org.eclipse.rdf4j.repository.sail.SailRepository Java Examples

@Setup(Level.Iteration)
public void beforeClass() {
	if (connection != null) {
		connection.close();
		connection = null;
	}
	i = 0;
	file = Files.newTemporaryFolder();

	NativeStore sail = new NativeStore(file, "spoc,ospc,psoc");
	sail.setForceSync(true);
	repository = new SailRepository(sail);
	connection = repository.getConnection();

	System.gc();

}
 

@Test
public void testRollbackClearSimple() {
	SailRepository elasticsearchStore = new SailRepository(this.elasticsearchStore);
	try (SailRepositoryConnection connection = elasticsearchStore.getConnection()) {

		BNode context = vf.createBNode();

		connection.begin(IsolationLevels.READ_COMMITTED);
		connection.add(RDF.TYPE, RDF.TYPE, RDFS.RESOURCE);
		connection.add(RDF.TYPE, RDF.TYPE, RDF.PROPERTY, context);
		connection.commit();

		connection.begin();
		connection.clear();
		assertEquals(0, connection.size());
		connection.rollback();

		assertEquals(2, connection.size());

	}

}
 

@Before
public void setUp()
{
    kb = new KnowledgeBase();
    kb.setDefaultLanguage("en");
    kb.setType(RepositoryType.LOCAL);
    kb.setFullTextSearchIri(null);
    kb.setMaxResults(1000);
    
    initRdfsMapping();
    
    // Local in-memory store - this should be used for most tests because we can
    // a) rely on its availability
    // b) import custom test data
    LuceneSail lucenesail = new LuceneSail();
    lucenesail.setParameter(LuceneSail.LUCENE_RAMDIR_KEY, "true");
    lucenesail.setBaseSail(new MemoryStore());
    rdf4jLocalRepo = new SailRepository(lucenesail);
    rdf4jLocalRepo.init();
    
    sut = new NoReification();
}
 

public TestSuite createTestSuite() throws Exception {
	// Create test suite
	TestSuite suite = new TestSuite(this.getClass().getName());

	// Add the manifest for W3C test cases to a repository and query it
	Repository w3cRepository = new SailRepository(new MemoryStore());
	w3cRepository.initialize();
	RepositoryConnection w3cCon = w3cRepository.getConnection();

	InputStream inputStream = this.getClass().getResourceAsStream(TEST_W3C_MANIFEST_URL);
	w3cCon.add(inputStream, TEST_W3C_MANIFEST_URI_BASE, RDFFormat.TURTLE);

	parsePositiveNTriplesSyntaxTests(suite, TEST_W3C_FILE_BASE_PATH, TEST_W3C_TEST_URI_BASE, w3cCon);
	parseNegativeNTriplesSyntaxTests(suite, TEST_W3C_FILE_BASE_PATH, TEST_W3C_TEST_URI_BASE, w3cCon);

	w3cCon.close();
	w3cRepository.shutDown();

	return suite;
}
 

@Benchmark
	public void shacl() throws Exception {

		SailRepository repository = new SailRepository(Utils.getInitializedShaclSail("shaclDatatype.ttl"));

//		((ShaclSail) repository.getSail()).setIgnoreNoShapesLoadedException(true);
//		((ShaclSail) repository.getSail()).disableValidation();

		try (SailRepositoryConnection connection = repository.getConnection()) {
			connection.begin(IsolationLevels.SERIALIZABLE);
			connection.commit();
		}

		try (SailRepositoryConnection connection = repository.getConnection()) {
			for (List<Statement> statements : allStatements) {
				connection.begin(IsolationLevels.SERIALIZABLE);
				connection.add(statements);
				connection.commit();
			}
		}

		repository.shutDown();

	}
 

List<NodeShape> refreshShapes(SailRepositoryConnection shapesRepoConnection) throws SailException {

		SailRepository shapesRepoCache = new SailRepository(new MemoryStore());
		shapesRepoCache.init();
		List<NodeShape> shapes;

		try (SailRepositoryConnection shapesRepoCacheConnection = shapesRepoCache.getConnection()) {
			shapesRepoCacheConnection.begin(IsolationLevels.NONE);
			try (RepositoryResult<Statement> statements = shapesRepoConnection.getStatements(null, null, null, false)) {
				shapesRepoCacheConnection.add(statements);
			}

			runInferencingSparqlQueries(shapesRepoCacheConnection);
			shapesRepoCacheConnection.commit();

			shapes = NodeShape.Factory.getShapes(shapesRepoCacheConnection, this);
		}

		shapesRepoCache.shutDown();
		return shapes;
	}
 

public TestSuite createTestSuite() throws Exception {
	// Create test suite
	TestSuite suite = new TestSuite(TurtleParserTestCase.class.getName());

