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Fix life science skill bugs#231

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kk-oai wants to merge 3 commits intomainfrom
codex/life-science-skill-smoke-fixes
Open

Fix life science skill bugs#231
kk-oai wants to merge 3 commits intomainfrom
codex/life-science-skill-smoke-fixes

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@kk-oai kk-oai commented May 7, 2026

Summary

  • refresh stale executable examples for ENCODE, eQTL Catalogue, NCBI Datasets, PharmGKB, QuickGO, and RNAcentral
  • embed NCBI RefSNP coordinate resolution directly in the locus-to-gene mapper and remove the missing variant-coordinate-finder dependency
  • add RefSNP parsing unit tests for coordinate and gene-symbol extraction

Tests

  • python plugins/life-science-research/skills/eqtl-catalogue-skill/scripts/test_rest_request.py
  • python plugins/life-science-research/skills/ncbi-blast-skill/scripts/test_ncbi_blast.py
  • python plugins/life-science-research/skills/locus-to-gene-mapper-skill/scripts/test_map_locus_to_gene.py

Notes

  • Local full smoke pass now reports 47 pass, 1 pass_with_limitations, and 1 docs_only

@kk-oai kk-oai requested a review from a team May 7, 2026 20:55
@kk-oai kk-oai changed the title Fix life science skill smoke failures Fix life science skill bugs May 7, 2026
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