Ruff and flake8 fixes

.github/workflows/lint.yaml

@@ -20,6 +20,7 @@ jobs:
     name: Test
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         python-version: ['3.7', '3.11']
     env:

lib/galaxy/authnz/managers.py

@@ -67,7 +67,7 @@ def _parse_oidc_config(self, config_file):
             if root.tag != "OIDC":
                 raise etree.ParseError(
                     "The root element in OIDC_Config xml file is expected to be `OIDC`, "
-                    "found `{}` instead -- unable to continue.".format(root.tag)
+                    f"found `{root.tag}` instead -- unable to continue."
                 )
             for child in root:
                 if child.tag != "Setter":
@@ -79,7 +79,7 @@ def _parse_oidc_config(self, config_file):
                 if "Property" not in child.attrib or "Value" not in child.attrib or "Type" not in child.attrib:
                     log.error(
                         "Could not find the node attributes `Property` and/or `Value` and/or `Type`;"
-                        " found these attributes: `{}`; skipping this node.".format(child.attrib)
+                        f" found these attributes: `{child.attrib}`; skipping this node."
                     )
                     continue
                 try:
@@ -110,7 +110,7 @@ def _parse_oidc_backends_config(self, config_file):
             if root.tag != "OIDC":
                 raise etree.ParseError(
                     "The root element in OIDC config xml file is expected to be `OIDC`, "
-                    "found `{}` instead -- unable to continue.".format(root.tag)
+                    f"found `{root.tag}` instead -- unable to continue."
                 )
             for child in root:
                 if child.tag != "provider":

lib/galaxy/jobs/__init__.py

@@ -1674,7 +1674,7 @@ def _set_object_store_ids_full(self, job):
                 # the outputs and set them accordingly
                 object_store_id_overrides = {o: preferred_outputs_object_store_id for o in output_names}
 
-                def split_object_stores(output_name):
+                def split_object_stores(output_name):  # noqa: F811 https://github.com/PyCQA/pyflakes/issues/783
                     if "|__part__|" in output_name:
                         output_name = output_name.split("|__part__|", 1)[0]
                     if output_name in output_names:

lib/galaxy/managers/workflows.py

@@ -1435,13 +1435,12 @@ def _workflow_to_dict_export(self, trans, stored=None, workflow=None, internal=F
                 if name:
                     input_dicts.append({"name": name, "description": annotation_str})
             for name, val in step_state.items():
-                input_type = type(val)
-                if input_type == RuntimeValue:
+                if isinstance(val, RuntimeValue):
                     input_dicts.append({"name": name, "description": f"runtime parameter for tool {module.get_name()}"})
-                elif input_type == dict:
+                elif isinstance(val, dict):
                     # Input type is described by a dict, e.g. indexed parameters.
                     for partval in val.values():
-                        if type(partval) == RuntimeValue:
+                        if isinstance(partval, RuntimeValue):
                             input_dicts.append(
                                 {"name": name, "description": f"runtime parameter for tool {module.get_name()}"}
                             )

lib/galaxy/model/__init__.py

@@ -604,7 +604,7 @@ def calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=F
         )
         if for_sqlite:
             # hacky alternative for older sqlite
-            statement = """
+            statement = f"""
 WITH new (user_id, quota_source_label, disk_usage) AS (
     VALUES(:id, :label, ({label_usage}))
 )
@@ -614,9 +614,7 @@ def calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=F
     LEFT JOIN user_quota_source_usage AS old
         ON new.user_id = old.user_id
             AND new.quota_source_label = old.quota_source_label
-""".format(
-                label_usage=label_usage
-            )
+"""
         else:
             statement = f"""
 INSERT INTO user_quota_source_usage(user_id, quota_source_label, disk_usage)
@@ -996,11 +994,7 @@ def calculate_disk_usage_default_source(self, object_store):
         exclude_objectstore_ids = quota_source_map.default_usage_excluded_ids()
         default_cond = "dataset.object_store_id IS NULL OR" if default_quota_enabled and exclude_objectstore_ids else ""
         default_usage_dataset_condition = (
-            (
-                "AND ( {default_cond} dataset.object_store_id NOT IN :exclude_object_store_ids )".format(
-                    default_cond=default_cond,
-                )
-            )
+            f"AND ( {default_cond} dataset.object_store_id NOT IN :exclude_object_store_ids )"
             if exclude_objectstore_ids
             else ""
         )

