chore(deps): bump biolink-model to 4.4.6 and drop the absorbed population_context_qualifier grants

CHANGELOG.md

@@ -4,6 +4,9 @@ All notable changes to this project are documented in this file.
 
 ## Unreleased
 
+### Changed
+- **`biolink-model` is bumped to 4.4.6 and the grant it absorbed is dropped.** Unlike the 4.4.5 wheel, whose bundled schema still carried the 4.4.4 version string, the 4.4.6 wheel's schema registers as 4.4.6, so `BIOLINK_VERSION` now reports the pinned version accurately. The release also attached `population_context_qualifier` to `EntityToDiseaseAssociation` / `EntityToPhenotypicFeatureAssociation`, so the `CLASS_FIELD_OVERRIDES` tripwire removed that grant from both classes (the removed entries stay in the source as commented examples for future grants); the remaining deliberate grants are `temporal_context_qualifier` on both classes plus `sex_qualifier` on `EntityToDiseaseAssociation`, and `prune_to_class` now keeps `population_context_qualifier` natively on the whole disease/phenotype family, including previously ungranted classes.
+
 ### Added
 - **`validate-infores` checks every emitted knowledge-source identifier against the Translator registry.** The new command classifies each `infores:` CURIE on the edges (`primary_knowledge_source`, `sources[].resource_id`, `sources[].upstream_resource_ids`), the nodes (`provided_by`), and optionally the RIG document against `biolink/information-resource-registry`'s `infores_catalog.yaml` -- the authoritative catalog translator-ingests' SOP points at but never checks programmatically. The registry ships as a bundled offline snapshot (vendored from upstream commit `a72dbc3b55d5`), `--registry refresh` fetches the live catalog through the bounded-retry network layer, and `--registry off` reports structure only. The default posture is advisory (exit 0 with warnings) because Tablassert legitimately mints graph-local CURIEs; repeatable `--allow-infores` exempts them and `--strict` makes unregistered CURIEs fail in CI. Values without the `infores:` prefix are malformed, not unregistered. This closes the validation gap that only the CURIE prefix was ever checked.
 

docs/configuration/table.md

@@ -590,7 +590,7 @@ annotations:
 
 Annotation names fall into three groups at build time:
 
