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

/**
 * Given a list of ontologies and a target ontology, remove all the axioms from the listed
 * ontologies and their import closure from the target ontology.
 *
 * @param ontologies the list of ontologies to unmerge
 * @param targetOntology the ontology to remove axioms from
 * @param includeAnnotations true if ontology annotations should be remove
 */
public static void unmergeFrom(
    List<OWLOntology> ontologies, OWLOntology targetOntology, boolean includeAnnotations) {
  for (OWLOntology ontology : ontologies) {
    logger.info("Removing axioms from: " + ontology);
    targetOntology.getOWLOntologyManager().removeAxioms(targetOntology, ontology.getAxioms());
    if (includeAnnotations) {
      for (OWLAnnotation annotation : ontology.getAnnotations()) {
        RemoveOntologyAnnotation remove =
            new RemoveOntologyAnnotation(targetOntology, annotation);
        targetOntology.getOWLOntologyManager().applyChange(remove);
      }
    }
    for (OWLOntology imported : ontology.getImportsClosure()) {
      targetOntology.getOWLOntologyManager().removeAxioms(targetOntology, imported.getAxioms());
    }
  }
}
 

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 void removeDirectives() {
	// TODO decide: move the set of directives into a constant/static collection?
	
	Set<IRI> directivesIRIs = new HashSet<IRI>();
	directivesIRIs.add(Obo2OWLVocabulary.IRI_OIO_LogicalDefinitionViewRelation.getIRI());
	directivesIRIs.add(Obo2OWLVocabulary.IRI_OIO_treatXrefsAsEquivalent.getIRI());
	directivesIRIs.add(Obo2OWLVocabulary.IRI_OIO_treatXrefsAsGenusDifferentia.getIRI());
	directivesIRIs.add(Obo2OWLVocabulary.IRI_OIO_treatXrefsAsHasSubClass.getIRI());
	directivesIRIs.add(Obo2OWLVocabulary.IRI_OIO_treatXrefsAsIsA.getIRI());
	directivesIRIs.add(Obo2OWLVocabulary.IRI_OIO_treatXrefsAsRelationship.getIRI());
	directivesIRIs.add(Obo2OWLVocabulary.IRI_OIO_treatXrefsAsReverseGenusDifferentia.getIRI());
	
	OWLOntology o = graph.getSourceOntology();
	for(OWLAnnotation ann : o.getAnnotations()) {
		final OWLAnnotationProperty property = ann.getProperty();
		if (directivesIRIs.contains(property.getIRI())) {
			manager.applyChange(new RemoveOntologyAnnotation(o, ann));
		}
	}
}
 

private String getOntologyAnnotationValue(OWLOntology o, OboFormatTag tag) {
	IRI dateTagIRI = Obo2Owl.trTagToIRI(tag.getTag());
	Set<OWLAnnotation> annotations = o.getAnnotations();
	for (OWLAnnotation annotation : annotations) {
		OWLAnnotationProperty property = annotation.getProperty();
		if(dateTagIRI.equals(property.getIRI())) {
			OWLAnnotationValue value = annotation.getValue();
			if (value != null) {
				if (value instanceof IRI) {
					return ((IRI) value).toString();
				}
				else if (value instanceof OWLLiteral) {
					return ((OWLLiteral) value).getLiteral();
				}
			}
		}
	}
	return null;
}
 

/**
 * Experimental method for trying out the loading of complex_annotation doc type
 * 
 * @param opts
 * @throws Exception
 */
@CLIMethod("--solr-load-complex-annotations")
public void experimentalLoadComplexAnnotationSolr(Opts opts) throws Exception {

	// Check to see if the global url has been set.
	String url = sortOutSolrURL(globalSolrURL);				

	// Only proceed if our environment was well-defined.
	if( legoCatalogs == null || legoFiles == null || legoCatalogs.isEmpty() || legoFiles.isEmpty() ){
		LOG.warn("Lego environment not well defined--skipping.");
	}else{

		// Ready the environment for every pass.
		ParserWrapper pw = new ParserWrapper();
		// Add all of the catalogs.
		for( File legoCatalog : legoCatalogs ){
			pw.addIRIMapper(new CatalogXmlIRIMapper(legoCatalog));				
		}
		OWLOntologyManager manager = pw.getManager();
		OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();

