Fix signature override of Tool.exec_after_process() method

Fix the following mypy 1.11 error:

```
lib/galaxy/tools/__init__.py:3212: error: Signature of "exec_after_process"
incompatible with supertype "Tool"  [override]
        def exec_after_process(self, app, inp_data, out_data, param_dict, ...
        ^
lib/galaxy/tools/__init__.py:3212: note:      Superclass:
lib/galaxy/tools/__init__.py:3212: note:          def exec_after_process(self, app: Any, inp_data: Any, out_data: Any, param_dict: Any, job: Any = ..., **kwds: Any) -> Any
lib/galaxy/tools/__init__.py:3212: note:      Subclass:
lib/galaxy/tools/__init__.py:3212: note:          def exec_after_process(self, app: Any, inp_data: Any, out_data: Any, param_dict: Any, job: Any, final_job_state: Any = ..., **kwds: Any) -> Any
```

Also:
- Add some type annotions
- Small refactorings

lib/galaxy/jobs/__init__.py

@@ -20,6 +20,7 @@
     Dict,
     Iterable,
     List,
+    Optional,
     TYPE_CHECKING,
 )
 
@@ -99,6 +100,7 @@
 
 if TYPE_CHECKING:
     from galaxy.jobs.handler import JobHandlerQueue
+    from galaxy.tools import Tool
 
 log = logging.getLogger(__name__)
 
@@ -984,11 +986,17 @@ class MinimalJobWrapper(HasResourceParameters):
 
     is_task = False
 
-    def __init__(self, job: model.Job, app: MinimalManagerApp, use_persisted_destination: bool = False, tool=None):
+    def __init__(
+        self,
+        job: model.Job,
+        app: MinimalManagerApp,
+        use_persisted_destination: bool = False,
+        tool: Optional["Tool"] = None,
+    ):
         self.job_id = job.id
         self.session_id = job.session_id
         self.user_id = job.user_id
-        self.app: MinimalManagerApp = app
+        self.app = app
         self.tool = tool
         self.sa_session = self.app.model.context
         self.extra_filenames: List[str] = []
@@ -2531,10 +2539,15 @@ def set_container(self, container):
 
 
 class JobWrapper(MinimalJobWrapper):
-    def __init__(self, job, queue: "JobHandlerQueue", use_persisted_destination=False, app=None):
-        super().__init__(job, app=queue.app, use_persisted_destination=use_persisted_destination)
+    def __init__(self, job, queue: "JobHandlerQueue", use_persisted_destination=False):
+        app = queue.app
+        super().__init__(
+            job,
+            app=app,
+            use_persisted_destination=use_persisted_destination,
+            tool=app.toolbox.get_tool(job.tool_id, job.tool_version, exact=True),
+        )
         self.queue = queue
-        self.tool = self.app.toolbox.get_tool(job.tool_id, job.tool_version, exact=True)
         self.job_runner_mapper = JobRunnerMapper(self, queue.dispatcher.url_to_destination, self.app.job_config)
         if use_persisted_destination:
             self.job_runner_mapper.cached_job_destination = JobDestination(from_job=job)

lib/galaxy/jobs/command_factory.py

@@ -142,6 +142,7 @@ def build_command(
 
     if job_wrapper.is_cwl_job:
         # Minimal metadata needed by the relocate script
+        assert job_wrapper.tool
         cwl_metadata_params = {
             "job_metadata": join("working", job_wrapper.tool.provided_metadata_file),
             "job_id_tag": job_wrapper.get_id_tag(),

lib/galaxy/jobs/runners/__init__.py

@@ -502,6 +502,7 @@ def get_job_file(self, job_wrapper: "MinimalJobWrapper", **kwds) -> str:
             env_setup_commands.append(env_to_statement(env))
         command_line = job_wrapper.runner_command_line
         tmp_dir_creation_statement = job_wrapper.tmp_dir_creation_statement
+        assert job_wrapper.tool
         options = dict(
             tmp_dir_creation_statement=tmp_dir_creation_statement,
             job_instrumenter=job_instrumenter,
@@ -538,13 +539,14 @@ def _find_container(
         if not compute_job_directory:
             compute_job_directory = job_wrapper.working_directory
 
