private void upload(URI graphURI, Resource context) throws Exception {
RepositoryConnection con = dataRep.getConnection();
con.setAutoCommit(false);
try {
RDFFormat rdfFormat = Rio.getParserFormatForFileName(graphURI.toString(), RDFFormat.TURTLE);
RDFParser rdfParser = Rio.createParser(rdfFormat, dataRep.getValueFactory());
rdfParser.setVerifyData(false);
rdfParser.setDatatypeHandling(DatatypeHandling.IGNORE);
// rdfParser.setPreserveBNodeIDs(true);
RDFInserter rdfInserter = new RDFInserter(con);
rdfInserter.enforceContext(context);
rdfParser.setRDFHandler(rdfInserter);
URL graphURL = new URL(graphURI.toString());
InputStream in = graphURL.openStream();
try {
rdfParser.parse(in, graphURI.toString());
} finally {
in.close();
}
con.setAutoCommit(true);
} finally {
con.close();
}
}
public void setupInMemory() throws Exception {
// create a sesame in-memory repository
String owlfile = "src/test/resources/onto2.owl";
repo = new SesameClassicInMemoryRepo("my_name", owlfile, false, "TreeWitness");
repo.initialize();
con = (RepositoryConnection) repo.getConnection();
}
protected void load(final String modelPathWithoutExtension)
throws RepositoryException, RDFParseException, IOException {
final File modelFile = new File(modelPathWithoutExtension + getPostfix());
repository.initialize();
connection = repository.getConnection();
connection.add(modelFile, RDFConstants.BASE_PREFIX, RDFFormat.TURTLE);
}
/**
* Creating local repository, the standard way to get a Sesame-RDF repository.
*
* @param tempDir Warning! if not <code>null</code> then it will reuse the data left in this
* directory from the previous session.
* @return
* @throws ConfigurationException
*/
public static Repository createLocalRepository(File tempDir) throws RepositoryException {
// initializing RDF repository
Repository myRepository =
new SailRepository(new ForwardChainingRDFSInferencer(new MemoryStore(tempDir))); // ,
// NB! MemoryStore(dir) will restore its contents!
myRepository.initialize();
return myRepository;
}
public static LoadStatementsResult loadStatements(String file, String tempDir, PrintStream... out)
throws Exception {
LoadStatementsResult result = new LoadStatementsResult();
// loading
Repository rdf = Helper.createLocalRepository();
RepositoryConnection con = rdf.getConnection();
try {
importRDFXMLFile(rdf, "http://localhost/namespace", new File(file));
RepositoryResult<Statement> statements = con.getStatements(null, null, null, false);
try {
while (statements.hasNext()) {
Statement st = statements.next();
if (st instanceof MemStatement) {
if (((MemStatement) (st)).isExplicit()) {
String property = st.getPredicate().toString();
result.subjects.add(st.getSubject().toString());
result.properties.add(st.getPredicate().toString());
String[] subject = st.getSubject().toString().split("#");
boolean isResource = (st.getObject() instanceof Resource);
if (isResource) {
result.values.add("R:" + st.getObject().stringValue());
} else {
result.values.add(
"L"
+ ((Literal) st.getObject()).getLanguage()
+ ":"
+ st.getObject().stringValue());
}
if (subject.length == 2) {
result.statements.add(
formatLine(
subject[0] + "#" /* ":" */ + subject[1],
property,
isResource,
st.getObject().toString()));
} else {
if (subject.length > 2)
throw new Exception("Multiple # in resource " + st.getSubject());
result.statements.add(
formatLine(subject[0], property, isResource, st.getObject().toString()));
}
}
} else throw new Exception("ERROR");
}
} finally {
statements.close();
}
} finally {
con.close();
}
return result;
}
/** Creating local repository, the standard way to get a Sesame-RDF repository. */
public static Repository createLocalRepository() throws RepositoryException {
// initializing RDF repository
Repository repository =
new SailRepository(
new DirectTypeHierarchyInferencer(
new ForwardChainingRDFSInferencer(new MemoryStore())));
// NB! MemoryStore(dir) will restore its contents!
