Examples with Sail org.eclipse.rdf4j.sail.Sail used on opensource projects

Example 51 with Sail

use of org.eclipse.rdf4j.sail.Sail in project incubator-rya by apache.

the class MongoBatchUpdatePCJ method updatePCJResults.

private void updatePCJResults(final String ryaInstanceName, final String pcjId, final MongoClient client) throws InstanceDoesNotExistException, PCJDoesNotExistException, RyaClientException {
    // Things that have to be closed before we exit.
    Sail sail = null;
    SailConnection sailConn = null;
    try (final PrecomputedJoinStorage pcjStorage = new MongoPcjStorage(client, ryaInstanceName)) {
        // Create an instance of Sail backed by the Rya instance.
        sail = connectToRya(ryaInstanceName);
        final SailRepository sailRepo = new SailRepository(sail);
        final SailRepositoryConnection sailRepoConn = sailRepo.getConnection();
        // Purge the old results from the PCJ.
        try {
            pcjStorage.purge(pcjId);
        } catch (final PCJStorageException e) {
            throw new RyaClientException("Could not batch update PCJ with ID '" + pcjId + "' because the old " + "results could not be purged from it.", e);
        }
        // Parse the PCJ's SPARQL query.
        final PcjMetadata metadata = pcjStorage.getPcjMetadata(pcjId);
        final String sparql = metadata.getSparql();
        sailConn = sail.getConnection();
        final TupleQuery tupleQuery = sailRepoConn.prepareTupleQuery(QueryLanguage.SPARQL, sparql);
        // Execute the query.
        final List<VisibilityBindingSet> batch = new ArrayList<>(1000);
        tupleQuery.evaluate(new AbstractTupleQueryResultHandler() {

            @Override
            public void handleSolution(final BindingSet bindingSet) throws TupleQueryResultHandlerException {
                final VisibilityBindingSet result = new VisibilityBindingSet(bindingSet, "");
                log.warn("Visibility information on the binding set is lost during a batch update." + "  This can create data leaks.");
                batch.add(result);
                if (batch.size() == 1000) {
                    try {
                        pcjStorage.addResults(pcjId, batch);
                    } catch (final PCJStorageException e) {
                        throw new TupleQueryResultHandlerException("Fail to batch load new results into the PCJ with ID '" + pcjId + "'.", e);
                    }
                    batch.clear();
                }
            }
        });
        if (!batch.isEmpty()) {
            pcjStorage.addResults(pcjId, batch);
            batch.clear();
        }
    } catch (final MalformedQueryException | PCJStorageException | SailException | QueryEvaluationException | RepositoryException | TupleQueryResultHandlerException e) {
        throw new RyaClientException("Fail to batch load new results into the PCJ with ID '" + pcjId + "'.", e);
    } finally {
        if (sailConn != null) {
            try {
                sailConn.close();
            } catch (final SailException e) {
                log.warn(e.getMessage(), e);
            }
        }
        if (sail != null) {
            try {
                sail.shutDown();
            } catch (final SailException e) {
                log.warn(e.getMessage(), e);
            }
        }
    }
}

Example 52 with Sail

use of org.eclipse.rdf4j.sail.Sail in project incubator-rya by apache.

the class FluoITBase method setupRya.

