feat: grant disease_context_qualifier to pinned EntityToDisease/PhenotypicFeature edge classes - #120
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…typicFeature edge classes Biolink declares disease_context_qualifier only on the ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation lineage, while FDA_regulatory_approvals lives only on the EntityToDisease / EntityToPhenotypicFeature classes DAKP pins via category_override -- so a contraindication edge could natively carry one slot or the other, never both. Add CLASS_FIELD_OVERRIDES (biolink.py): a class-scoped grant table in the DISABLED_EDGE_FIELDS / KNOWN_PENDING_EDGE_FIELDS policy style. prune_to_class keeps granted slots on rows resolved to a granted class instead of nulling and rescuing them, and _validation_record strips granted fields from its in-memory validation copy so the deliberate gap is not reported as extra_forbidden. A tripwire test asserts every granted field stays absent from its class, forcing removal of the stale grant when a biolink-model release widens the 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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Motivation
DAKP pins its contraindication/treats edges to
EntityToDiseaseAssociation/EntityToPhenotypicFeatureAssociationviastatement.category_override(#118), because only those classes declareFDA_regulatory_approvals. Biolink declaresdisease_context_qualifieronly on theChemicalEntityToDiseaseOrPhenotypicFeatureAssociationlineage — so one edge can natively carry one slot or the other, never both, andprune_to_classnulls the qualifier on the pinned rows (DAKP'sgraph.yamldocuments the gap: "Revisit if Biolink widens either slot").Change
New
CLASS_FIELD_OVERRIDEStable inbiolink.py, following theDISABLED_EDGE_FIELDS/KNOWN_PENDING_EDGE_FIELDSpolicy-table precedent:disease_context_qualifieris granted toEntityToDiseaseAssociationandEntityToPhenotypicFeatureAssociation, deliberately ahead of the pinned model.lib.prune_to_class: per-class acceptance now ORs the grant in, so granted rows keep the qualifier instead of nulling and rescuing it into the pruned column. The multivalued-wrap scan still keys on classes that declare the slot, so granted classes can't corrupt the wrap.biolink._validation_record: granted fields the record's own class doesn't declare are stripped from the in-memory validation copy (mirroring the existingRetrievalSource.idalias shim), so the deliberate gap is not reported asextra_forbidden. Emitted files are unchanged.Verification
prune_to_classkeeps the qualifier on granted rows and still prunes it on ungranted classes;validate_recordtolerates the grant on the granted class only; tripwire guards the grant against model releases.ruff check/ruff format --checkclean.