org.apache.jena.rdf.model.ResIterator Java Examples

private void acquireInstances() {
  // XXX: remove instances of DBkWik:Image and SKOS:Concept, Template. Under consideration.
  ResIterator it = null;

  if (m_inferred) {
    it = m_inferred_model.listSubjects();
  } else {
    it = m_raw_model.listSubjects();
  }

  while (it.hasNext()) {
    Resource r = it.nextResource();
    if (DBkWik.ownAsResource(r) && !DBkWik.ownAsTemplate(r) &&
        !r.hasProperty(RDF.type, SKOS.Concept) &&
        !r.hasProperty(RDF.type, DBkWik.Image)) {
      m_instances.add(r);
    }
  }
}
 

protected Set<Resource> getClasses(Model readModel) {
    ResIterator iterator = readModel.listSubjectsWithProperty(RDF.type, RDFS.Class);
    Resource r;
    Set<Resource> classes = new HashSet<Resource>();
    while (iterator.hasNext()) {
        r = iterator.next();
        if (!r.isAnon()) {
            classes.add(r);
        }
    }
    iterator = readModel.listSubjectsWithProperty(RDF.type, OWL.Class);
    while (iterator.hasNext()) {
        r = iterator.next();
        if (!r.isAnon()) {
            classes.add(r);
        }
    }
    return classes;
}
 

@Override
public Model process(Model model)
{
    if (getRequest().getMethod().equalsIgnoreCase("POST"))
    {
        ResIterator it = model.listSubjects();
        try
        {
            while (it.hasNext())
            {
                Resource resource = it.next();
                process(resource);
            }
        }
        finally
        {
            it.close();
        }
    
        return skolemize(getOntology(), getUriInfo().getBaseUriBuilder(), getUriInfo().getAbsolutePathBuilder(),
                super.process(model));
    }
    
    return super.process(model);
}
 

public Model process(Model model)
    {
//        if (getRequest().getMethod().equalsIgnoreCase("POST"))
//        {
            ResIterator it = model.listSubjects();
            try
            {
                while (it.hasNext())
                {
                    Resource resource = it.next();
                    process(resource);
                }
            }
            finally
            {
                it.close();
            }
        
            return skolemize(getOntology(), getUriInfo().getBaseUriBuilder(), getUriInfo().getAbsolutePathBuilder(), model);
//        }
//        
//        return model;
    }
 

private List<VCard> parseAddressBook(Resource selfResource, SolidUtilities utilities)
    throws IOException {

  String peopleUri = selfResource.getProperty(NAME_EMAIL_INDEX_PROPERTY).getResource().getURI();
  Model peopleModel = utilities.getModel(peopleUri);
  List<VCard> vcards = new ArrayList<>();
  ResIterator subjects = peopleModel.listSubjects();
  while (subjects.hasNext()) {
    Resource subject = subjects.nextResource();
    Model personModel = utilities.getModel(subject.getURI());
    Resource personResource = SolidUtilities.getResource(subject.getURI(), personModel);
    if (personResource == null) {
      throw new IllegalStateException(subject.getURI() + " not found in " + subject.toString());
    }
    vcards.add(parsePerson(personResource));
  }
  return vcards;
}
 

public RmlMappingDocument fromRdf(Model data, Function<RdfResource, Optional<DataSource>> dataSourceFactory) {
  ResIterator tripleMaps = data.listSubjectsWithProperty(data.createProperty(NS_RR + "subjectMap"));
  MappingDocumentBuilder resultBuilder = rmlMappingDocument();
  try {
    while (tripleMaps.hasNext()) {
      Resource resource = tripleMaps.nextResource();
      buildTripleMap(JenaResource.fromModel(data, resource), resultBuilder.withTripleMap(resource.getURI()));
    }
  } finally {
    tripleMaps.close();
  }
  return resultBuilder.build(dataSourceFactory);
}
 

private Set<Resource> acquireResources(ResIterator it) {
  Set<Resource> resources = new HashSet<>();
  while (it.hasNext()) {
    Resource r = it.nextResource();
    resources.add(r);
  }
  return resources;
}
 

@Test
public void initializeModel() {
    String testSubject = "http://www.example.org/test/subject";
    Map<String, String> params = new HashMap<String, String>();
    params.put("iut", testSubject);
    params.put("uuid", UUID.randomUUID().toString());
    when(xmlSuite.getAllParameters()).thenReturn(params);
    EarlReporter iut = new EarlReporter();
    Model model = iut.initializeModel(suite);
    assertNotNull(model);
    ResIterator itr = model.listSubjectsWithProperty(RDF.type, EARL.TestSubject);
    assertEquals("Unexpected URI for earl:TestSubject", testSubject, itr.next().getURI());
}
 

private void doConversion(Model model) throws JenaException {
  StatementHandler totm = new ToTMStatementHandler();
  AResourceWrapper subjw = new AResourceWrapper();
  AResourceWrapper propw = new AResourceWrapper();
  AResourceWrapper objtw = new AResourceWrapper();
  ALiteralWrapper litlw = new ALiteralWrapper();

