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

Example 26 with SailException

use of org.eclipse.rdf4j.sail.SailException 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 27 with SailException

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

the class MongoRyaSinkTask method makeSail.

@Override
protected Sail makeSail(final Map<String, String> taskConfig) {
    requireNonNull(taskConfig);
    // Parse the configuration object.
    final MongoRyaSinkConfig config = new MongoRyaSinkConfig(taskConfig);
    // Move the configuration into a Rya Configuration object.
    final MongoDBRdfConfiguration ryaConfig = new MongoDBRdfConfiguration();
    ConfigUtils.setUseMongo(ryaConfig, true);
    ryaConfig.setMongoDBName(config.getRyaInstanceName());
    ryaConfig.setTablePrefix(config.getRyaInstanceName());
    ryaConfig.setMongoHostname(config.getHostname());
    ryaConfig.setMongoPort("" + config.getPort());
    if (!Strings.isNullOrEmpty(config.getUsername()) && !Strings.isNullOrEmpty(config.getPassword())) {
        ryaConfig.setMongoUser(config.getUsername());
        ryaConfig.setMongoPassword(config.getPassword());
    }
    // Create the Sail object.
    try {
        return RyaSailFactory.getInstance(ryaConfig);
    } catch (final SailException | AccumuloException | AccumuloSecurityException | RyaDAOException | InferenceEngineException e) {
        throw new ConnectException("Could not connect to the Rya Instance named " + config.getRyaInstanceName(), e);
    }
}

Example 28 with SailException

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

the class RyaSinkTaskTest method singleRecord.

@Test
public void singleRecord() {
    // Create the Statements that will be put by the task.
    final ValueFactory vf = SimpleValueFactory.getInstance();
    final Set<Statement> statements = Sets.newHashSet(vf.createStatement(vf.createIRI("urn:Alice"), vf.createIRI("urn:WorksAt"), vf.createIRI("urn:Taco Shop"), vf.createIRI("urn:graph1")), vf.createStatement(vf.createIRI("urn:Bob"), vf.createIRI("urn:TalksTo"), vf.createIRI("urn:Charlie"), vf.createIRI("urn:graph2")), vf.createStatement(vf.createIRI("urn:Eve"), vf.createIRI("urn:ListensTo"), vf.createIRI("urn:Alice"), vf.createIRI("urn:graph1")));
    // Create the task that will be tested.
    final InMemoryRyaSinkTask task = new InMemoryRyaSinkTask();
    // Setup the properties that will be used to configure the task. We don't actually need to set anything
    // here since we're always returning true for ryaInstanceExists(...) and use an in memory RDF store.
    final Map<String, String> props = new HashMap<>();
    try {
        // Start the task.
        task.start(props);
        // Put the statements as a SinkRecord.
        task.put(Collections.singleton(new SinkRecord("topic", 1, null, "key", null, statements, 0)));
        // Flush the statements.
        task.flush(new HashMap<>());
        // Fetch the stored Statements to show they match the original set.
        final Set<Statement> fetched = new HashSet<>();
        final Sail sail = task.makeSail(props);
        try (SailConnection conn = sail.getConnection();
            CloseableIteration<? extends Statement, SailException> it = conn.getStatements(null, null, null, false)) {
            while (it.hasNext()) {
                fetched.add(it.next());
            }
        }
        assertEquals(statements, fetched);
    } finally {
        // Stop the task.
        task.stop();
    }
}

Example 29 with SailException

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

the class MergeDriverClient method main.

