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feat: fail the --qc study on edges whose subject and object are the same CURIE - #229
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SkyeAv
added this pull request to stack #230
October 21, 2026 20:19
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SkyeAv
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Oct 22, 2026
Cut 22.2.0 and bump the package version in pyproject.toml, CITATION.cff, and uv.lock. Minor: the --qc study stage fails the build on self-referential edges via a new self-loop-edges assertion (#229); eq/ne reindex filters can match cells with a Polars regex behind a default-off regex key (#232, #233, #234); source.reindex can filter rows by identifier membership with join/antijoin semi/anti hash joins (#236). Docs: the Taxon Filtering link in the table config reference now matches its section (#228, #231). Changelog: - Versioned the Unreleased section as 22.2.0 - 2026-10-22. - Added PR links to the three Added entries (#229; #232, #233, #234; #236). - Added the missing Fixed entry for the Taxon Filtering docs link (#228, #231). Docs: none needed here; the shipped docs changes are covered by the changelog entries above. Testing: - make check -> ruff, ruff format, pyright, pytest, cargo test, cargo clippy -D warnings: all green.
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Adds a
self-loop-edgesassertion to thebuild-kg --qcstage-7 study so an edge whosesubjectandobjectare the same CURIE fails the build instead of shipping.Study assertion
study._scan_ndjsontallies non-empty string pairs wheresubject == objectin the existing single edge pass, andstudy_kgxreports them asself-loop-edgeswith the repeated CURIE and per-CURIE count (examples capped like the other checks).incomplete-edges, and non-string slots are not flagged, so one broken edge never reports under two assertions.Design
studyKGtsvs.plnever checked this, and every other study assertion reports and exits 1. Reporting shows which mapping collapsed (two cell spellings resolving to one CURIE, or one cell in both slots) rather than silently deleting rows.--qcbuild too. Measured onMULTIOMICS_KG_3.0.0: 195 of 1,257,627 edges (0.0155%), 154biolink:regulatesand 39biolink:correlated_with.Docs
docs/cli.md--qcrow andCHANGELOG.md(Unreleased) updated.Testing
uv run pytest->1258 passed, 1 skippeduv run pytest tests/test_study.py -n 0 --no-cov->38 passeduv run ruff check ./uv run ruff format --check ./uv run pyright-> cleancargonot run locally.Questions for the reviewer
biolink:regulatesself-loops (a gene regulating itself) be exempt, or is failing the build the right default?