Add causal-graph structural-integrity audit + fix 2 orphan nodes#115
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LinkML/validate-strict check field types but not graph connectivity. New scripts/audit_causal_graphs.py flags two structural defects the schema can't: DANGLING_EDGE edge subject/object not a declared node_id ORPHAN_NODE declared node referenced by no edge Wired into `just qc` (and thus CI) alongside the other audits; exits non-zero on any defect. Unit-tested (tests/test_audit_causal_graphs.py: clean / orphan / dangling cases). Fixes the 2 orphan nodes the audit surfaced: - physiology/urease_activity.yaml: the trait node (urease_activity_trait) was disconnected; added urease_function -[manifests as / METPO:2007400]-> urease_activity_trait so the molecular function links to the observable trait. - morphology/capsule.yaml: capsular_polysaccharide was orphaned; added capsule_assembly -[produces / biolink:produces]-> capsular_polysaccharide. Both edges carry literature evidence; FIX_ORPHAN_NODE curation events appended. audit-graphs now reports 0 findings. validate-strict 0 errors; full qc passes; 90 tests pass. Pages regenerated. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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What
A diagnostic sweep of the corpus showed it's structurally clean (0 dangling edges, 0 edges missing evidence) except 2 orphan nodes — nodes declared in a causal graph that no edge references. Nothing currently catches this: LinkML/
validate-strictcheck field types, not graph connectivity.This adds a causal-graph structural-integrity audit and fixes the 2 it finds.
New audit (
scripts/audit_causal_graphs.py,just audit-graphs)Flags two defects the schema can't, exits non-zero on any:
subject/objectis not a declarednode_id(typo / deleted node)Wired into
just qc(and thus CI). Unit-tested (tests/test_audit_causal_graphs.py: clean / orphan / dangling).The 2 orphan fixes
urease_activity.yaml— the trait node itself was disconnected. Addedurease_function -[manifests as / METPO:2007400]-> urease_activity_traitso the molecular function links to the observable phenotype.capsule.yaml—capsular_polysaccharidewas orphaned. Addedcapsule_assembly -[produces / biolink:produces]-> capsular_polysaccharide.Both new edges carry literature evidence;
FIX_ORPHAN_NODEcuration events appended.Verification
just audit-graphs→ 0 findings.just validate-strict→ 477 files, 0 errors.just qc→ passes. 90 tests pass (+3 new).🤖 Generated with Claude Code