private synchronized void prepareModel() { m = ModelFactory.createDefaultModel(); m.read(new StringReader(baseModelString), ""); // m.read(GeneralJSONRDF.class.getResourceAsStream("rdf/base_usmf.rdf"), // ""); }
private LocalWorld() { File modelFile = new File(calculateComponentsDirectory(), FILENAME); model = createOntologyModel(); try { if (modelFile.exists()) model.read(new StringReader(readFileToString(modelFile)), null, ENCODING); } catch (IOException e) { logger.error("failed to construct local annotation world", e); } }
/** * Returns a pair of models. The first contains any statement containing at * least one blank node. The second contains all remaining statements. * @param g * @return */ private Model[] separateStatementsWithBlankNodes(Graph g) { Model gm = ModelFactory.createModelForGraph(g); Model blankNodeModel = ModelFactory.createDefaultModel(); Model nonBlankNodeModel = ModelFactory.createDefaultModel(); StmtIterator sit = gm.listStatements(); while (sit.hasNext()) { Statement stmt = sit.nextStatement(); if (!stmt.getSubject().isAnon() && !stmt.getObject().isAnon()) { nonBlankNodeModel.add(stmt); } else { blankNodeModel.add(stmt); } } Model[] result = new Model[2]; result[0] = blankNodeModel; result[1] = nonBlankNodeModel; return result; }
void applyReasoning(Reasoning r) { switch(r) { case rdfs: this.jenaModel = ModelFactory.createRDFSModel(this.jenaModel); break; case owl: this.jenaModel = ModelFactory.createInfModel(ReasonerRegistry.getOWLReasoner(), this.jenaModel); break; default: break; } }
/** * @param rdfXml * An RDF/XML String to be added to the model * @throws RDFHelperException * If <code>model</code> is <code>null</code> or empty. */ public void addToModel(final String rdfXml) { if (this.model == null) { this.model = ModelFactory.createDefaultModel(); } if (this.tempModel == null) { this.tempModel = ModelFactory.createDefaultModel(); } if ((rdfXml != null) && !rdfXml.equals("")) { final StringReader sr = new StringReader(rdfXml); this.model.read(sr, BackEndJenaHelper.BASE, BackEndJenaHelper.SYNTAX); sr.close(); } else { throw new RDFHelperException("Args was null or empty."); } }
public void setContents(String contentsAsString) { if (contentsAsString.startsWith("<rdf:RDF")) { Model model = ModelFactory.createDefaultModel(); model.read(new StringReader(contentsAsString), null); Set<Resource> subjects = model.listSubjects().toSet(); Set<RDFNode> objects = model.listObjects().toSet(); subjects.removeAll(objects); node = subjects.iterator().next(); } else { node = RdfUtils.createTypedLiteral(contentsAsString); } }
Model model = ModelFactory.createDefaultModel(); model.read(new StringReader(rdfString), String.format("%s#",nameSpace)); finally {qexec.close();} StringWriter writer = new StringWriter(); model.write(writer); return writer.toString();
@Override public final T fromString(final ConversionContext context, final String body) throws MessageConversionException { try { final Model model=ModelFactory.createDefaultModel(); RDFDataMgr. read( model, new StringReader(body), context.base().toString(), FORMAT.getLang()); return parse(model,getTargetResource(model)); } catch (final RiotException e) { throw new MessageConversionException("Could not parse body '"+body+"' as Turtle",e); } catch (final ValidationException e) { throw new InvalidDefinitionFoundException(messageType(),e); } }
/** * Test method for * {@link net.sf.taverna.t2.reference.sadi.RDFReference#setContents(java.lang.String)} * . */ @Test public void testSetContents() { rdfReference.setContents("5"); assertEquals("5", rdfReference.getContents()); rdfReference.setContents(rdfURIResourceString); assertTrue(rdfReference.getContents().contains( "UniProt_Record rdf:about=\"http://purl.uniprot.org/uniprot/P12345\"")); rdfReference.setContents(rdfResourceString); Model model1 = ModelFactory.createDefaultModel().read(new StringReader(rdfResourceString), null); Model model2 = ModelFactory.createDefaultModel().read( new StringReader(rdfReference.getContents()), null); assertTrue(model1.isIsomorphicWith(model2)); }
