fix(ontology): validate SHACL term kinds - #622
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…R 0205) Resolves #372. Supersedes ADR 0157: the repository-case public namespace https://contextualwisdomlab.github.io/LineageWeave/ontology# is the exact project path GitHub Pages serves and becomes the only spelling new runtime values, exports, fixtures, and database rows mint. The lowercase form stays published as a deprecated compatibility vocabulary with validated equivalentClass/equivalentProperty mappings, and scripts/migrate_legacy_namespace.py rewrites stored lowercase IRIs (dry-run by default; never touches provenance columns). Also lands the completeness increments that motivated the decision: grounded node-attribute datatype properties, the SKOS post-type scheme, person-side disjointness plus inverse affiliation, and a closed-world SHACL shapes graph (docs/ontology/lineageweave-kg-shapes.ttl) validated against every DB-to-RDF projection and published beside the ontology. Full unit suite: 1095 passed, 12 skipped.
…ory-case-namespace # Conflicts: # CHANGELOG.md # pyproject.toml
…as role=status Its resolved empty/unavailable state carried role="status" like sibling panels' transient loading text does, so mounting it inside the Board's collapsed Advanced Review Tools details collided with every other status region on the page (4 failing App.test.tsx assertions). RankingsPanel's own resolved placeholders carry no ARIA role for the same reason -- only the "Loading..." state announces.
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Closed as a duplicate of #618, which contains the same three-file review repair on current protected main with normal auto-merge enabled. Keeping both would duplicate the ontology/fixture changes and create an avoidable conflict. |
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📝 Info: Reversed migration guard reconstructs original IRI correctly
The reversed lowercase->repository-case migration rebuilds the pre-migration value via new.replace(CANONICAL_NAMESPACE, LEGACY_NAMESPACE) for the ontology_iri = $4 optimistic-lock guard. Since the replaced substring includes /ontology#, the local fragment cannot be mangled, and a re-run finds only canonical rows so it stays idempotent.
(Refers to this code)
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| - The repository-case public ontology namespace | ||
| `https://contextualwisdomlab.github.io/LineageWeave/ontology#` is canonical | ||
| (ADR 0207, superseding ADR 0157, resolving issue #372); the lowercase form | ||
| is a deprecated compatibility vocabulary with validated mappings and a | ||
| dry-run migration tool for stored values. |
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🟡 Changelog still calls the lowercase namespace canonical
The new entry names the repository-case namespace canonical, but three earlier bullets in the same Unreleased section still call the lowercase namespace canonical and the repository-case form deprecated (CHANGELOG.md, CHANGELOG.md). The changelog now states the namespace roles both ways.
Prompt for agents
After ADR 0207 flips the canonical ontology namespace to the repository-case spelling, three stale bullets in the [Unreleased]/Added and Fixed sections of CHANGELOG.md still describe the old lowercase-canonical direction and now contradict the new entry at the top. Update or remove: the bullet at CHANGELOG.md:74-75 ('publishes the deprecated repository-case compatibility vocabulary' -- repository-case is now canonical, lowercase is deprecated); the bullet at CHANGELOG.md:76-77 ('mints its product class mappings only in the canonical lowercase namespace'); and the Fixed bullet at CHANGELOG.md:128 ('uses its canonical lowercase deployed IRI'). Make them consistent with the repository-case-canonical direction.
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| <h3 id={`${headingId}-observed`}>{t("Observed calendar events")}</h3> | ||
| {events.length === 0 ? ( | ||
| <p className="popup-placeholder" role="status"> | ||
| <p className="popup-placeholder"> |
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📝 Info: Calendar fail-closed message no longer announced
The empty-events placeholder dropped role="status", so the fail-closed copy shown when Naruon is unavailable is no longer surfaced as a live region to screen readers. Tests still pass because they query by text. Unrelated to the PR's namespace/SHACL focus.
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| def validate_shapes_graph(shapes: Graph, canonical: Graph) -> None: | ||
| """Reject SHACL shapes whose targets dangle outside the ontology. | ||
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| A shape that targets a class absent from the canonical graph, or | ||
| constrains a path neither declared there nor one of RDF's three | ||
| reification predicates, would silently validate nothing -- the | ||
| publication boundary refuses it instead (ADR 0207 decision 10). | ||
| Only URI-valued targets and paths are checked; literal sh:path values | ||
| are not part of this contract. | ||
| """ | ||
| if not any(shapes.triples((None, RDF.type, SH.NodeShape))): | ||
| raise ValueError("SHACL shapes graph declares no sh:NodeShape") | ||
| for predicate in (SH.targetClass, SH.path): | ||
| for value in shapes.objects(None, predicate): | ||
| if ( | ||
| not isinstance(value, URIRef) | ||
| or str(value).startswith(CANONICAL_NAMESPACE) | ||
| or (predicate == SH.path and value in STANDARD_SHACL_PATHS) | ||
| ): | ||
| continue | ||
| kind = "targetClass" if predicate == SH.targetClass else "path" | ||
| raise ValueError( | ||
| f"SHACL {kind} target outside the canonical namespace: {value}" | ||
| ) | ||
| declared_classes = { | ||
| subject | ||
| for subject in canonical.subjects(RDF.type, OWL.Class) | ||
| if isinstance(subject, URIRef) | ||
| } | ||
| # Entailed classes: anything with a subclass assertion is a class. | ||
| declared_classes.update( | ||
| subject | ||
| for subject, _ in canonical.subject_objects(RDFS.subClassOf) | ||
| if isinstance(subject, URIRef) | ||
| ) | ||
| declared_properties = { | ||
| subject | ||
| for subject in canonical.subjects(RDF.type, OWL.ObjectProperty) | ||
| if isinstance(subject, URIRef) | ||
| } | ||
| declared_properties.update( | ||
| subject | ||
| for subject in canonical.subjects(RDF.type, OWL.DatatypeProperty) | ||
| if isinstance(subject, URIRef) | ||
| ) | ||
| declared_properties.update(STANDARD_SHACL_PATHS) | ||
| for target in shapes.objects(None, SH.targetClass): | ||
| if target not in declared_classes: | ||
| raise ValueError(f"SHACL targetClass is not an ontology class: {target}") | ||
| for path in shapes.objects(None, SH.path): | ||
| if path not in declared_properties: | ||
| raise ValueError(f"SHACL property path is not an ontology property: {path}") |
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📝 Info: SHACL target/path validation matches the shipped shapes
validate_shapes_graph rejects sh:targetClass/sh:path values outside the canonical namespace (bar RDF reification predicates) and dangling targets. Every targetClass in the shipped shapes is a declared or subclass-entailed class and every path is a declared property or reification predicate, so the real file passes; sh:class under sh:not is intentionally unchecked.
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Summary
Validation
uv run --extra dev pytest tests/test_publish_ontology_site.py -q(14 passed)uv run --extra dev pytest tests/test_public_docstrings.py -q(2 passed)Follow-up to #616 for review findings completed after its protected auto-merge.