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BUG: Failing Enrichment Analysis Tests #563

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ronjakrg opened this issue Jan 8, 2025 · 1 comment · Fixed by #564
Closed

BUG: Failing Enrichment Analysis Tests #563

ronjakrg opened this issue Jan 8, 2025 · 1 comment · Fixed by #564
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ronjakrg commented Jan 8, 2025

What is the issue?

For some commits, the a few tests for the enrichment analysis fail even though nothing has been changed in the associated code or section. This phenomenon has already been observed in some commits, for example here, here and here.

=========================== short test summary info ============================
FAILED tests/protzilla/data_integration/test_enrichment_analysis.py::test_GO_analysis_with_Enrichr - xml.etree.ElementTree.ParseError: mismatched tag: line 62, column 2
FAILED tests/protzilla/data_integration/test_enrichment_analysis.py::test_GO_analysis_Enrichr_wrong_background_file - xml.etree.ElementTree.ParseError: mismatched tag: line 62, column 2
====== 2 failed, 302 passed, 1 skipped, 102 warnings in 80.14s (0:01:20) =======

How to reproduce the issue?

Hard to say. It is not clear what similarities exist between the commits where the bug occurred.

What is the expected behavior?

The tests should run successfully if the code for the tests has not been changed.
@ronjakrg ronjakrg added the bug Something isn't working label Jan 8, 2025
@ronjakrg ronjakrg self-assigned this Jan 8, 2025
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/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/biomart/server.py:70: in fetch_databases
    xml = fromstring(r.text)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

text = '<html>\n\n<head>\n  <title>Service unavailable</title>\n  <meta name="robots" content="noindex">\n  <base href="//sta...   data centre.\n    </div>\n  </main>\n  <footer>\n    <p>&copy; 2024 EMBL-EBI</p>\n  </footer>\n</body>\n\n</html>\n'
parser = <xml.etree.ElementTree.XMLParser object at 0x7f36f822caf0>

The problem arises due to the (temporary?) non-availability of the BioMart database

@ronjakrg ronjakrg linked a pull request Jan 10, 2025 that will close this issue
Fixing tests regarding non-availability of BioMart database #564
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@ronjakrg ronjakrg mentioned this issue Jan 10, 2025
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Fixing tests regarding non-availability of BioMart database cschlaffner/PROTzilla2
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