[24.1] Extend on disk checks to running, queued and error states

[mvdbeek]

Fixes
https://sentry.galaxyproject.org/share/issue/c1c4c9b0ab324b4ea4f98c3b8c402d21/:

Message
Uncaught Exception
Stack Trace

Newest

FileNotFoundError: [Errno 2] No such file or directory: ''
  File "galaxy/web/framework/middleware/error.py", line 167, in __call__
    app_iter = self.application(environ, sr_checker)
  File "galaxy/web/framework/middleware/statsd.py", line 29, in __call__
    req = self.application(environ, start_response)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.11/site-packages/paste/httpexceptions.py", line 635, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/base.py", line 176, in __call__
    return self.handle_request(request_id, path_info, environ, start_response)
  File "galaxy/web/framework/base.py", line 271, in handle_request
    body = method(trans, **kwargs)
  File "galaxy/webapps/galaxy/controllers/dataset.py", line 155, in display
    display_data, headers = data.datatype.display_data(
  File "galaxy/datatypes/tabular.py", line 226, in display_data
    chunk=self.get_chunk(trans, dataset, 0),
  File "galaxy/datatypes/tabular.py", line 149, in get_chunk
    ck_data, last_read = self._read_chunk(trans, dataset, offset, ck_size)
  File "galaxy/datatypes/tabular.py", line 159, in _read_chunk
    with compression_utils.get_fileobj(dataset.get_file_name()) as f:
  File "galaxy/util/compression_utils.py", line 79, in get_fileobj
    return get_fileobj_raw(filename, mode, compressed_formats)[1]
  File "galaxy/util/compression_utils.py", line 139, in get_fileobj_raw
    return compressed_format, open(filename, mode, encoding="utf-8")

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How to test the changes?

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• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

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