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curation: fix getGeneData crash when a CDS's Parent resolves to no gene - #730
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Found while porting getGeneData to raven-toolbox (SysBioChalmers/raven-gecko-parity#53): parseGFF's emptyGene fallback struct had no uniProt field, so a CDS whose Parent chain doesn't resolve to any parsed gene feature crashed outright on g.uniProt with 'Unrecognized field name'. Added the missing field, empty like the rest of the fallback record.
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edkerk added a commit
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Sep 5, 2026
Landed in SysBioChalmers/raven-toolbox#132. Adds the parity scenario calling getGeneData.m directly (via a local GFF3 path, bypassing downloadGenomeData) against a hand-built fixture. Also notes SysBioChalmers/RAVEN#730, a crash found and fixed upstream while building the scenario.
Function test results306 tests 279 ✅ 1m 5s ⏱️ Results for commit 43408b1. |
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Summary
Found while porting
getGeneDatato raven-toolbox (SysBioChalmers/raven-gecko-parity#53):parseGFF'semptyGenefallback struct (used when a CDS'sParentchain doesn't resolve to any parsedgenefeature) has nouniProtfield, so hitting that fallback crashes outright:Added the missing field, empty like the rest of the fallback record.
Test plan
CDSwithParent=missing_gene) before the fix; confirmed it now returns a row with emptylocus_tag/old_locus_tag/GeneID/gene_name/UniProtand the CDS's ownprotein_id.tGenomeDatatest class: 6/6 passed.