Guard run_user_tool against legacy half-deactivated UDT rows

Before the manager fix in the prior commit, deactivate_unprivileged_tool
only flipped UserDynamicToolAssociation.active, leaving DynamicTool.active
true. Any deployment that deactivated UDTs through the existing
/api/unprivileged_tools DELETE endpoint before this branch landed has
rows in that half-state. Checking dynamic_tool.active alone would let
those legacy entries run via run_user_tool. Also verify the user's
association is active so legacy rows surface as "deactivated" instead.

Author: dannon

lib/galaxy/agents/operations.py

@@ -920,14 +920,28 @@ def delete_user_tool(self, uuid: str) -> dict[str, Any]:
         return {"uuid": uuid, "deactivated": True}
 
     def run_user_tool(self, history_id: str, tool_uuid: str, inputs: dict[str, Any]) -> dict[str, Any]:
+        from sqlalchemy import select
+
+        from galaxy.model import UserDynamicToolAssociation
+
         user = self.trans.user
         if not user:
             raise ValueError("User must be authenticated")
 
         dynamic_tool = self.dynamic_tools_manager.get_unprivileged_tool_by_uuid(user, tool_uuid)
         if dynamic_tool is None:
             raise ValueError(f"User-defined tool {tool_uuid!r} not found")
-        if not dynamic_tool.active:
+        # Check both DynamicTool.active and the user-association.active. Pre-fix
+        # rows may have only the association deactivated; checking just
+        # dynamic_tool.active would miss those legacy deletions.
+        session = self.dynamic_tools_manager.session()
+        assoc_active = session.scalar(
+            select(UserDynamicToolAssociation.active).where(
+                UserDynamicToolAssociation.user_id == user.id,
+                UserDynamicToolAssociation.dynamic_tool_id == dynamic_tool.id,
+            )
+        )
+        if not dynamic_tool.active or not assoc_active:
             raise ValueError(f"User-defined tool {tool_uuid!r} is deactivated")
 
         payload = {