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public OWLObjectRenderer(OWLOntologyManager man, OWLOntology ontology, Writer writer) { this.ontology = ontology; this.writer = writer; writeEnitiesAsURIs = true; prefixManager = new DefaultPrefixManager(); if (!ontology.isAnonymous()) { String defPrefix = ontology.getOntologyID().getOntologyIRI() + "#"; prefixManager.setDefaultPrefix(defPrefix); } focusedObject = man.getOWLDataFactory().getOWLThing(); }
/** * Sets the default namespace. This will also bind the prefix name ":" to this prefix * @param defaultPrefix The namespace to be used as the default namespace. Note that * the value may be <code>null</code> in order to clear the default namespace. */ public void setDefaultPrefix(String defaultPrefix) { setPrefix(":", defaultPrefix); }
public void writePrefixes() { for (String prefix : prefixManager.getPrefixName2PrefixMap().keySet()) { writePrefix(prefix, prefixManager.getPrefix(prefix)); } }
public TurtleRenderer(OWLOntology ontology, OWLOntologyManager manager, Writer writer) { super(ontology, manager); this.writer = new PrintWriter(writer); pending = new HashSet<RDFResourceNode>(); pm = new DefaultPrefixManager(); if(!ontology.isAnonymous()) { pm.setDefaultPrefix(ontology.getOntologyID().getOntologyIRI() + "#"); } base = ""; }
ont = ontology; this.writer = writer; defaultPrefixManager = new DefaultPrefixManager(); prefixManager = defaultPrefixManager; OWLDocumentFormat ontologyFormat = ontology.getNonnullFormat(); .setPrefixComparator(((PrefixDocumentFormat) ontologyFormat).getPrefixComparator()); if (!ontology.isAnonymous() && prefixManager.getDefaultPrefix() == null) { String existingDefault = prefixManager.getDefaultPrefix(); String ontologyIRIString = ontology.getOntologyID().getOntologyIRI().get().toString(); if (existingDefault == null || !existingDefault.startsWith(ontologyIRIString)) { String defaultPrefix = ontologyIRIString; OWLOntologyManager manager = ontology.getOWLOntologyManager(); OWLDataFactory df = manager.getOWLDataFactory(); OWLAnnotationProperty labelProp = df.getOWLAnnotationProperty(RDFS_LABEL.getIRI()); labelMaker = new AnnotationValueShortFormProvider(Collections.singletonList(labelProp), prefLangMap, manager, defaultPrefixManager);
/** * @param ontology ontology * @param writer writer * @param format format */ public TurtleRenderer(OWLOntology ontology, Writer writer, OWLDocumentFormat format) { super(ontology, format, ontology.getOWLOntologyManager().getOntologyWriterConfiguration()); this.format = checkNotNull(format, "format cannot be null"); this.writer = new PrintWriter(writer); pm = new DefaultPrefixManager(); if (!ontology.isAnonymous()) { String ontologyIRIString = ontology.getOntologyID().getOntologyIRI().get().toString(); String defaultPrefix = ontologyIRIString; if (!ontologyIRIString.endsWith("/") && !ontologyIRIString.endsWith("#")) { defaultPrefix = ontologyIRIString + '#'; } pm.setDefaultPrefix(defaultPrefix); } if (format instanceof PrefixDocumentFormat) { PrefixDocumentFormat prefixFormat = (PrefixDocumentFormat) format; pm.copyPrefixesFrom(prefixFormat); pm.setPrefixComparator(prefixFormat.getPrefixComparator()); } base = ""; }
