fix: leave number_of_cases alone instead of coercing it to study_size - #119
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number_of_cases is a legitimate Biolink Association slot (cases carrying the phenotype/disease), but STUDY_SIZE_PREFIX_PATTERN matched it via 'number of cases' and coerce_study_size_columns renamed it to study_size, destroying the edge field. Add STUDY_SIZE_EXEMPT_PATTERN so study_size_target returns None for the exact slot.
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SkyeAv
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Cut 15.1.0 and bump the package version in pyproject.toml, uv.lock, and CITATION.cff. Minor: one feature and one fix since 15.0.0, no breaking changes. A class-scoped policy override (CLASS_FIELD_OVERRIDES) grants disease_context_qualifier to the EntityToDisease / EntityToPhenotypicFeature edge classes DAKP pins via category_override, so prune_to_class keeps the qualifier instead of nulling and rescuing it, with a tripwire test that fails the suite once an upstream Biolink widening makes the grant stale (#120). Also fixes number_of_cases being matched by STUDY_SIZE_PREFIX_PATTERN and coerced into study_size, destroying the edge field; a new STUDY_SIZE_EXEMPT_PATTERN leaves the exact Biolink slot alone (#119). Changelog: - Versioned the Unreleased section as 15.1.0, gave the #120 entry its PR link, and added a Fixed entry for the number_of_cases coercion fix. Docs: none needed here. #120 shipped with no docs changes and #119 is a coercion fix with no user-facing surface. Testing: - uv run pytest -q -> 1092 passed, 15 skipped (94% coverage) - uv run ruff check . && uv run ruff format --check . && uv run pyright -> clean / 0 errors - uv lock --check -> up to date - uv run mkdocs build --strict -> clean
SkyeAv
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…, move FAERS count to number_of_cases - Bump tablassert[qc] floor to >=15.1.0. - Un-TODO the contraindication disease_context_qualifier: 15.1's CLASS_FIELD_OVERRIDES (SkyeAv/Tablassert#120) grants the slot to the pinned EntityToDisease/EntityToPhenotypicFeature classes, so the nullable Disease-guarded qualifier survives prune_to_class on the edge. - Migrate the FAERS case count annotation from the evidence_count alias to the literal Biolink slot number_of_cases: 15.1's STUDY_SIZE_EXEMPT_PATTERN (SkyeAv/Tablassert#119) stops the study-size classifier from renaming the column onto Study.study_size; the kgx_end_to_end tripwire fired as designed. legacy_tsv N_cases reads number_of_cases accordingly. - Regenerate tables/*.yaml from the generator; update RIG target consideration to note the grant pending upstream Biolink widening.
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Bugfix
number_of_casesis a legitimate BiolinkAssociationslot (declared onEntityToDiseaseAssociation/EntityToPhenotypicFeatureAssociation) that counts cases carrying the phenotype/disease — it is not the study population size.However,
STUDY_SIZE_PREFIX_PATTERNinsrc/tablassert/coerce.pymatched it via the "number of cases" quantity+unit form, socoerce_study_size_columnsrenamed the column tostudy_sizeduring the clean phase, silently destroying the edge field.Fix
STUDY_SIZE_EXEMPT_PATTERN(src/tablassert/coerce.py): a whole-name, separator-tolerant match on the exactnumber_of_casesslot.study_size_targetnow returnsNonefor it before any study-size pattern runs, so the column passes through untouched.Tests
test_study_size_target_leaves_number_of_cases_alonecovering underscored/spaced/hyphenated/fused spellings and the fullcoerce_study_size_columnspath.tests/test_lib.py+tests/test_biolink.py: 284 passed.