE_MESSAGE)
 
     def stop(self, job, job_wrapper):
@@ -1023,11 +1023,11 @@ class DefaultJobDispatcher:
         job_runner_name = job.get_job_runner_name()
         if job_runner_name is not None:
             runner_name = job_runner_name.split(":", 1)[0]
-            log.debug("Stopping job {} in {} runner".format(job_wrapper.get_id_tag(), runner_name))
+            log.debug(f"Stopping job {job_wrapper.get_id_tag()} in {runner_name} runner")
             try:
                 self.job_runners[runner_name].stop_job(job_wrapper)
             except KeyError:
-                log.error('stop(): ({}) Invalid job runner: {}'.format(job_wrapper.get_id_tag(), runner_name))
+                log.error(f'stop(): ({job_wrapper.get_id_tag()}) Invalid job runner: {runner_name}')
                 # Job and output dataset states have already been updated, so nothing is done here.
 
     def recover(self, job, job_wrapper):
@@ -1036,7 +1036,7 @@ class DefaultJobDispatcher:
         try:
             self.job_runners[runner_name].recover(job, job_wrapper)
         except KeyError:
-            log.error('recover(): ({}) Invalid job runner: {}'.format(job_wrapper.job_id, runner_name))
+            log.error(f'recover(): ({job_wrapper.job_id}) Invalid job runner: {runner_name}')
             job_wrapper.fail(DEFAULT_JOB_PUT_FAILURE_MESSAGE)
 
     def shutdown(self):

lib/galaxy/jobs/rule_helper.py

@@ -187,7 +187,7 @@ class RuleHelper:
         invocation for jobs outside of workflows.
         """
         if hash_by not in VALID_JOB_HASH_STRATEGIES:
-            message = "Do not know how to hash jobs by {}, must be one of {}".format(hash_by, VALID_JOB_HASH_STRATEGIES)
+            message = f"Do not know how to hash jobs by {hash_by}, must be one of {VALID_JOB_HASH_STRATEGIES}"
             raise Exception(message)
 
         if hash_by == "workflow_invocation":

lib/galaxy/jobs/runners/__init__.py

@@ -9,10 +9,9 @@ import sys
 import threading
 import time
 import traceback
-
-from six.moves.queue import (
+from queue import (
     Empty,
-    Queue
+    Queue,
 )
 
 import galaxy.jobs
@@ -90,7 +89,7 @@ class BaseJobRunner:
         """
         self.work_queue = Queue()
         self.work_threads = []
-        log.debug('Starting {} {} workers'.format(self.nworkers, self.runner_name))
+        log.debug(f'Starting {self.nworkers} {self.runner_name} workers')
         for i in range(self.nworkers):
             worker = threading.Thread(name="%s.work_thread-%d" % (self.runner_name, i), target=self.run_next)
             worker.daemon = True
@@ -129,7 +128,7 @@ class BaseJobRunner:
             except Exception:
                 name = 'unknown'
             try:
-                action_str = 'galaxy.jobs.runners.{}.{}'.format(self.__class__.__name__.lower(), name)
+                action_str = f'galaxy.jobs.runners.{self.__class__.__name__.lower()}.{name}'
                 action_timer = self.app.execution_timer_factory.get_timer(
                     'internals.%s' % action_str,
                     'job runner action %s for job ${job_id} executed' % (action_str)
@@ -137,7 +136,7 @@ class BaseJobRunner:
                 method(arg)
                 log.trace(action_timer.to_str(job_id=job_id))
             except Exception:
-                log.exception("({}) Unhandled exception calling {}".format(job_id, name))
+                log.exception(f"({job_id}) Unhandled exception calling {name}")
                 if not isinstance(arg, JobState):
                     job_state = JobState(job_wrapper=arg, job_destination={})
                 else:
@@ -151,7 +150,7 @@ class BaseJobRunner:
         put_timer = ExecutionTimer()
         job_wrapper.enqueue()
         self.mark_as_queued(job_wrapper)
-        log.debug("Job [{}] queued {}".format(job_wrapper.job_id, put_timer))
+        log.debug(f"Job [{job_wrapper.job_id}] queued {put_timer}")
 
     def mark_as_queued(self, job_wrapper):
         self.work_queue.put((self.queue_job, job_wrapper))
@@ -222,12 +221,12 @@ class BaseJobRunner:
 
         # Make sure the job hasn't been deleted
         if job_state == model.Job.states.DELETED:
-            log.debug("({}) Job deleted by user before it entered the {} queue".format(job_id, self.runner_name))
+            log.debug(f"({job_id}) Job deleted by user before it entered the {self.runner_name} queue")
             if self.app.config.cleanup_job in ("always", "onsuccess"):
                 job_wrapper.cleanup()
             return False
         elif job_state != model.Job.states.QUEUED:
-            log.info("({}) Job is in state {}, skipping execution".format(job_id, job_state))
+            log.info(f"({job_id}) Job is in state {job_state}, skipping execution")
             # cleanup may not be safe in all states
             return False
 
@@ -352,13 +351,13 @@ class BaseJobRunner:
                                                                            tmp_dir=job_wrapper.working_directory,
                                                                            # We don't want to overwrite metadata that was copied over in init_meta(), as per established behavior
                                                                            kwds={'overwrite' : False})
-            external_metadata_script = "{} {} {}".format(lib_adjust, venv, external_metadata_script)
+            external_metadata_script = f"{lib_adjust} {venv} {external_metadata_script}"
             if resolve_requirements:
                 dependency_shell_commands = self.app.datatypes_registry.set_external_metadata_tool.build_dependency_shell_commands(job_directory=job_wrapper.working_directory)
                 if dependency_shell_commands:
                     if isinstance(dependency_shell_commands, list):
                         dependency_shell_commands = "&&".join(dependency_shell_commands)
-                    external_metadata_script = "{}&&{}".format(dependency_shell_commands, external_metadata_script)
+                    external_metadata_script = f"{dependency_shell_commands}&&{external_metadata_script}"
             log.debug('executing external set_meta script for job %d: %s' % (job_wrapper.job_id, external_metadata_script))
             external_metadata_proc = subprocess.Popen(args=external_metadata_script,
                                                       shell=True,
@@ -396,7 +395,7 @@ class BaseJobRunner:
         # Additional logging to enable if debugging from_work_dir handling, metadata
         # commands, etc... (or just peak in the job script.)
         job_id = job_wrapper.job_id
-        log.debug('({}) command is: {}'.format(job_id, command_line))
+        log.debug(f'({job_id}) command is: {command_line}')
         options.update(**kwds)
         return job_script(**options)
 
@@ -600,7 +599,7 @@ class JobState:
                 if not hasattr(self, "job_id"):
                     prefix = "(%s)" % self.job_wrapper.get_id_tag()
                 else:
-                    prefix = "({}/{})".format(self.job_wrapper.get_id_tag(), self.job_id)
+                    prefix = f"({self.job_wrapper.get_id_tag()}/{self.job_id})"
                 log.debug("{} Unable to cleanup {}: {}".format(prefix, file, unicodify(e)))
 