-- **Allowed edge fields:** names on the edge allow-list: [Biolink Association](https://biolink.github.io/biolink-model/) slots, qualifier slots, and curated KGX/Tablassert edge fields (e.g. `p_value`, `adjusted_p_value`, `knowledge_level`, `supporting_text`, `publications`, `effect_size`, `effect_type`, `statistical_significance_qualifier`, qualifier slots like `severity_qualifier` / `disease_context_qualifier`) are written to edges verbatim. `effect_size` and `effect_type` became real Association slots in biolink-model 4.4.4 (PR #1774) and emit as real JSON numbers and enum tokens. Annotation names are matched case-insensitively against the allow-list and emitted under the canonical slot spelling. `regulatory_approvals` (multivalued, so declare [`split_by`](#split_by) for pipe-joined cells like `011111|022222`), `disease_context_qualifier`, `anatomical_context_qualifier`, and `frequency_qualifier` are declared natively on `EntityToDiseaseAssociation` / `EntityToPhenotypicFeatureAssociation` by biolink-model 4.4.5, and `sex_qualifier` on the phenotypic-feature class, so those rows keep them without any override. The remaining class-scoped grants cover DAKP's sparse qualifier stack ahead of the model: `population_context_qualifier` and `temporal_context_qualifier` on both classes, plus `sex_qualifier` on `EntityToDiseaseAssociation`; without a grant `prune_to_class` nulls those qualifiers off the pinned rows. `species_context_qualifier` stays disabled, and `temporal_interval_qualifier` / `severity_qualifier` stay unsatisfiable, so none of the three is granted.
+- **Allowed edge fields:** names on the edge allow-list: [Biolink Association](https://biolink.github.io/biolink-model/) slots, qualifier slots, and curated KGX/Tablassert edge fields (e.g. `p_value`, `adjusted_p_value`, `knowledge_level`, `supporting_text`, `publications`, `effect_size`, `effect_type`, `statistical_significance_qualifier`, qualifier slots like `severity_qualifier` / `disease_context_qualifier`) are written to edges verbatim. `effect_size` and `effect_type` became real Association slots in biolink-model 4.4.4 (PR #1774) and emit as real JSON numbers and enum tokens. Annotation names are matched case-insensitively against the allow-list and emitted under the canonical slot spelling. `regulatory_approvals` (multivalued, so declare [`split_by`](#split_by) for pipe-joined cells like `011111|022222`), `disease_context_qualifier`, `anatomical_context_qualifier`, and `frequency_qualifier` are declared natively on `EntityToDiseaseAssociation` / `EntityToPhenotypicFeatureAssociation` by biolink-model 4.4.5, and `sex_qualifier` on the phenotypic-feature class; biolink-model 4.4.6 added `population_context_qualifier` to both classes, so those rows keep them without any override. The remaining class-scoped grants cover DAKP's sparse qualifier stack ahead of the model: `temporal_context_qualifier` on both classes, plus `sex_qualifier` on `EntityToDiseaseAssociation`; without a grant `prune_to_class` nulls those qualifiers off the pinned rows. `species_context_qualifier` stays disabled, and `temporal_interval_qualifier` / `severity_qualifier` stay unsatisfiable, so none of the three is granted.
 - **Study metadata:** `study_size`, `study_cohort`, `study_context`, `study_date_range`, `study_method_description`, and `study_method_types` are current Biolink `Study` node properties ([biolink-model PR #1770](https://github.com/biolink/biolink-model/pull/1770)). They describe the study itself, not an association, so their values are carried on the edge's **inlined supporting Study** (`has_supporting_studies` to `Study`, the COHD/ICEES pattern) rather than emitted as edge fields. Deprecated `supporting_study_*` spellings and `sample_size` are accepted as aliases and renamed onto canonical `study_*` names by coercion. They never appear in final JSON. Declaring any of them is legal and emits a `BiolinkRelocationWarning` naming where the value went.
 - **Unsatisfiable slots:** names the Biolink LinkML schema declares but attaches to **no** Pydantic class, derived from the installed `biolink-model`. A record carrying one could never validate, so its value is preserved in the inlined supporting study's `StudyResult.description`. A slot leaves the set automatically once a release attaches it.
 

pyproject.toml

@@ -47,7 +47,7 @@ classifiers = [
 ]
 requires-python = ">=3.11"
 dependencies = [
-    "biolink-model>=4.4.5",
+    "biolink-model>=4.4.6",
     "polars>=2.0.0rc2",
     "pyarrow>=21.0.0",
     "rapidfuzz>=3.14.3",

src/tablassert/biolink.py

@@ -593,8 +593,12 @@ class EffectTypes(str, Enum):
 
 
 CLASS_FIELD_OVERRIDES: dict[str, frozenset[str]] = {
-    "EntityToDiseaseAssociation": frozenset({"population_context_qualifier", "sex_qualifier", "temporal_context_qualifier"}),
-    "EntityToPhenotypicFeatureAssociation": frozenset({"population_context_qualifier", "temporal_context_qualifier"}),
+    # Absorbed by biolink-model 4.4.6 (now declared natively on both pinned classes,
+    # removed by the tripwire; kept here commented as the pattern for future grants):
+    # "EntityToDiseaseAssociation": frozenset({"population_context_qualifier", "sex_qualifier", "temporal_context_qualifier"}),
+    # "EntityToPhenotypicFeatureAssociation": frozenset({"population_context_qualifier", "temporal_context_qualifier"}),
+    "EntityToDiseaseAssociation": frozenset({"sex_qualifier", "temporal_context_qualifier"}),
+    "EntityToPhenotypicFeatureAssociation": frozenset({"temporal_context_qualifier"}),
 }
 """Per-class grants of edge fields the resolved association class does not declare.
 