	// Add the manifest for W3C test cases to a repository and query it
	Repository w3cRepository = new SailRepository(new MemoryStore());
	w3cRepository.initialize();
	RepositoryConnection w3cCon = w3cRepository.getConnection();

	InputStream inputStream = this.getClass().getResourceAsStream(TEST_W3C_MANIFEST_URL);
	w3cCon.add(inputStream, TEST_W3C_MANIFEST_URI_BASE, RDFFormat.TURTLE);

	parsePositiveTurtleSyntaxTests(suite, TEST_W3C_FILE_BASE_PATH, TESTS_W3C_BASE_URL, TEST_W3C_TEST_URI_BASE,
			w3cCon);
	parseNegativeTurtleSyntaxTests(suite, TEST_W3C_FILE_BASE_PATH, TESTS_W3C_BASE_URL, TEST_W3C_TEST_URI_BASE,
			w3cCon);
	parsePositiveTurtleEvalTests(suite, TEST_W3C_FILE_BASE_PATH, TESTS_W3C_BASE_URL, TEST_W3C_TEST_URI_BASE,
			w3cCon);
	parseNegativeTurtleEvalTests(suite, TEST_W3C_FILE_BASE_PATH, TESTS_W3C_BASE_URL, TEST_W3C_TEST_URI_BASE,
			w3cCon);

	w3cCon.close();
	w3cRepository.shutDown();

	return suite;
}
 

@Test
public void testMinCountWithValidInitialDataset() throws Throwable {

	SailRepository sailRepository = new SailRepository(new ShaclSail(new MemoryStore()));

	try (SailRepositoryConnection connection = sailRepository.getConnection()) {
		connection.begin();
		connection.add(validPerson1, ssn, value1);
		connection.add(validPerson1, ssn, value2);
		connection.add(validPerson2, ssn, value1);
		connection.add(validPerson2, ssn, value2);
		connection.commit();

		connection.begin();
		connection.add(new StringReader(shaclShapes), "", RDFFormat.TURTLE, RDF4J.SHACL_SHAPE_GRAPH);
		connection.commit();
	} catch (Exception e) {
		throw e.getCause();
	}

}
 

@Test
public void testNamespace() {

	SailRepository elasticsearchStore = new SailRepository(this.elasticsearchStore);

	try (SailRepositoryConnection connection = elasticsearchStore.getConnection()) {
		connection.begin();
		connection.setNamespace(SHACL.PREFIX, SHACL.NAMESPACE);
		connection.commit();
	}

	try (SailRepositoryConnection connection = elasticsearchStore.getConnection()) {
		String namespace = connection.getNamespace(SHACL.PREFIX);
		assertEquals(SHACL.NAMESPACE, namespace);
	}
}
 

@Benchmark
public void shacl() throws Exception {

	SailRepository repository = new SailRepository(Utils.getInitializedShaclSail("shacl.ttl"));

	try (SailRepositoryConnection connection = repository.getConnection()) {
		connection.begin();
		connection.commit();
	}

	try (SailRepositoryConnection connection = repository.getConnection()) {
		for (List<Statement> statements : allStatements) {
			connection.begin();
			connection.add(statements);
			connection.commit();
		}
	}
	repository.shutDown();

}
 

@Benchmark
public void shacl() throws Exception {

	SailRepository repository = new SailRepository(Utils.getInitializedShaclSail("shaclMaxCountBenchmark.ttl"));

	try (SailRepositoryConnection connection = repository.getConnection()) {
		connection.begin();
		connection.commit();
	}

	try (SailRepositoryConnection connection = repository.getConnection()) {
		for (List<Statement> statements : allStatements) {
			connection.begin();
			connection.add(statements);
			connection.commit();
		}
	}
	repository.shutDown();

