feat(alliance): add gget alliance module for Alliance of Genome Resources (#162)#232
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feat(alliance): add gget alliance module for Alliance of Genome Resources (#162)#232Elarwei001 wants to merge 2 commits into
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…rces (scverse#162) New module `gget alliance` queries the Alliance of Genome Resources REST API (https://www.alliancegenome.org/). Passing an Alliance gene ID (HGNC/MGI/RGD/ZFIN/FB/WB/SGD/...) returns that gene's details; any other input is used as a free-text search returning matching objects of a chosen category (gene/allele/disease/go/variant/model) across the member model-organism databases. Exposed via the Python API and the command line. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## dev #232 +/- ##
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+ Coverage 56.14% 56.61% +0.46%
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Files 29 30 +1
Lines 9244 9325 +81
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+ Hits 5190 5279 +89
+ Misses 4054 4046 -8 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Add network-free mocked tests for empty search_term, _text passthrough, _alliance_get request-exception/404, gene-not-found, gene/search verbose logging, and save CSV/JSON branches. gget_alliance.py now 100%. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Resolves #162
Summary
gget alliance: New module to query the Alliance of Genome Resources. Pass an Alliance gene ID (e.g.HGNC:1101,MGI:109337,RGD:2219) to fetch the gene's details, or a free-text term to search genes/alleles/diseases/GO/variants/models across the member model-organism databases (selectable withcategory). Available in the Python API and on the command line. Resolves issue 162.Testing
Unit tests in
tests/test_alliance.pywith fixturetests/fixtures/test_alliance.json; run with pytest.