Annotations on DifferentIndividualsAxioms lost

[matthewhorridge]

Small test case below. Produced with 4.5.8. The axiom annotation is not saved in RDF/XML. Note, that it is saved in OWL/XML (I first thought that this was a Protege problem). Haven't tested with 5.x or later.

import org.hamcrest.MatcherAssert;
import org.hamcrest.Matchers;
import org.junit.Test;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat;
import org.semanticweb.owlapi.model.*;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.util.Collections;

import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.is;

/**
 * Matthew Horridge
 * Stanford Center for Biomedical Informatics Research
 * 2019-01-23
 */
public class DifferentIndividualsAxiom_Annotation_TestCase {

    @Test
    public void shouldSaveDifferentIndividualsAxiomWithAnnotations() throws OWLException {
        OWLOntologyManager man = OWLManager.createOWLOntologyManager();
        OWLOntology ontology = man.createOntology(IRI.create("http://stuff.com/ont"));
        OWLDataFactory dataFactory = man.getOWLDataFactory();

        OWLDifferentIndividualsAxiom ax = dataFactory.getOWLDifferentIndividualsAxiom(
                dataFactory.getOWLNamedIndividual(IRI.create("http://stuff.com/ont/a")),
                dataFactory.getOWLNamedIndividual(IRI.create("http://stuff.com/ont/b"))
        );
        OWLAnnotation anno = dataFactory.getOWLAnnotation(dataFactory.getRDFSLabel(), dataFactory.getOWLLiteral("Hello"));
        OWLAxiom annotatedAx = ax.getAnnotatedAxiom(Collections.singleton(anno));

        man.addAxiom(ontology, annotatedAx);

        ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
        man.saveOntology(ontology, new RDFXMLDocumentFormat(), byteArrayOutputStream);

        OWLOntologyManager man2 = OWLManager.createOWLOntologyManager();
        OWLOntology reloadedOntology = man2.loadOntologyFromOntologyDocument(new ByteArrayInputStream(byteArrayOutputStream.toByteArray()));

        assertThat(reloadedOntology.containsAxiom(annotatedAx), is(true));
    }
}

[ignazio1977]

Nasty one. Bug in rendering, bug in parsing, and the bug depends on how many individuals are in the axiom. Also, similar bug exists on OWLSameIndividuals.
I've fixed Different individuals for three and above for all syntaxes. Manchester syntax with two elements is still broken. Same individuals needs fixing.

[ignazio1977]

Bugs uncovered in RDF/XML and Manchester Syntax, for Different and Same individuals. Miraculously, part of the fix was deleting code. Nasty ones, 'm surprised we haven't met these before.