}
 

@Setup(Level.Trial)
public void beforeClass() throws IOException, InterruptedException {
	// JMH does not correctly set JAVA_HOME. Change the JAVA_HOME below if you the following error:
	// [EmbeddedElsHandler] INFO p.a.t.e.ElasticServer - could not find java; set JAVA_HOME or ensure java is in
	// PATH
	embeddedElastic = TestHelpers.startElasticsearch(installLocation,
			"/Library/Java/JavaVirtualMachines/adoptopenjdk-8.jdk/Contents/Home");

	repository = new SailRepository(
			new ElasticsearchStore("localhost", embeddedElastic.getTransportTcpPort(), "cluster1", "testindex"));
	try (SailRepositoryConnection connection = repository.getConnection()) {
		connection.begin(IsolationLevels.NONE);
		connection.add(getResourceAsStream("benchmarkFiles/datagovbe-valid.ttl"), "", RDFFormat.TURTLE);
		connection.commit();
	}

	System.gc();

}
 

@Before
public void setUp() throws Exception {
    repo = new SesameRepositoryWrapper(new SailRepository(new MemoryStore()));
    repo.initialize();

    activityIRI = VALUE_FACTORY.createIRI("http://test.com/activity");

    MockitoAnnotations.initMocks(this);
    when(registry.getFactoriesOfType(Activity.class)).thenReturn(Collections.singletonList(activityFactory));

    service = new SimpleProvenanceService();
    injectOrmFactoryReferencesIntoService(service);
    service.setRepo(repo);
    service.setVf(VALUE_FACTORY);
    service.setMf(MODEL_FACTORY);
    service.setFactoryRegistry(registry);
}
 

@Test
public void ensureInEventStore_Test() throws Exception {
    final Sail sail = GeoRyaSailFactory.getInstance(conf);
    final SailRepository repo = new SailRepository(sail);
    try(final MongoGeoTemporalIndexer indexer = new MongoGeoTemporalIndexer()) {
        indexer.setConf(conf);
        indexer.init();

        addStatements(repo.getConnection());
        final EventStorage events = indexer.getEventStorage();
        final RyaIRI subject = new RyaIRI("urn:event1");
        final Optional<Event> event = events.get(subject);
        assertTrue(event.isPresent());
    } finally {
        sail.shutDown();
    }
}
 

@Benchmark
@BenchmarkMode(Mode.AverageTime)
@OutputTimeUnit(TimeUnit.MILLISECONDS)
public void forwardChainingSchemaCachingRDFSInferencer() throws IOException {
	SailRepository sail = new SailRepository(new SchemaCachingRDFSInferencer(new MemoryStore()));

	try (SailRepositoryConnection connection = sail.getConnection()) {
		connection.begin();
		connection.add(resourceAsStream("schema.ttl"), "", RDFFormat.TURTLE, schemaGraph);
		connection.commit();

		addAllDataMultipleTransactions(connection);

	}

	checkSize(sail);
}
 

@Test(expected = RepositoryException.class)
public void testShapeWithoutTargetClassRemove() throws Exception {

	SailRepository shaclRepository = Utils.getInitializedShaclRepository("shacleNoTargetClass.ttl", true);
	shaclRepository.init();

	try (SailRepositoryConnection connection = shaclRepository.getConnection()) {

		connection.begin();
		connection.add(RDFS.CLASS, RDFS.LABEL, connection.getValueFactory().createLiteral("class1"));
		connection.add(RDFS.CLASS, RDF.TYPE, RDFS.RESOURCE);
		connection.commit();

		connection.begin();
		connection.remove(RDFS.CLASS, RDFS.LABEL, connection.getValueFactory().createLiteral("class1"));
		connection.commit();

	}

}
 

@Test()
public void checkForNoExceptionWithEmptyTransaction() {

	SailRepository sailRepository = new SailRepository(new ShaclSail(new MemoryStore()));
	sailRepository.init();

	try (SailRepositoryConnection connection = sailRepository.getConnection()) {
		connection.begin();
		connection.commit();
	}

}
 

public static void main(String[] args) throws Exception {
	MemoryStore baseSail = new MemoryStore();
	DedupingInferencer deduper = new DedupingInferencer(baseSail);
	SchemaCachingRDFSInferencer rdfsInferencer = new SchemaCachingRDFSInferencer(deduper);
	SpinSail spinSail = new SpinSail(rdfsInferencer);
	Repository repo = new SailRepository(spinSail);
	repo.initialize();
	try (FileWriter writer = new FileWriter("spin-full.ttl")) {
		try (RepositoryConnection conn = repo.getConnection()) {
			conn.exportStatements(null, null, null, true, Rio.createWriter(RDFFormat.TURTLE, writer));
		}
	}
	repo.shutDown();
}
 

@Test
public void testComplexPath() throws IOException {
	ch.qos.logback.classic.Logger root = (ch.qos.logback.classic.Logger) LoggerFactory
			.getLogger(ch.qos.logback.classic.Logger.ROOT_LOGGER_NAME);

