com.hp.hpl.jena.rdf.model.ResIterator Java Examples

protected void writeRDFStatements(Model model, PrintWriter writer) {
	ResIterator rIter = model.listSubjects();
	@SuppressWarnings("unused")
	Resource nextR = null;
	while (rIter.hasNext())
		writeRDFStatements(model, rIter.nextResource(), writer);
}
 

protected void doGet(HttpServletRequest request, HttpServletResponse response) 
		throws ServletException, IOException {
	D2RServer server = D2RServer.fromServletContext(getServletContext());
	server.checkMappingFileChanged();
	if (request.getPathInfo() == null) {
		response.sendError(404);
		return;
	}
	String classMapName = request.getPathInfo().substring(1);
	int limit = server.getConfig().getLimitPerClassMap();
	Model resourceList = server.getMapping().getResourceCollection(classMapName).getInventoryModel(limit);
	if (resourceList == null) {
		response.sendError(404, "Sorry, class map '" + classMapName + "' not found.");
		return;
	}
	Map<String,String> resources = new TreeMap<String,String>();
	ResIterator subjects = resourceList.listSubjects();
	while (subjects.hasNext()) {
		Resource resource = subjects.nextResource();
		if (!resource.isURIResource()) {
			continue;
		}
		String uri = resource.getURI();
		Statement labelStmt = PageServlet.getBestLabel(resource);
		String label = (labelStmt == null) ? resource.getURI() : labelStmt.getString();
		resources.put(uri, label);
	}
	Map<String,String> classMapLinks = new TreeMap<String,String>();
	for (String name: server.getMapping().getResourceCollectionNames()) {
		classMapLinks.put(name, server.baseURI() + "directory/" + name);
	}
	VelocityWrapper velocity = new VelocityWrapper(this, request, response);
	Context context = velocity.getContext();
	context.put("rdf_link", server.baseURI() + "all/" + classMapName);
	context.put("classmap", classMapName);
	context.put("classmap_links", classMapLinks);
	context.put("resources", resources);
	context.put("limit_per_class_map", server.getConfig().getLimitPerClassMap());
	velocity.mergeTemplateXHTML("directory_page.vm");
}
 

private static Set<Resource> generatePartitions(Model m, Resource type,
		Property p) {
	Set<Resource> partitions = new HashSet<Resource>();
	ResIterator classIt = m.listResourcesWithProperty(RDF.type, type);
	while (classIt.hasNext()) {
		Resource classMap = classIt.next();
		StmtIterator pIt = classMap.listProperties(p);
		while (pIt.hasNext()) {
			partitions.add((Resource) pIt.next().getObject());
		}
	}
	return partitions;
}
 

protected Resource findServerResource() {
	ResIterator it = this.model.listSubjectsWithProperty(RDF.type,
			D2RConfig.Server);
	if (!it.hasNext()) {
		return null;
	}
	return it.nextResource();
}
 

protected Resource findDatabaseResource() {
	ResIterator it = this.model.listSubjectsWithProperty(RDF.type,
			D2RQ.Database);
	if (!it.hasNext()) {
		return null;
	}
	return it.nextResource();
}
 

public Set<Resource> listResourcesWith(Property... properties) {
	Set<Resource> result = new HashSet<Resource>();
	for (Property property: properties) {
		ResIterator it = model.listResourcesWithProperty(property);
		while (it.hasNext()) {
			result.add(it.next());
		}
	}
	return result;
}
 

private void checkForSpuriousTypes() {
	// This doesn't catch spurious subclass triples, e.g., rr:SubjectMap,
	// rr:R2RMLView.
	for (ComponentType type: ComponentType.values()) {
		ResIterator it = model.listResourcesWithProperty(RDF.type, type.asResource());
		while (it.hasNext()) {
			Resource r = it.next();
			if (mapping.getMappingComponent(r, type) == null) {
				report.report(Problem.SPURIOUS_TYPE, r, RDF.type, type.asResource());
			}
		}
	}
	remainingTriples.removeAll(null, RDF.type, (RDFNode) null);
}
 

public static Set<Resource> getAllEntitiesOfType(Model model, String type) {
    Set<Resource> ret = new HashSet<Resource>();

    ResIterator list = model.listSubjectsWithProperty(RDF.type, model.createResource(type));
    while (list.hasNext()) {
        Resource entity = list.next();
        ret.add(entity);
    }

    return ret;
}
 

/**
 * Run the RDF generator pipeline for clinical trial data Before running
 * this, run the Mapping Discovery Test first to generate the mapping file
 * for clinical trials.
 *
 * @throws SAXException
 * @throws IOException
 * @throws ParserConfigurationException
 */
@Test
public void test_generateRdfs_clinical_trials() throws SAXException, IOException, ParserConfigurationException {
    // Setup deserializer
    mappingDeserialization = new XmlBasedMappingDeserialization(
            new FileInputStream("output/clinicaltrials-mapping.xml"), parser);