repository.initialize();
return repository;
}
public TestSuite createTestSuite() throws Exception {
// Create test suite
TestSuite suite = new TestSuite(N3ParserTestCase.class.getName());
// Add the manifest to a repository and query it
Repository repository = new SailRepository(new MemoryStore());
repository.initialize();
RepositoryConnection con = repository.getConnection();
URL url = url(MANIFEST_URL);
con.add(url, base(MANIFEST_URL), RDFFormat.TURTLE);
// Add all positive parser tests to the test suite
String query =
"SELECT testURI, inputURL, outputURL "
+ "FROM {testURI} rdf:type {n3test:PositiveParserTest}; "
+ " n3test:inputDocument {inputURL}; "
+ " n3test:outputDocument {outputURL} "
+ "USING NAMESPACE n3test = <http://www.w3.org/2004/11/n3test#>";
TupleQueryResult queryResult = con.prepareTupleQuery(QueryLanguage.SERQL, query).evaluate();
while (queryResult.hasNext()) {
BindingSet bindingSet = queryResult.next();
String testURI = bindingSet.getValue("testURI").toString();
String inputURL = bindingSet.getValue("inputURL").toString();
String outputURL = bindingSet.getValue("outputURL").toString();
suite.addTest(new PositiveParserTest(testURI, inputURL, outputURL));
}
queryResult.close();
// Add all negative parser tests to the test suite
query =
"SELECT testURI, inputURL "
+ "FROM {testURI} rdf:type {n3test:NegativeParserTest}; "
+ " n3test:inputDocument {inputURL} "
+ "USING NAMESPACE n3test = <http://www.w3.org/2004/11/n3test#>";
queryResult = con.prepareTupleQuery(QueryLanguage.SERQL, query).evaluate();
while (queryResult.hasNext()) {
BindingSet bindingSet = queryResult.next();
String testURI = bindingSet.getValue("testURI").toString();
String inputURL = bindingSet.getValue("inputURL").toString();
suite.addTest(new NegativeParserTest(testURI, inputURL));
}
queryResult.close();
con.close();
repository.shutDown();
return suite;
}
protected Repository createRepository() throws Exception {
Repository repo = newRepository();
repo.initialize();
RepositoryConnection con = repo.getConnection();
try {
con.clear();
con.clearNamespaces();
} finally {
con.close();
}
return repo;
}
@Override
public boolean toRdf(final Repository myRepository, final int modelVersion, final URI... keyToUse)
throws OpenRDFException {
super.toRdf(myRepository, modelVersion, keyToUse);
final RepositoryConnection con = myRepository.getConnection();
try {
if (SpinInferencingRuleImpl.DEBUG) {
SpinInferencingRuleImpl.log.debug(
"SparqlNormalisationRuleImpl.toRdf: keyToUse=" + keyToUse);
}
final URI keyUri = this.getKey();
con.setAutoCommit(false);
con.add(
keyUri, RDF.TYPE, SpinInferencingRuleSchema.getSpinInferencingRuleTypeUri(), keyToUse);
// If everything went as planned, we can commit the result
con.commit();
return true;
} catch (final RepositoryException re) {
// Something went wrong during the transaction, so we roll it back
con.rollback();
SpinInferencingRuleImpl.log.error("RepositoryException: " + re.getMessage());
} finally {
con.close();
}
return false;
}
/**
* Execute a SELECT SPARQL query against the graphs
*
* @param qs SELECT SPARQL query
* @return list of solutions, each containing a hashmap of bindings
*/
public List<HashMap<String, Value>> runSPARQL(String qs) {
try {
RepositoryConnection con = currentRepository.getConnection();
try {
TupleQuery query = con.prepareTupleQuery(org.openrdf.query.QueryLanguage.SPARQL, qs);
TupleQueryResult qres = query.evaluate();
ArrayList<HashMap<String, Value>> reslist = new ArrayList<HashMap<String, Value>>();
while (qres.hasNext()) {
BindingSet b = qres.next();
Set<String> names = b.getBindingNames();
HashMap<String, Value> hm = new HashMap<String, Value>();
for (String n : names) {
hm.put(n, b.getValue(n));
}
reslist.add(hm);
}
return reslist;
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
return null;
}
public ResponseHandler(String resource, Endpoint endpoint) throws RepositoryException {
this.resource = resource;
this.endpoint = endpoint;
triples = new SailRepository(new MemoryStore());
triples.initialize();
}
@Override
public void reInitialize() throws Exception {
log.info("Reinitializing repository and connection due to error in past results.");
if (conn.isOpen()) {
try {
log.debug("Trying to close connection, interrupt time is 10000");
Utils.closeConnectionTimeout(conn, 10000);
} catch (Exception e) {; /*ignore*/
}
}
if (sailRepo != null) {
boolean shutDown =
Utils.shutdownRepositoryTimeout(
sailRepo, 20 * 60 * 1000); // timeout of 20 min for shutdown
sailRepo = null;
if (shutDown) log.debug("Repository shut down.");
else log.debug("Failed to shut down repository within 20 minutes!");
}
// log.info("Waiting for 2 minutes to give server time for reinitialization");
