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Review failed test for BIA data #878

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tcompa opened this issue Dec 16, 2024 · 2 comments · Fixed by #879
Closed

Review failed test for BIA data #878

tcompa opened this issue Dec 16, 2024 · 2 comments · Fixed by #879
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@tcompa
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tcompa commented Dec 16, 2024

We've been hitting this test failure for a few days:

FAILED tests/tasks/test_import_ome_zarr.py::test_import_ome_zarr_image_BIA - TimeoutError: [Errno 60] Operation timed out

The failure has to do with FTP access to BIA

        # Download an existing OME-Zarr from BIA
        ftp = FTP("ftp.ebi.ac.uk")
        ftp.login()
        ftp.cwd("biostudies/fire/S-BIAD/843/S-BIAD843/Files")
        fname = "WD1_15-02_WT_confocalonly.ome.zarr.zip"
        with (tmp_path / fname).open("wb") as fp:
>           ftp.retrbinary(f"RETR {fname}", fp.write)

tests/tasks/test_import_ome_zarr.py:290: 

which fails with a TimeoutError.

This was a ConnectionRefusedError a few days back - see https://github.com/fractal-analytics-platform/fractal-tasks-core/actions/runs/12253006499/job/34183395372.

@jluethi
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jluethi commented Dec 16, 2024

Do we run this test regularly? I thought we had the BIA tested disabled to avoid such potential issues?

@tcompa
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tcompa commented Dec 17, 2024

Do we run this test regularly?

Yes, it is part of the test suite. But I am now deactivating it, since its irregular failures introduce too much noise.

If we ever decide to systematically test support for some BIA datasets, then we should first address #565.

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