public void hospitalQueryProcess() {
Model model = ModelFactory.createDefaultModel();
InputStream in = FileManager.get().open("cancer_rdf.owl");
if (in == null) {
throw new IllegalArgumentException("File: not found");
}
// read the RDF/XML file
model.read(in, null);
for (int i = 0; i < treatment_list.size(); i++) {
String treatment_name = treatment_list.get(i);
issueSPARQLTreatment_Hospital(model, treatment_name, hos_treatment);
}
// System.out.println("Hospital list for treatments: " + Hospital_list);
System.out.println("Hospital map for treatments: " + hos_treatment);
Set set = hos_treatment.entrySet();
// Get an iterator
Iterator i = set.iterator();
// Display elements
while (i.hasNext()) {
Map.Entry me = (Map.Entry) i.next();
System.out.print(me.getKey() + ": ");
System.out.println(me.getValue());
if (!Hospital_list.contains(me.getValue().toString())) {
Hospital_list.add(me.getValue().toString());
}
}
System.out.println("Hospital list for treatments: " + Hospital_list);
model.close();
}
/**
* Upload the given file of n3 data.
*
* @param sFileName the name of the file to upload.
* @param sMeetingID the id of the meeting whose data is being uploaded.
* @throws MalformedURLException {@Link #uploadModel(com.hp.hpl.jena.rdf.model.Model,String)
* uploadModel} method throw it back to this method.
*/
public void uploadFile(String sFileName, String sMeetingID) throws MalformedURLException {
com.hp.hpl.jena.rdf.model.Model model =
com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel();
model.read("file:///" + sFileName, "N3"); // $NON-NLS-1$ //$NON-NLS-2$
uploadModel(model, sMeetingID);
model.close();
}
/**
* Write the given model to a file with the given name.
*
* @param model the model to write to a file.
* @param sFileName the name of the file to write to.
* @throws FileNodeFountException if a new FileOutputStream cannot be created.
* @throws IOException if the FileOutputStream cannot be closed.
*/
public void writeFile(com.hp.hpl.jena.rdf.model.Model model, String sFileName)
throws FileNotFoundException, IOException {
FileOutputStream out = new FileOutputStream(sFileName);
model.write(out, "N3"); // $NON-NLS-1$
model.close();
out.close();
}
@After
public void tearDown() throws Exception {
if (httpclient != null) {
httpclient.getConnectionManager().shutdown();
httpclient = null;
}
if (model != null) {
model.close();
model = null;
}
}
/**
* @see org.caboto.jena.db.Database#updateProperty(java.lang.String, java.lang.String,
* com.hp.hpl.jena.rdf.model.Property, com.hp.hpl.jena.rdf.model.RDFNode)
*/
public boolean updateProperty(String uri, String resourceUri, Property property, RDFNode value) {
try {
log.info("Updting property in model: " + uri + " " + reasoner);
Data data = getData();
Model m = data.getModel(uri);
if (!m.containsResource(ResourceFactory.createResource(resourceUri))) {
m.close();
data.close();
return false;
}
Resource resource = m.getResource(resourceUri);
if (resource.hasProperty(property)) {
resource.getProperty(property).changeObject(value);
} else {
resource.addProperty(property, value);
}
m.close();
data.close();
return true;
} catch (DataException e) {
e.printStackTrace();
return false;
}
}
public boolean deleteAll(String uri) {
try {
log.info("Deleting model: " + uri + " " + reasoner);
Data data = getData();
Model m = data.getModel(uri);
m.removeAll();
if (reasoner != null) redoInferred(uri, m, true);
m.close();
data.close();
return true;
} catch (DataException e) {
e.printStackTrace();
return false;
}
}
/**
* @see org.caboto.jena.db.Database#addModel(java.lang.String, com.hp.hpl.jena.rdf.model.Model)
*/
public boolean addModel(String uri, Model model) {
try {
log.info("Adding data to model: " + uri + " " + reasoner);
Data data = getData();
Model m = data.getModel(uri);
m.withDefaultMappings(model);
m.add(model);
if (reasoner != null) redoInferred(uri, m, false);
m.close();
data.close();
return true;
} catch (DataException e) {
e.printStackTrace();
return false;
}
}
/**
* Upload the given model to the triplestore
*
* @param model, the model to upload.