	MyAppender newAppender = new MyAppender();
	root.addAppender(newAppender);

	SailRepository shaclRepository = Utils.getInitializedShaclRepository("complexPath.ttl", false);

	try (SailRepositoryConnection connection = shaclRepository.getConnection()) {
		connection.begin();
		connection.add(RDF.TYPE, RDF.TYPE, RDFS.RESOURCE);
		connection.commit();
	}

	Set<String> relevantLog = newAppender.logged.stream()
			.filter(m -> m.startsWith("Unsupported SHACL feature"))
			.map(s -> s.replaceAll("\r\n|\r|\n", " "))
			.map(String::trim)
			.collect(Collectors.toSet());

	Set<String> expected = new HashSet<>(Arrays.asList(
			"Unsupported SHACL feature with complex path. Only single predicate paths are supported. <http://example.com/ns#PersonPropertyShape> shape has been deactivated!  @prefix sh: <http://www.w3.org/ns/shacl#> .  <http://example.com/ns#PersonPropertyShape> sh:path [       sh:inversePath <http://example.com/ns#inverseThis>     ] .",
			"Unsupported SHACL feature with complex path. Only single predicate paths are supported. <http://example.com/ns#PersonPropertyShape2> shape has been deactivated!  @prefix sh: <http://www.w3.org/ns/shacl#> .  <http://example.com/ns#path> sh:inversePath <http://example.com/ns#inverseThis> .  <http://example.com/ns#PersonPropertyShape2> sh:path <http://example.com/ns#path> .",
			"Unsupported SHACL feature with complex path. Only single predicate paths are supported. <http://example.com/ns#PersonPropertyShape3> shape has been deactivated!  @prefix sh: <http://www.w3.org/ns/shacl#> .  <http://example.com/ns#pathList> <http://www.w3.org/1999/02/22-rdf-syntax-ns#first>     \"one\";   <http://www.w3.org/1999/02/22-rdf-syntax-ns#rest> <http://www.w3.org/1999/02/22-rdf-syntax-ns#nil> .  <http://example.com/ns#PersonPropertyShape3> sh:path <http://example.com/ns#pathList> ."));

	assertEquals(expected, relevantLog);
}
 

@Override
public void rebuildFullTextIndex(KnowledgeBase aKB) throws Exception
{
    if (!RepositoryType.LOCAL.equals(aKB.getType())) {
        throw new IllegalArgumentException("Reindexing is only supported on local KBs");
    }
    
    boolean reindexSupported = false;
    
    // Handle re-indexing of local repos that use a Lucene FTS
    if (repoManager.getRepository(aKB.getRepositoryId()) instanceof SailRepository) {
        SailRepository sailRepo = (SailRepository) repoManager
            .getRepository(aKB.getRepositoryId());
        if (sailRepo.getSail() instanceof LuceneSail) {
            reindexSupported = true;
            LuceneSail luceneSail = (LuceneSail) (sailRepo.getSail());
            try (RepositoryConnection conn = getConnection(aKB)) {
                luceneSail.reindex();
                conn.commit();
            }
        }
    }
    
    if (!reindexSupported) {
        throw new IllegalArgumentException(
                aKB + "] does not support rebuilding its full text index.");
    }
}
 

public static void loadShapeData(SailRepository repo, URL resourceName)
		throws RDF4JException, UnsupportedRDFormatException, IOException {
	((ShaclSail) repo.getSail()).disableValidation();

	try (RepositoryConnection conn = repo.getConnection()) {
		conn.begin();
		conn.add(resourceName, resourceName.toString(), RDFFormat.TURTLE, RDF4J.SHACL_SHAPE_GRAPH);

		conn.commit();
	}
	((ShaclSail) repo.getSail()).enableValidation();

}
 

/**
 * Shuts the repository down, releasing any resources that it keeps hold of.
 * Once shut down, the repository can no longer be used until it is
 * re-initialized.
 * @param repository the {@link SailRepository} to close.
 */
private static void close(final SailRepository repository) {
    if (repository != null) {
        try {
            repository.shutDown();
        } catch (final RepositoryException e) {
            log.error("Encountered an error while closing Sail Repository", e);
        }
    }
}
 

private SailRepository createSchema() throws IOException {
	SailRepository schema = new SailRepository(new MemoryStore());
	schema.initialize();

	try (SailRepositoryConnection schemaConnection = schema.getConnection()) {
		schemaConnection.begin();
		schemaConnection.add(resourceAsStream("schema.ttl"), "", RDFFormat.TURTLE);
		schemaConnection.commit();
	}
	return schema;
}
 

private static void closeQuietly(final SailRepository repository) {
    if (repository != null) {
        try {
            repository.shutDown();
        } catch (final RepositoryException e) {
            // quietly absorb this exception
        }
    }
}
 