// Thread.sleep(120000);
log.debug("loading repositories from scratch.");
System.gc();
sailRepo = SesameRepositoryLoader.loadRepositories(new VoidReportStream());
conn = sailRepo.getConnection();
log.debug("reinitialize done.");
}
@Override
protected void tearDown() throws Exception {
if (dataRep != null) {
dataRep.shutDown();
dataRep = null;
}
}
private void saveLog(DefaultQueryLog log) {
try {
RepositoryConnection conn = null;
try {
conn = repository.getConnection();
ValueFactory vf = conn.getValueFactory();
URI queryURI = vf.createURI(NS_QUERY + queryId);
URI logURI = vf.createURI(NS_QUERY + log.timestamp());
conn.add(queryURI, RDF.TYPE, vf.createURI(NS_QUERY + "Query"));
conn.add(queryURI, vf.createURI(NS_QUERY + "log"), logURI);
conn.add(logURI, RDF.TYPE, vf.createURI(NS_QUERY + "QueryLog"));
conn.add(logURI, vf.createURI(NS_QUERY + "timestamp"), vf.createLiteral(log.timestamp()));
for (QueryResultBindingSet set : log.result()) {
BNode setURI = vf.createBNode();
conn.add(logURI, vf.createURI(NS_QUERY + "bindingSet"), setURI);
for (QueryResultBinding binding : set) {
BNode bindingURI = vf.createBNode();
conn.add(setURI, vf.createURI(NS_QUERY + "binding"), bindingURI);
conn.add(bindingURI, vf.createURI(NS_QUERY + "name"), vf.createLiteral(binding.name()));
conn.add(
bindingURI, vf.createURI(NS_QUERY + "value"), vf.createLiteral(binding.value()));
}
}
} finally {
if (conn != null) {
conn.close();
}
}
} catch (Exception e) {
throw new RuntimeException(e);
}
}
private String serialize(final Repository repo) throws RDFHandlerException, RepositoryException {
ByteArrayOutputStream bos = new ByteArrayOutputStream();
RDFWriter w = Rio.createWriter(format, bos);
RepositoryConnection rc = repo.getConnection();
try {
rc.export(w);
} finally {
rc.close();
}
String s = new String(bos.toByteArray());
if (RDFFormat.RDFXML == format || RDFFormat.TRIX == format) {
// Chop off the XML declaration.
int i = s.indexOf('\n');
s = s.substring(i + 1);
}
s = s.replaceAll("\n", "");
s = "<" + TAGNAME + " xmlns='" + NAMESPACE + "'>" + s + "</" + TAGNAME + ">";
// s = s.replaceAll("<rdf:", "<");
// s = s.replaceAll("</rdf:", "</");
// System.out.println("s = " + s);
return s;
// return "<body><one>foo</two></body>";
// return "<content><one/></content>";
// return "<body></body>";
}
public void loadDataFromURL(String stringURL) {
RepositoryConnection con;
try {
con = currentRepository.getConnection();
try {
// upload a URL
URL url = new URL(stringURL);
con.add(url, null, RDFFormat.RDFXML);
} catch (RDFParseException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (RepositoryException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} finally {
try {
con.close();
} catch (RepositoryException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
} catch (RepositoryException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
}
/**
* Insert Triple/Statement into graph
*
* @param s subject uriref
* @param p predicate uriref
* @param o value object (URIref or Literal)
* @param contexts varArgs context objects (use default graph if null)
*/
public void add(Resource s, URI p, Value o, Resource... contexts) {
if (log.isDebugEnabled())
log.debug(
"[SesameDataSet:add] Add triple ("
+ s.stringValue()
+ ", "
+ p.stringValue()
+ ", "
+ o.stringValue()
+ ").");
try {
RepositoryConnection con = currentRepository.getConnection();
try {
ValueFactory myFactory = con.getValueFactory();
Statement st = myFactory.createStatement((Resource) s, p, (Value) o);
con.add(st, contexts);
con.commit();
} catch (Exception e) {
e.printStackTrace();
} finally {
con.close();
}
} catch (Exception e) {
// handle exception
}
}
/**
* Load data in specified graph (use default graph if contexts is null)
*
* @param filePath
* @param format
* @param contexts
*/
public void loadDataFromFile(String filePath, RDFFormat format, Resource... contexts) {
RepositoryConnection con;
try {
con = currentRepository.getConnection();
try {
// upload a file
File f = new File(filePath);
con.add(f, null, format, contexts);
} catch (RDFParseException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (RepositoryException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} finally {
try {
con.close();
} catch (RepositoryException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
} catch (RepositoryException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
}
private void calculateGraphsAndDataSets() {
try {
RepositoryConnection conn = repository.getConnection();
TupleQuery q = conn.prepareTupleQuery(QueryLanguage.SPARQL, SparqlUtils.PREFIXES + QUERY);
TupleQueryResult results = q.evaluate();
graphs = new LinkedList<DataCubeGraph>();
datasets = new LinkedList<DataSet>();
