Java Code Examples for org.semanticweb.owlapi.model.OWLOntology#getOntologyID()

public OntologyMetadata(OWLOntology ont) {
	super();
	OWLOntologyID id = ont.getOntologyID();
	if (id.getOntologyIRI().isPresent())
		ontologyIRI = id.getOntologyIRI().get().toString();
	if (id.getVersionIRI().isPresent())
		versionIRI = id.getVersionIRI().get().toString();
	importDirectives = new HashSet<String>();
	for (OWLImportsDeclaration oid : ont.getImportsDeclarations()) {
		importDirectives.add(oid.getIRI().toString());
	}
	classCount = ont.getClassesInSignature().size();
	namedIndividualCount = ont.getIndividualsInSignature().size();
	axiomCount = ont.getAxiomCount();
	annotations = new HashSet<OntologyAnnotation>();
	for (OWLAnnotation ann : ont.getAnnotations()) {
		annotations.add(new OntologyAnnotation(ann));
	}
}
 

private String handleVersion(String ontologyId) {
	// TODO add an option to set/overwrite the version manually via command-line
	// TODO re-use/create a method in obo2owl for creating an version IRI
	String version;
	OWLOntology ontology = mooncat.getOntology();
	OWLOntologyID owlOntologyId = ontology.getOntologyID();
	Optional<IRI> versionIRI = owlOntologyId.getVersionIRI();
	if (versionIRI.isPresent() == false) {
		// set a new version IRI using the current date
		version = OntologyVersionTools.format(new Date());
		versionIRI = Optional.of(IRI.create(Obo2OWLConstants.DEFAULT_IRI_PREFIX+ontologyId+"/"+oortConfig.getVersionSubdirectory()+"/"+version+"/"+ontologyId+".owl"));
		
		OWLOntologyManager m = mooncat.getManager();
		m.applyChange(new SetOntologyID(ontology, new OWLOntologyID(owlOntologyId.getOntologyIRI(), versionIRI)));
	}
	else {
		String versionIRIString = versionIRI.get().toString();
		version = OntologyVersionTools.parseVersion(versionIRIString);
		if (version == null) {
			// use the whole IRI? escape?
			logError("Could not parse a version from ontolgy version IRI: "+versionIRIString);
			version = versionIRIString;
		}
	}
	return version;
}
 

@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;
}
 

public static OWLOntology createOWLThingTypeDeclForIndividuals(OWLOntology ont) throws OWLOntologyCreationException, IOException  {
	OWLOntology ret = ont.getOntologyID()!=null && ont.getOntologyID().getOntologyIRI()!=null?
				ont.getOWLOntologyManager().createOntology(ont.getOntologyID().getOntologyIRI()):
				ont.getOWLOntologyManager().createOntology();
	
				OWLDataFactory fac = ret.getOWLOntologyManager().getOWLDataFactory();
	OWLClass owlThing = ret.getOWLOntologyManager().getOWLDataFactory().getOWLThing();
	for (OWLNamedIndividual ind: ont.getIndividualsInSignature()) {
		OWLNamedIndividual ni = fac.getOWLNamedIndividual(ind.getIRI());
		OWLAxiom ax = fac.getOWLClassAssertionAxiom(owlThing, ni);
		ret.getOWLOntologyManager().addAxiom(ret, ax);
	}
	return ret;
	
	
}
 

/**
 * 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 static String getIri(OWLOntology ontology) {
  String iri = "_:" + hash(ontology.toString());
  if (null != ontology.getOntologyID() && null != ontology.getOntologyID().getOntologyIRI()) {
    iri = ontology.getOntologyID().getOntologyIRI().toString();
  } else {
    if (!ontologiesWithoutIris.contains(ontology)) {
      ontologiesWithoutIris.add(ontology);
      logger.warning("Failed to find IRI for " + ontology + " - using hash code instead.");
    }
  }
  return iri;
}
 

