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change error handling for /curation REST errors #608

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merged 4 commits into from
Jul 6, 2023

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bkmartinjr
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@bkmartinjr bkmartinjr commented Jul 6, 2023

Fixes #606

Changes:

  • if the response from the upstream curation API is suspect, error out. Do not silently ignore and move on.
  • where we were logging as an Error, but it was really a Warning, change log level
  • raise RuntimeError in cases of intentionally "bailing" rather than raising AssertionError (save that for assertions)
  • fix unit test to match new (expected) behavior

@bkmartinjr bkmartinjr marked this pull request as ready for review July 6, 2023 19:10
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codecov bot commented Jul 6, 2023

Codecov Report

Merging #608 (b44a463) into main (33084b8) will decrease coverage by 0.03%.
The diff coverage is 63.63%.

@@            Coverage Diff             @@
##             main     #608      +/-   ##
==========================================
- Coverage   88.10%   88.07%   -0.03%     
==========================================
  Files          62       62              
  Lines        3740     3741       +1     
==========================================
  Hits         3295     3295              
- Misses        445      446       +1     
Flag Coverage Δ
unittests 88.07% <63.63%> (-0.03%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
.../cellxgene_census_builder/build_soma/build_soma.py 91.74% <0.00%> (ø)
...rc/cellxgene_census_builder/build_soma/manifest.py 94.02% <50.00%> (-1.36%) ⬇️
...src/cellxgene_census_builder/build_soma/anndata.py 86.90% <100.00%> (ø)
...ls/cellxgene_census_builder/tests/test_manifest.py 100.00% <100.00%> (ø)

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@bkmartinjr bkmartinjr merged commit 58bb4cc into main Jul 6, 2023
@bkmartinjr bkmartinjr deleted the bkmartinjr/606-manifest-errors branch July 6, 2023 22:39
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[builder] Error on reading manifest from Discover REST API
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