Refactor code for improved readability and consistency in function signatures across multiple files

Author: arash77

lib/galaxy/managers/credentials.py

@@ -48,7 +48,8 @@ def build_credentials_context_response(
             name=association.service_name,
             version=association.service_version,
             selected_group=SelectedGroupResponse(
-                id=association.selected_group_id, name=association.selected_group_name
+                id=association.selected_group_id,
+                name=association.selected_group_name,
             ),
         )
         service_credentials_list.append(service_credential)
@@ -189,27 +190,47 @@ def add_user_credentials(
         self.session.flush()
         return user_credentials.id
 
-    def update_group(self, credentials_group: CredentialsGroup, group_name: str) -> None:
+    def update_group(
+        self,
+        credentials_group: CredentialsGroup,
+        group_name: str,
+    ) -> None:
         credentials_group.name = group_name
         self.session.add(credentials_group)
 
-    def set_group_last_updated(self, credentials_group: CredentialsGroup) -> None:
+    def set_group_last_updated(
+        self,
+        credentials_group: CredentialsGroup,
+    ) -> None:
         credentials_group.update_time = now()
         self.session.add(credentials_group)
 
-    def add_group(self, user_credentials_id: DecodedDatabaseIdField, group_name: str) -> DecodedDatabaseIdField:
+    def add_group(
+        self,
+        user_credentials_id: DecodedDatabaseIdField,
+        group_name: str,
+    ) -> DecodedDatabaseIdField:
         credentials_group = CredentialsGroup(name=group_name, user_credentials_id=user_credentials_id)
         self.session.add(credentials_group)
         self.session.flush()
         return credentials_group.id
 
-    def update_credential(self, credential: Credential, value: Optional[str] = None, is_secret: bool = False) -> None:
+    def update_credential(
+        self,
+        credential: Credential,
+        value: Optional[str] = None,
+        is_secret: bool = False,
+    ) -> None:
         credential.is_set = bool(value)
         credential.value = value if not is_secret else None
         self.session.add(credential)
 
     def add_credential(
-        self, group_id: DecodedDatabaseIdField, name: str, value: Optional[str] = None, is_secret: bool = False
+        self,
+        group_id: DecodedDatabaseIdField,
+        name: str,
+        value: Optional[str] = None,
+        is_secret: bool = False,
     ) -> None:
         credential = Credential(
             group_id=group_id,

lib/galaxy/tool_util/verify/interactor.py

@@ -185,7 +185,11 @@ def stage_data_in_history(
         job[test_data["fname"]] = test_dict
     resolve_data = test_data_resolver.get_filename if test_data_resolver else None
     staging_interface.stage(
-        "tool", history_id=history, job=job, use_path_paste=force_path_paste, resolve_data=resolve_data
+        "tool",
+        history_id=history,
+        job=job,
+        use_path_paste=force_path_paste,
+        resolve_data=resolve_data,
     )
     staging_interface.handle_jobs()
     galaxy_interactor.uploads = job
@@ -200,6 +204,7 @@ class RunToolResponse(NamedTuple):
 
 
 class InteractorStagingInterface(StagingInterface):
+
     def __init__(self, galaxy_interactor: "GalaxyInteractorApi", maxseconds: Optional[int], upload_async: bool) -> None:
         super().__init__()
         self.galaxy_interactor = galaxy_interactor
@@ -787,7 +792,10 @@ def adapt_collections(test_input: JsonTestCollectionDefDict) -> DataCollectionRe
             jobs = submit_response_object["jobs"]
         try:
             return RunToolResponse(
-                inputs=inputs_tree, outputs=outputs, output_collections=output_collections, jobs=jobs
+                inputs=inputs_tree,
+                outputs=outputs,
+                output_collections=output_collections,
+                jobs=jobs,
             )
         except KeyError:
             message = (
@@ -1019,7 +1027,12 @@ def ensure_user_with_email(self, email, password=None):
             # If remote user middleware is enabled - this endpoint consumes
             # ``remote_user_email`` otherwise it requires ``email``, ``password``
             # and ``username``.
-            data = dict(remote_user_email=email, email=email, password=password, username=username)
+            data = dict(
+                remote_user_email=email,
+                email=email,
+                password=password,
+                username=username,
+            )
             test_user = self._post("users", data, key=admin_key, json=True).json()
         return test_user
 