  ResIterator it = model.listSubjects();
  while (it.hasNext()) {
    Resource subject = (Resource) it.next();

    StmtIterator it2 = subject.listProperties(); // get all statements
    while (it2.hasNext()) {
      Statement stmt = (Statement) it2.next();

      subjw.resource = stmt.getSubject();
      propw.resource = stmt.getPredicate();

      RDFNode obj = stmt.getObject();
      if (obj instanceof Resource) {
        objtw.resource = (Resource) obj;
        totm.statement(subjw, propw, objtw);
      } else {
        litlw.literal = (Literal) obj;
        totm.statement(subjw, propw, litlw);
      }
    }
  }
}
 

@Override
public Response toResponse(ConstraintViolationException ex)
{
    Resource exception = toResource(ex, Response.Status.BAD_REQUEST,
        ResourceFactory.createResource("http://www.w3.org/2011/http-statusCodes#BadRequest"));
    ex.getModel().add(exception.getModel());
    
    SPINConstraints.addConstraintViolationsRDF(ex.getConstraintViolations(), ex.getModel(), true);
    ResIterator it = ex.getModel().listSubjectsWithProperty(RDF.type, SPIN.ConstraintViolation);
    try
    {
        while (it.hasNext())
        {
            Resource violation = it.next();
            // connect Response to ConstraintViolations
            ex.getModel().add(exception, ResourceFactory.createProperty("http://www.w3.org/ns/prov#wasDerivedFrom"), violation);
        }
    }
    finally
    {
        it.close();
    }
    
    return getResponseBuilder(DatasetFactory.create(ex.getModel())).
            status(Response.Status.BAD_REQUEST).
            build();
}
 

public Model build(Model model)
{
    if (model == null) throw new IllegalArgumentException("Model cannot be null");

    Map<Resource, String> resourceURIMap = new HashMap<>();
    ResIterator resIt = model.listSubjects();
    try
    {
        while (resIt.hasNext())
        {
            Resource resource = resIt.next();
            if (resource.isAnon())
            {
                URI uri = build(resource);
                if (uri != null) resourceURIMap.put(resource, uri.toString());
            }
        }
    }
    finally
    {
        resIt.close();
    }
    
    Iterator<Map.Entry<Resource, String>> entryIt = resourceURIMap.entrySet().iterator();
    while (entryIt.hasNext())
    {
        Map.Entry<Resource, String> entry = entryIt.next();
        ResourceUtils.renameResource(entry.getKey(), entry.getValue());
    }

    return model;
}
 

List<RDFNode> getSubjectsOfObjectProperty(String predicateURI, String objectURI) {

        ResIterator iterator = this.model.listSubjectsWithProperty(getPropertyFromUri(predicateURI), getResourceFromUri(objectURI));
        List<RDFNode> nodeList = new ArrayList<>();
        iterator.forEachRemaining(nodeList::add);
        return nodeList;
    }
 

private Set<String> findRootIdentifiers(Model model, TypeConfig targetName) {

        Set<String> identifiers = new HashSet<>();
        Model currentmodel = ModelFactory.createDefaultModel();
        Resource res = currentmodel.createResource(targetName.getId());
        Property property = currentmodel.createProperty(RDF_TYPE);

        ResIterator iterator = model.listResourcesWithProperty(property, res);

        while (iterator.hasNext()) {
            identifiers.add(iterator.nextResource().toString());
        }
        return identifiers;
    }
 

List<RDFNode> getSubjectsOfObjectProperty(String predicateURI, String objectURI) {

        ResIterator iterator = this.model.listSubjectsWithProperty(getPropertyFromUri(predicateURI), getResourceFromUri(objectURI));
        List<RDFNode> nodeList = new ArrayList<>();
        iterator.forEachRemaining(nodeList::add);
        return nodeList;
    }
 

private Set<String> findRootIdentifiers(Model model, TypeConfig targetName) {

        Set<String> identifiers = new HashSet<>();
        Model currentmodel = ModelFactory.createDefaultModel();
        Resource res = currentmodel.createResource(targetName.getId());
        Property property = currentmodel.createProperty(RDF_TYPE);

        ResIterator iterator = model.listResourcesWithProperty(property, res);

        while (iterator.hasNext()) {
            identifiers.add(iterator.nextResource().toString());
        }
        return identifiers;
    }
 

