org.apache.jena.ontology.Individual Java Examples

@SuppressWarnings({"rawtypes", "unchecked"})
private Individual addIndividual(OntModel model, Vertex v, String className) {
  OntClass ontClass = model.getOntClass(namespace + className);
  if (ontClass != null) {
    Individual individual = ontClass.createIndividual(namespace + v.id());
    Map<String, List> propertyValueMap = ElementHelper.vertexPropertyValueMap(v);
    propertyValueMap
        .entrySet()
        .forEach(
            e -> {
              Property property = model.getProperty(namespace + e.getKey());
              if (property != null) {
                e.getValue().forEach(value -> individual.addProperty(property, value.toString()));
              }
            });
    return individual;
  } else {
    getMonitor().warn("Missing ontology class {}", className);
  }
  return null;
}
 

private ObjectProperty addRelationToModel(OntModel model, Edge e) {
  Individual source = model.getIndividual(namespace + e.outVertex().id());
  Individual target = model.getIndividual(namespace + e.inVertex().id());
  ObjectProperty property = model.getObjectProperty(namespace + e.label());

  if (source != null && target != null && property != null) {
    source.addProperty(property, target);
    return property;
  } else {
    getMonitor()
        .warn(
            "Missing individuals {} or {} or relation {}",
            e.outVertex(),
            e.inVertex(),
            e.label());
    return null;
  }
}
 

@SuppressWarnings({"rawtypes", "unchecked"})
private Individual addIndividual(OntModel model, Vertex v, String className) {
  OntClass ontClass = model.getOntClass(namespace + className);
  if (ontClass != null) {
    Individual individual = ontClass.createIndividual(namespace + v.id());
    Map<String, List> propertyValueMap = ElementHelper.vertexPropertyValueMap(v);
    propertyValueMap
        .entrySet()
        .forEach(
            e -> {
              Property property = model.getProperty(namespace + e.getKey());
              if (property != null) {
                e.getValue().forEach(value -> individual.addProperty(property, value.toString()));
              }
            });
    return individual;
  } else {
    getMonitor().warn("Missing ontology class {}", className);
  }
  return null;
}
 

private void acquireIndividuals() {
  for (ExtendedIterator<Individual> it = ontModel.listIndividuals(); it.hasNext(); ) {
    Individual i = it.next();
    if (isIgnoredIndividual(i)) continue;
    individuals.add(i);
  }
}
 

/**
 * Acquire the instances and skip the ignored one
 */
private void acquireInstances() {
  for (ExtendedIterator<Individual> it = m_ontology.listIndividuals(); it.hasNext(); ) {
    Individual i = it.next();
    if (isSkipInstance(i)) continue;
    m_instances.add(i);
  }
}
 

private Individual findRO(OntModel model, URI base) {
	try (ClosableIterable<? extends OntResource> instances = iterate(ore.Aggregation
			.listInstances())) {
		for (OntResource o : instances)
			// System.out.println("Woo " + o);
			return o.asIndividual();
	}
	// Fallback - resolve as "/"
	// TODO: Ensure it's an Aggregation?
	return model.getIndividual(base.toString());
}
 

private List<Agent> getAgents(URI base, Individual in,
		ObjectProperty property) {
	List<Agent> creators = new ArrayList<>();
	for (Individual agent : listObjectProperties(in, property)) {
		Agent a = new Agent();

		// Check for any ORCIDs, note that "orcid" is mapped as
		// prov:alternateOf in our modified bundle.jsonld
		for (Individual alternate : listObjectProperties(agent, prov.alternateOf)) {
			if (alternate.isURIResource() && (
					alternate.getURI().startsWith("https://orcid.org/") ||
					alternate.getURI().startsWith("http://orcid.org/"))) {
				// TODO: Check against https://support.orcid.org/knowledgebase/articles/116780-structure-of-the-orcid-identifier
				a.setOrcid(URI.create(alternate.getURI()));
				break;
			}
		}
		if (agent.isURIResource()) {
			URI agentURI = relativizeFromBase(agent.getURI(), base);
			if ("orcid.org".equals(agentURI.getHost()) && a.getOrcid() == null) {
				a.setOrcid(agentURI);
			} else {
				a.setUri(agentURI);
			}
		}

		RDFNode name = agent.getPropertyValue(foaf.name);
		if (name != null && name.isLiteral())
			a.setName(name.asLiteral().getLexicalForm());
		creators.add(a);
	}
	return creators;
}
 

private Set<Individual> listObjectProperties(OntResource ontResource,
		ObjectProperty prop) {
	LinkedHashSet<Individual> results = new LinkedHashSet<>();
	try (ClosableIterable<RDFNode> props = iterate(ontResource
			.listPropertyValues(prop))) {
		for (RDFNode node : props) {
			if (!node.isResource() || !node.canAs(Individual.class))
				continue;
			results.add(node.as(Individual.class));
		}
	}
	return results;
}
 

private void addRevision(OntModel model,
		Revision revision) {
	OntClass VersionableResource = model.createClass("http://purl.org/wf4ever/roevo#VersionableResource");
	VersionableResource.addSuperClass(prov.Entity);
	Individual revisionResource = model.createIndividual(revision.getIdentifier().toASCIIString(), 
			VersionableResource);
	revisionResource.addRDFType(prov.Entity);
}
 

private void addPrevious(OntModel model,
		Revision revision, Revision previous) {
	OntClass VersionableResource = model.createClass("http://purl.org/wf4ever/roevo#VersionableResource");
	VersionableResource.addSuperClass(prov.Entity);
	
	Individual revisionResource = model.createIndividual(revision.getIdentifier().toASCIIString(), 
			VersionableResource);
	Individual previousResource = model.createIndividual(previous.getIdentifier().toASCIIString(), 
			VersionableResource);
	revisionResource.addProperty(prov.wasRevisionOf, previousResource);
}
 

private ObjectProperty addRelationToModel(OntModel model, Edge e) {
  Individual source = model.getIndividual(namespace + e.outVertex().id());
  Individual target = model.getIndividual(namespace + e.inVertex().id());

  ObjectProperty property = model.getObjectProperty(namespace + e.label());
  source.addProperty(property, target);

  return property;
}
 

public Set<Individual> getIndividuals() {
  return individuals;
}
 

private static final boolean isIgnoredIndividual(Individual i) {
  return i.hasProperty(RDF.type, SKOS.Concept) || i.hasProperty(RDF.type, DBkWik.Image);
}
 

/**
 * Check whether the individual should be skipped
 *
 * @param i individual
 * @return true means the individual should be ignored
 */
private static final boolean isSkipInstance(Individual i) {
  return i.hasProperty(RDF.type, SKOS.Concept) ||
         i.hasProperty(RDF.type, DBkWik.Image);
}
 

/**
 * Get the hash set of instances
 *
 * @return m_instances
 */
public Set<Individual> getInstances() {
  return m_instances;
}