Examples with OntModel org.apache.jena.ontology.OntModel used on opensource projects

Example 26 with OntModel

use of org.apache.jena.ontology.OntModel in project Vitro by vivo-project.

the class RDFFilesLoader method loadEveryTimeFiles.

/**
 * Load the "every time" files.
 *
 * The location is based on the home directory and the model path: "abox",
 * "display", etc.
 *
 * The files from the directory become a sub-model of the model.
 */
public static void loadEveryTimeFiles(String modelPath, OntModel model) {
    OntModel everytimeModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
    String home = locateHomeDirectory();
    Set<Path> paths = getPaths(home, RDF, modelPath, EVERY_TIME);
    for (Path p : paths) {
        log.info("Loading " + relativePath(p, home));
        readOntologyFileIntoModel(p, everytimeModel);
    }
    model.addSubModel(everytimeModel);
}

Example 27 with OntModel

use of org.apache.jena.ontology.OntModel in project Vitro by vivo-project.

the class UpdateKnowledgeBase method replaceTboxAndDisplayMetadata.

// replace
private void replaceTboxAndDisplayMetadata(OntModel displayModel, Model addStatements, Model removeStatements, UpdateSettings settings) {
    OntModel oldDisplayModelTboxModel = settings.getOldDisplayModelTboxModel();
    OntModel oldDisplayModelDisplayMetadataModel = settings.getOldDisplayModelDisplayMetadataModel();
    OntModel newDisplayModelTboxModel = settings.getNewDisplayModelTboxModel();
    OntModel newDisplayModelDisplayMetadataModel = settings.getNewDisplayModelDisplayMetadataModel();
    OntModel loadedAtStartup = settings.getLoadedAtStartupDisplayModel();
    OntModel oldVivoListView = settings.getVivoListViewConfigDisplayModel();
    // Remove old display model tbox and display metadata statements from display model
    removeStatements.add(oldDisplayModelTboxModel);
    removeStatements.add(oldDisplayModelDisplayMetadataModel);
    // the old startup folder only contained by oldVivoListView
    removeStatements.add(oldVivoListView);
    StringWriter sw = new StringWriter();
    try {
        log.debug("Adding old display tbox model, display metadata model, and oldVivoListView to remove statements.  Remove statements now include:");
        removeStatements.write(sw, "N3");
        log.debug(sw.toString());
        sw.close();
    } catch (Exception ex) {
        log.error("Exception occurred", ex);
    }
    // Add statements from new tbox and display metadata
    addStatements.add(newDisplayModelTboxModel);
    addStatements.add(newDisplayModelDisplayMetadataModel);
    // this should include the list view in addition to other files
    addStatements.add(loadedAtStartup);
    try {
        sw = new StringWriter();
        log.debug("Adding new display tbox model, display metadata model, and loaded at startup to add statements.  Add statements now include:");
        addStatements.write(sw, "N3");
        log.debug(sw.toString());
        sw.close();
    } catch (Exception ex) {
        log.error("Exception occurred in adding new display model tbox/metadata info to add statements ", ex);
    }
    log.debug("Adding new display tbox model, display metadata model, and all models loaded at startup");
}

Example 28 with OntModel

use of org.apache.jena.ontology.OntModel in project Vitro by vivo-project.

the class UpdateKnowledgeBase method loadModelFromFile.

// load file from file path
private OntModel loadModelFromFile(String filePath) {
    log.debug("Load model from file " + filePath);
    OntModel om = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
    File file = new File(filePath);
    if (!file.isFile()) {
        throw new ModelFileNotFoundException(filePath + " must be a file " + "containing RDF files.");
    }
    readFile(file, om, filePath);
    return om;
}

Example 29 with OntModel

use of org.apache.jena.ontology.OntModel in project Vitro by vivo-project.

the class UpdateKnowledgeBase method updateDataGetterLabels.

// update any new labels
private void updateDataGetterLabels(OntModel displayModel, Model addStatements, Model removeStatements, UpdateSettings settings) {
    log.debug("Checking: BEFORE adding any statements, what do we have for pageList page");
    Resource testResource = ResourceFactory.createResource(DisplayVocabulary.DISPLAY_NS + "pageListPage");
    StmtIterator testIt = addStatements.listStatements(testResource, null, (RDFNode) null);
    if (!testIt.hasNext()) {
        log.debug("Add statements does not have the page list page resource " + testResource.getURI());
    }
    while (testIt.hasNext()) {
        log.debug("Statement for page list resource: " + testIt.nextStatement().toString());
    }
    log.debug("Triple checking -- before this method, the add statements model contains");
    StringWriter sw = new StringWriter();
    try {
        addStatements.write(sw, "N3");
        log.debug(sw.toString());
        sw.close();
    } catch (Exception ex) {
        log.error("Error occurred in adding resource labels ", ex);
    }
    OntModel newDisplayModel = settings.getNewDisplayModelFromFile();
    List<Resource> resourcesForLabels = new ArrayList<Resource>();
    resourcesForLabels.add(ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.ClassGroupPageData"));
    resourcesForLabels.add(ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.BrowseDataGetter"));
    resourcesForLabels.add(ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.IndividualsForClassesDataGetter"));
    resourcesForLabels.add(ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.InternalClassesDataGetter"));
    resourcesForLabels.add(ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SparqlQueryDataGetter"));
    for (Resource r : resourcesForLabels) {
        log.debug("Adding the following for " + r.getURI());
        log.debug(newDisplayModel.listStatements(r, RDFS.label, (RDFNode) null).toList().toString());
        addStatements.add(newDisplayModel.listStatements(r, RDFS.label, (RDFNode) null));
        log.debug("After adding statements, we now have the following in addStatements:::");
        sw = new StringWriter();
        try {
            addStatements.write(sw, "N3");
            log.debug(sw.toString());
            sw.close();
        } catch (Exception ex) {
            log.error("Error occurred in adding resource labels ", ex);
        }
    }
    // Add statements now includes
    log.debug("AFTER all resources added, Add statements now includes ");
    sw = new StringWriter();
    try {
        addStatements.write(sw, "N3");
        log.debug(sw.toString());
        sw.close();
    } catch (Exception ex) {
        log.error("Error occurred in adding resource labels ", ex);
    }
}