String reifiedModelFileName = destinationFileName.substring(0, dot) + "-reified" + destinationFileName.substring(dot); logModel = ModelFactory.createDefaultModel(); String logNs = properties.getProperty("default.namespace"); logModel.setNsPrefix("log", logNs); if (incremental) { InputStream isMap = FileManager.get().open(reifiedModelFileName); resultModel = ModelFactory.createDefaultModel(); try { resultModel.read(isMap, null, "N-TRIPLE"); } catch (Exception e) { log.error(e.toString()); log.error("Error reading last run model. Cannot proceed with incremental, going for a full run."); // Please change property default.incremental in file r2rml.properties to false. resultModel.setNsPrefixes(mappingDocument.getPrefixes()); incremental = false; writeReifiedModel = true; stmtIter.close(); Long reifiedModelFileSizeInLogFile = Long.valueOf(stmt2.getObject().toString()); Long actualReifiedModelFileSize = new Long(new File(reifiedModelFileName).length()); if (reifiedModelFileSizeInLogFile.longValue() != actualReifiedModelFileSize.longValue()) { Model cleanModel = ModelFactory.createDefaultModel(); logModel = ModelFactory.createDefaultModel();
thisMetaPage.addProperty( API.definition, uriForDefinition ); URI emv_uri = URIUtils.replaceQueryParam( URIUtils.newURI(thisMetaPage.getURI()), "_metadata", "all" ); thisMetaPage.addProperty( API.extendedMetadataVersion, metaModel.createResource( emv_uri.toString() ) ); thisMetaPage.addProperty( RDF.type, API.Page ); Resource l = licence.inModel(thisMetaPage.getModel()); thisMetaPage.addProperty(DCTerms.license, l); thisMetaPage.getModel().add(ResourceUtils.reachableClosure(l)); for (Resource d: notices) { thisMetaPage.addProperty(ELDA_API.notice, d); thisMetaPage.getModel().add(ResourceUtils.reachableClosure(d)); Resource exec = metaModel1.createResource(); Model versionsModel = ModelFactory.createDefaultModel(); Model formatsModel = ModelFactory.createDefaultModel(); Model bindingsModel = ModelFactory.createDefaultModel(); Model execution = ModelFactory.createDefaultModel(); mu.addGraph(execution.getGraph()); Model toScan = ModelFactory.createModelForGraph(mu); em.addBindings( toScan, bindingsModel, exec, cc ); Model toRemove = ModelFactory.createDefaultModel();
try { Model model = ModelFactory.createDefaultModel(); model.read((in), ""); StmtIterator iter; Statement stmt; iter = model.listStatements(); while (iter.hasNext()) { stmt = (Statement) iter.next(); String sub = stmt.getSubject().getURI(); String obj = stmt.getObject().toString(); if (sub != null) { try { if (stmt.getPredicate().getURI().indexOf("subClassOf") > 0) {
protected static void addRangeTypes( Model result, Model schema ) { Model toAdd = ModelFactory.createDefaultModel(); for (StmtIterator it = schema.listStatements( ANY, RDFS.range, ANY ); it.hasNext();) { Statement s = it.nextStatement(); RDFNode type = s.getObject(); Property property = s.getSubject().as( Property.class ); for (StmtIterator x = result.listStatements( ANY, property, ANY ); x.hasNext();) { RDFNode ob = x.nextStatement().getObject(); if (ob.isResource()) toAdd.add( (Resource) ob, RDF.type, type ); } } result.add( toAdd ); }
