Java Code Examples for org.semanticweb.owlapi.model.OWLOntologyID#getOntologyIRI()

/**
 * .
 */
public static OntologyId mobiOntologyId(OWLOntologyID owlId) {
    if (owlId == null) {
        return null;
    }
    Optional<org.semanticweb.owlapi.model.IRI> ontologyIRI = owlId.getOntologyIRI();
    Optional<org.semanticweb.owlapi.model.IRI> versionIRI = owlId.getVersionIRI();
    if (versionIRI.isPresent()) {
        return new SimpleOntologyId.Builder(factory).ontologyIRI(mobiIRI(ontologyIRI.get()))
            .versionIRI(mobiIRI(versionIRI.get())).build();
    } else if (ontologyIRI.isPresent()) {
        return new SimpleOntologyId.Builder(factory).ontologyIRI(mobiIRI(ontologyIRI.get())).build();
    } else {
        return new SimpleOntologyId.Builder(factory).build();
    }
}
 

@Override
public Void visit(OWLOntology ontology) {
  this.ontology = Optional.of(ontology);
  this.definingOntology = OwlApiUtils.getIri(ontology);
  Long versionNodeID = null;
  Long ontologyNodeID = null;
  OWLOntologyID id = ontology.getOntologyID();
  if (null == id.getOntologyIRI()) {
    logger.fine("Ignoring null ontology ID for " + ontology.toString());
  } else {
    ontologyNodeID = getOrCreateNode(id.getOntologyIRI().toString(), OwlLabels.OWL_ONTOLOGY);
  }
  if (null != id.getVersionIRI()){
    versionNodeID = getOrCreateNode(id.getVersionIRI().toString(), OwlLabels.OWL_ONTOLOGY);
  }
  if (null != ontologyNodeID && null != versionNodeID) {
    graph.createRelationship(ontologyNodeID, versionNodeID, OwlRelationships.OWL_VERSION_IRI);
  }
  return null;
}
 

private void appendOntologyId(OWLOntologyID ontologyID, StringBuilder sb) {
	Optional<IRI> ontologyIRI = ontologyID.getOntologyIRI();
	if (ontologyIRI.isPresent()) {
		sb.append("Ontology(id=").append(ontologyIRI.get());
		Optional<IRI> versionIRI = ontologyID.getVersionIRI();
		if (versionIRI .isPresent()) {
			sb.append(", version=").append(versionIRI.get());
		}
		sb.append(")");
		
	}
	else {
		sb.append("Ontology with no ID");
	}
}
 

/**
 * Create an instance for the given graph and reasoner.
 * 
 * @param graph
 * @param reasoner
 * @param disposeReasoner set to true, if the reasoner should also be disposed
 * @throws UnknownOWLOntologyException
 * @throws OWLOntologyCreationException
 * 
 * @see #dispose()
 */
public EcoTools (OWLGraphWrapper graph, OWLReasoner reasoner, boolean disposeReasoner) throws UnknownOWLOntologyException, OWLOntologyCreationException {

	// This has bitten me, so let's try and bew specific...
	if( reasoner == null ){ throw new Error("No reasoner was specified for use with the EcoTools. Add a reasoner for the command line"); }
	
	// assume the graph wrapper is more than eco
	// try to find ECO by its purl
	Set<OWLOntology> allOntologies = graph.getAllOntologies();
	OWLOntology eco = null;
	for (OWLOntology owlOntology : allOntologies) {
		OWLOntologyID id = owlOntology.getOntologyID();
		Optional<IRI> ontologyIRI = id.getOntologyIRI();
		if (ontologyIRI.isPresent()) {
			if (ECO_PURL.equals(ontologyIRI.get().toString())) {
				eco = owlOntology;
			}
		}
	}
	if (eco != null) {
		// found eco create new wrapper
		this.eco = new OWLGraphWrapper(eco);
	}
	else {
		// did not find eco, use whole wrapper
		this.eco = graph;
	}
	
	this.reasoner = reasoner;
	this.disposeReasonerP = disposeReasoner;
}
 

/**
 * Create a {@link TraversingEcoMapper} instance using the given
 * {@link OWLGraphWrapper}. It is assumed that ECO can be retrieved from the
 * graph using its default IRI. The mappings are retrieved using the PURL.
 * <p>
 * Uses the given reasoner in the traversal methods. If disposeReasoner is
 * set to true, dispose also the reasoner, while calling
 * {@link TraversingEcoMapper#dispose()}.
 * 
 * @param all
 *            graph containing all ontologies, including ECO
 * @param reasoner
 *            reasoner capable of traversing ECO
 * @param disposeReasoner
 *            set to true if the reasoner should be disposed, when calling
 *            {@link TraversingEcoMapper#dispose()}
 * @return mapper
 * @throws IOException
 * @throws OWLException
 * @throws IllegalArgumentException
 *             throw when the reasoner is null, or the
 *             {@link OWLGraphWrapper} does not contain ECO.
 * 
 * @see EcoMapper#ECO_PURL_IRI
 * @see EcoMapper#ECO_MAPPING_PURL
 */
public static TraversingEcoMapper createTraversingEcoMapper(OWLGraphWrapper all, OWLReasoner reasoner, boolean disposeReasoner) throws IOException, OWLException {
	