@@ -612,11 +616,12 @@ class EffectTypes(str, Enum):
 ``anatomical_context_qualifier``, and ``frequency_qualifier`` to the whole
 disease/phenotype family, renamed ``FDA_regulatory_approvals`` to the canonical
 ``regulatory_approvals`` on the pinned classes, and added ``sex_qualifier`` to
-``EntityToPhenotypicFeatureAssociation``); the tripwire removed those grants the day
-the release landed, and the remaining ones stay deliberately ahead of the model
-(pending an upstream Biolink widening). ``_validation_record`` strips granted fields
-before record validation so the deliberate gap is not reported as
-``extra_forbidden``.
+``EntityToPhenotypicFeatureAssociation``; biolink-model 4.4.6 then attached
+``population_context_qualifier`` to both pinned classes, so the tripwire removed
+those grants the day each release landed). The remaining ones stay deliberately
+ahead of the model (pending an upstream Biolink widening).
+``_validation_record`` strips granted fields before record validation so the
+deliberate gap is not reported as ``extra_forbidden``.
 
 A tripwire test asserts every granted field is still absent from its class: the moment
 a biolink-model release attaches the slot, the suite fails and the stale grant is

tests/test_biolink.py

@@ -415,18 +415,18 @@ def test_class_field_overrides_track_the_installed_model() -> None:
     philosophy as the ``UNSATISFIABLE_EDGE_FIELDS`` derivation guard). A field the
     family allow-list would strip anyway must never be granted. The biolink-model
     4.4.5 mixin consolidation (plus the ``regulatory_approvals`` rename and the
-    phenotypic-feature ``sex_qualifier`` attachment) fired exactly this tripwire for
-    the original seven-field grant stack; the remaining grants are DAKP's sparse
-    qualifier slots still absent from the pinned classes
-    (``population_context_qualifier`` / ``temporal_context_qualifier`` on both, and
-    ``sex_qualifier`` on the disease side only). Deliberately excluded from the
-    grants: ``species_context_qualifier`` (disabled) plus
-    ``temporal_interval_qualifier`` and ``severity_qualifier`` (unsatisfiable -- a
-    grant could never validate).
+    phenotypic-feature ``sex_qualifier`` attachment) and the 4.4.6
+    ``population_context_qualifier`` attachment to both pinned classes fired exactly
+    this tripwire for the original eight-field grant stack; the remaining grants are
+    DAKP's sparse qualifier slots still absent from the pinned classes
+    (``temporal_context_qualifier`` on both, and ``sex_qualifier`` on the disease
+    side only). Deliberately excluded from the grants: ``species_context_qualifier``
+    (disabled) plus ``temporal_interval_qualifier`` and ``severity_qualifier``
+    (unsatisfiable -- a grant could never validate).
     """
     assert {
-        "EntityToDiseaseAssociation": frozenset({"population_context_qualifier", "sex_qualifier", "temporal_context_qualifier"}),
-        "EntityToPhenotypicFeatureAssociation": frozenset({"population_context_qualifier", "temporal_context_qualifier"}),
+        "EntityToDiseaseAssociation": frozenset({"sex_qualifier", "temporal_context_qualifier"}),
+        "EntityToPhenotypicFeatureAssociation": frozenset({"temporal_context_qualifier"}),
     } == CLASS_FIELD_OVERRIDES
     for class_name, fields in CLASS_FIELD_OVERRIDES.items():
         cls: type[Any] = association_class(f"biolink:{class_name}")
@@ -442,9 +442,10 @@ def test_validate_record_tolerates_class_field_override_grants() -> None:
     The grant is a deliberate, class-scoped step ahead of the pinned model, so its
     ``extra_forbidden`` must not surface on either intended target -- while the same
     field on an ungranted class stays a real defect through the installed-model boundary.
-    ``population_context_qualifier`` is the probe because it is still granted on both
-    targets: ``regulatory_approvals`` was absorbed by the model itself in 4.4.5, so a
-    probe on it would pass natively and exercise nothing.
+    ``temporal_context_qualifier`` is the probe because it is still granted on both
+    targets: ``regulatory_approvals`` and ``population_context_qualifier`` were
+    absorbed by the model itself (in 4.4.5 and 4.4.6), so a probe on either would
+    pass natively and exercise nothing.
     """
     base: dict[str, Any] = {
         "id": "e1",
@@ -453,13 +454,16 @@ def test_validate_record_tolerates_class_field_override_grants() -> None:
         "object": "MONDO:0005148",
         "knowledge_level": "statistical_association",
         "agent_type": "data_analysis_pipeline",
+        "temporal_context_qualifier": "TIME:1",
+        # 4.4.6 attached population_context_qualifier to the whole family: native on
+        # both granted targets AND the control, so it cannot serve as a rejection probe.
         "population_context_qualifier": "NCIT:C25667",
     }
     for category in ("EntityToDiseaseAssociation", "EntityToPhenotypicFeatureAssociation"):
         record: dict[str, Any] = {**base, "category": [f"biolink:{category}"]}
         assert validate_record(record, edge=True) == []
     control: dict[str, Any] = {**base, "category": ["biolink:GeneToDiseaseAssociation"]}
-    assert "population_context_qualifier: extra_forbidden" in validate_record(control, edge=True)
+    assert "temporal_context_qualifier: extra_forbidden" in validate_record(control, edge=True)
     unknown: dict[str, Any] = {**base, "category": ["biolink:EntityToDiseaseAssociation"], "not_a_biolink_field": "x"}
     assert "not_a_biolink_field: extra_forbidden" in validate_record(unknown, edge=True)
 