/**
 * Sets up a Rya instance.
 */
protected RyaSailRepository setupRya() throws AccumuloException, AccumuloSecurityException, RepositoryException, RyaDAOException, NumberFormatException, UnknownHostException, InferenceEngineException, AlreadyInitializedException, RyaDetailsRepositoryException, DuplicateInstanceNameException, RyaClientException, SailException {
    checkNotNull(instanceName);
    checkNotNull(zookeepers);
    // Setup Rya configuration values.
    conf.setTablePrefix(getRyaInstanceName());
    conf.setDisplayQueryPlan(true);
    conf.setBoolean(ConfigUtils.USE_MOCK_INSTANCE, false);
    conf.set(ConfigUtils.CLOUDBASE_USER, clusterInstance.getUsername());
    conf.set(ConfigUtils.CLOUDBASE_PASSWORD, clusterInstance.getPassword());
    conf.set(ConfigUtils.CLOUDBASE_INSTANCE, clusterInstance.getInstanceName());
    conf.set(ConfigUtils.CLOUDBASE_ZOOKEEPERS, clusterInstance.getZookeepers());
    conf.set(ConfigUtils.USE_PCJ, "true");
    conf.set(ConfigUtils.FLUO_APP_NAME, getRyaInstanceName());
    conf.set(ConfigUtils.PCJ_STORAGE_TYPE, PrecomputedJoinIndexerConfig.PrecomputedJoinStorageType.ACCUMULO.toString());
    conf.set(ConfigUtils.PCJ_UPDATER_TYPE, PrecomputedJoinIndexerConfig.PrecomputedJoinUpdaterType.FLUO.toString());
    conf.set(ConfigUtils.CLOUDBASE_AUTHS, "");
    // Install the test instance of Rya.
    final Install install = new AccumuloInstall(createConnectionDetails(), accumuloConn);
    final InstallConfiguration installConfig = InstallConfiguration.builder().setEnableTableHashPrefix(true).setEnableEntityCentricIndex(true).setEnableFreeTextIndex(true).setEnableTemporalIndex(true).setEnablePcjIndex(true).setEnableGeoIndex(true).setFluoPcjAppName(getRyaInstanceName()).build();
    install.install(getRyaInstanceName(), installConfig);
    // Connect to the instance of Rya that was just installed.
    final Sail sail = RyaSailFactory.getInstance(conf);
    final RyaSailRepository ryaRepo = new RyaSailRepository(sail);
    return ryaRepo;
}

Example 53 with Sail

use of org.eclipse.rdf4j.sail.Sail in project incubator-rya by apache.

the class AccumuloRemoveUserIT method removedUserCanNotInsert.

/**
 * Ensure a user that has been removed from the Rya instance can not interact with it.
 */
@Test
public void removedUserCanNotInsert() throws Exception {
    final String adminUser = testInstance.createUniqueUser();
    final String user = testInstance.createUniqueUser();
    final SecurityOperations secOps = super.getConnector().securityOperations();
    // Create the user that will install the instance of Rya.
    secOps.createLocalUser(adminUser, new PasswordToken(adminUser));
    secOps.grantSystemPermission(adminUser, SystemPermission.CREATE_TABLE);
    final RyaClient userAClient = AccumuloRyaClientFactory.build(new AccumuloConnectionDetails(adminUser, adminUser.toCharArray(), getInstanceName(), getZookeepers()), super.getClusterInstance().getCluster().getConnector(adminUser, adminUser));
    // Create the user that will be added to the instance of Rya.
    secOps.createLocalUser(user, new PasswordToken(user));
    final RyaClient userCClient = AccumuloRyaClientFactory.build(new AccumuloConnectionDetails(user, user.toCharArray(), getInstanceName(), getZookeepers()), super.getClusterInstance().getCluster().getConnector(user, user));
    // Install the instance of Rya.
    userAClient.getInstall().install(getRyaInstanceName(), InstallConfiguration.builder().build());
    // Add userC.
    userAClient.getAddUser().get().addUser(getRyaInstanceName(), user);
    // Remove userA.
    userCClient.getRemoveUser().get().removeUser(getRyaInstanceName(), adminUser);
    // Show that userA can not insert anything.
    boolean securityExceptionThrown = false;
    Sail sail = null;
    SailConnection sailConn = null;
    try {
        final AccumuloRdfConfiguration userAConf = makeRyaConfig(getRyaInstanceName(), adminUser, adminUser, getInstanceName(), getZookeepers());
        sail = RyaSailFactory.getInstance(userAConf);
        sailConn = sail.getConnection();
        final ValueFactory vf = sail.getValueFactory();
        sailConn.addStatement(vf.createIRI("urn:Alice"), vf.createIRI("urn:talksTo"), vf.createIRI("urn:Bob"));
    } catch (final RuntimeException e) {
        final Throwable cause = e.getCause();
        if (cause instanceof AccumuloSecurityException) {
            securityExceptionThrown = true;
        }
    } finally {
        if (sailConn != null) {
            sailConn.close();
        }
        if (sail != null) {
            sail.shutDown();
        }
    }
    assertTrue(securityExceptionThrown);
}

