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[24.0] Don't serialize display application links for deleted datasets #18307

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mvdbeek
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@mvdbeek mvdbeek commented Jun 3, 2024

Doing that often requires datasets on disk, which we shouldn't guarantee for deleted datasets.

Fixes
https://sentry.galaxyproject.org/share/issue/0ae7a9d9ad564054bd11c9a43aa6994c/:

Message
Unexpected error
Stack Trace

Newest

FileNotFoundError: [Errno 2] No such file or directory: ''
  File "galaxy/datatypes/interval.py", line 914, in get_estimated_display_viewport
    with compression_utils.get_fileobj(dataset.get_file_name()) as fh:
  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")

(Also note how it's very bad to pull in the dataset from an object store just to generate the link if we request the extended dataset view ...).

How to test the changes?

(Select all options that apply)

  • 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.

Doing that often requires datasets on disk, which we shouldn't guarantee
for deleted datasets.

Fixes
https://sentry.galaxyproject.org/share/issue/0ae7a9d9ad564054bd11c9a43aa6994c/:
```
Message
Unexpected error
Stack Trace

Newest

FileNotFoundError: [Errno 2] No such file or directory: ''
  File "galaxy/datatypes/interval.py", line 914, in get_estimated_display_viewport
    with compression_utils.get_fileobj(dataset.get_file_name()) as fh:
  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")
```
@mvdbeek mvdbeek merged commit a4376d3 into galaxyproject:release_24.0 Jun 3, 2024
44 of 50 checks passed
@jdavcs jdavcs added this to the 24.1 milestone Jun 19, 2024
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3 participants