Examples with OWLOntologyCreationException org.semanticweb.owlapi.model.OWLOntologyCreationException used on opensource projects

Example 26 with OWLOntologyCreationException

use of org.semanticweb.owlapi.model.OWLOntologyCreationException in project stanbol by apache.

the class ConversionTester method testAxiomOwlToJenaResource.

public void testAxiomOwlToJenaResource() {
    JenaToOwlConvert j2o = new JenaToOwlConvert();
    OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();
    OWLOntology ont = null;
    try {
        ont = mgr.createOntology();
    } catch (OWLOntologyCreationException e) {
        e.printStackTrace();
        fail("Can not create ontology");
    }
    OWLDataFactory factory = mgr.getOWLDataFactory();
    StmtIterator resource = null;
    OWLClass cls = factory.getOWLClass(IRI.create(CLAZZ));
    OWLDataProperty dp = factory.getOWLDataProperty(IRI.create(DP));
    OWLObjectProperty op = factory.getOWLObjectProperty(IRI.create(OP));
    OWLAnnotationProperty oa = factory.getOWLAnnotationProperty(IRI.create(label));
    OWLAnnotation oav = factory.getOWLAnnotation(oa, factory.getOWLStringLiteral(clazzlabel, "en"));
    OWLDatatype dt = factory.getOWLDatatype(IRI.create(DATATYPE));
    OWLNamedIndividual sub = factory.getOWLNamedIndividual(IRI.create(SUBJECT));
    OWLNamedIndividual obj = factory.getOWLNamedIndividual(IRI.create(OBJECT));
    OWLLiteral literal1 = factory.getOWLTypedLiteral(VALUE, dt);
    // Classe
    OWLDeclarationAxiom daxiomcls = factory.getOWLDeclarationAxiom(cls);
    // obj prop
    OWLDeclarationAxiom daxiomop = factory.getOWLDeclarationAxiom(op);
    // data prop
    OWLDeclarationAxiom daxiomdp = factory.getOWLDeclarationAxiom(dp);
    // subject
    OWLDeclarationAxiom daxiomsub = factory.getOWLDeclarationAxiom(sub);
    // object
    OWLDeclarationAxiom daxiomobj = factory.getOWLDeclarationAxiom(obj);
    // Istanza
    OWLClassAssertionAxiom axiomsub = factory.getOWLClassAssertionAxiom(cls, sub);
    // Istanza
    OWLClassAssertionAxiom axiomobj = factory.getOWLClassAssertionAxiom(cls, obj);
    // Obj
    OWLObjectPropertyAssertionAxiom axiomop = factory.getOWLObjectPropertyAssertionAxiom(op, sub, obj);
    // prop
    // tra
    // individui
    OWLDataPropertyAssertionAxiom axiomvalue = factory.getOWLDataPropertyAssertionAxiom(dp, obj, // Dataprop all'istanza;
    literal1);
    // Annotazione
    OWLAnnotationAssertionAxiom axioman = factory.getOWLAnnotationAssertionAxiom(cls.getIRI(), oav);
    mgr.addAxiom(ont, daxiomcls);
    mgr.addAxiom(ont, daxiomop);
    mgr.addAxiom(ont, daxiomdp);
    mgr.addAxiom(ont, daxiomsub);
    mgr.addAxiom(ont, daxiomobj);
    mgr.addAxiom(ont, axiomsub);
    mgr.addAxiom(ont, axiomobj);
    mgr.addAxiom(ont, axiomop);
    mgr.addAxiom(ont, axiomvalue);
    mgr.addAxiom(ont, axioman);
    Set<OWLAxiom> setaxiom = ont.getAxioms();
    try {
        resource = j2o.AxiomOwlToJenaResource(setaxiom, RDFXML);
        if (resource == null) {
            fail("Some errors occur");
        } else {
            String statment = "[http://www.w3.org/2000/01/rdf-schema#label, http://www.w3.org/2000/01/rdf-schema#range, http://www.w3.org/2000/01/rdf-schema#Literal] " + "[http://example.org/dummy#hasAge, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#DatatypeProperty] " + "[http://example.org/dummy#Linus, http://example.org/dummy#hasAge, \"8\"^^http://www.w3.org/2001/XMLSchema#int] " + "[http://example.org/dummy#Linus, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://example.org/dummy#Peanut] " + "[http://example.org/dummy#hasSibling, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#ObjectProperty] " + "[http://example.org/dummy#Lucy, http://example.org/dummy#hasSibling, http://example.org/dummy#Linus] " + "[http://example.org/dummy#Lucy, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://example.org/dummy#Peanut] " + "[http://www.w3.org/2000/01/rdf-schema#label, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#AnnotationProperty] " + "[http://example.org/dummy#Peanut, http://www.w3.org/2000/01/rdf-schema#label, \"Peanut\"@en] " + "[http://example.org/dummy#Peanut, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class]";
            int size = setaxiom.size();
            int count = 0;
            while (resource.hasNext()) {
                Statement stm = resource.nextStatement();
                Resource jsubj = stm.getSubject();
                if (jsubj.getURI().equals(OP.toString()) || jsubj.getURI().equals(DP.toString()) || jsubj.getURI().equals(CLAZZ.toString()) || jsubj.getURI().equals(OBJECT.toString()) || jsubj.getURI().equals(SUBJECT.toString()) || jsubj.getURI().equals(label.toString()))
                    if (statment.contains(stm.toString()))
                        count++;
            }
            assertEquals(size, count);
        }
    } catch (Exception e) {
        e.printStackTrace();
        fail("Exception caugth");
    } finally {
        assertNotNull(resource);
    }
}

