Fix #1080: preserve ontology IRI when it is both import subject and annotation value

[Artemis-IA]

Summary

Fixes #1080 — when an ontology declares owl:imports and has a self-referencing annotation (an annotation whose IRI value equals the ontology IRI, e.g. rdfs:isDefinedBy → <ontology-iri>), the RDF/XML parser incorrectly assigns an imported ontology's IRI as the main ontology IRI.

Problem

When parsing RDF/XML, OWLRDFConsumer.chooseAndSetOntologyIRI() selects the ontology IRI from candidate IRIs. When multiple candidates exist (the ontology IRI + imported ontology IRIs), it removes any candidate that also appears as the value of an ontology annotation:

ontology.annotations().forEach(a -> a.getValue().asIRI().ifPresent(iri -> {
    if (ontologyIRIs.contains(iri)) {
        candidateIRIs.remove(iri);
    }
}));

This is meant to avoid picking an IRI that is merely an annotation value. However, the subject of an owl:imports triple (i.e. the importing ontology itself) is also added to ontologyIRIs by TPImportsHandler. If that same IRI appears as an annotation value (a self-referencing annotation), it gets incorrectly removed from candidates, and an imported ontology's IRI is chosen instead.

Self-referencing annotations are valid and standard semantic web practice:

• rdfs:isDefinedBy → <ontology-iri>
• omv:URI → <ontology-iri>
• omv:resourceLocator → <ontology-iri>
• rdfs:seeAlso → <ontology-iri>

Root Cause Analysis

The bug requires both conditions simultaneously:

1. The ontology has at least one owl:imports declaration
2. The ontology has at least one annotation whose IRI value equals the ontology IRI

If only one condition is met, the bug does not trigger (verified by tests).

Why some ontologies are not affected

OSO 1.0.0 has both conditions but is not affected by coincidence: its imports (rdfs#, owl#, skos/core#, foaf/) are also declared as values of omv:useImports annotations with exactly the same IRIs. This causes all candidates to be removed, leaving candidateIRIs empty — in which case the parser does not change the ontology IRI (it stays correct).

OSO 1.1.0 and 1.2.0 have imports (prov-o, wgs84_pos, skos/core, foaf/) that do not all appear as annotation values, so some candidates survive and an imported IRI is wrongly selected.

Fix

Three minimal changes across two files:

OWLRDFConsumer.java

1. New field ontologySubImportIRIs to track IRIs that are subjects of owl:imports triples.
2. New overload addOntology(IRI, boolean isImportSubject) that adds to ontologySubImportIRIs when isImportSubject is true.
3. In chooseAndSetOntologyIRI(), skip removal of candidates that are in ontologySubImportIRIs:

if (ontologyIRIs.contains(iri) && !ontologySubImportIRIs.contains(iri)) {
    candidateIRIs.remove(iri);
}

TripleHandlers.java

4. TPImportsHandler.handleTriple() calls consumer.addOntology(s, true) instead of consumer.addOntology(s) to mark the import subject.

Tests

7 regression tests in SelfReferenceAnnotationImportsTestCase:

Test	Without fix	With fix
testSelfReferenceWithImports	❌ FAIL	✅ PASS
testMultipleSelfReferencesWithImports	❌ FAIL	✅ PASS
testVersionIRIPreservedWithSelfRef	❌ FAIL	✅ PASS
testImportsWithoutSelfReference	✅ PASS	✅ PASS
testSelfReferenceWithoutImports	✅ PASS	✅ PASS
testSelfReferenceAsLiteral	✅ PASS	✅ PASS
testAnnotationWithDifferentIRI	✅ PASS	✅ PASS

3 tests fail without the fix and pass with it. 4 pass in both cases (no regression).

Broader Validation

Beyond unit tests, the fix was validated against:

• 3 OSO ontology versions (1.0.0, 1.1.0, 1.2.0): 1.1.0 and 1.2.0 were broken (returned prov-o instead of OSO), now fixed. 1.0.0 was unaffected by coincidence, remains correct.
• 9 real-world ontologies (DCAT2, SSN, PROV-O, GeoNames, GoodRelations, FOAF, IAO, RO, BFO): all return identical results before and after the fix — no regression.
• 8 edge cases (partial import matches, multiple self-refs, self-import, version IRI, no type declaration, multiple ontologies, literal self-ref, 20 imports): all handled correctly.

Impact

This bug affects any OWL API consumer that loads ontologies with both owl:imports and self-referencing annotations. Known affected consumers include:

• WebVOWL/OWL2VOWL — displays the wrong ontology IRI
• Protégé (reported in #1181)
• EarthPortal/AgroPortal ingestion pipelines

Test plan

• 7 unit tests pass with fix (3 fail without)
• 3 OSO versions tested (2 fixed, 1 no regression)
• 9 real-world ontologies tested (no regression)
• 8 edge cases tested (6 fixed, 2 no regression)

[Artemis-IA]

Closing this PR as the fix has already been merged upstream in commit b1768cd ("Fixed ontology iri parsing when annotation imports same iri") by @chavez-bermudez.

The upstream fix uses the same approach as this PR:

• New ontologySubImportIRIs set to track owl:imports subjects
• addOntology(IRI, boolean) overload
• !ontologySubImportIRIs.contains(iri) condition in chooseAndSetOntologyIRI()
• TPImportsHandler calls addOntology(s, true)

The regression tests in this PR may still be useful for validation. Thank you.