Examples with RyaDAOException org.apache.rya.api.persist.RyaDAOException used on opensource projects

Example 6 with RyaDAOException

use of org.apache.rya.api.persist.RyaDAOException in project incubator-rya by apache.

the class RyaOutputFormat method getRyaIndexer.

private static AccumuloRyaDAO getRyaIndexer(final Configuration conf) throws IOException {
    try {
        if (!conf.getBoolean(ENABLE_CORE, true)) {
            return null;
        }
        final AccumuloRyaDAO ryaIndexer = new AccumuloRyaDAO();
        final Connector conn = ConfigUtils.getConnector(conf);
        ryaIndexer.setConnector(conn);
        final AccumuloRdfConfiguration ryaConf = new AccumuloRdfConfiguration();
        final String tablePrefix = conf.get(OUTPUT_PREFIX_PROPERTY, null);
        if (tablePrefix != null) {
            ryaConf.setTablePrefix(tablePrefix);
        }
        ryaConf.setDisplayQueryPlan(false);
        ryaIndexer.setConf(ryaConf);
        ryaIndexer.init();
        return ryaIndexer;
    } catch (final AccumuloException e) {
        logger.error("Cannot create RyaIndexer", e);
        throw new IOException(e);
    } catch (final AccumuloSecurityException e) {
        logger.error("Cannot create RyaIndexer", e);
        throw new IOException(e);
    } catch (final RyaDAOException e) {
        logger.error("Cannot create RyaIndexer", e);
        throw new IOException(e);
    }
}

Example 7 with RyaDAOException

use of org.apache.rya.api.persist.RyaDAOException in project incubator-rya by apache.

the class AccumuloCreatePCJ method createPCJ.

@Override
public String createPCJ(final String instanceName, final String sparql, Set<ExportStrategy> strategies) throws InstanceDoesNotExistException, RyaClientException {
    requireNonNull(instanceName);
    requireNonNull(sparql);
    final Optional<RyaDetails> ryaDetailsHolder = getInstanceDetails.getDetails(instanceName);
    final boolean ryaInstanceExists = ryaDetailsHolder.isPresent();
    if (!ryaInstanceExists) {
        throw new InstanceDoesNotExistException(String.format("The '%s' instance of Rya does not exist.", instanceName));
    }
    final PCJIndexDetails pcjIndexDetails = ryaDetailsHolder.get().getPCJIndexDetails();
    final boolean pcjIndexingEnabeld = pcjIndexDetails.isEnabled();
    if (!pcjIndexingEnabeld) {
        throw new RyaClientException(String.format("The '%s' instance of Rya does not have PCJ Indexing enabled.", instanceName));
    }
    // Create the PCJ table that will receive the index results.
    final String pcjId;
    try (final PrecomputedJoinStorage pcjStorage = new AccumuloPcjStorage(getConnector(), instanceName)) {
        pcjId = pcjStorage.createPcj(sparql);
        // If a Fluo application is being used, task it with updating the PCJ.
        final Optional<FluoDetails> fluoDetailsHolder = pcjIndexDetails.getFluoDetails();
        if (fluoDetailsHolder.isPresent()) {
            final String fluoAppName = fluoDetailsHolder.get().getUpdateAppName();
            try {
                updateFluoApp(instanceName, fluoAppName, pcjId, sparql, strategies);
            } catch (RepositoryException | MalformedQueryException | SailException | QueryEvaluationException | PcjException | RyaDAOException e) {
                throw new RyaClientException("Problem while initializing the Fluo application with the new PCJ.", e);
            } catch (UnsupportedQueryException e) {
                throw new RyaClientException("The new PCJ could not be initialized because it either contains an unsupported query node " + "or an invalid ExportStrategy for the given QueryType.  Projection queries can be exported to either Rya or Kafka," + "unless they contain an aggregation, in which case they can only be exported to Kafka.  Construct queries can be exported" + "to Rya and Kafka, and Periodic queries can only be exported to Rya.");
            }
            // Update the Rya Details to indicate the PCJ is being updated incrementally.
            final RyaDetailsRepository detailsRepo = new AccumuloRyaInstanceDetailsRepository(getConnector(), instanceName);
            try {
                new RyaDetailsUpdater(detailsRepo).update(new RyaDetailsMutator() {

