Fix new UP037 errors from ruff 0.4.5

bgruening · Jun 10, 2024 · 70b5811 · 70b5811
1 parent 211c1d4
commit 70b5811
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Showing 7 changed files with 10 additions and 10 deletions.
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
@@ -864,7 +864,7 @@ def find_conversion_destination_for_dataset_by_extensions(
             ext = dataset_or_ext
             dataset = None
 
-        accepted_datatypes: List["Data"] = []
+        accepted_datatypes: List[Data] = []
         for accepted_format in accepted_formats:
             if isinstance(accepted_format, str):
                 accepted_datatype = self.get_datatype_by_extension(accepted_format)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
@@ -7989,8 +7989,8 @@ def __init__(self):
         self._inputs_by_name = None
         # Injected attributes
         # TODO: code using these should be refactored to not depend on these non-persistent fields
-        self.module: Optional["WorkflowModule"]
-        self.state: Optional["DefaultToolState"]
+        self.module: Optional[WorkflowModule]
+        self.state: Optional[DefaultToolState]
         self.upgrade_messages: Optional[Dict]
 
     @reconstructor

diff --git a/lib/galaxy/model/tags.py b/lib/galaxy/model/tags.py
@@ -61,7 +61,7 @@ def __init__(self, sa_session: galaxy_scoped_session, galaxy_session=None) -> No
         self.item_tag_assoc_info: Dict[str, ItemTagAssocInfo] = {}
         # Can't include type annotation in signature, because lagom will attempt to look up
         # GalaxySession, but can't find it due to the circular import
-        self.galaxy_session: Optional["GalaxySession"] = galaxy_session
+        self.galaxy_session: Optional[GalaxySession] = galaxy_session
 
     def create_tag_handler_session(self, galaxy_session: Optional["GalaxySession"]):
         # Creates a transient tag handler that avoids repeated flushes
@@ -502,7 +502,7 @@ class GalaxyTagHandlerSession(GalaxyTagHandler):
 
     def __init__(self, sa_session, galaxy_session: Optional["GalaxySession"]):
         super().__init__(sa_session, galaxy_session)
-        self.created_tags: Dict[str, "Tag"] = {}
+        self.created_tags: Dict[str, Tag] = {}
 
     def _get_tag(self, tag_name):
         """Get tag from cache or database."""

diff --git a/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py b/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py
@@ -74,7 +74,7 @@ def install_data_managers(
         repository,
         repository_tools_tups,
     ) -> List["DataManagerInterface"]:
-        rval: List["DataManagerInterface"] = []
+        rval: List[DataManagerInterface] = []
         if "data_manager" in metadata_dict:
             tpm = tool_panel_manager.ToolPanelManager(self.app)
             repository_tools_by_guid = {}

diff --git a/lib/galaxy/webapps/galaxy/services/dataset_collections.py b/lib/galaxy/webapps/galaxy/services/dataset_collections.py
@@ -252,7 +252,7 @@ def contents(
             raise exceptions.RequestParameterInvalidException(
                 "Parameter instance_type not being 'history' is not yet implemented."
             )
-        hdca: "HistoryDatasetCollectionAssociation" = self.collection_manager.get_dataset_collection_instance(
+        hdca: HistoryDatasetCollectionAssociation = self.collection_manager.get_dataset_collection_instance(
             trans, "history", hdca_id
         )
 

diff --git a/lib/galaxy/webapps/galaxy/services/history_contents.py b/lib/galaxy/webapps/galaxy/services/history_contents.py
@@ -697,7 +697,7 @@ def bulk_operation(
         history = self.history_manager.get_mutable(history_id, trans.user, current_history=trans.history)
         filters = self.history_contents_filters.parse_query_filters(filter_query_params)
         self._validate_bulk_operation_params(payload, trans.user, trans)
-        contents: List["HistoryItem"]
+        contents: List[HistoryItem]
         if payload.items:
             contents = self._get_contents_by_item_list(
                 trans,
@@ -1366,7 +1366,7 @@ def _apply_operation_to_item(
     def _get_contents_by_item_list(
         self, trans, history: History, items: List[HistoryContentItem]
     ) -> List["HistoryItem"]:
-        contents: List["HistoryItem"] = []
+        contents: List[HistoryItem] = []
 
         dataset_items = filter(lambda item: item.history_content_type == HistoryContentType.dataset, items)
         datasets_ids = (dataset.id for dataset in dataset_items)

diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
@@ -423,7 +423,7 @@ def replacement_for_input(self, trans, step: "WorkflowStep", input_dict: Dict[st
             modules.NoReplacement,
             model.DatasetCollectionInstance,
             List[model.DatasetCollectionInstance],
-            "HistoryItem",
+            HistoryItem,
         ] = modules.NO_REPLACEMENT
         prefixed_name = input_dict["name"]
         multiple = input_dict["multiple"]