@Before public void setUp() throws Exception { OWLOntologyManager man = OWLManager.createOWLOntologyManager(); OWLDataFactory df = man.getOWLDataFactory(); ontology = man.createOntology(); PrefixManager pm = new DefaultPrefixManager(); pm.setDefaultPrefix("http://dl-learner.org/test/"); OWLClass clsA = df.getOWLClass("A", pm); OWLClass clsB = df.getOWLClass("B", pm); OWLClass clsC = df.getOWLClass("C", pm); OWLObjectProperty op1 = df.getOWLObjectProperty("p1", pm); OWLObjectProperty op2 = df.getOWLObjectProperty("p2", pm); // A(a_i), 1<=i<=10 for(int i = 0; i < 10; i++) { man.addAxiom(ontology, df.getOWLClassAssertionAxiom(clsA, df.getOWLNamedIndividual("a" + i, pm))); } // B(a_i), 1<=i<=8 for(int i = 0; i < 7; i++) { man.addAxiom(ontology, df.getOWLClassAssertionAxiom(clsB, df.getOWLNamedIndividual("a" + i, pm))); } }
public OWLObjectRenderer(OWLOntology ontology, Writer writer) { this.ontology = ontology; this.writer = writer; writeEnitiesAsURIs = true; prefixManager = new DefaultPrefixManager(); OWLOntologyFormat ontologyFormat = ontology.getOWLOntologyManager() .getOntologyFormat(ontology); if (ontologyFormat instanceof PrefixOWLOntologyFormat) { PrefixOWLOntologyFormat prefixFormat = (PrefixOWLOntologyFormat) ontologyFormat; for (String prefixName : prefixFormat.getPrefixNames()) { String prefix = prefixFormat.getPrefix(prefixName); prefixManager.setPrefix(prefixName, prefix); } } if (!ontology.isAnonymous()) { String defPrefix = ontology.getOntologyID().getOntologyIRI() + "#"; prefixManager.setDefaultPrefix(defPrefix); } focusedObject = ontology.getOWLOntologyManager().getOWLDataFactory() .getOWLThing(); }
/** * @param ontology ontology * @param writer writer * @param format format * @param contexts contexts */ public RioRenderer(final OWLOntology ontology, final RDFHandler writer, final OWLDocumentFormat format, final Resource... contexts) { super(ontology, format, ontology.getOWLOntologyManager().getOntologyWriterConfiguration()); OpenRDFUtil.verifyContextNotNull(contexts); this.contexts = contexts; this.writer = writer; pm = new DefaultPrefixManager(); if (!ontology.isAnonymous()) { String ontologyIRIString = ontology.getOntologyID().getOntologyIRI().get().toString(); String defaultPrefix = ontologyIRIString; if (!ontologyIRIString.endsWith("/") && !ontologyIRIString.endsWith("#")) { defaultPrefix = ontologyIRIString + '#'; } pm.setDefaultPrefix(defaultPrefix); } // copy prefixes out of the given format if it is a // PrefixOWLDocumentFormat if (format instanceof PrefixDocumentFormat) { PrefixDocumentFormat prefixFormat = (PrefixDocumentFormat) format; pm.copyPrefixesFrom(prefixFormat); pm.setPrefixComparator(prefixFormat.getPrefixComparator()); } }
public Map<OWLIndividual, List<OWLAxiom>> toRDF(String defaultNamespace){ Map<OWLIndividual, List<OWLAxiom>> ind2Axioms = new HashMap<>(); OWLDataFactory f = new OWLDataFactoryImpl(); String id = DigestUtils.md5Hex(hypothesis.toString()) + score.getAccuracy(); OWLNamedIndividual ind = f.getOWLNamedIndividual(IRI.create(defaultNamespace + id)); StringWriter sw = new StringWriter(); PrintWriter pw = new PrintWriter(sw); ManchesterOWLSyntaxObjectRenderer r = new ManchesterOWLSyntaxObjectRenderer(pw, new ManchesterOWLSyntaxPrefixNameShortFormProvider(new DefaultPrefixManager())); hypothesis.accept(r); OWLAxiom ax1 = f.getOWLClassAssertionAxiom(EnrichmentVocabulary.AddSuggestion, ind); OWLAxiom ax2 = f.getOWLDataPropertyAssertionAxiom(EnrichmentVocabulary.hasAxiom, ind, sw.toString()); OWLAnnotation anno = f.getOWLAnnotation(EnrichmentVocabulary.belongsTo, ind.getIRI()); // OWLAxiom ax2 = ax.getAnnotatedAxiom(Collections.singleton(anno)); OWLAxiom ax3 = f.getOWLDataPropertyAssertionAxiom(EnrichmentVocabulary.confidence, ind, score.getAccuracy()); List<OWLAxiom> axioms = new ArrayList<>(); axioms.add(ax1); axioms.add(ax2); axioms.add(ax3); ind2Axioms.put(ind, axioms); return ind2Axioms; }
public static void main(String[] args) throws Exception { StringRenderer.setRenderer(Rendering.DL_SYNTAX); OWLOntologyManager man = OWLManager.createOWLOntologyManager(); OWLDataFactory df = man.getOWLDataFactory(); PrefixManager pm = new DefaultPrefixManager(); pm.setDefaultPrefix("http://example.org/"); OWLClassExpression ce = df.getOWLObjectIntersectionOf( df.getOWLClass("A", pm), df.getOWLObjectSomeValuesFrom( df.getOWLObjectProperty("p", pm), df.getOWLObjectSomeValuesFrom( df.getOWLObjectProperty("r", pm), df.getOWLObjectIntersectionOf( df.getOWLClass("A", pm), df.getOWLClass("B", pm)))) ); System.out.println(ce); QueryTreeConverter converter = new QueryTreeConverter(); QueryTree<String> tree = converter.asQueryTree(ce); tree.dump(); }
public IRI getIRI(String curie) { if(curie.startsWith("<")) { return IRI.create(curie.substring(1, curie.length() - 1)); } int sep = curie.indexOf(':'); if(sep == -1) { if (getDefaultPrefix() != null) { return IRI.create(getDefaultPrefix() + curie); } else { return IRI.create(curie); } } else { String prefixName = curie.substring(0, sep + 1); if(!containsPrefixMapping(prefixName)) { throw new RuntimeException("Prefix not registered for prefix name: " + prefixName); } String prefix = getPrefix(prefixName); String localName = curie.substring(sep + 1); return IRI.create(prefix + localName); } }
@Before public void setUp() throws Exception { df = new OWLDataFactoryImpl(); PrefixManager pm = new DefaultPrefixManager(); pm.setDefaultPrefix("http://examples.org/ontology#"); clsA = df.getOWLClass("A", pm); clsB = df.getOWLClass("B", pm); clsC = df.getOWLClass("C", pm); propR = df.getOWLObjectProperty("r", pm); propS = df.getOWLObjectProperty("s", pm); indA = df.getOWLNamedIndividual("a", pm); indB = df.getOWLNamedIndividual("b", pm); renamer = new OWLAxiomRenamer(df); }
public static void main(String[] args) { try { DefaultPrefixManager pm = new DefaultPrefixManager("http://protege.cim3.net/file/pub/ontologies/tambis/tambis-full.owl#"); SimpleShortFormProvider sfp = new SimpleShortFormProvider(); // SimpleRenderer ren = new SimpleRenderer(); ManchesterOWLSyntaxOWLObjectRendererImpl ren = new ManchesterOWLSyntaxOWLObjectRendererImpl(); ren.setShortFormProvider(sfp); ToStringRenderer.getInstance().setRenderer(ren); OWLOntologyManager man = OWLManager.createOWLOntologyManager(); // OWLOntology ont = man.loadOntologyFromOntologyDocument(URI.create("http://www.co-ode.org/ontologies/pizza/pizza.owl")); OWLOntology ont = man.loadOntologyFromOntologyDocument(IRI.create("http://owl.cs.manchester.ac.uk/repository/download?ontology=http://protege.cim3.net/file/pub/ontologies/tambis/tambis-full.owl&format=RDF/XML")); System.out.println("Loaded ontology"); check(ont, new OWL2Profile()); check(ont, new OWL2DLProfile()); check(ont, new OWL2ELProfile()); check(ont, new OWL2QLProfile()); check(ont, new OWL2RLProfile()); } catch (OWLOntologyCreationException e) { e.printStackTrace(); } }