tests/test_lib.py

@@ -1995,15 +1995,16 @@ def test_prune_to_class_keeps_class_field_override_grants() -> None:
 
     DAKP's sparse qualifier stack rides the pinned ``EntityToDiseaseAssociation`` /
     ``EntityToPhenotypicFeatureAssociation`` rows through ``prune_to_class`` via the
-    grants: ``population_context_qualifier`` / ``temporal_context_qualifier`` (both
-    classes) and ``sex_qualifier`` (disease side only) are kept even though the
-    installed model does not declare them there. ``regulatory_approvals`` needs no
-    grant anymore -- biolink-model 4.4.5 attached it natively to the two pinned
-    classes -- but the ungranted control class still prunes it, alongside the
-    still-granted qualifiers. The qualifiers the 4.4.5 mixin consolidation attached
-    to the whole disease/phenotype family (``disease_context_qualifier``,
-    ``anatomical_context_qualifier``, ``frequency_qualifier``) survive on every row
-    including the control.
+    grants: ``temporal_context_qualifier`` (both classes) and ``sex_qualifier``
+    (disease side only) are kept even though the installed model does not declare
+    them there. ``regulatory_approvals`` (biolink-model 4.4.5) needs no grant
+    anymore on the two pinned classes, but the ungranted control class still
+    prunes it, alongside the still-granted qualifiers; and biolink-model 4.4.6
+    attached ``population_context_qualifier`` to the whole disease/phenotype
+    family, so it survives on every row including the control. The qualifiers the
+    4.4.5 mixin consolidation attached to the family (``disease_context_qualifier``,
+    ``anatomical_context_qualifier``, ``frequency_qualifier``) also survive on
+    every row.
     """
     from tablassert.lib import PRUNED_COLUMN, prune_to_class
 
@@ -2029,10 +2030,14 @@ def test_prune_to_class_keeps_class_field_override_grants() -> None:
     assert out["anatomical_context_qualifier"].to_list() == [["UBERON:0001557"]] * 3
     assert out["frequency_qualifier"].to_list() == ["HP:0012823"] * 3
     assert out["regulatory_approvals"].to_list() == [["FDA:1"], None, ["FDA:3"]]
-    for col in ("sex_qualifier", "population_context_qualifier", "temporal_context_qualifier"):
+    # 4.4.6 attached population_context_qualifier to the whole disease/phenotype
+    # family (not just the two pinned classes): kept natively on the ungranted
+    # control row too.
+    assert out["population_context_qualifier"].to_list() == ["NCIT:C25667"] * 3
+    for col in ("sex_qualifier", "temporal_context_qualifier"):
         assert out[col].to_list() == [out[col].to_list()[0], None, out[col].to_list()[2]], col
     pruned_second: list[str] = out[PRUNED_COLUMN].to_list()[1]
-    for col in ("regulatory_approvals", "sex_qualifier", "population_context_qualifier", "temporal_context_qualifier"):
+    for col in ("sex_qualifier", "temporal_context_qualifier"):
         assert any(entry.startswith(f"{col}=") for entry in pruned_second), col
     assert out[PRUNED_COLUMN].to_list()[0] == []
     assert out[PRUNED_COLUMN].to_list()[2] == []