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ClinVar namespaced variant data export#684

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jstone-dev wants to merge 3 commits intorelease-2026.1.2from
clinvar-namespaced-variant-data-export
Open

ClinVar namespaced variant data export#684
jstone-dev wants to merge 3 commits intorelease-2026.1.2from
clinvar-namespaced-variant-data-export

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This pull request adds support for exporting ClinVar data alongside variant information in the score set CSV export endpoint. It introduces a new namespace pattern for ClinVar-versioned data (e.g., clinvar.2024_01), allowing users to request multiple ClinVar versions simultaneously. The changes update the API, CSV generation logic, and documentation to handle these new namespaces and ensure correct column naming and data retrieval.

ClinVar namespace support and CSV export enhancements:

  • Added support for ClinVar-versioned namespaces (e.g., clinvar.2024_01) in the CSV export endpoint, including validation of requested namespaces and documentation updates in src/mavedb/routers/score_sets.py. [1] [2] [3] [4] [5]
  • Updated CSV row generation functions (get_score_set_variants_as_csv, variant_to_csv_row, variants_to_csv_rows) to fetch and include per-variant ClinVar data, with proper column naming to avoid collisions when multiple ClinVar versions are requested. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10]

Internal and testing improvements:

  • Added helper function and test data for linking ClinVar clinical controls to mapped variants, supporting new export scenarios in test utilities and test cases. [1] [2] [3]
  • Updated imports and documentation to reflect new ClinVar namespace pattern and usage. [1] [2]

These changes collectively enable users to export variant data with ClinVar annotations for multiple versions, improving clinical relevance and flexibility for downstream analyses.

@jstone-dev jstone-dev linked an issue Mar 18, 2026 that may be closed by this pull request
@jstone-dev jstone-dev changed the title Clinvar namespaced variant data export ClinVar namespaced variant data export Mar 18, 2026
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Fully complete dataset export

1 participant