Example 27 with OWLOntologyCreationException

use of org.semanticweb.owlapi.model.OWLOntologyCreationException in project goci by EBISPOT.

the class ReasonedOntologyLoader method indexOntology.

protected OWLOntology indexOntology(OWLOntology ontology) throws OWLOntologyCreationException {
    getLog().debug("Trying to create a reasoner over ontology '" + getOntologyURI() + "'");
    OWLReasonerFactory factory = new Reasoner.ReasonerFactory();
    ReasonerProgressMonitor progressMonitor = new LoggingReasonerProgressMonitor(getLog());
    OWLReasonerConfiguration config = new SimpleConfiguration(progressMonitor);
    this.reasoner = factory.createReasoner(ontology, config);
    getLog().debug("Precomputing inferences...");
    reasoner.precomputeInferences();
    getLog().debug("Checking ontology consistency...");
    reasoner.isConsistent();
    getLog().debug("Checking for unsatisfiable classes...");
    if (reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size() > 0) {
        throw new OWLOntologyCreationException("Once classified, unsatisfiable classes were detected in '" + getOntologyIRI() + "'");
    } else {
        getLog().debug("Reasoning complete! ");
    }
    Set<OWLClass> allClasses = ontology.getClassesInSignature();
    removeExcludedClasses(ontology, allClasses, superclass -> reasoner.getSubClasses(superclass, false).getFlattened());
    int labelCount = 0;
    int labelledClassCount = 0;
    int synonymCount = 0;
    int synonymedClassCount = 0;
    getLog().debug("Loading " + allClasses.size() + " classes...");
    for (OWLClass ontologyClass : allClasses) {
        IRI clsIri = ontologyClass.getIRI();
        // get IRI fragment/path
        Optional<String> accession = evaluateAccessionValue(ontology, ontologyClass);
        if (accession.isPresent()) {
            addClassAccession(clsIri, accession.get());
        }
        // get label annotations
        Optional<String> label = evaluateLabelAnnotationValue(ontology, ontologyClass);
        if (label.isPresent()) {
            addClassLabel(clsIri, label.get());
            labelledClassCount++;
            labelCount++;
        }
        // get all synonym annotations
        getLog().trace("Loading synonyms of " + clsIri.toString() + "...");
        Set<String> synonyms = evaluateSynonymAnnotationValues(ontology, ontologyClass);
        if (!synonyms.isEmpty()) {
            addSynonyms(clsIri, synonyms);
            synonymCount += synonyms.size();
            synonymedClassCount++;
        }
        // get parent labels
        getLog().trace("Loading parents of " + clsIri.toString() + "...");
        Set<OWLClass> parents = reasoner.getSuperClasses(ontologyClass, false).getFlattened();
        // only add type if the parent isn't excluded
        Set<String> parentLabelSet = parents.stream().filter(allClasses::contains).peek(parent -> getLog().trace("Next parent of " + label + ": " + parent)).map(parent -> evaluateLabelAnnotationValue(ontology, parent)).filter(Optional::isPresent).map(Optional::get).collect(Collectors.toSet());
        // always also add current class to the parents
        label.ifPresent(parentLabelSet::add);
        addClassParentLabels(clsIri, parentLabelSet);
        // get child labels
        getLog().trace("Loading children of " + clsIri.toString() + "...");
        Set<OWLClass> children = reasoner.getSubClasses(ontologyClass, false).getFlattened();
        // only add type if the child isn't excluded
        Set<String> childLabelSet = children.stream().filter(allClasses::contains).peek(child -> getLog().trace("Next child of " + label + ": " + child)).map(child -> evaluateLabelAnnotationValue(ontology, child)).filter(Optional::isPresent).map(Optional::get).collect(Collectors.toSet());
        // always also add current class to the parents
        label.ifPresent(childLabelSet::add);
        addClassChildLabels(clsIri, childLabelSet);
    }
    getLog().debug("Successfully indexed " + labelCount + " labels on " + labelledClassCount + " classes and " + synonymCount + " synonyms on " + synonymedClassCount + " classes!");
    return ontology;
}