    Document dataDocument = parser.parse(RdfGeneratorTest2.class.getResourceAsStream(
            "/clinicaltrials/data/content.xml"), 10);
    rdfGenerator = new RdfGenerator(new DataDocument(dataDocument), new XmlBasedMapping());

    // Add steps
    rdfGenerator.addStep(mappingDeserialization);
    rdfGenerator.addStep(rdfGeneration);

    // Generate
    rdfGenerator.generateRdfs();

    // Verify
    Model model = TDBFactory.createModel(testTdbDir);
    Assert.assertFalse("No RDF was generated. TDB directory: " + testTdbDir, model.isEmpty());

    ResIterator iter = model.listResourcesWithProperty(RDF.type);
    while (iter.hasNext()) {
        Resource resource = iter.nextResource();
        System.out.println(resource.getLocalName());
        StmtIterator iterStm = resource.listProperties();
        while (iterStm.hasNext()) {
            System.out.println(iterStm.nextStatement().toString());
        }
    }
}
 

/**
 * Run the RDF generator pipeline for clinical trial data Before running
 * this, run the Mapping Discovery Test first to generate the mapping file
 * for clinical trials.
 *
 * @throws SAXException
 * @throws IOException
 * @throws ParserConfigurationException
 */
@Test
public void test_generateRdfs_clinical_trials() throws SAXException, IOException, ParserConfigurationException {
    // Setup deserializer
    mappingDeserialization = new XmlBasedMappingDeserialization(
            new FileInputStream("output/clinicaltrials-mapping.xml"), parser);

    Document dataDocument = parser.parse(RdfGeneratorTest.class.getResourceAsStream(
            "/clinicaltrials/data/content.xml"), 10);
    rdfGenerator = new RdfGenerator(new DataDocument(dataDocument), new XmlBasedMapping());

    // Add steps
    rdfGenerator.addStep(mappingDeserialization);
    rdfGenerator.addStep(rdfGeneration);

    // Generate
    rdfGenerator.generateRdfs();

    // Verify
    Model model = TDBFactory.createModel(testTdbDir);
    Assert.assertFalse("No RDF was generated. TDB directory: " + testTdbDir, model.isEmpty());

    ResIterator iter = model.listResourcesWithProperty(RDF.type);
    while (iter.hasNext()) {
        Resource resource = iter.nextResource();
        System.out.println(resource.getLocalName());
        StmtIterator iterStm = resource.listProperties();
        while (iterStm.hasNext()) {
            System.out.println(iterStm.nextStatement().toString());
        }
    }
}
 

private Map<String, String> populateColorPairMatcher() {
	Map<String, String> result = new HashMap<String, String>();
	ResIterator iter = confModel.listSubjectsWithProperty(confModel.createProperty(confModel.getNsPrefixURI("conf"), "hasColorPair"));
	while (iter.hasNext()) {
		Resource res = iter.next();
		NodeIterator values = confModel.listObjectsOfProperty(res, confModel.createProperty(confModel.getNsPrefixURI("conf"), "hasColorPair"));
		while (values.hasNext()) {
			RDFNode node = values.next();
			result.put(res.toString(), node.toString());
			break;
		}
	}
	return result;
}
 

@Test
// Run test_discoverMapping_multiple_XBRLs to generate the mapping file before running
// this test.
public void test_generateRdfs_multiple_XBRLs() throws SAXException, IOException, ParserConfigurationException {
    // Setup deserializer
    mappingDeserialization = new XmlBasedMappingDeserialization(
            new FileInputStream("output/xbrl-mapping.xml"), parser);

    Document fb2013 = parser.parse(BasicEntityDiscoveryTest.class.getResourceAsStream(
            "/secxbrls/data/fb-20131231.xml"), -1);

    Document msft2013 = parser.parse(BasicEntityDiscoveryTest.class.getResourceAsStream(
            "/secxbrls/data/msft-20130630.xml"), -1);

    Document goog2013 = parser.parse(BasicEntityDiscoveryTest.class.getResourceAsStream(
            "/secxbrls/data/goog-20131231.xml"), -1);

    rdfGenerator = new RdfGenerator(new XmlBasedMapping());

    // Add document and steps
    rdfGenerator.addDataDocument(new DataDocument(fb2013, "http://example.org/resource/fb-20131231"))
            .addDataDocument(new DataDocument(msft2013, "http://example.org/resource/msft-20130630"))
            .addDataDocument(new DataDocument(goog2013, "http://example.org/resource/goog-20131231"))
            .addStep(mappingDeserialization)
            .addStep(rdfGeneration);

    // Generate
    rdfGenerator.generateRdfs();