String lastG = null;
String lastDSD = null;
SparqlDCGraph dcGraph;
SparqlStructure dcStructure = null;
Collection<DataSet> graphDataSets = null;
Collection<Structure> graphStructures = null;
Collection<DataSet> structDataSets = null;
while (results.hasNext()) {
BindingSet set = results.next();
String g = set.getValue("g").stringValue();
String ds = set.getValue("ds").stringValue();
String dsd = set.getValue("dsd").stringValue();
if (!g.equals(lastG)) {
// new Graph
dcGraph = new SparqlDCGraph(repository, g);
graphDataSets = new LinkedList<DataSet>();
graphStructures = new LinkedList<Structure>();
dcGraph.setDatasets(graphDataSets);
dcGraph.setStructures(graphStructures);
graphs.add(dcGraph);
// new structure
dcStructure = new SparqlStructure(repository, dsd, g);
structDataSets = new LinkedList<DataSet>();
dcStructure.setDatasets(structDataSets);
graphStructures.add(dcStructure);
} else if (!dsd.equals(lastDSD)) {
// new structure
dcStructure = new SparqlStructure(repository, dsd, g);
structDataSets = new LinkedList<DataSet>();
dcStructure.setDatasets(structDataSets);
graphStructures.add(dcStructure);
}
SparqlDataSet dcDataSet = new SparqlDataSet(repository, ds, g);
dcDataSet.setStructure(dcStructure);
graphDataSets.add(dcDataSet);
structDataSets.add(dcDataSet);
datasets.add(dcDataSet);
lastG = g;
lastDSD = dsd;
}
} catch (RepositoryException ex) {
Logger.getLogger(SparqlDCRepository.class.getName()).log(Level.SEVERE, null, ex);
} catch (MalformedQueryException ex) {
Logger.getLogger(SparqlDCRepository.class.getName()).log(Level.SEVERE, null, ex);
} catch (QueryEvaluationException ex) {
Logger.getLogger(SparqlDCRepository.class.getName()).log(Level.SEVERE, null, ex);
}
}
/**
* This test verifies whether the transparent caching works for the three resources provided by
* our dummy provider.
*
* @throws Exception
*/
@Test
public void testCachedResources() throws Exception {
String uri1 = "http://localhost/resource1";
String uri2 = "http://localhost/resource2";
String uri3 = "http://localhost/resource3";
RepositoryConnection con = repository.getConnection();
try {
con.begin();
List<Statement> list1 =
Iterations.asList(
con.getStatements(con.getValueFactory().createURI(uri1), null, null, true));
Assert.assertEquals(3, list1.size());
Assert.assertThat(
list1,
allOf(
CoreMatchers.<Statement>hasItem(hasProperty("object", hasToString("\"Value 1\""))),
CoreMatchers.<Statement>hasItem(hasProperty("object", hasToString("\"Value X\"")))));
con.commit();
con.begin();
List<Statement> list2 =
Iterations.asList(
con.getStatements(con.getValueFactory().createURI(uri2), null, null, true));
Assert.assertEquals(2, list2.size());
Assert.assertThat(
list2,
allOf(
CoreMatchers.<Statement>hasItem(hasProperty("object", hasToString("\"Value 2\"")))));
con.commit();
con.begin();
List<Statement> list3 =
Iterations.asList(
con.getStatements(con.getValueFactory().createURI(uri3), null, null, true));
Assert.assertEquals(2, list3.size());
Assert.assertThat(
list3,
allOf(
CoreMatchers.<Statement>hasItem(hasProperty("object", hasToString("\"Value 3\""))),
CoreMatchers.<Statement>hasItem(hasProperty("object", hasToString("\"Value 4\"")))));
con.commit();
} catch (RepositoryException ex) {
con.rollback();
} finally {
con.close();
}
}
public SesameDataSet(String sesameServer, String repositoryID) {
currentRepository = new HTTPRepository(sesameServer, repositoryID);
try {
currentRepository.initialize();
} catch (RepositoryException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
public ValueLoader(String host, String port, String user, String pwd) {
String connectionString = "jdbc:virtuoso://" + host + ':' + port;
repository = new VirtuosoRepository(connectionString, user, pwd, true);
try {
RepositoryConnection con = repository.getConnection();
} catch (RepositoryException e) {
throw new IllegalArgumentException(e.getMessage(), e);
}
}
@Override
public void initialize() throws Exception {
log.info("Performing Sesame Initialization...");
sailRepo = SesameRepositoryLoader.loadRepositories(report);
if (!Config.getConfig().isFill()) conn = sailRepo.getConnection();
log.info("Sesame Repository successfully initialized.");
}
@Before
public void setUp() throws Exception {
repository = new SailRepository(new MemoryStore());
repository.initialize();
ObjectRepositoryFactory factory = new ObjectRepositoryFactory();
ObjectRepository objectRepository = factory.createRepository(repository);
connection = objectRepository.getConnection();
}
/**
* Compares the models of the default context of two repositories and returns true if rep1 is a
* subset of rep2. Note that the method pulls the entire default context of both repositories into
* main memory. Use with caution.