Example 28 with OWLOntologyCreationException

use of org.semanticweb.owlapi.model.OWLOntologyCreationException in project stanbol by apache.

the class ConversionTester method testEntityOwlToJenaResource.

public void testEntityOwlToJenaResource() {
    JenaToOwlConvert j2o = new JenaToOwlConvert();
    OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();
    OWLOntology ont = null;
    StmtIterator resource = null;
    try {
        ont = mgr.createOntology();
    } catch (OWLOntologyCreationException e) {
        e.printStackTrace();
        fail("Could not load ontology");
    }
    OWLDataFactory factory = mgr.getOWLDataFactory();
    OWLClass cls = factory.getOWLClass(IRI.create(CLAZZ));
    OWLDataProperty dp = factory.getOWLDataProperty(IRI.create(DP));
    OWLObjectProperty op = factory.getOWLObjectProperty(IRI.create(OP));
    OWLAnnotationProperty oa = factory.getOWLAnnotationProperty(IRI.create(label));
    OWLAnnotation oav = factory.getOWLAnnotation(oa, factory.getOWLStringLiteral(clazzlabel, "en"));
    OWLDatatype dt = factory.getOWLDatatype(IRI.create(DATATYPE));
    OWLNamedIndividual sub = factory.getOWLNamedIndividual(IRI.create(SUBJECT));
    OWLNamedIndividual obj = factory.getOWLNamedIndividual(IRI.create(OBJECT));
    OWLLiteral literal1 = factory.getOWLTypedLiteral(VALUE, dt);
    // Classe
    OWLDeclarationAxiom daxiomcls = factory.getOWLDeclarationAxiom(cls);
    // obj prop
    OWLDeclarationAxiom daxiomop = factory.getOWLDeclarationAxiom(op);
    // data prop
    OWLDeclarationAxiom daxiomdp = factory.getOWLDeclarationAxiom(dp);
    // subject
    OWLDeclarationAxiom daxiomsub = factory.getOWLDeclarationAxiom(sub);
    // object
    OWLDeclarationAxiom daxiomobj = factory.getOWLDeclarationAxiom(obj);
    // Istanza
    OWLClassAssertionAxiom axiomsub = factory.getOWLClassAssertionAxiom(cls, sub);
    // Istanza
    OWLClassAssertionAxiom axiomobj = factory.getOWLClassAssertionAxiom(cls, obj);
    // Obj
    OWLObjectPropertyAssertionAxiom axiomop = factory.getOWLObjectPropertyAssertionAxiom(op, sub, obj);
    // prop
    // tra
    // individui
    OWLDataPropertyAssertionAxiom axiomvalue = factory.getOWLDataPropertyAssertionAxiom(dp, sub, // Dataprop all'istanza;
    literal1);
    // Annotazione
    OWLAnnotationAssertionAxiom axioman = factory.getOWLAnnotationAssertionAxiom(cls.getIRI(), oav);
    mgr.addAxiom(ont, daxiomcls);
    mgr.addAxiom(ont, daxiomop);
    mgr.addAxiom(ont, daxiomdp);
    mgr.addAxiom(ont, daxiomsub);
    mgr.addAxiom(ont, daxiomobj);
    mgr.addAxiom(ont, axiomsub);
    mgr.addAxiom(ont, axiomobj);
    mgr.addAxiom(ont, axiomop);
    mgr.addAxiom(ont, axiomvalue);
    mgr.addAxiom(ont, axioman);
    Set<OWLIndividualAxiom> ind = ont.getAxioms(sub);
    try {
        resource = j2o.EntityOwlToJenaResource(daxiomsub.getEntity(), ont, RDFXML);
        if (resource == null) {
            fail("Some errors accour");
        } else {
            int cont = 0;
            while (resource.hasNext()) {
                Statement stm = resource.nextStatement();
                IRI subres = IRI.create(stm.getSubject().getURI());
                if (("<" + subres + ">").equals(daxiomsub.getEntity().toString()))
                    cont++;
            }
            assertEquals(ind.size(), (cont - 1));
        }
    } catch (Exception e) {
        e.printStackTrace();
        fail("Exception caugth");
    } finally {
        assertNotNull(resource);
    }
}