/**
 * Acquire the categories
 */
private void acquireCategories() {
  for (ResIterator it = m_ontology.listResourcesWithProperty(RDF.type, SKOS.Concept); it.hasNext(); ) {
    Resource c = it.nextResource();
    m_categories.add(c);
  }
}
 

private void acquireCategories() {
  for (ResIterator it = ontModel.listResourcesWithProperty(RDF.type, SKOS.Concept); it.hasNext(); ) {
    Resource r = it.nextResource();
    if (isIgnoredCategory(r)) continue;
    categories.add(r);
  }
}
 

private void acquireClasses() {
  ResIterator it = null;

  if (m_inferred) {
    it = m_inferred_model.listResourcesWithProperty(RDF.type, OWL.Class);
  } else {
    it = m_raw_model.listResourcesWithProperty(RDF.type, OWL.Class);
  }

  m_classes = acquireResources(it);
}
 

private void acquireProperties() {
  ResIterator it = null;

  if (m_inferred) {
    it = m_inferred_model.listResourcesWithProperty(RDF.type, RDF.Property);
  } else {
    it = m_raw_model.listResourcesWithProperty(RDF.type, RDF.Property);
  }

  m_properties = acquireResources(it);
}
 

public SortedSet<ClassPrecedence> match(Ontology ontology, Resource resource, Property property, int level)
{
    if (ontology == null) throw new IllegalArgumentException("Ontology cannot be null");
    if (resource == null) throw new IllegalArgumentException("Resource cannot be null");
    if (property == null) throw new IllegalArgumentException("Property cannot be null");

    SortedSet<ClassPrecedence> matchedClasses = new TreeSet<>();
    ResIterator it = ontology.getOntModel().listResourcesWithProperty(LDT.path);
    try
    {
        while (it.hasNext())
        {
            Resource ontClassRes = it.next();
            OntClass ontClass = ontology.getOntModel().getOntResource(ontClassRes).asClass();
            // only match templates defined in this ontology - maybe reverse loops?
            if (ontClass.getIsDefinedBy() != null && ontClass.getIsDefinedBy().equals(ontology) &&
                    resource.hasProperty(property, ontClass))
            {
                ClassPrecedence precedence = new ClassPrecedence(ontClass, level * -1);
                if (log.isTraceEnabled()) log.trace("Resource {} matched OntClass {}", resource, ontClass);
                matchedClasses.add(precedence);
            } 
        }
    }
    finally
    {
        it.close();
    }

    ExtendedIterator<OntResource> imports = ontology.listImports();
    try
    {
        while (imports.hasNext())
        {
            OntResource importRes = imports.next();
            if (importRes.canAs(Ontology.class))
            {
                Ontology importedOntology = importRes.asOntology();
                // traverse imports recursively
                Set<ClassPrecedence> matchedImportClasses = match(importedOntology, resource, property, level + 1);
                matchedClasses.addAll(matchedImportClasses);
            }
        }
    }
    finally
    {
        imports.close();
    }
    
    return matchedClasses;
}
 

/**
 * Workaround for TAVERNA-71 to find annotations in WorkflowBundle
 * <p>
 * FIXME: The annotation links should instead be stored in the 
 * {@link Manifest} using taverna-robundle - see TAVERNA-71
 * 
 * @param wb
 * @throws IOException
 */
private void parseAnnotations(final WorkflowBundle wb) throws IOException {
	if (! wb.getAnnotations().isEmpty()) {
		// Assume already parsed
		return;
	}
	URITools uriTools = new URITools();		
	for (ResourceEntry resource : wb.getResources().listResources("annotation").values()) {
		Lang lang = RDFLanguages.contentTypeToLang(resource.getMediaType());
		if (lang == null) {
			// Not a semantic annotation
			continue;
		}
		//System.out.println(resource.getPath());
		//System.out.println(resource.getMediaType());
		Annotation ann = new Annotation();
		// Hackish way to generate a name from the annotation filename
		// as these typically are UUIDs
		String name = resource.getPath().replace("annotation/", "").replaceAll("\\..*", ""); // strip extension
		ann.setName(name);
		ann.setParent(wb);
		
		String path = resource.getPath();
		ann.setBody(URI.create("/" + path));		
		URI base = wb.getGlobalBaseURI().resolve(path);
		Model model = ModelFactory.createDefaultModel();			
		InputStream inputStream = resource.getUcfPackage().getResourceAsInputStream(path);
		if (inputStream == null) {
			// Not found!
			continue;
		}
		RDFDataMgr.read(model, inputStream, 
				base.toASCIIString(), lang);
		ResIterator subjs = model.listSubjects();			
		while (subjs.hasNext()) { 
			Resource r = subjs.next();
			//System.out.println(r);
			WorkflowBean b = uriTools.resolveUri(URI.create(r.getURI()), wb);
			//System.out.println(b);
			if (b != null) {
				ann.setTarget(b);
			}
			break;
		}
	}
}