ProvenanceVocab.EXECUTED_PROCESS_RUN.getURI(), "urn:processrun"); Model model = ModelFactory.createDefaultModel(); Resource workflowRun = model.createResource("urn:workflowrun"); String workFlowRunUri = workflowRun.getURI(); Resource processRun = model.createResource("urn:processrun"); Model retrievedGraphModel = metadataService .retrieveGraphModel(workFlowRunUri); retrievedGraphModel.write(System.out, "N3"); retrievedGraphModel.contains(workflowRun, ProvenanceVocab.EXECUTED_PROCESS_RUN, processRun); StmtIterator listStatements = retrievedGraphModel.listStatements(); int statementsCount = 0; while (listStatements.hasNext()) { listStatements.next(); statementsCount++; listStatements.close(); assertEquals(2, statementsCount); metadataService.removeGraph(workFlowRunUri);
private void verbModel(Model model, String verb) { Model m = ModelFactory.createDefaultModel(); int testLimit = 1000; StmtIterator stmtIt = model.listStatements(); int count = 0; try { while (stmtIt.hasNext()) { count++; m.add(stmtIt.nextStatement()); if (count % testLimit == 0 || !stmtIt.hasNext()) { StringWriter sw = new StringWriter(); m.write(sw, "N-TRIPLE"); StringBuffer updateStringBuff = new StringBuffer(); String graphURI = graph.getGraphURI(); updateStringBuff.append(verb + " DATA { " + ((graphURI != null) ? "GRAPH <" + graphURI + "> { " : "")); updateStringBuff.append(sw); updateStringBuff.append(((graphURI != null) ? " } " : "") + " }"); String updateString = updateStringBuff.toString(); //log.info(updateString); graph.executeUpdate(updateString); m.removeAll(); } } } finally { stmtIt.close(); } }
private static URI getSWRLVariable(String argument){ Resource variableResource = null; String variableString = argument.substring(1); variableResource = ModelFactory.createDefaultModel().createResource(kb.getPrefixURI("var")+variableString); try { return new URI(variableResource.getURI()); } catch (URISyntaxException e) { // TODO Auto-generated catch block e.printStackTrace(); return null; } }
private Model normaliseLiterals(Model m) { Model result = ModelFactory.createDefaultModel(); for (StmtIterator it = m.listStatements(); it.hasNext();) { result.add(normaliseLiterals(it.next())); } return result; }
new SimpleSelector(null, ResourceMapConstants.IS_DESCRIBED_BY_PROPERTY, (Object) null); StmtIterator sItr = m.listStatements(isDescribedBySelector); while (sItr.hasNext()) { final Statement stmt = sItr.next(); final String rdfUri = stmt.getObject().toString(); if (loadedRems.contains(rdfUri)) { LOG.trace("Already loaded ReM from {}", rdfUri); Model loaded = ModelFactory.createDefaultModel(); RDFReader reader = loaded.getReader(); reader.setProperty(ResourceMapConstants.JENA_ERROR_MODE_URI, ResourceMapConstants.JENA_ERROR_MODE_STRICT); ResourceMapUtil.loadRDF(reader, loaded, baseDir, rdfUri); loadedRems.add(rdfUri); m = load(m.union(loaded), baseDir, loadedRems);
Model m = ModelFactory.createDefaultModel(); for (StmtIterator i = r.listProperties(); i.hasNext(); ) { Statement s = i.nextStatement(); m.add( s ); if (s.getObject() instanceof Resource) { queue.add( s.getObject() );
Model model = ModelFactory.createDefaultModel(); Resource cC = model.createResource(ONDEXRdf.ccToUri(graphURI, cc)); rdfMetadata(cC, cc); if (cc.getSpecialisationOf() != null) cC.addProperty(RDFS.subClassOf, model.createResource(ONDEXRdf.ccToUri(graphURI, cc.getSpecialisationOf()))); Resource rT = model.createResource(ONDEXRdf.rtToUri(graphURI, rt)); rdfMetadata(rT, rt); if (rt.getSpecialisationOf() != null) rT.addProperty(RDFS.subPropertyOf, model.createResource(ONDEXRdf.rtToUri(graphURI, rt.getSpecialisationOf()))); cRap(cR, model.createProperty(ONDEXRdf.annotationUri), c.getAnnotation()); for(ConceptAccession ca : c.getConceptAccessions()) { cR.addProperty(model.createProperty(ONDEXRdf.conceptAccessionUri), ca.getAccession()); Statement stmt = model.createStatement(f, rt, t); model.add(stmt); ReifiedStatement rel = stmt.createReifiedStatement(ONDEXRdf.relationToUri(graphURI, r));