Example 29 with OWLOntologyCreationException

use of org.semanticweb.owlapi.model.OWLOntologyCreationException in project stanbol by apache.

the class ConversionTester method testModelOwlToJenaConvert.

public void testModelOwlToJenaConvert() {
    JenaToOwlConvert j2o = new JenaToOwlConvert();
    OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();
    OWLOntologyManager mgrf = OWLManager.createOWLOntologyManager();
    OWLDataFactory factory = mgrf.getOWLDataFactory();
    String dul = "http://www.loa-cnr.it/ontologies/DUL.owl";
    OWLOntology owl = null;
    OntModel jena = null;
    try {
        owl = mgr.loadOntologyFromOntologyDocument(IRI.create(dul));
    } catch (OWLOntologyCreationException e) {
        e.printStackTrace();
        fail("Could not load ontology");
    }
    try {
        jena = j2o.ModelOwlToJenaConvert(owl, "RDF/XML");
        if (jena == null) {
            fail("Some errors occur");
        } else {
            ExtendedIterator<OntClass> jenaclass = jena.listNamedClasses();
            int jenaclassset = jenaclass.toSet().size();
            jenaclass = jena.listNamedClasses();
            Set<OWLClass> owlclass = owl.getClassesInSignature();
            int countclass = 0;
            while (jenaclass.hasNext()) if (owlclass.contains(factory.getOWLClass(IRI.create(jenaclass.next().getURI()))))
                countclass++;
            if (countclass == jenaclassset)
                assertEquals(countclass, jenaclassset);
            else
                fail("Error in number of classes");
            ExtendedIterator<ObjectProperty> jenaprop = jena.listObjectProperties();
            int jenapropset = jenaprop.toSet().size();
            jenaprop = jena.listObjectProperties();
            Set<OWLObjectProperty> owlprop = owl.getObjectPropertiesInSignature();
            int countprop = 0;
            while (jenaprop.hasNext()) if (owlprop.contains(factory.getOWLObjectProperty(IRI.create(jenaprop.next().getURI()))))
                countprop++;
            if (countprop == jenapropset)
                assertEquals(countprop, jenapropset);
            else
                fail("Error in number of object properties");
            ExtendedIterator<DatatypeProperty> jenadata = jena.listDatatypeProperties();
            int jenadataset = jenadata.toSet().size();
            jenadata = jena.listDatatypeProperties();
            Set<OWLDataProperty> owldata = owl.getDataPropertiesInSignature();
            int countdata = 0;
            while (jenadata.hasNext()) if (owldata.contains(factory.getOWLDataProperty(IRI.create(jenadata.next().getURI()))))
                countdata++;
            if (countdata == jenadataset)
                assertEquals(countdata, jenadataset);
            else
                fail("Error in number of data properties");
        }
    } catch (Exception e) {
        e.printStackTrace();
        fail("Exception caugth");
    } finally {
        assertNotNull(jena);
    }
}

Example 30 with OWLOntologyCreationException

use of org.semanticweb.owlapi.model.OWLOntologyCreationException in project stanbol by apache.

the class JenaToOwlConvert method DataPropOwlToJena.

// //////////////////////////////////////////////////////////////////////////////
/**
     * This function converts a single OWLDataProperty of OWL to DatatypeProperty of Jena
     * 
     * @param data
     *            {An OWLDataProperty object}
     * @param format
     *            {RDF/XML or TURTLE}
     * @return {A DatatypeProperty object}
     */
public synchronized DatatypeProperty DataPropOwlToJena(OWLDataProperty data, String format) {
    while (available == false) {
        try {
            wait();
        } catch (InterruptedException e) {
            System.err.println("DataPropOwlToJena::: " + e);
        }
    }
    available = false;
    try {
        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
        OWLOntology ontology = manager.createOntology(IRI.create("http://www.semanticweb.org/owlapi/ontologies/ontology"));
        OWLDataFactory factory = manager.getOWLDataFactory();
        OWLDeclarationAxiom declarationAxiom = factory.getOWLDeclarationAxiom(data);
        manager.addAxiom(ontology, declarationAxiom);
        OntModel jenamodel = ModelOwlToJenaConvert(ontology, format);
        available = true;
        notifyAll();
        return jenamodel.getDatatypeProperty(data.getIRI().toString());
    } catch (OWLOntologyCreationException eoc) {
        System.err.print("DataPropOwlToJena::: ");
        eoc.printStackTrace();
        return null;
    }
}