Example 54 with Sail

use of org.eclipse.rdf4j.sail.Sail in project incubator-rya by apache.

the class MongoRyaDirectExample method main.

public static void main(final String[] args) throws Exception {
    if (IS_DETAILED_LOGGING_ENABLED) {
        setupLogging();
    }
    final Configuration conf = getConf();
    conf.setBoolean(ConfigUtils.DISPLAY_QUERY_PLAN, PRINT_QUERIES);
    SailRepository repository = null;
    SailRepositoryConnection conn = null;
    try {
        log.info("Connecting to Indexing Sail Repository.");
        final Sail sail = RyaSailFactory.getInstance(conf);
        repository = new SailRepository(sail);
        conn = repository.getConnection();
        final long start = System.currentTimeMillis();
        if (USE_LUBM_QUERIES) {
            log.info("Running LUBM Sample Queries");
            testLubmFile(conn);
        }
        log.info("Running SPARQL Example: Add and Delete");
        testAddAndDelete(conn);
        testAddAndDeleteNoContext(conn);
        testAddNamespaces(conn);
        // testAddPointAndWithinSearch(conn);
        testAddAndFreeTextSearchWithPCJ(conn);
        // to test out inference, set inference to true in the conf
        if (USE_INFER) {
            testInfer(conn, sail);
            testPropertyChainInference(conn, sail);
            testPropertyChainInferenceAltRepresentation(conn, sail);
            testSomeValuesFromInference(conn, sail);
            testAllValuesFromInference(conn, sail);
            testIntersectionOfInference(conn, sail);
            testOneOfInference(conn, sail);
        }
        log.info("TIME: " + (System.currentTimeMillis() - start) / 1000.);
    } finally {
        log.info("Shutting down");
        closeQuietly(conn);
        closeQuietly(repository);
    }
}

Example 55 with Sail

use of org.eclipse.rdf4j.sail.Sail in project incubator-rya by apache.

the class RyaClientExample method main.