lib/galaxy/model/security.py

@@ -605,21 +605,21 @@ def __active_folders_have_accessible_library_datasets(self, trans, folder, user,
         return False
 
     def can_access_library_item(self, roles, item, user):
-        if type(item) == self.model.Library:
+        if isinstance(item, self.model.Library):
             return self.can_access_library(roles, item)
-        elif type(item) == self.model.LibraryFolder:
+        elif isinstance(item, self.model.LibraryFolder):
             return (
                 self.can_access_library(roles, item.parent_library) and self.check_folder_contents(user, roles, item)[0]
             )
-        elif type(item) == self.model.LibraryDataset:
+        elif isinstance(item, self.model.LibraryDataset):
             return self.can_access_library(roles, item.folder.parent_library) and self.can_access_dataset(
                 roles, item.library_dataset_dataset_association.dataset
             )
-        elif type(item) == self.model.LibraryDatasetDatasetAssociation:
+        elif isinstance(item, self.model.LibraryDatasetDatasetAssociation):
             return self.can_access_library(
                 roles, item.library_dataset.folder.parent_library
             ) and self.can_access_dataset(roles, item.dataset)
-        elif type(item) == self.model.LibraryDatasetCollectionAssociation:
+        elif isinstance(item, self.model.LibraryDatasetCollectionAssociation):
             return self.can_access_library(roles, item.folder.parent_library)
         else:
             log.warning(f"Unknown library item type: {type(item)}")

lib/galaxy/quota/__init__.py

@@ -179,16 +179,14 @@ def _default_unregistered_quota(self, quota_source_label):
     def _default_quota(self, default_type, quota_source_label):
         label_condition = "IS NULL" if quota_source_label is None else "= :label"
         query = text(
-            """
+            f"""
 SELECT bytes
 FROM quota as default_quota
 LEFT JOIN default_quota_association on default_quota.id = default_quota_association.quota_id
 WHERE default_quota_association.type = :default_type
     AND default_quota.deleted != :is_true
     AND default_quota.quota_source_label {label_condition}
-""".format(
-                label_condition=label_condition
-            )
+"""
         )
 
         conn = self.sa_session.connection()

lib/galaxy/tool_util/verify/script.py

@@ -362,7 +362,7 @@ def build_case_references(
                 filtered_test_references.append(test_reference)
         if log is not None:
             log.info(
-                f"Skipping {len(test_references)-len(filtered_test_references)} out of {len(test_references)} tests."
+                f"Skipping {len(test_references) - len(filtered_test_references)} out of {len(test_references)} tests."
             )
         test_references = filtered_test_references
 

lib/galaxy/tools/actions/__init__.py

@@ -757,7 +757,7 @@ def _remap_job_on_rerun(self, trans, galaxy_session, rerun_remap_job_id, current
                 assert (
                     old_job.user_id == trans.user.id
                 ), f"({old_job.id}/{current_job.id}): Old user id ({old_job.user_id}) does not match rerun user id ({trans.user.id})"
-            elif trans.user is None and type(galaxy_session) == trans.model.GalaxySession:
+            elif trans.user is None and isinstance(galaxy_session, trans.model.GalaxySession):
                 assert (
                     old_job.session_id == galaxy_session.id
                 ), f"({old_job.id}/{current_job.id}): Old session id ({old_job.session_id}) does not match rerun session id ({galaxy_session.id})"
@@ -847,7 +847,7 @@ def _new_job_for_session(self, trans, tool, history):
         if hasattr(trans, "get_galaxy_session"):
             galaxy_session = trans.get_galaxy_session()
             # If we're submitting from the API, there won't be a session.
-            if type(galaxy_session) == trans.model.GalaxySession:
+            if isinstance(galaxy_session, trans.model.GalaxySession):
                 job.session_id = model.cached_id(galaxy_session)
         if trans.user is not None:
             job.user_id = model.cached_id(trans.user)