/**
 * Mirrors ontologies on local filesystem.
 *
 * @param rootOntology The ontology to mirror.
 * @param baseFolder The folder.
 * @param catalogFile The catalog file to write to.
 * @throws IOException on most problems.
 * @throws OWLOntologyStorageException if the ontology cannot be saved.
 */
public static void mirror(OWLOntology rootOntology, File baseFolder, File catalogFile)
    throws IOException, OWLOntologyStorageException {

  logger.info("Mirroring ontologies: " + rootOntology);
  Map<IRI, String> iriMap = new HashMap<>();
  for (OWLOntology ont : rootOntology.getImportsClosure()) {
    logger.info("Mirroring: " + ont);
    validateImports(ont);

    OWLOntologyID ontologyID = ont.getOntologyID();
    IRI ontologyIRI = ontologyID.getOntologyIRI().orNull();

    // 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 (ontologyIRI == null) {
      ontologyIRI = IRI.generateDocumentIRI();
    }
    // Always write the actualIRI
    String localFilePath = getMirrorPathOfOntologyIRI(ontologyIRI);
    IRI outputStream = IRI.create(new File(baseFolder, localFilePath));
    ont.getOWLOntologyManager().saveOntology(ont, outputStream);
    iriMap.put(ontologyIRI, localFilePath);

    //
    // 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.toString().startsWith("file:") && documentIRI != ontologyIRI) {
      String sourceLocalFile = getMirrorPathOfOntologyIRI(ontologyIRI);
      logger.info("Mirroring " + documentIRI + " in " + sourceLocalFile);
      iriMap.put(documentIRI, sourceLocalFile);
    }
  }
  writeCatalog(catalogFile, iriMap);
}
 

/**
 * Create the GCIs for BioChEBI. Add the axioms into the given ontology.
 * 
 * @param ontology
 * @param ignoredClasses
 */
public void expand(OWLOntology ontology, Set<OWLClass> ignoredClasses) {
	final OWLOntologyManager manager = ontology.getOWLOntologyManager();
	final OWLDataFactory factory = manager.getOWLDataFactory();
	
	// scan axioms
	Set<OWLSubClassOfAxiom> axioms = ontology.getAxioms(AxiomType.SUBCLASS_OF, Imports.INCLUDED);
	for (OWLSubClassOfAxiom axiom : axioms) {
		OWLClassExpression superCE = axiom.getSuperClass();
		OWLClassExpression subCE = axiom.getSubClass();
		if (subCE.isAnonymous()) {
			// sub class needs to be an named OWLClass
			continue;
		}

		if (superCE instanceof OWLObjectSomeValuesFrom == false) {
			continue;
		}
		OWLObjectSomeValuesFrom some = (OWLObjectSomeValuesFrom) superCE;

		OWLObjectPropertyExpression expression = some.getProperty();
		if (expression.isAnonymous()) {
			// object property expression needs to be a named OWLObjectProperty 
			continue;
		}

		OWLObjectProperty p = (OWLObjectProperty) expression;
		
		Set<OWLObjectProperty> expansions = expansionMap.get(p);
		if (expansions == null) {
			continue;
		}

		// get content for GCI
		OWLClassExpression y = some.getFiller();
		OWLClass x = subCE.asOWLClass();
		if (ignoredClasses.contains(x)) {
			continue;
		}
		for (OWLObjectProperty createProperty : expansions) {
			OWLClassExpression ce1 = factory.getOWLObjectSomeValuesFrom(createProperty, x);
			OWLClassExpression ce2 = factory.getOWLObjectSomeValuesFrom(createProperty, y);
			OWLEquivalentClassesAxiom eq = factory.getOWLEquivalentClassesAxiom(ce1, ce2);
			manager.addAxiom(ontology, eq);
		}
	}
	
	Set<OWLOntology> imports = ontology.getImports();
	StringBuilder sb = new StringBuilder();
	DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd");
	sb.append("Generated on ").append(dateFormat.format(new Date())).append(" using the following import chain:");
	for (OWLOntology owlOntology : imports) {
		OWLOntologyID ontologyID = owlOntology.getOntologyID();
		sb.append(" ");
		appendOntologyId(ontologyID, sb);
	}
	addComment(sb.toString(), ontology);
}
 

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();
}