		// Actual loading--iterate over our list and load individually.
		for( File legoFile : legoFiles ){
			String fname = legoFile.getName();
			OWLReasoner currentReasoner = null;
			OWLOntology ontology = null;

			// TODO: Temp cover for missing group labels and IDs.
			//String agID = legoFile.getCanonicalPath();
			String agLabel = StringUtils.removeEnd(fname, ".owl");
			String agID = new String(agLabel);

			try {
				ontology = pw.parseOWL(IRI.create(legoFile));
				currentReasoner = reasonerFactory.createReasoner(ontology);

				// Some sanity checks--some of the genereated ones are problematic.
				boolean consistent = currentReasoner.isConsistent();
				if( consistent == false ){
					LOG.info("Skip since inconsistent: " + fname);
					continue;
				}
				Set<OWLClass> unsatisfiable = currentReasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();

				// TODO - make configurable to allow fail fast
				if (unsatisfiable.isEmpty() == false) {
					LOG.info("Skip since unsatisfiable: " + fname);
					continue;
				}

				Set<OWLNamedIndividual> individuals = ontology.getIndividualsInSignature();
				Set<OWLAnnotation> modelAnnotations = ontology.getAnnotations();

				OWLGraphWrapper currentGraph = new OWLGraphWrapper(ontology);						
				try {
					LOG.info("Trying complex annotation load of: " + fname);
					ComplexAnnotationSolrDocumentLoader loader =
							new ComplexAnnotationSolrDocumentLoader(url, currentGraph, currentReasoner, individuals, modelAnnotations, agID, agLabel, fname);
					loader.load();
				} catch (SolrServerException e) {
					LOG.info("Complex annotation load of " + fname + " at " + url + " failed!");
					e.printStackTrace();
					System.exit(1);
				}
			} finally {
				// Cleanup reasoner and ontology.
				if (currentReasoner != null) {
					currentReasoner.dispose();
				}
				if (ontology != null) {
					manager.removeOntology(ontology);
				}
			}
		}
	}
}
 

/**
 * Experimental method for trying out the loading of complex_annotation doc type.
 * Works with --read-ca-list <file>.
 * 
 * @param opts
 * @throws Exception
 */
@CLIMethod("--solr-load-complex-exp")
public void loadComplexAnnotationSolr(Opts opts) throws Exception {

	// Check to see if the global url has been set.
	String url = sortOutSolrURL(globalSolrURL);				

	// Only proceed if our environment was well-defined.
	if( caFiles == null || caFiles.isEmpty() ){
		LOG.warn("LEGO environment not well defined--will skip loading LEGO/CA.");
	}else{

		// NOTE: These two lines are remainders from old code, and I'm not sure of their place in this world of ours.
		// I wish there was an arcitecture diagram somehwere...
		OWLOntologyManager manager = pw.getManager();
		OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();

		// Actual loading--iterate over our list and load individually.
		for( String fname : caFiles ){
			OWLReasoner currentReasoner = null;
			OWLOntology ontology = null;

			// TODO: Temp cover for missing group labels and IDs.
			//String agID = legoFile.getCanonicalPath();
			String pretmp = StringUtils.removeEnd(fname, ".owl");
			String[] bits = StringUtils.split(pretmp, "/");
			String agID = bits[bits.length -1];
			String agLabel = new String(StringUtils.replaceOnce(agID, ":", "_"));

			try {
				ontology = pw.parseOWL(IRI.create(fname));
				currentReasoner = reasonerFactory.createReasoner(ontology);

				// Some sanity checks--some of the genereated ones are problematic.
				boolean consistent = currentReasoner.isConsistent();
				if( consistent == false ){
					LOG.info("Skip since inconsistent: " + fname);
					continue;
				}
				Set<OWLClass> unsatisfiable = currentReasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
				if (unsatisfiable.isEmpty() == false) {
					LOG.info("Skip since unsatisfiable: " + fname);
					continue;
				}