lib/galaxy/tools/actions/upload_common.py

@@ -393,7 +393,7 @@ def create_job(trans, params, tool, json_file_path, outputs, folder=None, histor
     trans.sa_session.add(job)
     job.galaxy_version = trans.app.config.version_major
     galaxy_session = trans.get_galaxy_session()
-    if type(galaxy_session) == trans.model.GalaxySession:
+    if isinstance(galaxy_session, trans.model.GalaxySession):
         job.session_id = galaxy_session.id
     if trans.user is not None:
         job.user_id = trans.user.id

lib/galaxy/tools/parameters/validation.py

@@ -409,7 +409,7 @@ def from_element(cls, param, elem):
         message = elem.get("message")
         negate = elem.get("negate", "false")
         if not message:
-            message = f"The selected dataset is {'non-' if negate == 'true' else ''}empty, this tool expects {'non-' if negate=='false' else ''}empty files."
+            message = f"The selected dataset is {'non-' if negate == 'true' else ''}empty, this tool expects {'non-' if negate == 'false' else ''}empty files."
         return cls(message, negate)
 
     def validate(self, value, trans=None):

lib/galaxy/util/dictifiable.py

@@ -38,9 +38,9 @@ def get_value(key, item):
                 assert value_mapper is not None
                 if key in value_mapper:
                     return value_mapper[key](item)
-                if type(item) == datetime.datetime:
+                if isinstance(item, datetime.datetime):
                     return item.isoformat()
-                elif type(item) == uuid.UUID:
+                elif isinstance(item, uuid.UUID):
                     return str(item)
                 # Leaving this for future reference, though we may want a more
                 # generic way to handle special type mappings going forward.

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

@@ -467,7 +467,7 @@ def send_report(rep, exc_data, html=True):
 
 
 def error_template(head_html, exception, extra):
-    return """
+    return f"""
     <!DOCTYPE HTML>
     <html>
     <head>
@@ -476,24 +476,22 @@ def error_template(head_html, exception, extra):
     .content {{ max-width: 720px; margin: auto; margin-top: 50px; }}
     </style>
     <title>Internal Server Error</title>
-    {}
+    {head_html}
     </head>
     <body>
     <div class="content">
     <h1>Internal Server Error</h1>
 
     <h2>Galaxy was unable to successfully complete your request</h2>
 
-    <p>{}</p>
+    <p>{exception}</p>
 
     This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.
 
-    {}
+    {extra}
     </div>
     </body>
-    </html>""".format(
-        head_html, exception, extra
-    )
+    </html>"""
 
 
 def make_error_middleware(app, global_conf, **kw):

lib/galaxy/webapps/galaxy/api/cloudauthz.py

@@ -93,11 +93,11 @@ def create(self, trans, payload, **kwargs):
             *   status:     HTTP response code
             *   message:    A message complementary to the response code.
         """
-        msg_template = f"Rejected user `{str(trans.user.id)}`'s request to create cloudauthz config because of {{}}."
+        msg_template = f"Rejected user `{trans.user.id}`'s request to create cloudauthz config because of {{}}."
         if not isinstance(payload, dict):
             raise ActionInputError(
                 "Invalid payload data type. The payload is expected to be a dictionary, but "
-                "received data of type `{}`.".format(str(type(payload)))
+                f"received data of type `{type(payload)}`."
             )
 