 

lib/galaxy/jobs/runners/chronos.py

@@ -196,7 +196,7 @@ class ChronosJobRunner(AsynchronousJobRunner):
                 msg = 'Job {name!r} failed more than {retries!s} times'
                 reason = msg.format(name=job_name, retries=str(max_retries))
                 return self._mark_as_failed(job_state, reason)
-        reason = 'Job {name!r} not found'.format(name=job_name)
+        reason = f'Job {job_name!r} not found'
         return self._mark_as_failed(job_state, reason)
 
     def _mark_as_successful(self, job_state):
@@ -264,7 +264,7 @@ class ChronosJobRunner(AsynchronousJobRunner):
         jobs = self._chronos_client.list()
         job = [x for x in jobs if x['name'] == job_id]
         if len(job) > 1:
-            msg = 'Multiple jobs found with name {name!r}'.format(name=job_id)
+            msg = f'Multiple jobs found with name {job_id!r}'
             LOGGER.error(msg)
             raise ChronosRunnerException(msg)
         return job[0] if job else None

lib/galaxy/jobs/runners/cli.py

@@ -47,7 +47,7 @@ class ShellJobRunner(AsynchronousJobRunner):
         job_params = {'job_' + k: v for k, v in [kv.split('=', 1) for kv in job_params.split('&')]}
         params.update(shell_params)
         params.update(job_params)
-        log.debug("Converted URL '{}' to destination runner=cli, params={}".format(url, params))
+        log.debug(f"Converted URL '{url}' to destination runner=cli, params={params}")
         # Create a dynamic JobDestination
         return JobDestination(runner='cli', params=params)
 
@@ -94,7 +94,7 @@ class ShellJobRunner(AsynchronousJobRunner):
                 job_wrapper.cleanup()
             return
 
-        log.debug("({}) submitting file: {}".format(galaxy_id_tag, ajs.job_file))
+        log.debug(f"({galaxy_id_tag}) submitting file: {ajs.job_file}")
 
         returncode, stdout = self.submit(shell, job_interface, ajs.job_file, galaxy_id_tag, retry=MAX_SUBMIT_RETRY)
         if returncode != 0:
@@ -108,7 +108,7 @@ class ShellJobRunner(AsynchronousJobRunner):
             job_wrapper.fail("failure submitting job")
             return
 
-        log.info("({}) queued with identifier: {}".format(galaxy_id_tag, external_job_id))
+        log.info(f"({galaxy_id_tag}) queued with identifier: {external_job_id}")
 
         # store runner information for tracking if Galaxy restarts
         job_wrapper.set_external_id(external_job_id)
@@ -131,8 +131,8 @@ class ShellJobRunner(AsynchronousJobRunner):
         cmd_out = shell.execute(job_interface.submit(job_file))
         if cmd_out.returncode == 0:
             return cmd_out.returncode, cmd_out.stdout
-        stdout = '({}) submission failed (stdout): {}'.format(galaxy_id_tag, cmd_out.stdout)
-        stderr = '({}) submission failed (stderr): {}'.format(galaxy_id_tag, cmd_out.stderr)
+        stdout = f'({galaxy_id_tag}) submission failed (stdout): {cmd_out.stdout}'
+        stderr = f'({galaxy_id_tag}) submission failed (stderr): {cmd_out.stderr}'
         if retry > 0:
             log.debug("%s, retrying in %s seconds", stdout, timeout)
             log.debug("%s, retrying in %s seconds", stderr, timeout)
@@ -161,15 +161,15 @@ class ShellJobRunner(AsynchronousJobRunner):
                 if ajs.job_wrapper.get_state() == model.Job.states.DELETED:
                     continue
 
-                log.debug("({}/{}) job not found in batch state check".format(id_tag, external_job_id))
+                log.debug(f"({id_tag}/{external_job_id}) job not found in batch state check")
                 shell_params, job_params = self.parse_destination_params(ajs.job_destination.params)
                 shell, job_interface = self.get_cli_plugins(shell_params, job_params)
                 cmd_out = shell.execute(job_interface.get_single_status(external_job_id))
                 state = job_interface.parse_single_status(cmd_out.stdout, external_job_id)
                 if not state == model.Job.states.OK:
-                    log.warning('({}/{}) job not found in batch state check, but found in individual state check'.format(id_tag, external_job_id))
+                    log.warning(f'({id_tag}/{external_job_id}) job not found in batch state check, but found in individual state check')
             if state != old_state:
-                log.debug("({}/{}) state change: from {} to {}".format(id_tag, external_job_id, old_state, state))
+                log.debug(f"({id_tag}/{external_job_id}) state change: from {old_state} to {state}")
                 if not state == model.Job.states.OK:
                     # No need to change_state when the state is OK, this will be handled by `self.finish_job`
                     ajs.job_wrapper.change_state(state)
@@ -186,7 +186,7 @@ class ShellJobRunner(AsynchronousJobRunner):
                 external_metadata = not asbool(ajs.job_wrapper.job_destination.params.get("embed_metadata_in_job", DEFAULT_EMBED_METADATA_IN_JOB))
                 if external_metadata:
                     self.work_queue.put((self.handle_metadata_externally, ajs))
-                log.debug('({}/{}) job execution finished, running job wrapper finish method'.format(id_tag, external_job_id))
+                log.debug(f'({id_tag}/{external_job_id}) job execution finished, running job wrapper finish method')
                 self.work_queue.put((self.finish_job, ajs))
             else:
                 new_watched.append(ajs)
@@ -234,9 +234,9 @@ class ShellJobRunner(AsynchronousJobRunner):
             shell, job_interface = self.get_cli_plugins(shell_params, job_params)
             cmd_out = shell.execute(job_interface.delete(job.job_runner_external_id))
             assert cmd_out.returncode == 0, cmd_out.stderr
-            log.debug("({}/{}) Terminated at user's request".format(job.id, job.job_runner_external_id))
+            log.debug(f"({job.id}/{job.job_runner_external_id}) Terminated at user's request")
         except Exception as e:
-            log.debug("({}/{}) User killed running job, but error encountered during termination: {}".format(job.id, job.job_runner_external_id, e))
+            log.debug(f"({job.id}/{job.job_runner_external_id}) User killed running job, but error encountered during termination: {e}")
 
     def recover(self, job, job_wrapper):
         """Recovers jobs stuck in the queued/running state when Galaxy started"""
@@ -250,12 +250,12 @@ class ShellJobRunner(AsynchronousJobRunner):
         ajs.job_wrapper = job_wrapper
         ajs.job_destination = job_wrapper.job_destination
         if job.state == model.Job.states.RUNNING:
-            log.debug("({}/{}) is still in running state, adding to the runner monitor queue".format(job.id, job.job_runner_external_id))
+            log.debug(f"({job.id}/{job.job_runner_external_id}) is still in running state, adding to the runner monitor queue")
             ajs.old_state = model.Job.states.RUNNING
             ajs.running = True
             self.monitor_queue.put(ajs)
         elif job.state == model.Job.states.QUEUED:
-            log.debug("({}/{}) is still in queued state, adding to the runner monitor queue".format(job.id, job.job_runner_external_id))
+            log.debug(f"({job.id}/{job.job_runner_external_id}) is still in queued state, adding to the runner monitor queue")
             ajs.old_state = model.Job.states.QUEUED
             ajs.running = False
             self.monitor_queue.put(ajs)

lib/galaxy/jobs/runners/condor.py

@@ -63,7 +63,7 @@ class CondorJobRunner(AsynchronousJobRunner):
         Remove this function in 21.01
         """
         if cjs.job_wrapper is not None:
-            job_file = "{}/galaxy_{}.sh".format(self.app.config.cluster_files_directory, cjs.job_wrapper.job_id)
+            job_file = f"{self.app.config.cluster_files_directory}/galaxy_{cjs.job_wrapper.job_id}.sh"
             if not os.path.exists(cjs.job_file) and os.path.exists(job_file):
                 cluster_files_dir_and_id = (self.app.config.cluster_files_directory, cjs.job_wrapper.get_id_tag())
                 cjs.output_file = "%s/galaxy_%s.o" % cluster_files_dir_and_id
@@ -155,11 +155,11 @@ class CondorJobRunner(AsynchronousJobRunner):
                 job_wrapper.cleanup()
             return
 