* @param sMeetingID the id of the meeting whose data is being uploaded.
* @throws MalformedURLException if the urls used to create the HttpRemove and HttpAdd is
* malformed.
*/
public void uploadModel(com.hp.hpl.jena.rdf.model.Model oModel, String sMeetingID)
throws MalformedURLException {
// System.out.println("About to try and upload: "+oModel.toString());
com.hp.hpl.jena.rdf.model.Model oInnerModel = ModelFactory.createDefaultModel();
Resource meeting = oInnerModel.createResource(sMeetingID);
Property comp_is_proc =
oInnerModel.createProperty(MEMETIC_NS, "compendium-is-processed"); // $NON-NLS-1$
meeting.addProperty(comp_is_proc, "true"); // $NON-NLS-1$
HttpRemove removeOp = new HttpRemove(sUrl);
removeOp.setModel(oInnerModel);
removeOp.exec();
oInnerModel.close();
HttpAdd addOp = new HttpAdd(sUrl);
addOp.setModel(oModel);
addOp.exec();
}
public void start() {
String directory = TriplestoreUtil.getTriplestoreLocation();
Dataset dataset = TDBFactory.createDataset(directory);
ClientConfig clientConfig = new ClientConfig();
for (Class providerClass : JenaProvidersRegistry.getProviders()) {
clientConfig.register(providerClass);
}
Client rdfclient = ClientBuilder.newClient(clientConfig);
System.out.println(
AMESimAdapterAndTDBSubversionSyncClientWithRevision.oslcServiceProviderCatalogURI);
Response response =
rdfclient
.target(
AMESimAdapterAndTDBSubversionSyncClientWithRevision.oslcServiceProviderCatalogURI)
.request("application/rdf+xml")
.get();
System.out.println(response.getStatus());
ServiceProviderCatalog serviceProviderCatalog =
response.readEntity(ServiceProviderCatalog.class);
// list to collect all AMESim resources
ArrayList<AbstractResource> oslcResourcesArrayList = new ArrayList<AbstractResource>();
for (ServiceProvider serviceProvider : serviceProviderCatalog.getServiceProviders()) {
System.out.println("serviceProvider " + serviceProvider.getAbout());
if (serviceProvider.getAbout().toString().endsWith("/serviceProviders/" + fileName)) {
for (Service service : serviceProvider.getServices()) {
for (QueryCapability queryCapability : service.getQueryCapabilities()) {
System.out.println(queryCapability.getQueryBase());
Response queryCapabilityResponse =
rdfclient
.target(queryCapability.getQueryBase())
.request("application/rdf+xml")
.get();
System.out.println(queryCapabilityResponse.getStatus());
if (queryCapability.getQueryBase().toString().endsWith("components")) {
AMESimComponent[] oslcResources =
queryCapabilityResponse.readEntity(AMESimComponent[].class);
oslcResourcesArrayList.addAll(
Arrays.asList(getResourcesWithVersion(oslcResources, revision)));
}
// else if(queryCapability.getQueryBase().toString().endsWith("lines")){
// AMESimLine[] oslcResources =
// queryCapabilityResponse.readEntity(AMESimLine[].class);
//
// oslcResourcesArrayList.addAll(Arrays.asList(getResourcesWithVersion(oslcResources,
// revision)));
// }
else if (queryCapability.getQueryBase().toString().endsWith("parameters")) {
AMESimParameter[] oslcResources =
queryCapabilityResponse.readEntity(AMESimParameter[].class);
oslcResourcesArrayList.addAll(
Arrays.asList(getResourcesWithVersion(oslcResources, revision)));
}
// else if(queryCapability.getQueryBase().toString().endsWith("outputports")){
// AMESimOutputPort[] oslcResources =
// queryCapabilityResponse.readEntity(AMESimOutputPort[].class);
//
// oslcResourcesArrayList.addAll(Arrays.asList(getResourcesWithVersion(oslcResources,
// revision)));
// }
// else if(queryCapability.getQueryBase().toString().endsWith("inputports")){
// AMESimInputPort[] oslcResources =
// queryCapabilityResponse.readEntity(AMESimInputPort[].class);
//
// oslcResourcesArrayList.addAll(Arrays.asList(getResourcesWithVersion(oslcResources,