	// This has bitten me, so let's try and be specific...
	if( reasoner == null )	{
		throw new IllegalArgumentException("No reasoner was specified for use with the EcoTools. Add a reasoner for the command line");
	}
			
	OWLOntology eco = null;
	
	// assume the graph wrapper is more than eco
	// try to find ECO by its purl
	Set<OWLOntology> allOntologies = all.getAllOntologies();
	for (OWLOntology owlOntology : allOntologies) {
		OWLOntologyID id = owlOntology.getOntologyID();
		Optional<IRI> ontologyIRI = id.getOntologyIRI();
		if (ontologyIRI.isPresent()) {
			if (EcoMapper.ECO_PURL_IRI.equals(ontologyIRI.get())) {
				eco = owlOntology;
			}
		}
	}
	if (eco == null) {
		throw new IllegalArgumentException("The specified graph did not contain ECO with the IRI: "+EcoMapper.ECO_PURL_IRI);
	}

	OWLGraphWrapper ecoGraph = new OWLGraphWrapper(eco);
	Reader reader = null;
	try {
		reader = createReader(EcoMapper.ECO_MAPPING_PURL);
		EcoMappings<OWLClass> mappings = loadEcoMappings(reader, ecoGraph);
		return new TraversingEcoMapperImpl(mappings, reasoner, disposeReasoner);
	}
	finally {
		IOUtils.closeQuietly(reader);
	}
}
 

public void save(File baseFolder, BufferedWriter w) throws IOException, OWLOntologyStorageException {
	w.write("<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n");
	w.write("<catalog prefer=\"public\" xmlns=\"urn:oasis:names:tc:entity:xmlns:xml:catalog\">\n");
	
	for (OWLOntology ont : ontology.getImportsClosure()) {
		validateImports(ont);
		
		OWLOntologyID ontologyID = ont.getOntologyID();
		IRI actualIRI = null;
		Optional<IRI> optional = ontologyID.getOntologyIRI();
		if (optional.isPresent()) {
			actualIRI = optional.get();
		}

		// Not really sure why this is here, but apparently we can get
		// an ontology without an IRI, in which case we'll generate one
		// that is 'sort of' unique (only fails if two different machines run
		// this tool at the exact same time).
		//
		if (actualIRI == null) {
			IRI generatedIRI = IRI.generateDocumentIRI();
			actualIRI = generatedIRI;
		}
		// Always write the actualIRI
		String actualLocalFile = createLocalFileName(actualIRI);
		IRI outputStream = IRI.create(new File(baseFolder, actualLocalFile));
		ont.getOWLOntologyManager().saveOntology(ont, outputStream);
		
		if (LOGGER.isInfoEnabled()) {
			LOGGER.info("name: "+ actualIRI +" local: "+actualLocalFile);
		}
		w.write("  <uri name=\""+ actualIRI  +"\" uri=\""+ actualLocalFile +"\"/>\n");

		//
		// In case there is a difference between the source document IRI
		// and the IRI of the resolved target (e.g., there is an HTTP
		// redirect from a legacy IRI to a newer IRI), then write an entry
		// in the catalog that points the legacy IRI to the newer, canonical one.
		// Examples of this include:
		//  http://purl.obolibrary.org/obo/so.owl
		// which redirects to:
		//  http://purl.obolibrary.org/obo/so-xp.obo.owl
		//

		IRI 			documentIRI = ont.getOWLOntologyManager().getOntologyDocumentIRI(ont);
		if (documentIRI != actualIRI) {
			String sourceLocalFile = createLocalFileName(actualIRI);
			if (LOGGER.isInfoEnabled()) {
				LOGGER.info("alias: "+ documentIRI + " ==> " + actualIRI + " local: "+ sourceLocalFile);
			}
			w.write("  <uri name=\""+ documentIRI +"\" uri=\""+ sourceLocalFile +"\"/>\n");
		}
	}
	w.write("</catalog>\n");
	w.flush();
}