-        log.debug("({}) submitting file {}".format(galaxy_id_tag, executable))
+        log.debug(f"({galaxy_id_tag}) submitting file {executable}")
 
         external_job_id, message = condor_submit(submit_file)
         if external_job_id is None:
-            log.debug("condor_submit failed for job {}: {}".format(job_wrapper.get_id_tag(), message))
+            log.debug(f"condor_submit failed for job {job_wrapper.get_id_tag()}: {message}")
             if self.app.config.cleanup_job == "always":
                 os.unlink(submit_file)
                 cjs.cleanup()
@@ -168,7 +168,7 @@ class CondorJobRunner(AsynchronousJobRunner):
 
         os.unlink(submit_file)
 
-        log.info("({}) queued as {}".format(galaxy_id_tag, external_job_id))
+        log.info(f"({galaxy_id_tag}) queued as {external_job_id}")
 
         # store runner information for tracking if Galaxy restarts
         job_wrapper.set_external_id(external_job_id)
@@ -201,8 +201,8 @@ class CondorJobRunner(AsynchronousJobRunner):
                 cjs.user_log_size = log_size
             except Exception:
                 # so we don't kill the monitor thread
-                log.exception("({}/{}) Unable to check job status".format(galaxy_id_tag, job_id))
-                log.warning("({}/{}) job will now be errored".format(galaxy_id_tag, job_id))
+                log.exception(f"({galaxy_id_tag}/{job_id}) Unable to check job status")
+                log.warning(f"({galaxy_id_tag}/{job_id}) job will now be errored")
                 cjs.fail_message = "Cluster could not complete job"
                 self.work_queue.put((self.fail_job, cjs))
                 continue
@@ -212,10 +212,10 @@ class CondorJobRunner(AsynchronousJobRunner):
                 cjs.job_wrapper.check_for_entry_points()
 
             if job_running and not cjs.running:
-                log.debug("({}/{}) job is now running".format(galaxy_id_tag, job_id))
+                log.debug(f"({galaxy_id_tag}/{job_id}) job is now running")
                 cjs.job_wrapper.change_state(model.Job.states.RUNNING)
             if not job_running and cjs.running:
-                log.debug("({}/{}) job has stopped running".format(galaxy_id_tag, job_id))
+                log.debug(f"({galaxy_id_tag}/{job_id}) job has stopped running")
                 # Will switching from RUNNING to QUEUED confuse Galaxy?
                 # cjs.job_wrapper.change_state( model.Job.states.QUEUED )
             if job_complete:
@@ -223,11 +223,11 @@ class CondorJobRunner(AsynchronousJobRunner):
                     external_metadata = not asbool(cjs.job_wrapper.job_destination.params.get("embed_metadata_in_job", True))
                     if external_metadata:
                         self._handle_metadata_externally(cjs.job_wrapper, resolve_requirements=True)
-                    log.debug("({}/{}) job has completed".format(galaxy_id_tag, job_id))
+                    log.debug(f"({galaxy_id_tag}/{job_id}) job has completed")
                     self.work_queue.put((self.finish_job, cjs))
                 continue
             if job_failed:
-                log.debug("({}/{}) job failed".format(galaxy_id_tag, job_id))
+                log.debug(f"({galaxy_id_tag}/{job_id}) job failed")
                 cjs.failed = True
                 self.work_queue.put((self.finish_job, cjs))
                 continue
@@ -243,7 +243,7 @@ class CondorJobRunner(AsynchronousJobRunner):
         galaxy_id_tag = job_wrapper.get_id_tag()
         if job.container:
             try:
-                log.info("stop_job(): {}: trying to stop container .... ({})".format(job.id, external_id))
+                log.info(f"stop_job(): {job.id}: trying to stop container .... ({external_id})")
                 # self.watched = [cjs for cjs in self.watched if cjs.job_id != external_id]
                 new_watch_list = list()
                 cjs = None
@@ -260,21 +260,21 @@ class CondorJobRunner(AsynchronousJobRunner):
                     external_metadata = not asbool(cjs.job_wrapper.job_destination.params.get("embed_metadata_in_job", True))
                     if external_metadata:
                         self._handle_metadata_externally(cjs.job_wrapper, resolve_requirements=True)
-                    log.debug("({}/{}) job has completed".format(galaxy_id_tag, external_id))
+                    log.debug(f"({galaxy_id_tag}/{external_id}) job has completed")
                     self.work_queue.put((self.finish_job, cjs))
             except Exception as e:
-                log.warning("stop_job(): {}: trying to stop container failed. ({})".format(job.id, e))
+                log.warning(f"stop_job(): {job.id}: trying to stop container failed. ({e})")
                 try:
                     self._kill_container(job_wrapper)
                 except Exception as e:
-                    log.warning("stop_job(): {}: trying to kill container failed. ({})".format(job.id, e))
+                    log.warning(f"stop_job(): {job.id}: trying to kill container failed. ({e})")
                     failure_message = condor_stop(external_id)
                     if failure_message:
-                        log.debug("({}). Failed to stop condor {}".format(external_id, failure_message))
+                        log.debug(f"({external_id}). Failed to stop condor {failure_message}")
         else:
             failure_message = condor_stop(external_id)
             if failure_message:
-                log.debug("({}). Failed to stop condor {}".format(external_id, failure_message))
+                log.debug(f"({external_id}). Failed to stop condor {failure_message}")
 
     def recover(self, job, job_wrapper):
         """Recovers jobs stuck in the queued/running state when Galaxy started"""
@@ -293,11 +293,11 @@ class CondorJobRunner(AsynchronousJobRunner):
         cjs.register_cleanup_file_attribute('user_log')
         self.__old_state_paths(cjs)  # remove in 21.01
         if job.state == model.Job.states.RUNNING:
-            log.debug("({}/{}) is still in running state, adding to the DRM queue".format(job.id, job.job_runner_external_id))
+            log.debug(f"({job.id}/{job.job_runner_external_id}) is still in running state, adding to the DRM queue")
             cjs.running = True
             self.monitor_queue.put(cjs)
         elif job.state == model.Job.states.QUEUED:
-            log.debug("({}/{}) is still in DRM queued state, adding to the DRM queue".format(job.id, job.job_runner_external_id))
+            log.debug(f"({job.id}/{job.job_runner_external_id}) is still in DRM queued state, adding to the DRM queue")
             cjs.running = False
             self.monitor_queue.put(cjs)
 
@@ -317,7 +317,7 @@ class CondorJobRunner(AsynchronousJobRunner):
                     return self._run_command(cont.container_info['commands'][command], external_id)[0]
 
     def _run_command(self, command, external_job_id):
-        command = 'condor_ssh_to_job {} {}'.format(external_job_id, command)
+        command = f'condor_ssh_to_job {external_job_id} {command}'
 
         p = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True, close_fds=True, preexec_fn=os.setpgrp)
         stdout, stderr = p.communicate()

lib/galaxy/jobs/runners/drmaa.py

@@ -106,7 +106,7 @@ class DRMAAJobRunner(AsynchronousJobRunner):
         native_spec = url.split('/')[2]
         if native_spec:
             params = dict(nativeSpecification=native_spec)
-            log.debug("Converted URL '{}' to destination runner=drmaa, params={}".format(url, params))
+            log.debug(f"Converted URL '{url}' to destination runner=drmaa, params={params}")
             return JobDestination(runner='drmaa', params=params)
         else:
             log.debug("Converted URL '%s' to destination runner=drmaa" % url)
@@ -218,7 +218,7 @@ class DRMAAJobRunner(AsynchronousJobRunner):
             if external_job_id is None:
                 job_wrapper.fail("(%s) could not queue job" % galaxy_id_tag)
                 return
-        log.info("({}) queued as {}".format(galaxy_id_tag, external_job_id))
+        log.info(f"({galaxy_id_tag}) queued as {external_job_id}")
 