    // Verify
    Model model = TDBFactory.createModel(testTdbDir);
    Assert.assertFalse("No RDF was generated. TDB directory: " + testTdbDir, model.isEmpty());

    ResIterator iter = model.listResourcesWithProperty(RDF.type);
    while (iter.hasNext()) {
        Resource resource = iter.nextResource();
        System.out.println(resource.getLocalName());
        StmtIterator iterStm = resource.listProperties();
        while (iterStm.hasNext()) {
            System.out.println(iterStm.nextStatement().toString());
        }
    }

}
 

@Test
// Run test_discoverMapping_multiple_XBRLs to generate the mapping file before running
// this test.
public void test_generateRdfs_multiple_XBRLs() throws SAXException, IOException, ParserConfigurationException {
    // Setup deserializer
    mappingDeserialization = new XmlBasedMappingDeserialization(
            new FileInputStream("output/xbrl-mapping.xml"), parser);

    Document fb2013 = parser.parse(BasicEntityDiscoveryTest.class.getResourceAsStream(
            "/secxbrls/data/fb-20131231.xml"), -1);

    Document msft2013 = parser.parse(BasicEntityDiscoveryTest.class.getResourceAsStream(
            "/secxbrls/data/msft-20130630.xml"), -1);

    Document goog2013 = parser.parse(BasicEntityDiscoveryTest.class.getResourceAsStream(
            "/secxbrls/data/goog-20131231.xml"), -1);

    rdfGenerator = new RdfGenerator(new XmlBasedMapping());

    // Add document and steps
    rdfGenerator.addDataDocument(new DataDocument(fb2013, "http://example.org/resource/fb-20131231"))
            .addDataDocument(new DataDocument(msft2013, "http://example.org/resource/msft-20130630"))
            .addDataDocument(new DataDocument(goog2013, "http://example.org/resource/goog-20131231"))
            .addStep(mappingDeserialization)
            .addStep(rdfGeneration);

    // Generate
    rdfGenerator.generateRdfs();

    // Verify
    Model model = TDBFactory.createModel(testTdbDir);
    Assert.assertFalse("No RDF was generated. TDB directory: " + testTdbDir, model.isEmpty());

    ResIterator iter = model.listResourcesWithProperty(RDF.type);
    while (iter.hasNext()) {
        Resource resource = iter.nextResource();
        System.out.println(resource.getLocalName());
        StmtIterator iterStm = resource.listProperties();
        while (iterStm.hasNext()) {
            System.out.println(iterStm.nextStatement().toString());
        }
    }

}
 

public LinkedList<LogicalTableView> findLogicalTableViews() {
	LinkedList<LogicalTableView> results = new LinkedList<LogicalTableView>();
	Property sqlQuery = mapModel.getProperty(rrNs + "sqlQuery");
	ResIterator iter = mapModel.listSubjectsWithProperty(sqlQuery);
	while (iter.hasNext()) {
	    Resource r = iter.nextResource();
	    NodeIterator iter2 = mapModel.listObjectsOfProperty(r, sqlQuery);
	    while (iter2.hasNext()) { //should only have one
	    	RDFNode rn = iter2.next();
	    	LogicalTableView logicalTableView = new LogicalTableView();
	    	logicalTableView.setUri(r.getURI());
	    	String query = rn.asLiteral().toString();
	    	//Windows standard line separator is "\r\n"--a carriage-return followed by a linefeed. The regex below matches any number of either of the two characters
	    	query = query.replaceAll("[\r\n]+", " ");
	    	if (query.indexOf(';') != -1) query = query.replace(';', ' ');
	    	
	    	log.info("Testing query: <" + r.getURI() + "> with value: " + query);
	    	db.testQuery(query);
	    	
	    	SelectQuery selectQuery = new SelectQuery(query, properties);

	    	//if the dump is incremental, add an order by to ensure results are retrieved in the same order
	    	if (properties.containsKey("jena.jena.storeOutputModelUsingTdb")
	    		&& properties.getProperty("jena.jena.storeOutputModelUsingTdb").contains("false")
	    		&& properties.containsKey("default.incremental")
	    		&& properties.getProperty("default.incremental").contains("true")) {
	    		String q = selectQuery.getQuery();
	    		if (q.toLowerCase().indexOf("order by") == -1) {
	    			String fieldName = selectQuery.getFields().get(0).getName();
	    			int as = fieldName.toLowerCase().indexOf(" as ");
	    			if (as > -1) {
	    				fieldName = fieldName.substring(0, as);
		    			q += " order by " + fieldName;
	    				selectQuery.setQuery(q);
	    				log.info("Added ORDER BY to query that now is: " + q);
	    			}
	    		}
	    	}
	    	
	    	logicalTableView.setSelectQuery(selectQuery);
	    	results.add(logicalTableView);
	    }
	}
	return results;
}