Example 30 with OntModel

use of org.apache.jena.ontology.OntModel in project Vitro by vivo-project.

the class SimpleReasonerSameAsTest method mostSpecificTypeTest1.

/*
	 * test that mostSpecificType inferences propagate to sameAs
	 * individuals
	 */
@Test
public void mostSpecificTypeTest1() {
    // Create a Tbox with a simple class hierarchy. B is a subclass of A.
    OntModel tBox = createTBoxModel();
    OntClass classA = createClass(tBox, "http://test.vivo/A", "class A");
    OntClass classC = createClass(tBox, "http://test.vivo/C", "class C");
    OntClass classD = createClass(tBox, "http://test.vivo/D", "class D");
    OntClass classE = createClass(tBox, "http://test.vivo/E", "class E");
    // A is superclass of C, C is superclass of D and E
    addSubclass(classA, classC);
    addSubclass(classC, classD);
    addSubclass(classC, classE);
    // SimpleReasonerTBoxListener is not being used.
    AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
    // this will receive the abox inferences
    Model inf = ModelFactory.createDefaultModel();
    // abox
    OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
    // set up SimpleReasoner and register it with abox
    SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
    aBox.register(simpleReasoner);
    // add & remove ABox type statements and verify inferences
    Resource a = aBox.createResource("http://test.vivo/a");
    Resource b = aBox.createResource("http://test.vivo/b");
    Resource c = aBox.createResource("http://test.vivo/c");
    Resource d = aBox.createResource("http://test.vivo/d");
    // Assert a, b, c and d are the same
    aBox.add(a, OWL.sameAs, b);
    aBox.add(c, OWL.sameAs, b);
    aBox.add(d, OWL.sameAs, a);
    // Assert a is D, and d ic C
    // All resources will therefore be C and D
    aBox.add(a, RDF.type, classD);
    aBox.add(d, RDF.type, classC);
    // All resources should be inferred as C and D, except a and d which have direct assertions
    // D is asserted for a
    Assert.assertFalse(inf.contains(a, RDF.type, classD));
    Assert.assertTrue(inf.contains(a, RDF.type, classC));
    Assert.assertTrue(inf.contains(b, RDF.type, classD));
    Assert.assertTrue(inf.contains(b, RDF.type, classC));
    Assert.assertTrue(inf.contains(c, RDF.type, classD));
    Assert.assertTrue(inf.contains(c, RDF.type, classC));
    Assert.assertTrue(inf.contains(d, RDF.type, classD));
    // C is asserted for d
    Assert.assertFalse(inf.contains(d, RDF.type, classC));
    // In all cases, mostSpecificType should be D, not C
    Assert.assertTrue(inf.contains(a, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
    Assert.assertTrue(inf.contains(b, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
    Assert.assertTrue(inf.contains(c, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
    Assert.assertTrue(inf.contains(d, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
    Assert.assertFalse(inf.contains(a, mostSpecificType, ResourceFactory.createResource(classC.getURI())));
    Assert.assertFalse(inf.contains(b, mostSpecificType, ResourceFactory.createResource(classC.getURI())));
    Assert.assertFalse(inf.contains(c, mostSpecificType, ResourceFactory.createResource(classC.getURI())));
    Assert.assertFalse(inf.contains(d, mostSpecificType, ResourceFactory.createResource(classC.getURI())));
    aBox.remove(a, RDF.type, classD);
    Assert.assertFalse(inf.contains(a, RDF.type, classD));
    Assert.assertTrue(inf.contains(a, RDF.type, classC));
    Assert.assertFalse(inf.contains(b, RDF.type, classD));
    Assert.assertTrue(inf.contains(b, RDF.type, classC));
    Assert.assertFalse(inf.contains(c, RDF.type, classD));
    Assert.assertTrue(inf.contains(c, RDF.type, classC));
    Assert.assertFalse(inf.contains(d, RDF.type, classD));
    Assert.assertFalse(inf.contains(d, RDF.type, classC));
    Assert.assertTrue(inf.contains(a, mostSpecificType, ResourceFactory.createResource(classC.getURI())));
    Assert.assertTrue(inf.contains(b, mostSpecificType, ResourceFactory.createResource(classC.getURI())));
    Assert.assertTrue(inf.contains(c, mostSpecificType, ResourceFactory.createResource(classC.getURI())));
    Assert.assertTrue(inf.contains(d, mostSpecificType, ResourceFactory.createResource(classC.getURI())));
    Assert.assertFalse(inf.contains(a, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
    Assert.assertFalse(inf.contains(b, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
    Assert.assertFalse(inf.contains(c, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
    Assert.assertFalse(inf.contains(d, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
}