         # store runner information for tracking if Galaxy restarts
         job_wrapper.set_external_id(external_job_id)
@@ -274,7 +274,7 @@ class DRMAAJobRunner(AsynchronousJobRunner):
         galaxy_id_tag = ajs.job_wrapper.get_id_tag()
         state = None
         try:
-            assert external_job_id not in (None, 'None'), '({}/{}) Invalid job id'.format(galaxy_id_tag, external_job_id)
+            assert external_job_id not in (None, 'None'), f'({galaxy_id_tag}/{external_job_id}) Invalid job id'
             state = self.ds.job_status(external_job_id)
             # Reset exception retries
             for retry_exception in RETRY_EXCEPTIONS_LOWER:
@@ -306,8 +306,8 @@ class DRMAAJobRunner(AsynchronousJobRunner):
             return None
         except Exception:
             # so we don't kill the monitor thread
-            log.exception("({}/{}) unable to check job status".format(galaxy_id_tag, external_job_id))
-            log.warning("({}/{}) job will now be errored".format(galaxy_id_tag, external_job_id))
+            log.exception(f"({galaxy_id_tag}/{external_job_id}) unable to check job status")
+            log.warning(f"({galaxy_id_tag}/{external_job_id}) job will now be errored")
             ajs.fail_message = "Cluster could not complete job"
             self.work_queue.put((self.fail_job, ajs))
             return None
@@ -361,13 +361,13 @@ class DRMAAJobRunner(AsynchronousJobRunner):
                 cmd = shlex.split(kill_script)
                 cmd.extend([str(ext_id), str(self.userid)])
                 commands.execute(cmd)
-            log.info("({}/{}) Removed from DRM queue at user's request".format(job.id, ext_id))
+            log.info(f"({job.id}/{ext_id}) Removed from DRM queue at user's request")
         except drmaa.InvalidJobException:
-            log.exception("({}/{}) User killed running job, but it was already dead".format(job.id, ext_id))
+            log.exception(f"({job.id}/{ext_id}) User killed running job, but it was already dead")
         except commands.CommandLineException as e:
             log.error("({}/{}) User killed running job, but command execution failed: {}".format(job.id, ext_id, unicodify(e)))
         except Exception:
-            log.exception("({}/{}) User killed running job, but error encountered removing from DRM queue".format(job.id, ext_id))
+            log.exception(f"({job.id}/{ext_id}) User killed running job, but error encountered removing from DRM queue")
 
     def recover(self, job, job_wrapper):
         """Recovers jobs stuck in the queued/running state when Galaxy started"""
@@ -381,12 +381,12 @@ class DRMAAJobRunner(AsynchronousJobRunner):
         ajs.job_wrapper = job_wrapper
         ajs.job_destination = job_wrapper.job_destination
         if job.state == model.Job.states.RUNNING:
-            log.debug("({}/{}) is still in running state, adding to the DRM queue".format(job.id, job.get_job_runner_external_id()))
+            log.debug(f"({job.id}/{job.get_job_runner_external_id()}) is still in running state, adding to the DRM queue")
             ajs.old_state = drmaa.JobState.RUNNING
             ajs.running = True
             self.monitor_queue.put(ajs)
         elif job.get_state() == model.Job.states.QUEUED:
-            log.debug("({}/{}) is still in DRM queued state, adding to the DRM queue".format(job.id, job.get_job_runner_external_id()))
+            log.debug(f"({job.id}/{job.get_job_runner_external_id()}) is still in DRM queued state, adding to the DRM queue")
             ajs.old_state = drmaa.JobState.QUEUED_ACTIVE
             ajs.running = False
             self.monitor_queue.put(ajs)
@@ -395,10 +395,10 @@ class DRMAAJobRunner(AsynchronousJobRunner):
         """ Stores the content of a DRMAA JobTemplate object in a file as a JSON string.
         Path is hard-coded, but it's no worse than other path in this module.
         Uses Galaxy's JobID, so file is expected to be unique."""
-        filename = "{}/{}.jt_json".format(self.app.config.cluster_files_directory, job_wrapper.get_id_tag())
+        filename = f"{self.app.config.cluster_files_directory}/{job_wrapper.get_id_tag()}.jt_json"
         with open(filename, 'w+') as fp:
             json.dump(jt, fp)
-        log.debug('({}) Job script for external submission is: {}'.format(job_wrapper.job_id, filename))
+        log.debug(f'({job_wrapper.job_id}) Job script for external submission is: {filename}')
         return filename
 
     def external_runjob(self, external_runjob_script, jobtemplate_filename, username):

lib/galaxy/jobs/runners/godocker.py

@@ -253,13 +253,13 @@ class GodockerJobRunner(AsynchronousJobRunner):
         job_wrapper.command_line = job.command_line
         ajs.job_wrapper = job_wrapper
         if job.state == model.Job.states.RUNNING:
-            log.debug("({}/{}) is still in running state, adding to the god queue".format(job.id, job.get_job_runner_external_id()))
+            log.debug(f"({job.id}/{job.get_job_runner_external_id()}) is still in running state, adding to the god queue")
             ajs.old_state = 'R'
             ajs.running = True
             self.monitor_queue.put(ajs)
 
         elif job.state == model.Job.states.QUEUED:
-            log.debug("({}/{}) is still in god queued state, adding to the god queue".format(job.id, job.get_job_runner_external_id()))
+            log.debug(f"({job.id}/{job.get_job_runner_external_id()}) is still in god queued state, adding to the god queue")
             ajs.old_state = 'Q'
             ajs.running = False
             self.monitor_queue.put(ajs)

lib/galaxy/jobs/runners/kubernetes.py

@@ -527,7 +527,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
                 self.__cleanup_k8s_job(job_to_delete)
             # TODO assert whether job parallelism == 0
             # assert not job_to_delete.exists(), "Could not delete job,"+job.job_runner_external_id+" it still exists"
-            log.debug("({}/{}) Terminated at user's request".format(job.id, job.job_runner_external_id))
+            log.debug(f"({job.id}/{job.job_runner_external_id}) Terminated at user's request")
         except Exception as e:
             log.exception("({}/{}) User killed running job, but error encountered during termination: {}".format(
                 job.id, job.job_runner_external_id, e))

lib/galaxy/jobs/runners/local.py

@@ -94,7 +94,7 @@ class LocalJobRunner(BaseJobRunner):
         try:
             stdout_file = tempfile.NamedTemporaryFile(mode='wb+', suffix='_stdout', dir=job_wrapper.working_directory)
             stderr_file = tempfile.NamedTemporaryFile(mode='wb+', suffix='_stderr', dir=job_wrapper.working_directory)
-            log.debug('({}) executing job script: {}'.format(job_id, job_file))
+            log.debug(f'({job_id}) executing job script: {job_file}')
             # The preexec_fn argument of Popen() is used to call os.setpgrp() in
             # the child process just before the child is executed. This will set
             # the PGID of the child process to its PID (i.e. ensures that it is

lib/galaxy/jobs/runners/pbs.py

@@ -130,7 +130,7 @@ class PBSJobRunner(AsynchronousJobRunner):
         pbs_destination = '@%s' % server
         pbs_queue = url_split[3] or None
         if pbs_queue is not None:
-            pbs_destination = '{}{}'.format(pbs_queue, pbs_destination)
+            pbs_destination = f'{pbs_queue}{pbs_destination}'
 
         params = dict(destination=pbs_destination)
 
@@ -147,7 +147,7 @@ class PBSJobRunner(AsynchronousJobRunner):
             param, value = opt.split(None, 1)
             params[param] = value
 
-        log.debug("Converted URL '{}' to destination runner=pbs, params={}".format(url, params))
+        log.debug(f"Converted URL '{url}' to destination runner=pbs, params={params}")
 
