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Suppress logging for selected InvalidReferenceViolations #568

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merged 2 commits into from
Sep 12, 2019
Merged

Suppress logging for selected InvalidReferenceViolations #568

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ee04c8f
Suppress logging for selected InvalidReferenceViolations
jamesaoverton Sep 12, 2019
c41794d
Use isOWLThing, filter then count
jamesaoverton Sep 12, 2019
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41 changes: 41 additions & 0 deletions robot-core/src/main/java/org/obolibrary/robot/ReasonOperation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -505,6 +505,47 @@ private static void checkReferenceViolations(OWLOntology ontology, Map<String, S
int maxDanglings = 10;
int danglings = 0;
for (InvalidReferenceViolation v : referenceViolations) {
// Don't log errors for:
// - annotations
// - subclass of ObsoleteClass
// - subproperty of ObsoleteProperty
// - rdf:type owl:Thing
if (v.getAxiom() instanceof OWLAnnotationAxiom) {
continue;
}
if (v.getAxiom() instanceof OWLSubClassOfAxiom) {
OWLSubClassOfAxiom sub = (OWLSubClassOfAxiom) v.getAxiom();
OWLClassExpression sup = sub.getSuperClass();
if (!sup.isAnonymous()
&& sup.asOWLClass()
.getIRI()
.toString()
.equals("http://www.geneontology.org/formats/oboInOwl#ObsoleteClass")) {
continue;
}
}
if (v.getAxiom() instanceof OWLSubObjectPropertyOfAxiom) {
OWLSubObjectPropertyOfAxiom sub = (OWLSubObjectPropertyOfAxiom) v.getAxiom();
OWLObjectPropertyExpression sup = sub.getSuperProperty();
if (!sup.isAnonymous()
&& sup.asOWLObjectProperty()
.getIRI()
.toString()
.equals("http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty")) {
continue;
}
}
if (v.getAxiom() instanceof OWLClassAssertionAxiom) {
OWLClassAssertionAxiom sub = (OWLClassAssertionAxiom) v.getAxiom();
OWLClassExpression sup = sub.getClassExpression();
if (!sup.isAnonymous()
&& sup.asOWLClass()
.getIRI()
.toString()
.equals("http://www.w3.org/2002/07/owl#Thing")) {
continue;
}
}

if (v.getCategory().equals(InvalidReferenceViolation.Category.DANGLING)
&& danglings < maxDanglings) {
Expand Down