// revision)));
// }
// else if(queryCapability.getQueryBase().toString().endsWith("model")){
// AMESimModel oslcResource =
// queryCapabilityResponse.readEntity(AMESimModel.class);
// oslcResourcesArrayList.add(getResourceWithVersion(oslcResource,revision));
// }
}
}
}
}
Object[] objects = oslcResourcesArrayList.toArray();
Model model;
Model tdbModel = dataset.getDefaultModel();
try {
model = JenaModelHelper.createJenaModel(objects);
tdbModel.add(model);
} catch (IllegalAccessException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IllegalArgumentException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (InvocationTargetException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (DatatypeConfigurationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (OslcCoreApplicationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
tdbModel.close();
dataset.close();
}
protected void tearDown() throws java.lang.Exception {
model.close();
model = null;
conn.cleanDB();
conn.close();
}
// Using Stardog with the [Jena](http://jena.apache.org) API
// -------------------
// In this example we'll show how to use the Stardog Jena API bindings.
public static void main(String[] args) throws Exception {
// Creating a Server
// -----------------
// You'll need a server to connect to, obviously. For the example, lets create an embedded
// server.
Server aServer = Stardog.buildServer().bind(SNARLProtocolConstants.EMBEDDED_ADDRESS).start();
try {
// Next we'll establish a admin connection to Stardog so we can create a database to use for
// the example
AdminConnection aAdminConnection =
AdminConnectionConfiguration.toEmbeddedServer().credentials("admin", "admin").connect();
try {
// If the database already exists, we'll drop it and create a fresh copy
if (aAdminConnection.list().contains("testJena")) {
aAdminConnection.drop("testJena");
}
aAdminConnection.createMemory("testJena");
} finally {
aAdminConnection.close();
}
// Now we open a Connection our new database
Connection aConn =
ConnectionConfiguration.to("testJena").credentials("admin", "admin").connect();
// Then we obtain a Jena `Model` for the specified stardog database which is backed by our
// `Connection`
Model aModel = SDJenaFactory.createModel(aConn);
try {
// Start a transaction before adding the data. This is not required, but it is faster to
// group the entire add into a single transaction rather
// than rely on the auto commit of the underlying stardog connection.
aModel.begin();
// Read data into the model. note, this will add statement at a time. Bulk loading needs
// to be performed directly with the BulkUpdateHandler provided
// by the underlying graph, or read in files in RDF/XML format, which uses the bulk loader
// natively. Alternatively, you can load data into the stardog
// database using it's native API via the command line client.
aModel.getReader("N3").read(aModel, new FileInputStream("data/sp2b_10k.n3"), "");
// When you're done adding, you need to commit the changes
aModel.commit();
// Query that we will run against the data we just loaded
String aQueryString =
"select * where { ?s ?p ?o. filter(?s = <http://localhost/publications/articles/Journal1/1940/Article1>).}";
// Create a query...
Query aQuery = QueryFactory.create(aQueryString);
// ... and run it
QueryExecution aExec = QueryExecutionFactory.create(aQuery, aModel);
try {
// Now print the results
ResultSetFormatter.out(aExec.execSelect(), aModel);
} finally {
// Always close the execution
aExec.close();
}
} finally {
// close the model to free up the connection to the stardog database
aModel.close();
}
} finally {
// You must stop the server when you're done
aServer.stop();
}
}
