Fix job directory not being cleaned up

[davelopez]

Fixes:

galaxy.jobs ERROR 2024-10-15 13:11:57,570 [pN:main.1,p:610368,tN:LocalRunner.work_thread-2] Unable to cleanup job 11703
Traceback (most recent call last):
  File "/home/dlopez/dev/galaxy/lib/galaxy/jobs/__init__.py", line 2160, in cleanup
    self.object_store.delete(self.get_job(), base_dir="job_work", entire_dir=True, obj_dir=True)
  File "/home/dlopez/dev/galaxy/lib/galaxy/objectstore/__init__.py", line 580, in delete
    return self._invoke(
           ^^^^^^^^^^^^^
  File "/home/dlopez/dev/galaxy/lib/galaxy/objectstore/__init__.py", line 485, in _invoke
    return self.__getattribute__(f"_{delegate}")(obj=obj, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/dlopez/dev/galaxy/lib/galaxy/objectstore/__init__.py", line 1202, in _delete
    return self._call_method("_delete", obj, False, False, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/dlopez/dev/galaxy/lib/galaxy/objectstore/__init__.py", line 1524, in _call_method
    return self._resolve_backend(object_store_id).__getattribute__(method)(obj, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/dlopez/dev/galaxy/lib/galaxy/objectstore/__init__.py", line 1068, in _delete
    path = self._get_filename(obj, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/dlopez/dev/galaxy/lib/galaxy/objectstore/__init__.py", line 1114, in _get_filename
    raise ObjectNotFound
galaxy.exceptions.ObjectNotFound: No such object found.

How to test the changes?

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  • Run any tool
  • Check the server log and observe there is no exception when cleaning the job directory and it is indeed deleted.

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[mvdbeek]

Do we know when that started happening and why ?

[davelopez]

Do we know when that started happening and why ?

I think it might have been introduced unintentionally here https://github.com/galaxyproject/galaxy/pull/18608/files#diff-0acc3f85a991471b3f76a7d6431a244f7a06d4b4010f8f7531f59453d8e22f66R2133 while trying to figure out the exposed parameters without kwargs.

[nsoranzo]

Oops, sorry about that! Thanks @davelopez for the fix!