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feat(genes): multi-gene symbol/Ensembl search in CLI, MCP, and Catalog - #16
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…e bronze by default
Shared fixture (Ensembl-keyed, legacy NA feature_id, bronze dataset) and the expected memberships from spec §3, mirrored by the engine's A tests.
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Related: producer theislab/spatialdata-db#143 (builds the gene index); website consumer theislab/spatialdata-db-web#13. This PR is independent of the website rollout — it reads the existing |
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What
Python-side multi-gene search over the published
gene_index.parquet, surfaced in the Catalog API, CLI, and MCP tools.src/sddb/genes.py—GeneIndexreader bound to a Catalog; resolve symbols or Ensembl ids to dataset uids, union within a token and AND across tokens, with casefolded symbol/feature_id caches for speed over the ~10M-row index.Why
Gives the CLI/MCP the same cross-dataset gene search the website offers, over the same release artifact.
Scope
Independent of the website fix — this consumes the existing
gene_index.parquetdirectly and needs no release change. Producer: theislab/spatialdata-dbfeat/gene-search-foundation; web consumer: theislab/spatialdata-db-webfeat/gene-search-web.