protected IRI getIRI(String inputName) { String name = inputName; boolean fullIRI = "<".equals(name); if (fullIRI) { name = consumeToken(); consumeToken(); } IRI uri = nameIRIMap.get(name); if (uri != null) { return uri; } if (fullIRI) { uri = IRI.create(name); } else { int colonIndex = name.indexOf(':'); if (colonIndex == -1) { name = ":" + name; } uri = pm.getIRI(name); } nameIRIMap.put(name, uri); return uri; }
public static void main(String[] args) { PrefixManager pm = new DefaultPrefixManager("http://www.sematicweb.org/myOnt#"); OWLIndividual matt = NamedIndividual("Matt", pm); OWLIndividual peter = NamedIndividual("Peter", pm); ObjectPropertyDomain(hasMother, person) ); manager.saveOntology(ont, System.out); manager.saveOntology(ont, IRI.create("file:/tmp/out.txt"));
@NonNull @Override public Optional<@NonNull IRI> variableName2IRI(@NonNull String variableName) { String defaultPrefix = prefixManager.getDefaultPrefix(); if (defaultPrefix != null && defaultPrefix.matches(".*[0-9A-Za-z]$")) return Optional.of(IRI.create("", "#" + variableName)); else return Optional.of(this.prefixManager.getIRI(variableName)); }
@Override public void updatePrefixes(@NonNull OWLOntology ontology) { OWLOntologyManager owlOntologyManager = ontology.getOWLOntologyManager(); OWLDocumentFormat ontologyFormat = owlOntologyManager.getOntologyFormat(ontology); this.prefixManager.clear(); if (this.defaultPrefix != null) this.prefixManager.setDefaultPrefix(this.defaultPrefix); if (ontologyFormat != null && ontologyFormat.isPrefixOWLOntologyFormat()) { PrefixDocumentFormat prefixOntologyFormat = ontologyFormat.asPrefixOWLOntologyFormat(); Map<@NonNull String, String> map = prefixOntologyFormat.getPrefixName2PrefixMap(); for (String prefix : map.keySet()) this.prefixManager.setPrefix(prefix, map.get(prefix)); } addSWRLAPIPrefixes(); }
private PrefixManager buildPrefixManager() { PrefixManager prefixManager = new DefaultPrefixManager(); OWLDocumentFormat format = ontology.getOWLOntologyManager().getOntologyFormat(ontology); if (format.isPrefixOWLOntologyFormat()) { Map<String, String> prefixMap = format.asPrefixOWLOntologyFormat().getPrefixName2PrefixMap(); for (String prefixName : prefixMap.keySet()) { prefixManager.setPrefix(prefixName, prefixMap.get(prefixName)); } } return prefixManager; } }
TestRunner(String prefix, String owlfile, OWLDatatype restrictionType, int maxNrOfSplits) throws OWLOntologyCreationException, ComponentInitException { this.prefix = prefix; this.restrictionType = restrictionType; this.maxNrOfSplits = maxNrOfSplits; // StringRenderer.setRenderer(Rendering.MANCHESTER_SYNTAX); // StringRenderer.setRenderer(Rendering.DL_SYNTAX); File file = new File(owlfile); OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(file); df = new OWLDataFactoryImpl(); pm = new DefaultPrefixManager(); pm.setDefaultPrefix(prefix); ks = new OWLAPIOntology(ontology); ks.init(); } TestRunner(String prefix, String owlfile, OWLDatatype restrictionType) throws OWLOntologyCreationException, ComponentInitException {