         # Create a dynamic JobDestination
         return JobDestination(runner='pbs', params=params)
@@ -186,7 +186,7 @@ class PBSJobRunner(AsynchronousJobRunner):
                 try:
                     rval.append(dict(name=getattr(pbs, 'ATTR_' + arg), value=value))
                 except AttributeError as e:
-                    raise Exception("Invalid parameter '{}': {}".format(arg, e))
+                    raise Exception(f"Invalid parameter '{arg}': {e}")
         return rval
 
     def __get_pbs_server(self, job_destination_params):
@@ -230,13 +230,13 @@ class PBSJobRunner(AsynchronousJobRunner):
         if c <= 0:
             errno, text = pbs.error()
             job_wrapper.fail("Unable to queue job for execution.  Resubmitting the job may succeed.")
-            log.error("Connection to PBS server for submit failed: {}: {}".format(errno, text))
+            log.error(f"Connection to PBS server for submit failed: {errno}: {text}")
             return
 
         # define job attributes
-        ofile = "{}/{}.o".format(self.app.config.cluster_files_directory, job_wrapper.job_id)
-        efile = "{}/{}.e".format(self.app.config.cluster_files_directory, job_wrapper.job_id)
-        ecfile = "{}/{}.ec".format(self.app.config.cluster_files_directory, job_wrapper.job_id)
+        ofile = f"{self.app.config.cluster_files_directory}/{job_wrapper.job_id}.o"
+        efile = f"{self.app.config.cluster_files_directory}/{job_wrapper.job_id}.e"
+        ecfile = f"{self.app.config.cluster_files_directory}/{job_wrapper.job_id}.ec"
 
         output_fnames = job_wrapper.get_output_fnames()
 
@@ -262,7 +262,7 @@ class PBSJobRunner(AsynchronousJobRunner):
             ]
 
         # define PBS job options
-        attrs.append(dict(name=pbs.ATTR_N, value=str("{}_{}_{}".format(job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user))))
+        attrs.append(dict(name=pbs.ATTR_N, value=str(f"{job_wrapper.job_id}_{job_wrapper.tool.id}_{job_wrapper.user}")))
         job_attrs = pbs.new_attropl(len(attrs) + len(pbs_options))
         for i, attr in enumerate(attrs + pbs_options):
             job_attrs[i].name = attr['name']
@@ -287,7 +287,7 @@ class PBSJobRunner(AsynchronousJobRunner):
 
         env_setup_commands = [stage_commands]
         script = self.get_job_file(job_wrapper, exit_code_path=ecfile, env_setup_commands=env_setup_commands, shell=job_wrapper.shell)
-        job_file = "{}/{}.sh".format(self.app.config.cluster_files_directory, job_wrapper.job_id)
+        job_file = f"{self.app.config.cluster_files_directory}/{job_wrapper.job_id}.sh"
         self.write_executable_script(job_file, script)
         # job was deleted while we were preparing it
         if job_wrapper.get_state() == model.Job.states.DELETED:
@@ -302,7 +302,7 @@ class PBSJobRunner(AsynchronousJobRunner):
         # The job tag includes the job and the task identifier
         # (if a TaskWrapper was passed in):
         galaxy_job_id = job_wrapper.get_id_tag()
-        log.debug("({}) submitting file {}".format(galaxy_job_id, job_file))
+        log.debug(f"({galaxy_job_id}) submitting file {job_file}")
 
         tries = 0
         while tries < 5:
@@ -320,9 +320,9 @@ class PBSJobRunner(AsynchronousJobRunner):
             return
 
         if pbs_queue_name is None:
-            log.debug("({}) queued in default queue as {}".format(galaxy_job_id, job_id))
+            log.debug(f"({galaxy_job_id}) queued in default queue as {job_id}")
         else:
-            log.debug("({}) queued in {} queue as {}".format(galaxy_job_id, pbs_queue_name, job_id))
+            log.debug(f"({galaxy_job_id}) queued in {pbs_queue_name} queue as {job_id}")
 
         # persist destination
         job_wrapper.set_job_destination(job_destination, job_id)
@@ -356,7 +356,7 @@ class PBSJobRunner(AsynchronousJobRunner):
             old_state = pbs_job_state.old_state
             pbs_server_name = self.__get_pbs_server(pbs_job_state.job_destination.params)
             if pbs_server_name in failures:
-                log.debug("({}/{}) Skipping state check because PBS server connection failed".format(galaxy_job_id, job_id))
+                log.debug(f"({galaxy_job_id}/{job_id}) Skipping state check because PBS server connection failed")
                 new_watched.append(pbs_job_state)
                 continue
             try:
@@ -367,13 +367,13 @@ class PBSJobRunner(AsynchronousJobRunner):
                 try:
                     # Recheck to make sure it wasn't a communication problem
                     self.check_single_job(pbs_server_name, job_id)
-                    log.warning("({}/{}) PBS job was not in state check list, but was found with individual state check".format(galaxy_job_id, job_id))
+                    log.warning(f"({galaxy_job_id}/{job_id}) PBS job was not in state check list, but was found with individual state check")
                     new_watched.append(pbs_job_state)
                 except Exception:
                     errno, text = pbs.error()
                     if errno == 15001:
                         # 15001 == job not in queue
-                        log.debug("({}/{}) PBS job has left queue".format(galaxy_job_id, job_id))
+                        log.debug(f"({galaxy_job_id}/{job_id}) PBS job has left queue")
                         self.work_queue.put((self.finish_job, pbs_job_state))
                     else:
                         # Unhandled error, continue to monitor
@@ -381,7 +381,7 @@ class PBSJobRunner(AsynchronousJobRunner):
                         new_watched.append(pbs_job_state)
                 continue
             if status.job_state != old_state:
-                log.debug("({}/{}) PBS job state changed from {} to {}".format(galaxy_job_id, job_id, old_state, status.job_state))
+                log.debug(f"({galaxy_job_id}/{job_id}) PBS job state changed from {old_state} to {status.job_state}")
             if status.job_state == "R" and not pbs_job_state.running:
                 pbs_job_state.running = True
                 pbs_job_state.job_wrapper.change_state(model.Job.states.RUNNING)
@@ -396,18 +396,18 @@ class PBSJobRunner(AsynchronousJobRunner):
                 # "keep_completed" is enabled in PBS, so try to check exit status
                 try:
                     assert int(status.exit_status) == 0
-                    log.debug("({}/{}) PBS job has completed successfully".format(galaxy_job_id, job_id))
+                    log.debug(f"({galaxy_job_id}/{job_id}) PBS job has completed successfully")
                 except AssertionError:
                     exit_status = int(status.exit_status)
                     error_message = JOB_EXIT_STATUS.get(exit_status, 'Unknown error: %s' % status.exit_status)
                     pbs_job_state.fail_message = CLUSTER_ERROR_MESSAGE % error_message
-                    log.error('({}/{}) PBS job failed: {}'.format(galaxy_job_id, job_id, error_message))
+                    log.error(f'({galaxy_job_id}/{job_id}) PBS job failed: {error_message}')
                     pbs_job_state.stop_job = False
                     self.work_queue.put((self.fail_job, pbs_job_state))
                     continue
                 except AttributeError:
                     # No exit_status, can't verify proper completion so we just have to assume success.
-                    log.debug("({}/{}) PBS job has completed".format(galaxy_job_id, job_id))
+                    log.debug(f"({galaxy_job_id}/{job_id}) PBS job has completed")
                 self.work_queue.put((self.finish_job, pbs_job_state))
                 continue
             pbs_job_state.old_state = status.job_state
@@ -497,14 +497,14 @@ class PBSJobRunner(AsynchronousJobRunner):
                     stage_name = os.path.join(self.app.config.pbs_stage_path, os.path.split(fname)[1])
                 else:
                     stage_name = fname
-                stage += "{}@{}:{}".format(stage_name, self.app.config.pbs_dataset_server, fname)
+                stage += f"{stage_name}@{self.app.config.pbs_dataset_server}:{fname}"
         return stage
 
     def stop_job(self, job_wrapper):
         """Attempts to delete a job from the PBS queue"""
         job = job_wrapper.get_job()
         job_id = job.get_job_runner_external_id().encode('utf-8')
-        job_tag = "({}/{})".format(job.get_id_tag(), job_id)
+        job_tag = f"({job.get_id_tag()}/{job_id})"
         log.debug("%s Stopping PBS job" % job_tag)
 