public static void main(final String[] args) throws Exception {
    final String accumuloUsername = "root";
    final String accumuloPassword = "password";
    MiniAccumuloCluster cluster = null;
    MiniFluo fluo = null;
    Sail ryaSail = null;
    try {
        // Setup a Mini Accumulo Cluster to host the Rya instance.
        log.info("Setting up the Mini Accumulo Cluster used by this example.");
        final File miniDataDir = Files.createTempDir();
        final MiniAccumuloConfig cfg = new MiniAccumuloConfig(miniDataDir, accumuloPassword);
        cluster = new MiniAccumuloCluster(cfg);
        cluster.start();
        // Setup a Mini Fluo application that will be used to incrementally update the PCJ indicies.
        log.info("Setting up the Mini Fluo application used by this example.");
        final String fluoAppName = "demoInstance_pcjUpdater";
        fluo = makeMiniFluo(accumuloUsername, accumuloPassword, cluster.getInstanceName(), cluster.getZooKeepers(), fluoAppName);
        // Give the root user the 'U' authorizations.
        final Connector connector = cluster.getConnector(accumuloUsername, accumuloPassword);
        connector.securityOperations().changeUserAuthorizations(accumuloUsername, new Authorizations("U"));
        // Setup a Rya Client that is able to interact with the mini cluster.
        final AccumuloConnectionDetails connectionDetails = new AccumuloConnectionDetails(accumuloUsername, accumuloPassword.toCharArray(), cluster.getInstanceName(), cluster.getZooKeepers());
        final RyaClient ryaClient = AccumuloRyaClientFactory.build(connectionDetails, connector);
        // Install an instance of Rya that has all of the secondary indexers turned on.
        final String ryaInstanceName = "demoInstance_";
        final InstallConfiguration installConfig = InstallConfiguration.builder().setEnableTableHashPrefix(true).setEnableEntityCentricIndex(true).setEnableGeoIndex(true).setEnableFreeTextIndex(true).setEnableTemporalIndex(true).setEnablePcjIndex(true).setFluoPcjAppName(fluoAppName).build();
        ryaClient.getInstall().install(ryaInstanceName, installConfig);
        // Add a PCJ index.
        final String sparql = "SELECT ?patron ?employee " + "WHERE { " + "?patron <http://talksTo> ?employee. " + "?employee <http://worksAt> <http://CoffeeShop>. " + "}";
        // Load some statements into the Rya instance.
        final AccumuloIndexingConfiguration conf = AccumuloIndexingConfiguration.builder().setAuths("U").setAccumuloUser(accumuloUsername).setAccumuloPassword(accumuloPassword).setAccumuloInstance(cluster.getInstanceName()).setAccumuloZooKeepers(cluster.getZooKeepers()).setRyaPrefix(ryaInstanceName).setPcjUpdaterFluoAppName(fluoAppName).build();
        ryaSail = RyaSailFactory.getInstance(conf);
        final ValueFactory vf = ryaSail.getValueFactory();
        final List<Statement> statements = Lists.newArrayList(vf.createStatement(vf.createIRI("http://Eve"), vf.createIRI("http://talksTo"), vf.createIRI("http://Charlie")), vf.createStatement(vf.createIRI("http://David"), vf.createIRI("http://talksTo"), vf.createIRI("http://Alice")), vf.createStatement(vf.createIRI("http://Alice"), vf.createIRI("http://worksAt"), vf.createIRI("http://CoffeeShop")), vf.createStatement(vf.createIRI("http://Bob"), vf.createIRI("http://worksAt"), vf.createIRI("http://CoffeeShop")), vf.createStatement(vf.createIRI("http://George"), vf.createIRI("http://talksTo"), vf.createIRI("http://Frank")), vf.createStatement(vf.createIRI("http://Frank"), vf.createIRI("http://worksAt"), vf.createIRI("http://CoffeeShop")), vf.createStatement(vf.createIRI("http://Eve"), vf.createIRI("http://talksTo"), vf.createIRI("http://Bob")), vf.createStatement(vf.createIRI("http://Charlie"), vf.createIRI("http://worksAt"), vf.createIRI("http://CoffeeShop")));
        SailConnection ryaConn = ryaSail.getConnection();
        log.info("");
        log.info("Loading the following statements:");
        ryaConn.begin();
        for (final Statement statement : statements) {
            log.info("    " + statement.toString());
            ryaConn.addStatement(statement.getSubject(), statement.getPredicate(), statement.getObject());
        }
        log.info("");
        ryaConn.close();
        fluo.waitForObservers();
        // Execute the SPARQL query and print the results.
        log.info("Executing the following query: ");
        prettyLogSparql(sparql);
        log.info("");
        final ParsedQuery parsedQuery = new SPARQLParser().parseQuery(sparql, null);
        ryaConn = ryaSail.getConnection();
        final CloseableIteration<? extends BindingSet, QueryEvaluationException> result = ryaConn.evaluate(parsedQuery.getTupleExpr(), null, null, false);
        log.info("Results:");
        while (result.hasNext()) {
            log.info("    " + result.next());
        }
        log.info("");
    } finally {
        if (ryaSail != null) {
            log.info("Shutting down the Rya Sail instance.");
            ryaSail.shutDown();
        }
        if (fluo != null) {
            try {
                log.info("Shutting down the Mini Fluo instance.");
                fluo.close();
            } catch (final Exception e) {
                log.error("Could not shut down the Mini Fluo instance.", e);
            }
        }
        if (cluster != null) {
            log.info("Sutting down the Mini Accumulo Cluster.");
            cluster.stop();
        }
    }
}