*/
public static boolean isSubset(Repository rep1, Repository rep2) throws RepositoryException {
Set<Statement> model1, model2;
RepositoryConnection con1 = rep1.getConnection();
try {
model1 = Iterations.asSet(con1.getStatements(null, null, null, true));
} finally {
con1.close();
}
RepositoryConnection con2 = rep2.getConnection();
try {
model2 = Iterations.asSet(con2.getStatements(null, null, null, true));
} finally {
con2.close();
}
return ModelUtil.isSubset(model1, model2);
}
/**
* Evaluates the SPARQL SELECT query from the specified query pair on the repository.
*
* @param query Query pair.
* @return Query result set.
* @throws RepositoryException If no connection could be established, or connection fails.
* @throws MalformedQueryException On query-related errors.
* @throws QueryEvaluationException On query-related errors.
*/
public SparqlResultSet query(QueryPair query)
throws RepositoryException, MalformedQueryException, QueryEvaluationException {
RepositoryConnection conn = repo.getConnection();
TupleQuery tq = conn.prepareTupleQuery(QueryLanguage.SPARQL, query.getSparqlQuery());
SparqlResultSet ret =
new SparqlResultSet(tq.evaluate(), query.getName(), query.getSparqlEntityIdVariables());
conn.close();
return ret;
}
public RepositoryConnection getConnection() {
if (this.connection.get() == null) {
try {
this.connection.set(repository.getConnection());
this.connection.get().setAutoCommit(false);
} catch (RepositoryException e) {
throw new IllegalStateException(e);
}
}
return connection.get();
}
/**
* Compares two models defined by the default context of two repositories and returns the
* difference between the first and the second model (that is, all statements that are present in
* rep1 but not in rep2). Blank node IDs are not relevant for model equality, they are mapped from
* one model to the other by using the attached properties. Note that the method pulls the entire
* default context of both repositories into main memory. Use with caution.
*
* <p><b>NOTE: this algorithm is currently broken; it doesn't actually map blank nodes between the
* two models.</b>
*
* @return The collection of statements that is the difference between rep1 and rep2.
*/
public static Collection<? extends Statement> difference(Repository rep1, Repository rep2)
throws RepositoryException {
Collection<Statement> model1 = new HashSet<Statement>();
Collection<Statement> model2 = new HashSet<Statement>();
RepositoryConnection con1 = rep1.getConnection();
try {
Iterations.addAll(con1.getStatements(null, null, null, false), model1);
} finally {
con1.close();
}
RepositoryConnection con2 = rep2.getConnection();
try {
Iterations.addAll(con2.getStatements(null, null, null, false), model2);
} finally {
con2.close();
}
return difference(model1, model2);
}
/**
* Import RDF data from a file
*
* @param location of file (/path/file) with RDF data
* @param format RDF format of the string (used to select parser)
*/
public void addFile(String filepath, RDFFormat format) {
try {
RepositoryConnection con = currentRepository.getConnection();
try {
con.add(new File(filepath), "", format);
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Runs a SPARQL UPDATE query as specified.
*
* @param sparqlString Query string.
* @throws RepositoryException
* @throws MalformedQueryException
* @throws QueryEvaluationException
* @throws UpdateExecutionException
*/
public void plainSparqlUpdate(String sparqlString)
throws RepositoryException, MalformedQueryException, QueryEvaluationException,
UpdateExecutionException {
RepositoryConnection conn = repo.getConnection();
Update query = conn.prepareUpdate(QueryLanguage.SPARQL, sparqlString);
query.execute();
conn.close();
}
