Fix signature override of DatabaseOperationTool.produce_outputs() m…

…ethod

Fix the following mypy 1.11 errors:

```
lib/galaxy/tools/__init__.py:3989: error: Signature of "produce_outputs"
incompatible with supertype "DatabaseOperationTool"  [override]
        def produce_outputs(self, trans, out_data, output_collections, inc...
        ^
lib/galaxy/tools/__init__.py:3989: note:      Superclass:
lib/galaxy/tools/__init__.py:3989: note:          def produce_outputs(self, trans: Any, out_data: Any, output_collections: Any, incoming: Any, history: Any, **kwds: Any) -> Any
lib/galaxy/tools/__init__.py:3989: note:      Subclass:
lib/galaxy/tools/__init__.py:3989: note:          def produce_outputs(self, trans: Any, out_data: Any, output_collections: Any, incoming: Any, history: Any, tag_handler: Any, **kwds: Any) -> Any
lib/galaxy/tools/__init__.py:4026: error: Signature of "produce_outputs"
incompatible with supertype "DatabaseOperationTool"  [override]
        def produce_outputs(self, trans, out_data, output_collections, inc...
        ^
lib/galaxy/tools/__init__.py:4026: note:      Superclass:
lib/galaxy/tools/__init__.py:4026: note:          def produce_outputs(self, trans: Any, out_data: Any, output_collections: Any, incoming: Any, history: Any, **kwds: Any) -> Any
lib/galaxy/tools/__init__.py:4026: note:      Subclass:
lib/galaxy/tools/__init__.py:4026: note:          def produce_outputs(self, trans: Any, out_data: Any, output_collections: Any, incoming: Any, history: Any, tag_handler: Any, **kwds: Any) -> Any
```

lib/galaxy/tools/__init__.py

@@ -214,6 +214,7 @@
 
 if TYPE_CHECKING:
     from galaxy.app import UniverseApplication
+    from galaxy.managers.context import ProvidesUserContext
     from galaxy.managers.jobs import JobSearch
     from galaxy.tools.actions.metadata import SetMetadataToolAction
 
@@ -3402,7 +3403,7 @@ def _add_datasets_to_history(self, history, elements, datasets_visible=False):
                 element_object.visible = datasets_visible
                 history.stage_addition(element_object)
 
-    def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
+    def produce_outputs(self, trans: "ProvidesUserContext", out_data, output_collections, incoming, history, **kwds):
         return self._outputs_dict()
 
     def _outputs_dict(self):
@@ -3579,7 +3580,7 @@ class ExtractDatasetCollectionTool(DatabaseOperationTool):
     require_terminal_states = False
     require_dataset_ok = False
 
-    def produce_outputs(self, trans, out_data, output_collections, incoming, history, tags=None, **kwds):
+    def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         has_collection = incoming["input"]
         if hasattr(has_collection, "element_type"):
             # It is a DCE
@@ -3992,15 +3993,15 @@ def add_copied_value_to_new_elements(new_label, dce_object):
 class ApplyRulesTool(DatabaseOperationTool):
     tool_type = "apply_rules"
 
-    def produce_outputs(self, trans, out_data, output_collections, incoming, history, tag_handler, **kwds):
+    def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         hdca = incoming["input"]
         rule_set = RuleSet(incoming["rules"])
         copied_datasets = []
 
         def copy_dataset(dataset, tags):
             copied_dataset = dataset.copy(copy_tags=dataset.tags, flush=False)
             if tags is not None:
-                tag_handler.set_tags_from_list(
+                trans.tag_handler.set_tags_from_list(
                     trans.get_user(),
                     copied_dataset,
                     tags,
@@ -4029,14 +4030,15 @@ class TagFromFileTool(DatabaseOperationTool):
     # require_terminal_states = True
     # require_dataset_ok = False
 
-    def produce_outputs(self, trans, out_data, output_collections, incoming, history, tag_handler, **kwds):
+    def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         hdca = incoming["input"]
         how = incoming["how"]
         new_tags_dataset_assoc = incoming["tags"]
         new_elements = {}
         new_datasets = []
 
         def add_copied_value_to_new_elements(new_tags_dict, dce):
+            tag_handler = trans.tag_handler
             if getattr(dce.element_object, "history_content_type", None) == "dataset":
                 copied_value = dce.element_object.copy(copy_tags=dce.element_object.tags, flush=False)
                 # copy should never be visible, since part of a collection

lib/galaxy/tools/actions/model_operations.py

@@ -139,7 +139,6 @@ def execute(
     def _produce_outputs(
         self, trans: "ProvidesUserContext", tool, out_data, output_collections, incoming, history, tags, hdca_tags, skip
     ):
-        tag_handler = trans.tag_handler
         tool.produce_outputs(
             trans,
             out_data,
@@ -148,7 +147,6 @@ def _produce_outputs(
             history=history,
             tags=tags,
             hdca_tags=hdca_tags,
-            tag_handler=tag_handler,
         )
         if mapped_over_elements := output_collections.dataset_collection_elements:
             for name, value in out_data.items():