public static void main(final String[] args) throws ParseException, MergeConfigurationException, UnknownHostException, MergerException, java.text.ParseException, SailException, AccumuloException, AccumuloSecurityException, InferenceEngineException, RepositoryException, MalformedQueryException, UpdateExecutionException {
    final String log4jConfiguration = System.getProperties().getProperty("log4j.configuration");
    if (StringUtils.isNotBlank(log4jConfiguration)) {
        final String parsedConfiguration = PathUtils.clean(StringUtils.removeStart(log4jConfiguration, "file:"));
        final File configFile = new File(parsedConfiguration);
        if (configFile.exists()) {
            DOMConfigurator.configure(parsedConfiguration);
        } else {
            BasicConfigurator.configure();
        }
    }
    final MergeConfigurationCLI config = new MergeConfigurationCLI(args);
    try {
        configuration = config.createConfiguration();
    } catch (final MergeConfigurationException e) {
        LOG.error("Configuration failed.", e);
    }
    final boolean useTimeSync = configuration.getUseNtpServer();
    Optional<Long> offset = Optional.absent();
    if (useTimeSync) {
        final String tomcat = configuration.getChildTomcatUrl();
        final String ntpHost = configuration.getNtpServerHost();
        try {
            offset = Optional.fromNullable(TimeUtils.getNtpServerAndMachineTimeDifference(ntpHost, tomcat));
        } catch (final IOException e) {
            LOG.error("Unable to get time difference between time server: " + ntpHost + " and the server: " + tomcat, e);
        }
    }
    final StatementStoreFactory storeFactory = new StatementStoreFactory(configuration);
    try {
        final RyaStatementStore parentStore = storeFactory.getParentStatementStore();
        final RyaStatementStore childStore = storeFactory.getChildStatementStore();
        LOG.info("Starting Merge Tool");
        if (configuration.getParentDBType() == ACCUMULO && configuration.getChildDBType() == ACCUMULO) {
            final AccumuloRyaStatementStore childAStore = (AccumuloRyaStatementStore) childStore;
            final AccumuloRyaStatementStore parentAStore = (AccumuloRyaStatementStore) parentStore;
        // do map reduce merging.
        // TODO: Run Merger
        } else {
            if (configuration.getMergePolicy() == TIMESTAMP) {
                final TimestampPolicyMergeConfiguration timeConfig = (TimestampPolicyMergeConfiguration) configuration;
                final Long timeOffset;
                if (offset.isPresent()) {
                    timeOffset = offset.get();
                } else {
                    timeOffset = 0L;
                }
                final MemoryTimeMerger merger = new MemoryTimeMerger(parentStore, childStore, new VisibilityStatementMerger(), timeConfig.getToolStartTime(), configuration.getParentRyaInstanceName(), timeOffset);
                merger.runJob();
            }
        }
    } catch (final Exception e) {
        LOG.error("Something went wrong creating a Rya Statement Store connection.", e);
    }
    Thread.setDefaultUncaughtExceptionHandler(new Thread.UncaughtExceptionHandler() {

        @Override
        public void uncaughtException(final Thread thread, final Throwable throwable) {
            LOG.error("Uncaught exception in " + thread.getName(), throwable);
        }
    });
    LOG.info("Finished running Merge Tool");
    System.exit(1);
}

Example 30 with SailException

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

the class RdfCloudTripleStoreConnection method addStatementInternal.

@Override
protected void addStatementInternal(final Resource subject, final IRI predicate, final Value object, final Resource... contexts) throws SailException {
    try {
        final String cv_s = conf.getCv();
        final byte[] cv = cv_s == null ? null : cv_s.getBytes(StandardCharsets.UTF_8);
        final List<RyaStatement> ryaStatements = new ArrayList<>();
        if (contexts != null && contexts.length > 0) {
            for (final Resource context : contexts) {
                final RyaStatement statement = new RyaStatement(RdfToRyaConversions.convertResource(subject), RdfToRyaConversions.convertIRI(predicate), RdfToRyaConversions.convertValue(object), RdfToRyaConversions.convertResource(context), null, new StatementMetadata(), cv);
                ryaStatements.add(statement);
            }
        } else {
            final RyaStatement statement = new RyaStatement(RdfToRyaConversions.convertResource(subject), RdfToRyaConversions.convertIRI(predicate), RdfToRyaConversions.convertValue(object), null, null, new StatementMetadata(), cv);
            ryaStatements.add(statement);
        }
        ryaDAO.add(ryaStatements.iterator());
    } catch (final RyaDAOException e) {
        throw new SailException(e);
    }
}