@Override public Component getListCellRendererComponent(JList<?> list, Object value, int index, boolean isSelected, boolean cellHasFocus) { super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus); if (value instanceof OWLOntology) { OWLOntologyID id = ((OWLOntology) value).getOntologyID(); if (id.isAnonymous()) { this.setText(id.toString()); } else { this.setText(id.getOntologyIRI().get().toString()); } } return this; }
/** * Translate the given {@link GafDocument} into an OWL representation of the LEGO model. * * @param gaf * @return lego ontology * @throws OWLException * @throws UnknownIdentifierException */ public OWLOntology translate(GafDocument gaf) throws OWLException, UnknownIdentifierException { final OWLOntologyManager m = graph.getManager(); OWLOntology lego = m.createOntology(IRI.generateDocumentIRI()); OWLOntology sourceOntology = graph.getSourceOntology(); OWLOntologyID ontologyID = sourceOntology.getOntologyID(); if (ontologyID != null) { Optional<IRI> ontologyIRI = ontologyID.getOntologyIRI(); if (ontologyIRI.isPresent()) { OWLDataFactory f = m.getOWLDataFactory(); OWLImportsDeclaration importDeclaration = f.getOWLImportsDeclaration(ontologyIRI.get()); m.applyChange(new AddImport(lego, importDeclaration )); } } translate(gaf.getGeneAnnotations(), lego); return lego; }
public static OWLOntologyManager createOWLOntologyManager() { OWLOntologyManager man = new OWLOntologyManagerImpl(df, new NoOpReadWriteLock()); man.getOntologyFactories() .set(new OWLOntologyFactoryImpl(new OWLOntologyBuilder() { private static final long serialVersionUID = -7962454739789851685L; @Override public OWLOntology createOWLOntology(OWLOntologyManager om, OWLOntologyID id) { return new OWLOntologyImpl(om, id); } })); man.getOntologyParsers().set(MASTER_MANAGER_.getOntologyParsers()); man.getOntologyStorers().set(MASTER_MANAGER_.getOntologyStorers()); man.getIRIMappers().set(MASTER_MANAGER_.getIRIMappers()); return man; }
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 Map<String, Set<OWLAnnotationValue>> getOntologyAnnotationsOrderedByOntology( String annotation) { Map<String, Set<OWLAnnotationValue>> annotationValuesByOntologyIri = new HashMap<String, Set<OWLAnnotationValue>>(); final OWLDataFactory factory = manager.getOWLDataFactory(); final OWLAnnotationProperty dcProperty = factory .getOWLAnnotationProperty(IRI.create(annotation)); for (OWLOntology ontology : manager.getOntologies()) { Set<OWLAnnotationValue> annotationValues = new HashSet<OWLAnnotationValue>(); for (OWLAnnotation owlAnnotation : ontology.getAnnotations()) { if (owlAnnotation.getProperty().equals(dcProperty)) { annotationValues.add(owlAnnotation.getValue()); } } if (!annotationValues.isEmpty()) { final OWLOntologyID ontologyID = ontology.getOntologyID(); annotationValuesByOntologyIri.put(ontologyID.getOntologyIRI() .toString(), annotationValues); } } return annotationValuesByOntologyIri; }
public List<OntologyChangeRecordRun> getRuns() { List<OntologyChangeRecordRun> result = new ArrayList<OntologyChangeRecordRun>(); if (!changeRecords.isEmpty()) { OWLOntologyID currentRunId = null; List<OWLOntologyChangeData> runInfoList = new ArrayList<OWLOntologyChangeData>(); for(OWLOntologyChangeRecord record : changeRecords) { if(currentRunId == null) { // First run currentRunId = record.getOntologyID(); } else if(!currentRunId.equals(record.getOntologyID())) { // Store current run result.add(new OntologyChangeRecordRun(currentRunId, new ArrayList<OWLOntologyChangeData>(runInfoList))); // Reset for fresh run currentRunId = record.getOntologyID(); runInfoList.clear(); } // Add to current run runInfoList.add(record.getData()); } result.add(new OntologyChangeRecordRun(currentRunId, new ArrayList<OWLOntologyChangeData>(runInfoList))); } return result; }
@Override public OWLOntology createOntology() { try { return modelManager.createNewOntology(new OWLOntologyID(), null); } catch (OWLOntologyCreationException ex) { throw new RuntimeException(ex); } }
/** * Executed before the init call {@link #init()}. * * @param graph * @return IRI, never null * @throws OWLOntologyCreationException */ protected IRI getTboxIRI(OWLGraphWrapper graph) throws OWLOntologyCreationException { OWLOntology tbox = graph.getSourceOntology(); OWLOntologyID ontologyID = tbox.getOntologyID(); if (ontologyID != null) { Optional<IRI> ontologyIRI = ontologyID.getOntologyIRI(); if (ontologyIRI.isPresent()) { return ontologyIRI.get(); } } throw new OWLOntologyCreationException("No ontology id available for tbox. An ontology IRI is required for the import into the abox."); }
/** * Export the ABox, will try to set the ontologyID to the given modelId (to * ensure import assumptions are met) * * @param model * @param ontologyFormat * @return modelContent * @throws OWLOntologyStorageException */ public String exportModel(ModelContainer model, OWLDocumentFormat ontologyFormat) throws OWLOntologyStorageException { final OWLOntology aBox = model.getAboxOntology(); final OWLOntologyManager manager = aBox.getOWLOntologyManager(); // make sure the exported ontology has an ontologyId and that it maps to the modelId final IRI expectedABoxIRI = model.getModelId(); Optional<IRI> currentABoxIRI = aBox.getOntologyID().getOntologyIRI(); if (currentABoxIRI.isPresent() == false) { manager.applyChange(new SetOntologyID(aBox, expectedABoxIRI)); } else { if (expectedABoxIRI.equals(currentABoxIRI) == false) { OWLOntologyID ontologyID = new OWLOntologyID(Optional.of(expectedABoxIRI), Optional.of(expectedABoxIRI)); manager.applyChange(new SetOntologyID(aBox, ontologyID)); } } // write the model into a buffer ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); if (ontologyFormat != null) { manager.saveOntology(aBox, ontologyFormat, outputStream); } else { manager.saveOntology(aBox, outputStream); } // extract the string from the buffer String modelString = outputStream.toString(); return modelString; }
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); } }
private OWLGraphWrapper getTargetGraph() throws Exception { OWLOntologyManager targetManager = OWLManager.createOWLOntologyManager(); OWLOntologyID ontologyID = new OWLOntologyID(Optional.of(IRI.create("http://test.owltools.org/dynamic")), Optional.absent()); OWLOntology targetOntology = targetManager.createOntology(ontologyID); OWLGraphWrapper targetGraph = new OWLGraphWrapper(targetOntology); return targetGraph; }
/** * Instantiates a {@link OWLExporter} from the specified parameters. * * @param fileOutputStream the file output stream * @throws Exception if something goes wrong in constructor */ public OWLExporter(OutputStream fileOutputStream) throws Exception { dos = new DataOutputStream(new BufferedOutputStream(fileOutputStream)); if (snomed == null) { // Create a new ontology snomed = manager .createOntology(new OWLOntologyID(snomedIRI, snomedVersionIRI)); format.setParameter("xml:base", snomedNamespace); // Obtain SNOMED root concept // TODO: this needs to be generalized UUID snomedRootUUID = Taxonomies.SNOMED.getUuids()[0]; ConceptVersionBI snomedRootConcept = OTFUtility.getConceptVersion(snomedRootUUID); // Add annotation based on root concept for (DescriptionVersionBI<?> desc : snomedRootConcept .getDescriptionsActive()) { if (desc.getText().contains("Release")) { manager.applyChange(new AddOntologyAnnotation(snomed, factory .getOWLAnnotation(factory .getOWLAnnotationProperty(OWLRDFVocabulary.OWL_VERSION_INFO .getIRI()), factory.getOWLLiteral(desc.getText())))); } if (desc.getText().contains("IHTSDO")) { manager.applyChange(new AddOntologyAnnotation(snomed, factory .getOWLAnnotation(factory .getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_COMMENT .getIRI()), factory.getOWLLiteral(desc.getText())))); } } manager.applyChange(new AddOntologyAnnotation(snomed, factory .getOWLAnnotation(factory .getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI()), factory.getOWLLiteral(snomedOntologyName)))); } }
/** * Splits the given ontology into two partitions: The set of OWL EL * compliant axioms and the set of axioms which are not compliant with the * OWL EL profile. The EL compliant partition is stored in the left part of * resulting pair, and the EL non-compliant partition is stored in the right * part. * * @param sourceOnto * The source ontology to be partitioned. * @param compatibilityMode * Specifies the reasoner with which the resulting partition * should be compatible (e.g. Pellet has a different notion of EL * than other reasoners). * @return A pair containing two ontologies. The left part is the partition * of the source ontology with all EL-compliant axioms. The right * part is the partition of the source ontology with all * non-EL-compliant axioms. If the source ontology already conforms * to the OWL-EL profile, then the left part of the result contains * the source ontology, and the right part is null. * @throws OWLOntologyCreationException * If there is an error loading the source ontology. * @throws IllegalAccessException * @throws InstantiationException */ public static Pair<OWLOntology, OWLOntology> partition(OWLOntology sourceOnto, ReasonerCompatibilityMode compatibilityMode) throws OWLOntologyCreationException, InstantiationException, IllegalAccessException { OWLProfile elProfile = compatibilityMode.getProfileClass().newInstance(); OWLProfileReport report = elProfile.checkOntology(sourceOnto); if (report.isInProfile()) { return new ImmutablePair<OWLOntology, OWLOntology>(sourceOnto, null); } HashSet<OWLAxiom> nonELAxioms = new HashSet<OWLAxiom>(); Set<OWLProfileViolation> violations = report.getViolations(); for (OWLProfileViolation violation : violations) { nonELAxioms.add(violation.getAxiom()); } OWLOntologyID ontologyID = sourceOnto.getOntologyID(); IRI ontologyIRI = ontologyID.getOntologyIRI(); IRI targetELOntologyIRI = IRI.create(ontologyIRI.toString() + "/ELpart"); IRI targetNonELOntologyIRI = IRI.create(ontologyIRI.toString() + "/nonELpart"); OWLOntologyManager targetELOntoManager = OWLManager.createOWLOntologyManager(); targetELOntoManager.addIRIMapper(new NonMappingOntologyIRIMapper()); OWLOntology targetELOnto = targetELOntoManager.createOntology(new OWLOntologyID(targetELOntologyIRI)); OWLOntologyManager targetNonELOntoManager = OWLManager.createOWLOntologyManager(); targetNonELOntoManager.addIRIMapper(new NonMappingOntologyIRIMapper()); OWLOntology targetNonELOnto = targetNonELOntoManager.createOntology(new OWLOntologyID(targetNonELOntologyIRI)); Set<OWLAxiom> allAxioms = sourceOnto.getAxioms(); for (OWLAxiom axiom : allAxioms) { if (nonELAxioms.contains(axiom)) { targetNonELOntoManager.addAxiom(targetNonELOnto, axiom); System.out.println("- " + axiom); } else { targetELOntoManager.addAxiom(targetELOnto, axiom); System.out.println("+ " + axiom); } } return new ImmutablePair<OWLOntology, OWLOntology>(targetELOnto, targetNonELOnto); }
public OntologyChangeDataList(List<OWLOntologyChange> ontologyChanges, OWLOntologyID targetOntology, long timeStamp, BinaryOWLMetadata metadata) { List<OWLOntologyChangeData> infoList = new ArrayList<OWLOntologyChangeData>(); for(OWLOntologyChange change : ontologyChanges) { if(change.getOntology().getOntologyID().equals(targetOntology)) { infoList.add(change.getChangeData()); } } this.timestamp = timeStamp; this.metadata = metadata; this.list = Collections.unmodifiableList(infoList); }
/** * Try to load (or replace) a model with the given ontology. It is expected * that the content is an A-Box ontology, which imports the T-BOX. Also the * ontology ID is used to extract the modelId.<br> * <br> * This method will currently <b>NOT<b> work due to a bug in the OWL-API. * The functional syntax parser does not properly report the exceptions and * will return an ontology with an wrong ontology ID! * * @param modelData * @return modelId * @throws OWLOntologyCreationException */ public ModelContainer importModel(String modelData) throws OWLOntologyCreationException { // load data from String final OWLOntologyManager manager = graph.getManager(); final OWLOntologyDocumentSource documentSource = new StringDocumentSource(modelData); OWLOntology modelOntology; final Set<OWLParserFactory> originalFactories = removeOBOParserFactories(manager); try { modelOntology = manager.loadOntologyFromOntologyDocument(documentSource); } catch (OWLOntologyAlreadyExistsException e) { // exception is thrown if there is an ontology with the same ID already in memory OWLOntologyID id = e.getOntologyID(); IRI existingModelId = id.getOntologyIRI().orNull(); // remove the existing memory model unlinkModel(existingModelId); // try loading the import version (again) modelOntology = manager.loadOntologyFromOntologyDocument(documentSource); } finally { resetOBOParserFactories(manager, originalFactories); } // try to extract modelId IRI modelId = null; Optional<IRI> ontologyIRI = modelOntology.getOntologyID().getOntologyIRI(); if (ontologyIRI.isPresent()) { modelId = ontologyIRI.get(); } if (modelId == null) { throw new OWLOntologyCreationException("Could not extract the modelId from the given model"); } // paranoia check ModelContainer existingModel = modelMap.get(modelId); if (existingModel != null) { unlinkModel(modelId); } // add to internal model ModelContainer newModel = addModel(modelId, modelOntology); // update imports updateImports(newModel); return newModel; }
private void catOntologies(Opts opts) throws OWLOntologyCreationException, IOException { opts.info("[-r|--ref-ont ONT] [-i|--use-imports]", "Catenate ontologies taking only referenced subsets of supporting onts.\n"+ " See Mooncat docs"); Mooncat m = new Mooncat(g); ParserWrapper pw = new ParserWrapper(); String newURI = null; while (opts.hasOpts()) { //String opt = opts.nextOpt(); if (opts.nextEq("-r") || opts.nextEq("--ref-ont")) { LOG.error("DEPRECATED - list all ref ontologies on main command line"); String f = opts.nextOpt(); m.addReferencedOntology(pw.parseOWL(f)); } else if (opts.nextEq("-s") || opts.nextEq("--src-ont")) { m.setOntology(pw.parseOWL(opts.nextOpt())); } else if (opts.nextEq("-p") || opts.nextEq("--prefix")) { m.addSourceOntologyPrefix(opts.nextOpt()); } else if (opts.nextEq("-i") || opts.nextEq("--use-imports")) { System.out.println("using everything in imports closure"); g.addSupportOntologiesFromImportsClosure(); } else if (opts.nextEq("-n") || opts.nextEq("--new-uri")) { System.out.println("new URI for merged ontology"); newURI = opts.nextOpt(); } else { break; //opts.fail(); } } //if (m.getReferencedOntologies().size() == 0) { // m.setReferencedOntologies(g.getSupportOntologySet()); //} //g.useImportClosureForQueries(); //for (OWLAxiom ax : m.getClosureAxiomsOfExternalReferencedEntities()) { // System.out.println("M_AX:"+ax); //} m.mergeOntologies(); m.removeDanglingAxioms(); if (newURI != null) { SetOntologyID soi = new SetOntologyID(g.getSourceOntology(), new OWLOntologyID(Optional.of(IRI.create(newURI)), Optional.<IRI>absent())); g.getManager().applyChange(soi); /* HashSet<OWLOntology> cpOnts = new HashSet<OWLOntology>(); LOG.info("srcOnt annots:"+g.getSourceOntology().getAnnotations().size()); cpOnts.add(g.getSourceOntology()); OWLOntology newOnt = g.getManager().createOntology(IRI.create(newURI), cpOnts); LOG.info("newOnt annots:"+newOnt.getAnnotations().size()); //g.getDataFactory().getOWLOn g.setSourceOntology(newOnt); */ } }
/** * 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(); }
@Override public void handleOntologyID(OWLOntologyID ontologyID) throws E { }
public <E extends Throwable> void read(DataInputStream dis, BinaryOWLOntologyDocumentHandler<E> handler, OWLDataFactory df) throws IOException, BinaryOWLParseException, UnloadableImportException, E { BinaryOWLInputStream inputStream = new BinaryOWLInputStream(dis, df, VERSION); // Metadata BinaryOWLMetadataChunk chunk = new BinaryOWLMetadataChunk(inputStream); BinaryOWLMetadata metadata = chunk.getMetadata(); handler.handleDocumentMetaData(metadata); handler.handleBeginInitialDocumentBlock(); // Ontology ID BinaryOWLOntologyID serializer = new BinaryOWLOntologyID(inputStream); OWLOntologyID ontologyID = serializer.getOntologyID(); handler.handleOntologyID(ontologyID); // Imported ontologies BinaryOWLImportsDeclarationSet importsDeclarationSet = new BinaryOWLImportsDeclarationSet(inputStream); Set<OWLImportsDeclaration> importsDeclarations = importsDeclarationSet.getImportsDeclarations(); handler.handleImportsDeclarations(importsDeclarations); // IRI Table IRILookupTable iriLookupTable = new IRILookupTable(dis); // Used to be literal table // Skip 1 byte - the interning marker inputStream.skip(1); LookupTable lookupTable = new LookupTable(iriLookupTable); BinaryOWLInputStream lookupTableStream = new BinaryOWLInputStream(dis, lookupTable, df, VERSION); // Ontology Annotations Set<OWLAnnotation> annotations = lookupTableStream.readOWLObjects(); handler.handleOntologyAnnotations(annotations); // Axiom tables - axioms by type for (int i = 0; i < AxiomType.AXIOM_TYPES.size(); i++) { Set<OWLAxiom> axiomsOfType = lookupTableStream.readOWLObjects(); handler.handleAxioms(axiomsOfType); } handler.handleEndInitialDocumentBlock(); handler.handleBeginDocumentChangesBlock(); BinaryOWLInputStream changesInputStream = new BinaryOWLInputStream(dis, df, VERSION); // Read any changes that have been appended to the end of the file - no look up table for this readOntologyChanges(changesInputStream, handler); handler.handleEndDocumentChangesBlock(); handler.handleEndDocument(); }
public OntologyChangeRecordRun(OWLOntologyID ontologyID, List<OWLOntologyChangeData> records) { this.ontologyID = ontologyID; this.records = new ArrayList<OWLOntologyChangeData>(records); }
public OWLOntologyID getOntologyID() { return ontologyID; }
@Override public void write(SetOntologyIDData recordData, BinaryOWLOutputStream outputStream) throws IOException { OWLOntologyID id = recordData.getNewId(); BinaryOWLOntologyID serializer = new BinaryOWLOntologyID(id); serializer.write(outputStream); }
public BinaryOWLOntologyID(OWLOntologyID ontologyID) { this.ontologyID = ontologyID; }
void handleOntologyID(OWLOntologyID ontologyID) throws E;
OWLOntologyID getOntologyID();
