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BACKGROUND & CHANGES

This update adds fallback validation via OLS for taxon IDs not found in the minified list. This was brought about by a user adding mayfly (Cloeon dipterum, NCBI Taxonomy ID: 197152) data. Before, this data would not validate as the ID does not exist in our cache, and the user was blocked from adding data. Now, this data will validate server-side.

More work is needed to enable this in CSFV as we do not have a mechanism for doing OLS validation.

MANUAL TESTING

  1. Initialize your environment as normal
  2. Run the following command from the ingest/validation directory:
python metadata_validation.py --study-id dec0dedfeed1111111111111 --study-file-id addedfeed000000000000000 --study-accession SCPtest ../../tests/data/annotation/metadata/convention/valid_extended_taxon_v3.0.0.txt
  1. Confirm you see the following message:
Using fallback EBI OLS call with ['https://www.ebi.ac.uk/ols/api/ontologies/ncbitaxon'], NCBITaxon_197152, species
  1. Confirm there is no validation error

@bistline bistline requested a review from eweitz November 25, 2025 18:45
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codecov bot commented Nov 25, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.02%. Comparing base (a52b3bd) to head (579c257).

Additional details and impacted files

Impacted file tree graph

@@               Coverage Diff               @@
##           development     #402      +/-   ##
===============================================
+ Coverage        77.30%   78.02%   +0.71%     
===============================================
  Files               31       31              
  Lines             4635     4641       +6     
===============================================
+ Hits              3583     3621      +38     
+ Misses            1052     1020      -32     
Files with missing lines Coverage Δ
ingest/validation/validate_metadata.py 85.06% <100.00%> (+4.85%) ⬆️
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2 participants