         # Declare the connection handle c so that it can be cleaned up:
@@ -526,7 +526,7 @@ class PBSJobRunner(AsynchronousJobRunner):
                       % job_tag)
         except Exception:
             e = traceback.format_exc()
-            log.debug("{} Unable to stop job: {}".format(job_tag, e))
+            log.debug(f"{job_tag} Unable to stop job: {e}")
         finally:
             # Cleanup: disconnect from the server.
             if (None is not c):
@@ -536,22 +536,22 @@ class PBSJobRunner(AsynchronousJobRunner):
         """Recovers jobs stuck in the queued/running state when Galaxy started"""
         job_id = job.get_job_runner_external_id()
         pbs_job_state = AsynchronousJobState()
-        pbs_job_state.output_file = "{}/{}.o".format(self.app.config.cluster_files_directory, job.id)
-        pbs_job_state.error_file = "{}/{}.e".format(self.app.config.cluster_files_directory, job.id)
-        pbs_job_state.exit_code_file = "{}/{}.ec".format(self.app.config.cluster_files_directory, job.id)
-        pbs_job_state.job_file = "{}/{}.sh".format(self.app.config.cluster_files_directory, job.id)
+        pbs_job_state.output_file = f"{self.app.config.cluster_files_directory}/{job.id}.o"
+        pbs_job_state.error_file = f"{self.app.config.cluster_files_directory}/{job.id}.e"
+        pbs_job_state.exit_code_file = f"{self.app.config.cluster_files_directory}/{job.id}.ec"
+        pbs_job_state.job_file = f"{self.app.config.cluster_files_directory}/{job.id}.sh"
         pbs_job_state.job_id = str(job_id)
         pbs_job_state.runner_url = job_wrapper.get_job_runner_url()
         pbs_job_state.job_destination = job_wrapper.job_destination
         job_wrapper.command_line = job.command_line
         pbs_job_state.job_wrapper = job_wrapper
         if job.state == model.Job.states.RUNNING:
-            log.debug("({}/{}) is still in running state, adding to the PBS queue".format(job.id, job.get_job_runner_external_id()))
+            log.debug(f"({job.id}/{job.get_job_runner_external_id()}) is still in running state, adding to the PBS queue")
             pbs_job_state.old_state = 'R'
             pbs_job_state.running = True
             self.monitor_queue.put(pbs_job_state)
         elif job.state == model.Job.states.QUEUED:
-            log.debug("({}/{}) is still in PBS queued state, adding to the PBS queue".format(job.id, job.get_job_runner_external_id()))
+            log.debug(f"({job.id}/{job.get_job_runner_external_id()}) is still in PBS queued state, adding to the PBS queue")
             pbs_job_state.old_state = 'Q'
             pbs_job_state.running = False
             self.monitor_queue.put(pbs_job_state)

lib/galaxy/jobs/runners/pulsar.py

@@ -539,7 +539,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
     def get_client_from_wrapper(self, job_wrapper):
         job_id = job_wrapper.job_id
         if hasattr(job_wrapper, 'task_id'):
-            job_id = "{}_{}".format(job_id, job_wrapper.task_id)
+            job_id = f"{job_id}_{job_wrapper.task_id}"
         params = job_wrapper.job_destination.params.copy()
         user = job_wrapper.get_job().user
         if user:
@@ -685,7 +685,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
             # Remote kill
             pulsar_url = job.job_runner_name
             job_id = job.job_runner_external_id
-            log.debug("Attempt remote Pulsar kill of job with url {} and id {}".format(pulsar_url, job_id))
+            log.debug(f"Attempt remote Pulsar kill of job with url {pulsar_url} and id {job_id}")
             client = self.get_client(job.destination_params, job_id)
             client.kill()
 
@@ -1010,7 +1010,7 @@ class PulsarComputeEnvironment(ComputeEnvironment):
         # first but that adds untested logic that wouln't ever be used.
         remote_input_path = self.path_mapper.remote_input_path_rewrite(metadata_val, client_input_path_type=CLIENT_INPUT_PATH_TYPES.INPUT_METADATA_PATH)
         if remote_input_path:
-            log.info("input_metadata_rewrite is {} from {}".format(remote_input_path, metadata_val))
+            log.info(f"input_metadata_rewrite is {remote_input_path} from {metadata_val}")
             self.path_rewrites_input_metadata[metadata_val] = remote_input_path
             return remote_input_path
 

lib/galaxy/jobs/runners/state_handlers/resubmit.py

@@ -93,7 +93,7 @@ def _handle_resubmit_definitions(resubmit_definitions, app, job_runner, job_stat
 
         external_id = getattr(job_state, "job_id", None)
         if external_id:
-            job_log_prefix = "({}/{})".format(job_state.job_wrapper.job_id, job_state.job_id)
+            job_log_prefix = f"({job_state.job_wrapper.job_id}/{job_state.job_id})"
         else:
             job_log_prefix = "(%s)" % (job_state.job_wrapper.job_id)
 

lib/galaxy/jobs/runners/univa.py

@@ -91,13 +91,13 @@ class UnivaJobRunner(DRMAAJobRunner):
                 ajs.fail_message = "This job failed because it was cancelled."
                 drmaa_state = self.drmaa.JobState.FAILED
             elif ("signal" in extinfo and extinfo["signal"] == "SIGKILL") and time_wasted > time_granted:
-                log.error('({tag}/{jobid}) Job hit walltime'.format(tag=ajs.job_wrapper.get_id_tag(), jobid=ajs.job_id))
+                log.error(f'({ajs.job_wrapper.get_id_tag()}/{ajs.job_id}) Job hit walltime')
                 ajs.fail_message = "This job was terminated because it ran longer than the maximum allowed job run time."
                 ajs.runner_state = ajs.runner_states.WALLTIME_REACHED
                 drmaa_state = self.drmaa.JobState.FAILED
             # test wasted>granted memory only if failed != 0 and exit_status != 0, ie if marked as failed
             elif state == self.drmaa.JobState.FAILED and mem_wasted > mem_granted * slots:
-                log.error('({idtag}/{jobid}) Job hit memory limit ({used}>{limit})'.format(idtag=ajs.job_wrapper.get_id_tag(), jobid=ajs.job_id, used=mem_wasted, limit=mem_granted))
+                log.error(f'({ajs.job_wrapper.get_id_tag()}/{ajs.job_id}) Job hit memory limit ({mem_wasted}>{mem_granted})')
                 ajs.fail_message = "This job was terminated because it used more than the maximum allowed memory."
                 ajs.runner_state = ajs.runner_states.MEMORY_LIMIT_REACHED
                 drmaa_state = self.drmaa_job_states.FAILED
@@ -106,10 +106,10 @@ class UnivaJobRunner(DRMAAJobRunner):
             # TODO return True?
             return True  # job was not actually terminal
         elif state == self.drmaa.JobState.UNDETERMINED:
-            log.warning('({tag}/{jobid}) Job state could not be determined'.format(tag=ajs.job_wrapper.get_id_tag(), jobid=ajs.job_id))
+            log.warning(f'({ajs.job_wrapper.get_id_tag()}/{ajs.job_id}) Job state could not be determined')
             drmaa_state = self.drmaa_job_states.FAILED
         else:
-            log.error("DRMAAUniva: job {job_id} determined unknown state {state}".format(job_id=ajs.job_id, state=state))
+            log.error(f"DRMAAUniva: job {ajs.job_id} determined unknown state {state}")
             drmaa_state = self.drmaa_job_states.FAILED
         # by default, finish the job with the state from drmaa
         return super()._complete_terminal_job(ajs, drmaa_state=drmaa_state)
@@ -203,7 +203,7 @@ class UnivaJobRunner(DRMAAJobRunner):
             try:
                 stdout = commands.execute(cmd).strip()
             except commands.CommandLineException as e:
-                if slp <= 32 and "job id {jobid} not found".format(jobid=job_id) in e.stderr:
+                if slp <= 32 and f"job id {job_id} not found" in e.stderr:
                     time.sleep(slp)
                     slp *= 2
                     continue
@@ -397,7 +397,7 @@ class UnivaJobRunner(DRMAAJobRunner):
         extinfo["slots"] = float(rv.resourceUsage['slots'])
         # log.debug("wait -> \texitStatus {0}\thasCoreDump {1}\thasExited {2}\thasSignal {3}\tjobId {4}\t\tterminatedSignal {5}\twasAborted {6}\tresourceUsage {7}".format(rv.exitStatus, rv.hasCoreDump, rv.hasExited, rv.hasSignal, rv.jobId, rv.terminatedSignal, rv.wasAborted, rv.resourceUsage))
         if rv.wasAborted:
-            log.error("DRMAAUniva: job {job_id} was aborted according to wait()".format(job_id=job_id))
+            log.error(f"DRMAAUniva: job {job_id} was aborted according to wait()")
             extinfo["deleted"] = True
             return self.drmaa.JobState.FAILED
 