@@ -1235,7 +1248,9 @@ def prepare_request_params(
                 new_items[key] = dumps(val)
         data.update(new_items)
 
-    kwd: Dict[str, Any] = {"files": files}
+    kwd: Dict[str, Any] = {
+        "files": files,
+    }
     if headers:
         kwd["headers"] = headers
     if as_json:
@@ -1542,7 +1557,11 @@ def verify_tool(
     if tool_version is None and "tool_version" in tool_test_dict:
         tool_version = tool_test_dict.get("tool_version")
 
-    job_data: JobDataT = {"tool_id": tool_id, "tool_version": tool_version, "test_index": test_index}
+    job_data: JobDataT = {
+        "tool_id": tool_id,
+        "tool_version": tool_version,
+        "test_index": test_index,
+    }
     client_config = client_test_config.get_test_config(job_data)
     skip_message = None
     if client_config is not None:

lib/galaxy/tool_util/verify/parse.py

@@ -78,7 +78,10 @@ def parse_tool_test_descriptions(
                 validated_test_case = case_state(
                     raw_test_dict, tool_parameter_bundle.parameters, profile, validate=True
                 )
-                request_and_schema = TestRequestAndSchema(validated_test_case.tool_state, tool_parameter_bundle)
+                request_and_schema = TestRequestAndSchema(
+                    validated_test_case.tool_state,
+                    tool_parameter_bundle,
+                )
             except Exception as e:
                 validation_exception = e
 

lib/galaxy/tools/actions/__init__.py

@@ -339,7 +339,8 @@ def process_dataset(data, formats=None):
                     )
                     collection_builder = CollectionBuilder(collection_type_description)
                     collection_builder.replace_elements_in_collection(
-                        template_collection=collection, replacement_dict=processed_dataset_dict
+                        template_collection=collection,
+                        replacement_dict=processed_dataset_dict,
                     )
                     new_collection = collection_builder.build()
                     if child_collection:
@@ -435,7 +436,7 @@ def _collect_inputs(self, tool, trans, incoming, history, current_user_roles, co
                     for tag in collection.auto_propagated_tags:
                         preserved_hdca_tags[tag.value] = tag
         preserved_tags.update(preserved_hdca_tags)
-        return (history, inp_data, inp_dataset_collections, preserved_tags, preserved_hdca_tags, all_permissions)
+        return history, inp_data, inp_dataset_collections, preserved_tags, preserved_hdca_tags, all_permissions
 
     def execute(
         self,
@@ -468,9 +469,14 @@ def execute(
         if execution_cache is None:
             execution_cache = ToolExecutionCache(trans)
         current_user_roles = execution_cache.current_user_roles
-        history, inp_data, inp_dataset_collections, preserved_tags, preserved_hdca_tags, all_permissions = (
-            self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
-        )
+        (
+            history,
+            inp_data,
+            inp_dataset_collections,
+            preserved_tags,
+            preserved_hdca_tags,
+            all_permissions,
+        ) = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
         assert history  # tell type system we've set history and it is no longer optional
         # Build name for output datasets based on tool name and input names
         on_text = self._get_on_text(inp_data, inp_dataset_collections)
@@ -674,7 +680,12 @@ def handle_output(name, output, hidden=None):
                                 else:
                                     index = name_to_index[parent_id]
                             current_element_identifiers = cast(
-                                list[dict[str, Union[str, list[dict[str, Union[str, list[Any]]]]]]],
+                                list[
+                                    dict[
+                                        str,
+                                        Union[str, list[dict[str, Union[str, list[Any]]]]],
+                                    ]
+                                ],
                                 current_element_identifiers[index]["element_identifiers"],
                             )
 
