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@bencap bencap commented Dec 18, 2025

This pull request adds support for exporting ClinGen allele IDs in the variant data export endpoint, alongside improvements to the handling of namespaces in both the backend and API documentation. It also includes new tests to ensure that the ClinGen, VEP, and gnomAD namespaces are correctly exported in the CSV variant data.

API and Backend Enhancements:

  • Added "clingen" as a supported namespace for variant data export in both the backend logic (score_sets.py) and the API endpoint (score_sets.py). [1] [2] [3] [4]
  • Updated the CSV export logic to include the clingen_allele_id column when the "clingen" namespace is requested. [1] [2]

Testing Improvements:

  • Added tests for the export of VEP, ClinGen, and gnomAD namespaces in the variant data endpoint, verifying that the correct columns and values are present in the exported CSVs.

Additionally, adds a few tests for existing namespaces to increase coverage of namespaced CSV export.
@bencap bencap linked an issue Dec 18, 2025 that may be closed by this pull request
@bencap bencap requested review from jstone-dev and sallybg December 18, 2025 22:53
@bencap bencap marked this pull request as ready for review December 18, 2025 22:53
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Add clingen namespace in CSV export

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