@@ -405,19 +405,19 @@ class UnivaJobRunner(DRMAAJobRunner):
         # but also violation of scheduler constraints
         state = self.drmaa.JobState.DONE
         if rv.exitStatus != 0:
-            log.error("DRMAAUniva: job {job_id} has exit status {status}".format(job_id=job_id, status=rv.exitStatus))
+            log.error(f"DRMAAUniva: job {job_id} has exit status {rv.exitStatus}")
             extinfo["state"] = self.drmaa.JobState.FAILED
 
         if not rv.hasExited or rv.hasSignal:
             if rv.hasCoreDump != 0:
-                log.error("DRMAAUniva: job {job_id} has core dump".format(job_id=job_id))
+                log.error(f"DRMAAUniva: job {job_id} has core dump")
                 extinfo["state"] = self.drmaa.JobState.FAILED
             elif len(rv.terminatedSignal) > 0:
-                log.error("DRMAAUniva: job {job_id} was kill by signal {signal}".format(job_id=job_id, signal=rv.terminatedSignal))
+                log.error(f"DRMAAUniva: job {job_id} was kill by signal {rv.terminatedSignal}")
                 state = self.drmaa.JobState.FAILED
                 extinfo["signal"] = rv.terminatedSignal
             elif rv.wasAborted == 0:
-                log.error("DRMAAUniva: job {job_id} has finished in unclear condition".format(job_id=job_id))
+                log.error(f"DRMAAUniva: job {job_id} has finished in unclear condition")
                 state = self.drmaa.JobState.FAILED
         # log.debug("UnivaJobRunner._get_drmaa_state_wait ({jobid}) -> {state}".format(jobid=job_id, state=self.drmaa_job_state_strings[state]))
         return state
@@ -535,7 +535,7 @@ class UnivaJobRunner(DRMAAJobRunner):
         elif "w" in state:
             return self.drmaa.JobState.QUEUED_ACTIVE
         else:
-            log.error("DRMAAUniva: job {job_id} unknown state from qstat: {state}".format(job_id=job_id, state=state))
+            log.error(f"DRMAAUniva: job {job_id} unknown state from qstat: {state}")
             return self.drmaa.JobState.UNDETERMINED
 
 
@@ -569,12 +569,12 @@ def _parse_native_specs(job_id, native_spec):
     if m is not None:
         tme = _parse_time(m.group(1))
         if tme is None:
-            log.error("DRMAAUniva: job {job_id} has unparsable time native spec {spec}".format(job_id=job_id, spec=native_spec))
+            log.error(f"DRMAAUniva: job {job_id} has unparsable time native spec {native_spec}")
     # parse memory
     m = re.search(r"mem=([\d.]+[KGMT]?)[\s,]*", native_spec)
     if m is not None:
         mem = size_to_bytes(m.group(1))
         # mem = _parse_mem(m.group(1))
         if mem is None:
-            log.error("DRMAAUniva: job {job_id} has unparsable memory native spec {spec}".format(job_id=job_id, spec=native_spec))
+            log.error(f"DRMAAUniva: job {job_id} has unparsable memory native spec {native_spec}")
     return tme, mem

lib/galaxy/jobs/runners/util/cli/__init__.py

@@ -39,7 +39,7 @@ class CliInterface:
         def __load_from_path(module_path):
             base_module = importlib.import_module(module_path)
             for module_info in pkgutil.iter_modules(base_module.__path__):
-                module = importlib.import_module('{}.{}'.format(module_path, module_info.name))
+                module = importlib.import_module(f'{module_path}.{module_info.name}')
                 yield module
 
         def __load(module_path, d):

lib/galaxy/jobs/runners/util/cli/job/lsf.py

@@ -52,7 +52,7 @@ class LSF(BaseJobExec):
         # Generated template.
         template_scriptargs = ''
         for k, v in scriptargs.items():
-            template_scriptargs += '#BSUB {} {}\n'.format(k, v)
+            template_scriptargs += f'#BSUB {k} {v}\n'
         return dict(headers=template_scriptargs)
 
     def submit(self, script_file):

lib/galaxy/jobs/runners/util/cli/job/slurm.py

@@ -47,7 +47,7 @@ class Slurm(BaseJobExec):
         # Generated template.
         template_scriptargs = ''
         for k, v in scriptargs.items():
-            template_scriptargs += '#SBATCH {} {}\n'.format(k, v)
+            template_scriptargs += f'#SBATCH {k} {v}\n'
         return dict(headers=template_scriptargs)
 
     def submit(self, script_file):

lib/galaxy/jobs/runners/util/cli/job/torque.py

@@ -59,7 +59,7 @@ class Torque(BaseJobExec):
                 log.warning(ERROR_MESSAGE_UNRECOGNIZED_ARG % k)
         template_pbsargs = ''
         for k, v in pbsargs.items():
-            template_pbsargs += '#PBS {} {}\n'.format(k, v)
+            template_pbsargs += f'#PBS {k} {v}\n'
         return dict(headers=template_pbsargs)
 
     def submit(self, script_file):

lib/galaxy/jobs/runners/util/condor/__init__.py

@@ -58,7 +58,7 @@ def build_submit_description(executable, output, error, user_log, query_params):
 
     submit_description = []
     for key, value in all_query_params.items():
-        submit_description.append('{} = {}'.format(key, value))
+        submit_description.append(f'{key} = {value}')
     submit_description.append('executable = ' + executable)
     submit_description.append('output = ' + output)
     submit_description.append('error = ' + error)

lib/galaxy/jobs/runners/util/env.py

@@ -29,7 +29,7 @@ def env_to_statement(env):
         return execute
     name = env['name']
     value = __escape(env['value'], env)
-    return '{}={}; export {}'.format(name, value, name)
+    return f'{name}={value}; export {name}'
 
 
 def __escape(value, env):

lib/galaxy/jobs/transfer_manager.py

@@ -5,12 +5,11 @@ IPC with multiple process configurations.
 import json
 import logging
 import os
+import shlex
 import socket
 import subprocess
 import threading
 
