Package org.semanticweb.owlapi.model

Examples of org.semanticweb.owlapi.model.OWLOntology

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public class RoundTripOboAnnotations extends RoundTripTest {

    @Test
    public void testIsInferredAnnotation() throws Exception {
        OBODoc input = parseOBOFile("is_inferred_annotation.obo");
        OWLOntology owl = convert(input);
        // check round trip
        OBODoc output = convert(owl);
        String outObo = renderOboToString(output);
        assertEquals(readResource("is_inferred_annotation.obo"), outObo);
        // check owl
        IRI t1 = IRI.create("http://purl.obolibrary.org/obo/TEST_0001");
        IRI t3 = IRI.create("http://purl.obolibrary.org/obo/TEST_0003");
        IRI isInferredIRI = IRI.create(Obo2OWLConstants.OIOVOCAB_IRI_PREFIX,
                "is_inferred");
        boolean hasAnnotation = false;
        Set<OWLSubClassOfAxiom> axioms = owl.getAxioms(AxiomType.SUBCLASS_OF);
        for (OWLSubClassOfAxiom axiom : axioms) {
            OWLClassExpression superClassCE = axiom.getSuperClass();
            OWLClassExpression subClassCE = axiom.getSubClass();
            if (!superClassCE.isAnonymous() && !subClassCE.isAnonymous()) {
                OWLClass superClass = (OWLClass) superClassCE;
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@SuppressWarnings("javadoc")
public class Obo2OwlTest extends OboFormatTestBasics {

    @Test
    public void testConvertCARO() {
        OWLOntology owlOnt = convertOBOFile("caro.obo");
        assertNotNull(owlOnt);
    }
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        assertNotNull(owlOnt);
    }

    @Test
    public void testConvertXPWithQV() {
        OWLOntology owlOnt = convertOBOFile("testqvs.obo");
        assertNotNull(owlOnt);
    }
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    }

    @Test
    public void testWriteReadConvertedOWL() throws Exception {
        OBODoc oboDoc = parseOBOFile("namespace-id-rule.obo");
        OWLOntology owlOntology = convert(oboDoc);
        OWLOntologyManager manager = owlOntology.getOWLOntologyManager();
        StringDocumentTarget documentTarget = new StringDocumentTarget();
        manager.saveOntology(owlOntology, new OWLXMLDocumentFormat(),
                documentTarget);
        String owlString = documentTarget.toString();
        OWLOntologyDocumentSource documentSource = new StringDocumentSource(
                owlString);
        OWLOntology reloadedOwl = OWLManager.createOWLOntologyManager()
                .loadOntologyFromOntologyDocument(documentSource);
        assertEquals(owlOntology.getAxiomCount(), reloadedOwl.getAxiomCount());
    }
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public class TransitiveOverTest extends RoundTripTest {