@Benchmark
public void remove() {
	SailRepository spinSail = new SailRepository(new SpinSail(new MemoryStore()));
	spinSail.init();

	try (SailRepositoryConnection connection = spinSail.getConnection()) {
		connection.remove(bob, name, nameBob);
		connection.remove(alice, null, null);
	}

	spinSail.shutDown();

}
 

@Test
public void testGetSailRepositoryConneciton() {
	SailRepository elasticsearchStore = new SailRepository(
			new ElasticsearchStore("localhost", embeddedElastic.getTransportTcpPort(), "cluster1", "testindex"));
	try (SailRepositoryConnection connection = elasticsearchStore.getConnection()) {
	}
	elasticsearchStore.shutDown();
}
 

private static void closeQuietly(final SailRepository repository) {
	if (repository != null) {
		try {
			repository.shutDown();
		} catch (final RepositoryException e) {
			// quietly absorb this exception
		}
	}
}
 

@Test
public void testAdd() throws Exception {

	SailRepository shaclRepository = Utils.getInitializedShaclRepository("empty.ttl", false);
	((ShaclSail) shaclRepository.getSail()).setIgnoreNoShapesLoadedException(true);
	shaclRepository.init();

	try (SailRepositoryConnection connection = shaclRepository.getConnection()) {
		connection.begin();
		// System.out.println(size(connection));

		connection.add(RDFS.RESOURCE, RDF.TYPE, RDFS.RESOURCE);
		// System.out.println(size(connection));

		connection.remove(RDFS.RESOURCE, RDF.TYPE, RDFS.RESOURCE);
		// System.out.println(size(connection));

		connection.add(RDFS.RESOURCE, RDF.TYPE, RDFS.RESOURCE);
		// System.out.println(size(connection));

		ShaclSailConnection shaclSailConnection = (ShaclSailConnection) connection.getSailConnection();
		shaclSailConnection.fillAddedAndRemovedStatementRepositories();
		try (ConnectionsGroup connectionsGroup = shaclSailConnection.getConnectionsGroup()) {

			assertEquals(1, size(connectionsGroup.getAddedStatements()));
			assertEquals(0, size(connectionsGroup.getRemovedStatements()));
		}

		connection.commit();

		System.out.println(size(connection));

	}
}
 

private static void addTriples(final SailRepository repo, final InputStream triplesStream, final RDFFormat rdfFormat) throws RDFParseException, RepositoryException, IOException {
    SailRepositoryConnection conn = null;
    try {
        conn = repo.getConnection();
        conn.begin();
        conn.add(triplesStream, "", rdfFormat);
        conn.commit();
    } finally {
        closeQuietly(conn);
    }
}
 

@Test
public void partialQuery_Test() throws Exception {
    final Sail sail = RyaSailFactory.getInstance(conf);
    final SailRepositoryConnection conn = new SailRepository(sail).getConnection();
    conn.begin();

    try(MongoEntityIndexer indexer = new MongoEntityIndexer()) {
        indexer.setConf(conf);
        indexer.init();

        setupTypes(indexer);
        addStatements(conn);
        conn.commit();

        final String query = "SELECT * WHERE { " +
                "<urn:george> <" + RDF.TYPE + "> <urn:person> ."+
                "<urn:george> <urn:name> ?name . " +
                "<urn:george> <urn:eye> ?eye . " +
                "}";

        final TupleQueryResult rez = conn.prepareTupleQuery(QueryLanguage.SPARQL, query).evaluate();
        final Set<BindingSet> results = new HashSet<>();
        while(rez.hasNext()) {
            final BindingSet bs = rez.next();
            System.out.println(bs);
            results.add(bs);
        }
        final MapBindingSet expected = new MapBindingSet();
        //expected.addBinding("name", VF.createIRI("http://www.w3.org/2001/SMLSchema#string", "George"));
        expected.addBinding("name", VF.createLiteral("George"));
        expected.addBinding("eye", VF.createLiteral("blue"));

        assertEquals(1, results.size());
        assertEquals(expected, results.iterator().next());
    } finally {
        conn.close();
    }
}