				Set<OWLNamedIndividual> individuals = ontology.getIndividualsInSignature();
				Set<OWLAnnotation> modelAnnotations = ontology.getAnnotations();
				OWLGraphWrapper currentGraph = new OWLGraphWrapper(ontology);						
				try {
					LOG.info("Trying complex annotation load of: " + fname);
					ComplexAnnotationSolrDocumentLoader loader =
							new ComplexAnnotationSolrDocumentLoader(url, currentGraph, currentReasoner, individuals, modelAnnotations, agID, agLabel, fname);
					loader.load();
				} catch (SolrServerException e) {
					LOG.info("Complex annotation load of " + fname + " at " + url + " failed!");
					e.printStackTrace();
					System.exit(1);
				}
			} finally {
				// Cleanup reasoner and ontology.
				if (currentReasoner != null) {
					currentReasoner.dispose();
				}
				if (ontology != null) {
					manager.removeOntology(ontology);
				}
			}
		}
	}
}
 

public static String renderMarkdown(OWLGraphWrapper g, String baseDir, boolean isIncludeImage) {

		OWLOntology ont = g.getSourceOntology();
		StringBuilder out = new StringBuilder();

		String ontId = g.getOntologyId();

		Set<OWLAnnotation> oAnns = ont.getAnnotations();
		System.err.println("NUM1:"+oAnns.size());

		String title = getVal("title", oAnns);

		out.append("## Ontology: "+title+"\n\n");
		out.append("IRI: "+rurl(ont)+"\n\n");

		String desc = getVal("description", oAnns);
		out.append("### Description\n\n");
		out.append(desc+"\n\n");

		Set<OWLOntology> imports = ont.getImports();
		if (imports.size() > 0) {
			out.append("### Imports\n\n");
			for (OWLOntology im : imports) {
				out.append(" * "+rurl(im)+"\n");
			}
		}
		if (isIncludeImage) {
			String imgFn = baseDir + "/" + ontId + ".png";
			out.append("![]("+imgFn+")\n\n");
		}

		System.err.println("NUM:"+oAnns.size());
		if (oAnns.size() > 0) {
			out.append("### Annotations:\n\n");
			for (OWLAnnotation ann : oAnns) {
				String annLabel = g.getLabelOrDisplayId(ann.getProperty());
				OWLAnnotationValue v = ann.getValue();
				String dv = v.toString();
				if (v instanceof OWLLiteral) {
					OWLLiteral lv = ((OWLLiteral)v);
					dv = lv.getLiteral();
					IRI dt = lv.getDatatype().getIRI();
					//System.out.println("DT = "+dt);
					if (dt.equals(OWL2Datatype.XSD_ANY_URI.getIRI())) {
						dv = href(lv.getLiteral());
					}
				}
				out.append(" * "+href(ann.getProperty().getIRI().toString(),annLabel)+" : "+dv+"\n");
			}
		}

		return out.toString();
	}
 

@Before
public void setup() throws Exception {
  if (builtGraph) {
    // TODO: UGH - need a better pattern for this
    return;
  }
  graph = createInstance();

  String uri = Resources.getResource("ontologies/family.owl").toURI().toString();
  manager.loadOntologyFromOntologyDocument(IRI.create(uri));

  List<MappedProperty> propertyMap = new ArrayList<>();
  MappedProperty age = mock(MappedProperty.class);
  when(age.getName()).thenReturn("isAged");
  when(age.getProperties()).thenReturn(newArrayList(ROOT + "/hasAge"));
  propertyMap.add(age);
  MappedProperty versionInfo = mock(MappedProperty.class);
  when(versionInfo.getName()).thenReturn("versionInfo");
  when(versionInfo.getProperties()).thenReturn(newArrayList(OWL + "versionInfo"));
  propertyMap.add(versionInfo);
  OWLOntologyWalker walker = new OWLOntologyWalker(manager.getOntologies());
  GraphOwlVisitor visitor = new GraphOwlVisitor(walker, graph, propertyMap);
  walker.walkStructure(visitor);
  
  for (OWLOntology ontology : manager.getOntologies()){
    String ontologyIri = OwlApiUtils.getIri(ontology);
    for (OWLAnnotation annotation : ontology.getAnnotations()) { // Get annotations on ontology iri
      OWLAnnotationSubject ontologySubject = IRI.create(ontologyIri);
      OWLAnnotationAssertionAxiom object = 
          new OWLAnnotationAssertionAxiomImpl(ontologySubject,
              annotation.getProperty(), annotation.getValue(),
              new ArrayList<OWLAnnotation>());
      visitor.visit(object);
    }
  }
  graph.shutdown();
  graphDb = new TestGraphDatabaseFactory().newEmbeddedDatabase(new File(path));
  tx = graphDb.beginTx();
  nodeIndex = graphDb.index().getNodeAutoIndexer().getAutoIndex();
  builtGraph = true;
}