@@ -688,14 +699,20 @@ def handle_output(name, output, hidden=None):
                         # Following hack causes dataset to no be added to history...
                         trans.sa_session.add(element)
                         current_element_identifiers.append(
-                            {"__object__": element, "name": output_part_def.element_identifier}
+                            {
+                                "__object__": element,
+                                "name": output_part_def.element_identifier,
+                            }
                         )
 
                     if output.dynamic_structure:
                         assert not element_identifiers  # known_outputs must have been empty
                         element_kwds = dict(elements=collections_manager.ELEMENTS_UNINITIALIZED)
                     else:
-                        element_kwds = dict(element_identifiers=element_identifiers, fields=output.structure.fields)
+                        element_kwds = dict(
+                            element_identifiers=element_identifiers,
+                            fields=output.structure.fields,
+                        )
                     output_collections.create_collection(
                         output=output, name=name, completed_job=completed_job, **element_kwds
                     )
@@ -705,7 +722,8 @@ def handle_output(name, output, hidden=None):
                     log.info(f"Handled output named {name} for tool {tool.id} {handle_output_timer}")
 
         add_datasets_timer = tool.app.execution_timer_factory.get_timer(
-            "internals.galaxy.tools.actions.add_datasets", "Added output datasets to history"
+            "internals.galaxy.tools.actions.add_datasets",
+            "Added output datasets to history",
         )
         # Add all the top-level (non-child) datasets to the history unless otherwise specified
         for name, data in out_data.items():

lib/galaxy/tools/evaluation.py

@@ -117,6 +117,7 @@ def add_error(self, file, phase, exception):
 
 
 class ToolTemplatingException(Exception):
+
     def __init__(self, *args: object, tool_id: Optional[str], tool_version: str, is_latest: bool) -> None:
         super().__init__(*args)
         self.tool_id = tool_id
@@ -208,11 +209,21 @@ def set_compute_environment(self, compute_environment: ComputeEnvironment, get_s
             incoming.update(model.User.user_template_environment(self._user))
 
             # Build params, done before hook so hook can use
-            self.param_dict = self.build_param_dict(incoming, inp_data, out_data, output_collections=out_collections)
+            self.param_dict = self.build_param_dict(
+                incoming,
+                inp_data,
+                out_data,
+                output_collections=out_collections,
+            )
             self.execute_tool_hooks(inp_data=inp_data, out_data=out_data, incoming=incoming)
 
         else:
-            self.param_dict = self.build_param_dict(incoming, inp_data, out_data, output_collections=out_collections)
+            self.param_dict = self.build_param_dict(
+                incoming,
+                inp_data,
+                out_data,
+                output_collections=out_collections,
+            )
 
     def execute_tool_hooks(self, inp_data: InpDataDictT, out_data: OutDataDictT, incoming):
         # Certain tools require tasks to be completed prior to job execution
@@ -376,7 +387,11 @@ def validate_inputs(input, value, context, **kwargs):
 
         visit_input_values(self.tool.inputs, incoming, validate_inputs)
 
-    def _deferred_objects(self, input_datasets: InpDataDictT, incoming: dict) -> dict[str, DeferrableObjectsT]:
+    def _deferred_objects(
+        self,
+        input_datasets: InpDataDictT,
+        incoming: dict,
+    ) -> dict[str, DeferrableObjectsT]:
         """Collect deferred objects required for execution.
 
         Walk input datasets and collections and find inputs that need to be materialized.
@@ -460,6 +475,7 @@ def do_walk(inputs, input_values):
         do_walk(inputs, input_values)
 
     def __populate_wrappers(self, param_dict, input_datasets, job_working_directory):
+
         element_identifier_mapper = ElementIdentifierMapper(input_datasets)
 
         def wrap_input(input_values, input):
@@ -709,7 +725,12 @@ def build(self):
         global_tool_logs(
             self._create_interactivetools_entry_points, config_file, "Building Interactive Tool Entry Points", self.tool
         )
-        global_tool_logs(self._build_config_files, config_file, "Building Config Files", self.tool)
+        global_tool_logs(
+            self._build_config_files,
+            config_file,
+            "Building Config Files",
+            self.tool,
+        )
         global_tool_logs(self._build_param_file, config_file, "Building Param File", self.tool)
         global_tool_logs(self._build_command_line, config_file, "Building Command Line", self.tool)
         global_tool_logs(self._build_version_command, config_file, "Building Version Command Line", self.tool)
@@ -1024,6 +1045,7 @@ def build(self):
 
 
 class UserToolEvaluator(ToolEvaluator):
+
     param_dict_style = "json"
 
     def _build_config_files(self):