+        tool = job_wrapper.tool
+        assert tool
         if not compute_tool_directory:
-            compute_tool_directory = job_wrapper.tool.tool_dir
+            compute_tool_directory = tool.tool_dir
 
         if not compute_tmp_directory:
             compute_tmp_directory = job_wrapper.tmp_directory()
 
-        tool = job_wrapper.tool
         guest_ports = job_wrapper.guest_ports
         tool_info = ToolInfo(
             tool.containers,

lib/galaxy/tools/__init__.py

@@ -2346,7 +2346,7 @@ def call_hook(self, hook_name, *args, **kwargs):
     def exec_before_job(self, app, inp_data, out_data, param_dict=None):
         pass
 
-    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kwds):
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state: Optional[str] = None):
         pass
 
     def job_failed(self, job_wrapper, message, exception=False):
@@ -2977,7 +2977,7 @@ def exec_before_job(self, app, inp_data, out_data, param_dict=None):
         with open(expression_inputs_path, "w") as f:
             json.dump(expression_inputs, f)
 
-    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kwds):
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state=None):
         for key, val in self.outputs.items():
             if key not in out_data:
                 # Skip filtered outputs
@@ -3157,7 +3157,7 @@ def regenerate_imported_metadata_if_needed(
             )
             self.app.job_manager.enqueue(job=job, tool=self)
 
-    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kwds):
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state=None):
         working_directory = app.object_store.get_filename(job, base_dir="job_work", dir_only=True, obj_dir=True)
         for name, dataset in inp_data.items():
             external_metadata = get_metadata_compute_strategy(app.config, job.id, tool_id=self.id)
@@ -3215,8 +3215,8 @@ class ExportHistoryTool(Tool):
 class ImportHistoryTool(Tool):
     tool_type = "import_history"
 
-    def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state=None, **kwds):
-        super().exec_after_process(app, inp_data, out_data, param_dict, job=job, **kwds)
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state=None):
+        super().exec_after_process(app, inp_data, out_data, param_dict, job=job, final_job_state=final_job_state)
         if final_job_state != DETECTED_JOB_STATE.OK:
             return
         JobImportHistoryArchiveWrapper(self.app, job.id).cleanup_after_job()
@@ -3240,9 +3240,8 @@ def __remove_interactivetool_by_job(self, job):
         else:
             log.warning("Could not determine job to stop InteractiveTool: %s", job)
 
-    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kwds):
-        # run original exec_after_process
-        super().exec_after_process(app, inp_data, out_data, param_dict, job=job, **kwds)
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state=None):
+        super().exec_after_process(app, inp_data, out_data, param_dict, job=job, final_job_state=final_job_state)
         self.__remove_interactivetool_by_job(job)
 
     def job_failed(self, job_wrapper, message, exception=False):
@@ -3261,12 +3260,11 @@ def __init__(self, config_file, root, app, guid=None, data_manager_id=None, **kw
         if self.data_manager_id is None:
             self.data_manager_id = self.id
 
-    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, final_job_state=None, **kwds):
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state=None):
         assert self.allow_user_access(job.user), "You must be an admin to access this tool."
         if final_job_state != DETECTED_JOB_STATE.OK:
             return
-        # run original exec_after_process
-        super().exec_after_process(app, inp_data, out_data, param_dict, job=job, **kwds)
+        super().exec_after_process(app, inp_data, out_data, param_dict, job=job, final_job_state=final_job_state)
         # process results of tool
         data_manager_id = job.data_manager_association.data_manager_id
         data_manager = self.app.data_managers.get_manager(data_manager_id)