    @Test
    public void testConvert() {
        // PARSE TEST FILE, CONVERT TO OWL
        OWLOntology ontology = convert(parseOBOFile("relation_shorthand_test.obo"));
        // TEST CONTENTS OF OWL ONTOLOGY
        IRI regulatesIRI = getIriByLabel(ontology, "regulates");
        assertNotNull(regulatesIRI);
        boolean ok = false;
        // test that transitive over is translated to a property chain
        Set<OWLSubPropertyChainOfAxiom> axioms = ontology
                .getAxioms(AxiomType.SUB_PROPERTY_CHAIN_OF);
        for (OWLSubPropertyChainOfAxiom axiom : axioms) {
            OWLObjectProperty p = (OWLObjectProperty) axiom.getSuperProperty();
            if (regulatesIRI.equals(p.getIRI())) {
                List<OWLObjectPropertyExpression> chain = axiom
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    @Test
    public void testConvert() throws Exception {
        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
        String input = "Prefix(:=<http://www.example.org/#>)\nOntology(<http://example.org/>\nSubClassOf(:a :b) )";
        StringDocumentSource source = new StringDocumentSource(input);
        OWLOntology origOnt = manager.loadOntologyFromOntologyDocument(source);
        assertNotNull(origOnt);
        assertEquals(1, manager.getOntologies().size());
        assertFalse(origOnt.getOntologyID().getVersionIRI().isPresent());
        assertTrue(origOnt.getAxiomCount() > 0);
        Optional<IRI> ontologyIRI = origOnt.getOntologyID().getOntologyIRI();
        assertTrue(ontologyIRI.isPresent());
        OWLOntology newOnt = manager.getOntology(ontologyIRI.get());
        assertNotNull(newOnt);
    }
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                        "Sequential hermaphroditic organism that produces\ngametes first of the male sex, and then later of the\nfemale sex."));
        oboDocSource.addTermFrame(sourceFrame);
        // convert to OWL and retrieve def
        OWLAPIObo2Owl bridge = new OWLAPIObo2Owl(
                OWLManager.createOWLOntologyManager());
        OWLOntology owlOntology = bridge.convert(oboDocSource);
        OWLDataFactory factory = owlOntology.getOWLOntologyManager()
                .getOWLDataFactory();
        // IRI
        IRI iri = bridge.oboIdToIRI("CARO:0000049");
        OWLClass c = factory.getOWLClass(iri);
        // Def
        OWLAnnotationProperty defProperty = factory
                .getOWLAnnotationProperty(Obo2OWLVocabulary.IRI_IAO_0000115
                        .getIRI());
        int counter = 0;
        for (OWLAnnotationAssertionAxiom ax : owlOntology
                .getAnnotationAssertionAxioms(c.getIRI())) {
            if (ax.getProperty().equals(defProperty)) {
                counter++;
                assertTrue(ax.getValue() instanceof OWLLiteral);
                String owlDef = ((OWLLiteral) ax.getValue()).getLiteral();
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public class GCIQualifierTest extends OboFormatTestBasics {

    @Test
    public void testConvert() {
        // PARSE TEST FILE, CONVERT TO OWL, AND WRITE TO OWL FILE
        OWLOntology ontology = convert(parseOBOFile("gci_qualifier_test.obo"));
        Set<OWLSubClassOfAxiom> scas = ontology
                .getAxioms(AxiomType.SUBCLASS_OF);
        boolean ok = !scas.isEmpty();
        assertTrue(ok);
        // CONVERT BACK TO OBO
        OBODoc obodoc = convert(ontology);
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public class RelationShorthandTest extends OboFormatTestBasics {

    @Test
    public void testConvert() {
        // PARSE TEST FILE, CONVERT TO OWL, AND WRITE TO OWL FILE
        OWLOntology ontology = convert(parseOBOFile("relation_shorthand_test.obo"));
        // TEST CONTENTS OF OWL ONTOLOGY
        Set<OWLSubClassOfAxiom> scas = ontology
                .getAxioms(AxiomType.SUBCLASS_OF);
        boolean ok = false;
        for (OWLSubClassOfAxiom sca : scas) {
            OWLClassExpression sup = sca.getSuperClass();
            if (sup instanceof OWLObjectSomeValuesFrom) {
                OWLObjectProperty p = (OWLObjectProperty) ((OWLObjectSomeValuesFrom) sup)
                        .getProperty();
                OWLClass v = (OWLClass) ((OWLObjectSomeValuesFrom) sup)
                        .getFiller();
                if (p.getIRI().toString()
                        .equals("http://purl.obolibrary.org/obo/BFO_0000051")
                        && v.getIRI()
                                .toString()
                                .equals("http://purl.obolibrary.org/obo/GO_0004055")) {
                    ok = true;
                }
            }
        }
        assertTrue(ok);
        scas = ontology.getAxioms(AxiomType.SUBCLASS_OF);
        ok = false;
        for (OWLSubClassOfAxiom sca : scas) {
            OWLClassExpression sup = sca.getSuperClass();
            if (sup instanceof OWLObjectSomeValuesFrom) {
                OWLObjectProperty p = (OWLObjectProperty) ((OWLObjectSomeValuesFrom) sup)
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@SuppressWarnings("javadoc")
public class XPBridgeFileTest extends OboFormatTestBasics {

    @Test
    public void testConvertXPs() {
        OWLOntology owlOnt = convertOBOFile("xptest.obo");
        assertNotNull(owlOnt);
    }
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