         missing_arguments = []
@@ -116,7 +116,7 @@ def create(self, trans, payload, **kwargs):
         if len(missing_arguments) > 0:
             log.debug(msg_template.format(f"missing required config {missing_arguments}"))
             raise RequestParameterMissingException(
-                "The following required arguments are missing in the payload: " "{}".format(missing_arguments)
+                f"The following required arguments are missing in the payload: {missing_arguments}"
             )
 
         description = payload.get("description", "")
@@ -200,9 +200,7 @@ def delete(self, trans, encoded_authz_id, **kwargs):
             return view
         except Exception as e:
             log.exception(
-                msg_template.format(
-                    "exception while deleting the cloudauthz record with " "ID: `{}`.".format(encoded_authz_id)
-                )
+                msg_template.format(f"exception while deleting the cloudauthz record with ID: `{encoded_authz_id}`.")
             )
             raise InternalServerError(
                 "An unexpected error has occurred while responding to the DELETE request of the "
@@ -270,9 +268,7 @@ def update(self, trans, encoded_authz_id, payload, **kwargs):
             raise e
         except Exception as e:
             log.exception(
-                msg_template.format(
-                    "exception while updating the cloudauthz record with " "ID: `{}`.".format(encoded_authz_id)
-                )
+                msg_template.format(f"exception while updating the cloudauthz record with ID: `{encoded_authz_id}`.")
             )
             raise InternalServerError(
                 "An unexpected error has occurred while responding to the PUT request of the "

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

@@ -312,7 +312,7 @@ def create(self, trans, library_id, payload, **kwd):
                         trans.sa_session.add(meta_i)
                     with transaction(trans.sa_session):
                         trans.sa_session.commit()
-                if type(v) == trans.app.model.LibraryDatasetDatasetAssociation:
+                if isinstance(v, trans.app.model.LibraryDatasetDatasetAssociation):
                     v = v.library_dataset
                 encoded_id = trans.security.encode_id(v.id)
                 if create_type == "folder":

lib/galaxy_test/api/test_folder_contents.py

@@ -275,7 +275,7 @@ def test_index_order_by(self, history_id):
                 history_id,
                 folder_id,
                 name,
-                content=f"{'0'*dataset_sizes[index]}",
+                content=f"{'0' * dataset_sizes[index]}",
                 ldda_message=ldda_messages[index],
                 file_type=file_types[index],
             )

test/integration/test_recalculate_user_disk_usage.py

@@ -37,7 +37,7 @@ def test_recalculate_user_disk_usage(self):
         assert current_usage["total_disk_usage"] == 0
         size = 100
         history_id = self.dataset_populator.new_history()
-        hda_id = self.dataset_populator.new_dataset(history_id, content=f"{'0'*size}", wait=True)["id"]
+        hda_id = self.dataset_populator.new_dataset(history_id, content=f"{'0' * size}", wait=True)["id"]
         expected_usage = size + 1  # +1 for the new line character in the dataset
         # The usage should be the total of the datasets
         current_usage = self.dataset_populator.get_usage_for(None)

test/integration/test_storage_cleaner.py

@@ -164,7 +164,7 @@ def _create_histories_with(
             history_ids.append(history_id)
             # Create a dataset with content equal to the expected size of the history
             if history_data.size:
-                self.dataset_populator.new_dataset(history_id, content=f"{'0'*(history_data.size-1)}\n")
+                self.dataset_populator.new_dataset(history_id, content=f"{'0' * (history_data.size - 1)}\n")
         if wait_for_histories:
             for history_id in history_ids:
                 self.dataset_populator.wait_for_history(history_id)
@@ -176,7 +176,7 @@ def _create_datasets_in_history_with(
         dataset_ids = []
         for dataset_data in test_datasets:
             dataset = self.dataset_populator.new_dataset(
-                history_id, name=dataset_data.name, content=f"{'0'*(dataset_data.size-1)}\n"
+                history_id, name=dataset_data.name, content=f"{'0' * (dataset_data.size - 1)}\n"
             )
             dataset_ids.append(dataset["id"])
         if wait_for_history: