public OWLOntologyManager createOwlOntologyManager( OWLOntologyLoaderConfiguration config, IRI excludeDocumentIRI ) throws Exception { OWLOntologyManager m = OWLManager.createOWLOntologyManager(); config.setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT); loadOntologyFiles(m, config, excludeDocumentIRI); return m; }
@Nonnull private static OWLOntologyLoaderConfiguration createLoaderConfig() { return new OWLOntologyLoaderConfiguration() .setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT) .setReportStackTraces(true) // It is safe to turn of illegal punning fixing as we've already parsed // (and saved) the ontology using a manager with this turned on. .setRepairIllegalPunnings(false); }
private static void adjustImports(OWLOntology ontology, List<OWLOntologyChange> changes) { OWLOntologyLoaderConfiguration configuration = new OWLOntologyLoaderConfiguration(); configuration = configuration.setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT); configuration = configuration.setMissingOntologyHeaderStrategy(MissingOntologyHeaderStrategy.IMPORT_GRAPH); try { adjustImports(ontology, changes, configuration); } catch (UnloadableImportException uie) { throw new RuntimeException("This shouldn't happen because the configuration says import problems should be ignored.", uie); } }
private OWLOntology loadOwlOntology() throws OWLOntologyCreationException { FileDocumentSource fileDocumentSource = new FileDocumentSource(ontologyFile); // use silent import handling strategy to enable ontology loading without internet access // see: https://github.com/molgenis/molgenis/issues/5301 OWLOntologyLoaderConfiguration owlOntologyLoaderConfiguration = new OWLOntologyLoaderConfiguration() .setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT); return manager.loadOntologyFromOntologyDocument( fileDocumentSource, owlOntologyLoaderConfiguration); }
public void createProjectFromSources(DocumentId sourcesId, UserId owner) throws IOException, OWLOntologyCreationException, OWLOntologyStorageException { File uploadedFile = new File(uploadsDirectory, sourcesId.getDocumentId()); if (uploadedFile.exists()) { OWLOntologyManager rootOntologyManager = WebProtegeOWLManager.createOWLOntologyManager(); RawProjectSources projectSources = uploadedProjectSourcesExtractor.extractProjectSources(uploadedFile); OWLOntologyLoaderConfiguration loaderConfig = new OWLOntologyLoaderConfiguration() .setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT); RawProjectSourcesImporter importer = new RawProjectSourcesImporter(rootOntologyManager, loaderConfig); OWLOntology ontology = importer.importRawProjectSources(projectSources); generateInitialChanges(owner, rootOntologyManager); writeNewProject(rootOntologyManager, ontology); deleteSourceFile(uploadedFile); } else { throw new FileNotFoundException(uploadedFile.getAbsolutePath()); } }
public OWLAPILoader() { _manager.setOntologyLoaderConfiguration(_manager.getOntologyLoaderConfiguration().setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT)); _manager.addMissingImportListener(new MissingImportListener() { /** * TODO * * @since */ private static final long serialVersionUID = -1580704502184270618L; @Override public void importMissing(final MissingImportEvent event) { if (!_ignoreImports) { final IRI importURI = event.getImportedOntologyURI(); System.err.println("WARNING: Cannot import " + importURI); event.getCreationException().printStackTrace(); } } }); clear(); }
public OWLAPILoader() { _manager.setOntologyLoaderConfiguration(_manager.getOntologyLoaderConfiguration().setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT)); _manager.addMissingImportListener(new MissingImportListener() { /** * TODO * * @since */ private static final long serialVersionUID = -1580704502184270618L; @Override public void importMissing(final MissingImportEvent event) { if (!_ignoreImports) { final IRI importURI = event.getImportedOntologyURI(); System.err.println("WARNING: Cannot import " + importURI); event.getCreationException().printStackTrace(); } } }); clear(); }
public OWLAPILoader() { _manager.setOntologyLoaderConfiguration(_manager.getOntologyLoaderConfiguration().setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT)); _manager.addMissingImportListener(new MissingImportListener() { /** * TODO * * @since */ private static final long serialVersionUID = -1580704502184270618L; @Override public void importMissing(final MissingImportEvent event) { if (!_ignoreImports) { final IRI importURI = event.getImportedOntologyURI(); System.err.println("WARNING: Cannot import " + importURI); event.getCreationException().printStackTrace(); } } }); clear(); }
OWLOntologyLoaderConfiguration configuration = new OWLOntologyLoaderConfiguration(); configuration = configuration.setLoadAnnotationAxioms(false); configuration = configuration.setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT); OWLOntology ontology = manager.loadOntology(iri); Set<URI> suggestions = new TreeSet<>();
/** * Returns the ontology for the entry. * @param entry the entry * @return the OWL ontology */ public OWLOntology getOntology(OntologyRepositoryEntry entry) { try(InputStream is = getInputStream(entry.getPhysicalURI().toURL())) { OWLOntologyManager man = OWLManager.createOWLOntologyManager(); man.addMissingImportListener(e -> { System.out.println("Missing import: " + e.getImportedOntologyURI()); }); OWLOntologyLoaderConfiguration conf = new OWLOntologyLoaderConfiguration(); conf.setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT); conf.addIgnoredImport(IRI.create("http://www.co-ode.org/ontologies/lists/2008/09/11/list.owl")); man.setOntologyLoaderConfiguration(conf); OWLOntology ont = man.loadOntologyFromOntologyDocument(is); return ont; } catch (Exception e) { e.printStackTrace(); } return null; }
public OWLAPILoader() { iriMapper = new LimitedMapIRIMapper(); manager = OWLManager.createOWLOntologyManager(); manager.setOntologyLoaderConfiguration(manager .getOntologyLoaderConfiguration() .setMissingImportHandlingStrategy( MissingImportHandlingStrategy.SILENT)); manager.addMissingImportListener(new MissingImportListener() { @Override public void importMissing(MissingImportEvent event) { if (!ignoreImports) { IRI importURI = event.getImportedOntologyURI(); System.err.println("WARNING: Cannot import " + importURI); event.getCreationException().printStackTrace(); } } }); clear(); }
/** * Method that will download the ontology to document with Widoco. * @param c Widoco configuration object. * @throws java.lang.Exception */ public static void loadModelToDocument(Configuration c) throws Exception{ if(!c.isFromFile()){ String newOntologyPath = c.getTmpFile().getAbsolutePath()+File.separator+"Ontology"; downloadOntology(c.getOntologyURI(), newOntologyPath); c.setFromFile(true); c.setOntologyPath(newOntologyPath); } //reding the model with Jena (deprecated) // OntModel model = ModelFactory.createOntologyModel();//ModelFactory.createDefaultModel(); // readOntModel(model, c); // c.getMainOntology().setMainModel(model); OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); OWLOntologyLoaderConfiguration loadingConfig = new OWLOntologyLoaderConfiguration(); loadingConfig = loadingConfig.setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT); OWLOntology ontology= manager.loadOntologyFromOntologyDocument(new FileDocumentSource(new File(c.getOntologyPath())),loadingConfig); c.getMainOntology().setMainOntology(ontology); c.getMainOntology().setMainOntologyManager(manager); c.getMainOntology().getOWLAPIModel().setOWLOntologyManager(manager); }
@Override public OWLOntology parsePremiseOntology(SerializationFormat format) throws OntologyParseException { try { final OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); manager.setOntologyLoaderConfiguration(manager.getOntologyLoaderConfiguration().setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT)); manager.getIRIMappers().clear(); ImportsHelper.loadImports(manager, this, format); OWLOntology o = parsedPremise.get(format); if (o == null) { final String l = getPremiseOntology(format); if (l == null) { return null; } final StringDocumentSource source = new StringDocumentSource(l); o = manager.loadOntologyFromOntologyDocument(source); parsedPremise.put(format, o); } return o; } catch (final OWLOntologyCreationException e) { throw new OntologyParseException(e); } } }
@Override public OWLOntology parsePremiseOntology(SerializationFormat format) throws OntologyParseException { try { final OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); manager.setOntologyLoaderConfiguration(manager.getOntologyLoaderConfiguration().setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT)); manager.getIRIMappers().clear(); ImportsHelper.loadImports(manager, this, format); OWLOntology o = parsedPremise.get(format); if (o == null) { final String l = getPremiseOntology(format); if (l == null) { return null; } final StringDocumentSource source = new StringDocumentSource(l); o = manager.loadOntologyFromOntologyDocument(source); parsedPremise.put(format, o); } return o; } catch (final OWLOntologyCreationException e) { throw new OntologyParseException(e); } } }
@Override public OWLOntology parsePremiseOntology(SerializationFormat format) throws OntologyParseException { try { final OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); manager.setOntologyLoaderConfiguration(manager.getOntologyLoaderConfiguration().setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT)); manager.getIRIMappers().clear(); ImportsHelper.loadImports(manager, this, format); OWLOntology o = parsedPremise.get(format); if (o == null) { final String l = getPremiseOntology(format); if (l == null) { return null; } final StringDocumentSource source = new StringDocumentSource(l); o = manager.loadOntologyFromOntologyDocument(source); parsedPremise.put(format, o); } return o; } catch (final OWLOntologyCreationException e) { throw new OntologyParseException(e); } } }
@Override public OWLOntology parseConclusionOntology(SerializationFormat format) throws OntologyParseException { try { final OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); manager.setOntologyLoaderConfiguration(manager.getOntologyLoaderConfiguration().setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT)); manager.getIRIMappers().clear(); ImportsHelper.loadImports(manager, this, format); OWLOntology o = parsedConclusion.get(format); if (o == null) { final String l = getConclusionOntology(format); if (l == null) { return null; } final StringDocumentSource source = new StringDocumentSource(l); o = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(source); parsedConclusion.put(format, o); } return o; } catch (final OWLOntologyCreationException e) { throw new OntologyParseException(e); } }
@Override public OWLOntology parseConclusionOntology(SerializationFormat format) throws OntologyParseException { try { final OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); manager.setOntologyLoaderConfiguration(manager.getOntologyLoaderConfiguration().setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT)); manager.getIRIMappers().clear(); ImportsHelper.loadImports(manager, this, format); OWLOntology o = parsedConclusion.get(format); if (o == null) { final String l = getConclusionOntology(format); if (l == null) { return null; } final StringDocumentSource source = new StringDocumentSource(l); o = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(source); parsedConclusion.put(format, o); } return o; } catch (final OWLOntologyCreationException e) { throw new OntologyParseException(e); } }
/** * @return a new OWLOntologyLoaderConfiguration from the builder current settings */ public OWLOntologyLoaderConfiguration buildLoaderConfiguration() { return new OWLOntologyLoaderConfiguration() .setAcceptingHTTPCompression(shouldAcceptHTTPCompression()) .setConnectionTimeout(getConnectionTimeout()) .setFollowRedirects(shouldFollowRedirects()) .setLoadAnnotationAxioms(shouldLoadAnnotations()) .setMissingImportHandlingStrategy(getMissingImportHandlingStrategy()) .setMissingOntologyHeaderStrategy(getMissingOntologyHeaderStrategy()) .setPriorityCollectionSorting(getPriorityCollectionSorting()) .setReportStackTraces(shouldReportStackTraces()) .setRetriesToAttempt(getRetriesToAttempt()) .setStrict(shouldParseWithStrictConfiguration()) .setTreatDublinCoreAsBuiltIn(shouldTreatDublinCoreAsBuiltin()) .setBannedParsers(getBannedParsers()) .setRepairIllegalPunnings(shouldRepairIllegalPunnings()); }
/** * @return a new OWLOntologyLoaderConfiguration from the builder current settings */ public OWLOntologyLoaderConfiguration buildLoaderConfiguration() { return new OWLOntologyLoaderConfiguration() .setAcceptingHTTPCompression(shouldAcceptHTTPCompression()) .setConnectionTimeout(getConnectionTimeout()) .setFollowRedirects(shouldFollowRedirects()) .setLoadAnnotationAxioms(shouldLoadAnnotations()) .setMissingImportHandlingStrategy(getMissingImportHandlingStrategy()) .setMissingOntologyHeaderStrategy(getMissingOntologyHeaderStrategy()) .setPriorityCollectionSorting(getPriorityCollectionSorting()) .setReportStackTraces(shouldReportStackTraces()) .setRetriesToAttempt(getRetriesToAttempt()) .setStrict(shouldParseWithStrictConfiguration()) .setTreatDublinCoreAsBuiltIn(shouldTreatDublinCoreAsBuiltin()) .setBannedParsers(getBannedParsers()) .setRepairIllegalPunnings(shouldRepairIllegalPunnings()); }
/** * @return a new OWLOntologyLoaderConfiguration from the builder current settings */ public OWLOntologyLoaderConfiguration buildLoaderConfiguration() { return new OWLOntologyLoaderConfiguration() .setAcceptingHTTPCompression(shouldAcceptHTTPCompression()) .setConnectionTimeout(getConnectionTimeout()) .setFollowRedirects(shouldFollowRedirects()) .setLoadAnnotationAxioms(shouldLoadAnnotations()) .setMissingImportHandlingStrategy(getMissingImportHandlingStrategy()) .setMissingOntologyHeaderStrategy(getMissingOntologyHeaderStrategy()) .setPriorityCollectionSorting(getPriorityCollectionSorting()) .setReportStackTraces(shouldReportStackTraces()) .setRetriesToAttempt(getRetriesToAttempt()) .setStrict(shouldParseWithStrictConfiguration()) .setTreatDublinCoreAsBuiltIn(shouldTreatDublinCoreAsBuiltin()) .setBannedParsers(getBannedParsers()) .setRepairIllegalPunnings(shouldRepairIllegalPunnings()); }