-from six.moves import shlex_quote
-
 from galaxy.util import (
     listify,
     sleeper,
@@ -75,12 +74,12 @@ class TransferManager:
             # not the case, this process will need to be moved to a
             # non-blocking method.
             cmd = self.command + [tj.id]
-            log.debug('Transfer command is: %s', ' '.join(map(shlex_quote, cmd)))
+            log.debug('Transfer command is: %s', ' '.join(map(shlex.quote, cmd)))
             p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
             p.wait()
             output = p.stdout.read(32768)
             if p.returncode != 0:
-                log.error('Spawning transfer job failed: {}: {}'.format(tj.id, output))
+                log.error(f'Spawning transfer job failed: {tj.id}: {output}')
                 tj.state = tj.states.ERROR
                 tj.info = 'Spawning transfer job failed: %s' % output.splitlines()[-1]
                 self.sa_session.add(tj)
@@ -154,7 +153,7 @@ class TransferManager:
                 except Exception:
                     self.sa_session.refresh(tj)
                     if tj.state == tj.states.RUNNING:
-                        log.error('Transfer job {} is marked as running but pid {} appears to be dead.'.format(tj.id, tj.pid))
+                        log.error(f'Transfer job {tj.id} is marked as running but pid {tj.pid} appears to be dead.')
                         dead.append(tj)
             if dead:
                 self.run(dead)

lib/galaxy/managers/base.py

@@ -114,8 +114,8 @@ def get_object(trans, id, class_name, check_ownership=False, check_accessible=Fa
         item = trans.sa_session.query(item_class).get(decoded_id)
         assert item is not None
     except Exception:
-        log.exception("Invalid {} id ( {} ) specified.".format(class_name, id))
-        raise exceptions.MessageException("Invalid {} id ( {} ) specified".format(class_name, id), type="error")
+        log.exception(f"Invalid {class_name} id ( {id} ) specified.")
+        raise exceptions.MessageException(f"Invalid {class_name} id ( {id} ) specified", type="error")
 
     if check_ownership or check_accessible:
         security_check(trans, item, check_ownership, check_accessible)

lib/galaxy/managers/citations.py

@@ -67,7 +67,7 @@ def parse_citation(elem, citation_manager):
     try:
         citation = citation_class(elem, citation_manager)
     except Exception as e:
-        raise Exception("Invalid citation of type '{}' with content '{}': {}".format(citation_type, elem.text, e))
+        raise Exception(f"Invalid citation of type '{citation_type}' with content '{elem.text}': {e}")
     return citation
 
 

lib/galaxy/managers/cloud.py

@@ -248,7 +248,7 @@ class CloudManager(sharable.SharableModelManager):
         try:
             bucket = connection.storage.buckets.get(bucket_name)
             if bucket is None:
-                raise RequestParameterInvalidException("The bucket `{}` not found.".format(bucket_name))
+                raise RequestParameterInvalidException(f"The bucket `{bucket_name}` not found.")
         except Exception as e:
             raise ItemAccessibilityException("Could not get the bucket `{}`: {}".format(bucket_name, util.unicodify(e)))
 
@@ -354,7 +354,7 @@ class CloudManager(sharable.SharableModelManager):
                     incoming = (util.Params(args, sanitize=False)).__dict__
                     d2c = trans.app.toolbox.get_tool(SEND_TOOL, SEND_TOOL_VERSION)
                     if not d2c:
-                        log.debug("Failed to get the `send` tool per user `{}` request.".format(trans.user.id))
+                        log.debug(f"Failed to get the `send` tool per user `{trans.user.id}` request.")
                         failed.append(json.dumps(
                             {
                                 "object": object_label,

lib/galaxy/managers/cloudauthzs.py

@@ -110,7 +110,7 @@ class CloudAuthzsDeserializer(base.ModelDeserializer):
             decoded_authn_id = self.app.security.decode_id(val)
         except Exception:
             log.debug("cannot decode authz_id `" + str(val) + "`")
-            raise MalformedId("Invalid `authz_id` {}!".format(val))
+            raise MalformedId(f"Invalid `authz_id` {val}!")
 
         trans = context.get("trans")
         if trans is None:

lib/galaxy/managers/collections_util.py

@@ -78,12 +78,12 @@ def get_collection(collection, name=""):
     hdas = []
     if collection.has_subcollections:
         for element in collection.elements:
-            subnames, subhdas = get_collection_elements(element.child_collection, name="{}/{}".format(name, element.element_identifier))
+            subnames, subhdas = get_collection_elements(element.child_collection, name=f"{name}/{element.element_identifier}")
             names.extend(subnames)
             hdas.extend(subhdas)
     else:
         for element in collection.elements:
-            names.append("{}/{}".format(name, element.element_identifier))
+            names.append(f"{name}/{element.element_identifier}")
             hdas.append(element.dataset_instance)
     return names, hdas
 
@@ -92,7 +92,7 @@ def get_collection_elements(collection, name=""):
     names = []
     hdas = []
     for element in collection.elements:
-        full_element_name = "{}/{}".format(name, element.element_identifier)
+        full_element_name = f"{name}/{element.element_identifier}"
         if element.is_collection:
             subnames, subhdas = get_collection(element.child_collection, name=full_element_name)
             names.extend(subnames)

lib/galaxy/managers/jobs.py

@@ -38,7 +38,7 @@ def get_path_key(path_tuple):
             # we remove the last 2 items of the path tuple (values and list index)
             return path_key
         if path_key:
-            path_key = "{}{}{}".format(path_key, sep, p)
+            path_key = f"{path_key}{sep}{p}"
         else:
             path_key = p
     return path_key

lib/galaxy/managers/library_datasets.py

@@ -123,7 +123,7 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
                 continue
             if key in ('name'):
                 if len(val) < MINIMUM_STRING_LENGTH:
-                    raise RequestParameterInvalidException('{} must have at least length of {}'.format(key, MINIMUM_STRING_LENGTH))
+                    raise RequestParameterInvalidException(f'{key} must have at least length of {MINIMUM_STRING_LENGTH}')
                 val = validation.validate_and_sanitize_basestring(key, val)
                 validated_payload[key] = val
             if key in ('misc_info', 'message'):
@@ -136,7 +136,7 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
                 validated_payload[key] = val
             if key in ('genome_build'):
                 if len(val) < MINIMUM_STRING_LENGTH:
-                    raise RequestParameterInvalidException('{} must have at least length of {}'.format(key, MINIMUM_STRING_LENGTH))
+                    raise RequestParameterInvalidException(f'{key} must have at least length of {MINIMUM_STRING_LENGTH}')
                 val = validation.validate_and_sanitize_basestring(key, val)
                 validated_payload[key] = val
             if key in ('tags'):

lib/galaxy/managers/markdown_parse.py

@@ -42,7 +42,7 @@ GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = r'(?P<container>%s)' % "|".join(GALAX
 ARG_VAL_REGEX = r'''[\w_\-]+|\"[^\"]+\"|\'[^\']+\''''
 FUNCTION_ARG = r'\s*\w+\s*=\s*(?:%s)\s*' % ARG_VAL_REGEX
 # embed commas between arguments
-FUNCTION_MULTIPLE_ARGS = r'(?P<firstargcall>{})(?P<restargcalls>(?:,{})*)'.format(FUNCTION_ARG, FUNCTION_ARG)
+FUNCTION_MULTIPLE_ARGS = fr'(?P<firstargcall>{FUNCTION_ARG})(?P<restargcalls>(?:,{FUNCTION_ARG})*)'
 FUNCTION_MULTIPLE_ARGS_PATTERN = re.compile(FUNCTION_MULTIPLE_ARGS)
 FUNCTION_CALL_LINE_TEMPLATE = r'\s*%s\s*\((?:' + FUNCTION_MULTIPLE_ARGS + r')?\)\s*'
 GALAXY_MARKDOWN_FUNCTION_CALL_LINE = re.compile(FUNCTION_CALL_LINE_TEMPLATE % GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX)
@@ -119,7 +119,7 @@ def validate_galaxy_markdown(galaxy_markdown, internal=True):
 
     if expecting_container_close_for:
         template = "Invalid line %d: %s"
-        msg = template % (last_line_no, "close of block for [{expected_for}] expected".format(expected_for=expecting_container_close_for))
+        msg = template % (last_line_no, f"close of block for [{expecting_container_close_for}] expected")
         raise ValueError(msg)