feat(reactome): add gget reactome module to query the Reactome pathway database (#114)#236
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Elarwei001 wants to merge 3 commits into
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feat(reactome): add gget reactome module to query the Reactome pathway database (#114)#236Elarwei001 wants to merge 3 commits into
Elarwei001 wants to merge 3 commits into
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…y database (scverse#114) New module `gget reactome` (Python API + CLI) querying the Reactome ContentService REST API (https://reactome.org/). Supports three query types via the `resource` argument: - pathways (default): the Reactome pathways an identifier (e.g. a UniProt accession) participates in - search: full-text search of the Reactome knowledgebase - entity: details for a Reactome stable ID Returns a pandas DataFrame (or JSON with json=True / --csv on the CLI). Reuses the shared http_json helper for retries/error handling, strips HTML highlight tags from search results, and maps Reactome 404s to empty results (pathways/search) or a clear ValueError (entity). Adds unit tests (offline argument validation via fixture + release-robust network smoke tests that skip when Reactome is unreachable), docs page docs/src/en/reactome.md, a SUMMARY.md entry, and an updates.md note. Resolves scverse#114. Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
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## dev #236 +/- ##
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+ Coverage 56.14% 56.93% +0.79%
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Files 29 30 +1
Lines 9244 9337 +93
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+ Hits 5190 5316 +126
+ Misses 4054 4021 -33 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Add a network-free TestReactomeOffline class that mocks http_json to cover _strip_html passthrough, the pathways/search/entity parsing, verbose logging, 404 and non-404 error branches, the entity name fallback/summation, and resource/query validation. gget_reactome.py now 98% (only the import-time PackageNotFoundError version fallback, lines 16-17, remains, which is un-coverable in an installed environment). Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
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Resolves #114
Summary
gget reactome: New module to query the Reactome pathway knowledgebase via its ContentService REST API. Supports three query types via theresourceargument:pathways(the Reactome pathways an identifier such as a UniProt accession participates in),search(full-text search of the knowledgebase), andentity(details for a Reactome stable ID). Resolves issue 114.Testing
Unit tests in
tests/test_reactome.py(offline argument-validation viatests/fixtures/test_reactome.jsonplus release-robust network smoke tests that skip when Reactome is unreachable); run with pytest.