                    @Override
                    public RyaDetails mutate(final RyaDetails originalDetails) throws CouldNotApplyMutationException {
                        // Update the original PCJ Details to indicate they are incrementally updated.
                        final PCJDetails originalPCJDetails = originalDetails.getPCJIndexDetails().getPCJDetails().get(pcjId);
                        final PCJDetails.Builder mutatedPCJDetails = PCJDetails.builder(originalPCJDetails).setUpdateStrategy(PCJUpdateStrategy.INCREMENTAL);
                        // Replace the old PCJ Details with the updated ones.
                        final RyaDetails.Builder builder = RyaDetails.builder(originalDetails);
                        builder.getPCJIndexDetails().addPCJDetails(mutatedPCJDetails);
                        return builder.build();
                    }
                });
            } catch (RyaDetailsRepositoryException | CouldNotApplyMutationException e) {
                throw new RyaClientException("Problem while updating the Rya instance's Details to indicate the PCJ is being incrementally updated.", e);
            }
        }
        // Return the ID that was assigned to the PCJ.
        return pcjId;
    } catch (final PCJStorageException e) {
        throw new RyaClientException("Problem while initializing the PCJ table.", e);
    }
}

Example 8 with RyaDAOException

use of org.apache.rya.api.persist.RyaDAOException in project incubator-rya by apache.

the class MergeToolTest method testMergeTool.

@Test
public void testMergeTool() throws Exception {
    // This statement was in both parent/child instances a month ago and is before the start time of yesterday
    // but it was left alone.  It should remain in the parent after merging.
    final RyaStatement ryaStatementOutOfTimeRange = createRyaStatement("coach", "called", "timeout", LAST_MONTH);
    // This statement was in both parent/child instances a month ago but after the start time of yesterday
    // the parent deleted it and the child still has it.  It should stay deleted in the parent after merging.
    final RyaStatement ryaStatementParentDeletedAfter = createRyaStatement("parent", "deleted", "after", LAST_MONTH);
    // This statement was added by the parent after the start time of yesterday and doesn't exist in the child.
    // It should stay in the parent after merging.
    final RyaStatement ryaStatementParentAddedAfter = createRyaStatement("parent", "added", "after", TODAY);
    // This statement was in both parent/child instances a month ago but after the start time of yesterday
    // the child deleted it and the parent still has it.  It should be deleted from the parent after merging.
    final RyaStatement ryaStatementChildDeletedAfter = createRyaStatement("child", "deleted", "after", LAST_MONTH);
    // This statement was added by the child after the start time of yesterday and doesn't exist in the parent.
    // It should be added to the parent after merging.
    final RyaStatement ryaStatementChildAddedAfter = createRyaStatement("child", "added", "after", TODAY);
    // This statement was modified by the child after the start of yesterday (The timestamp changes after updating)
    // It should be updated in the parent to match the child.
    final RyaStatement ryaStatementUpdatedByChild = createRyaStatement("bob", "catches", "ball", LAST_MONTH);
    final RyaStatement ryaStatementUntouchedByChild = createRyaStatement("bill", "talks to", "john", LAST_MONTH);
    final RyaStatement ryaStatementDeletedByChild = createRyaStatement("susan", "eats", "burgers", LAST_MONTH);
    final RyaStatement ryaStatementAddedByChild = createRyaStatement("ronnie", "plays", "guitar", TODAY);
    // This statement was modified by the child to change the column visibility.
    // The parent should combine the child's visibility with its visibility.
    final RyaStatement ryaStatementVisibilityDifferent = createRyaStatement("I", "see", "you", LAST_MONTH);
    ryaStatementVisibilityDifferent.setColumnVisibility(PARENT_COLUMN_VISIBILITY.getExpression());
    // Setup initial parent instance with 7 rows
    // This is the state of the parent data (as it is today) before merging occurs which will use the specified start time of yesterday.
    // Merging should keep statement
    parentDao.add(ryaStatementOutOfTimeRange);
    // Merging should update statement
    parentDao.add(ryaStatementUpdatedByChild);
    // Merging should keep statement
    parentDao.add(ryaStatementUntouchedByChild);
    // Merging should delete statement
    parentDao.add(ryaStatementDeletedByChild);
    // Merging should update statement
    parentDao.add(ryaStatementVisibilityDifferent);
    // Merging should keep statement
    parentDao.add(ryaStatementParentAddedAfter);
    // Merging should delete statement
    parentDao.add(ryaStatementChildDeletedAfter);
    // Simulate the child coming back with a modified data set before the merging occurs.
    // (1 updated row, 1 row left alone because it was unchanged, 1 row outside time range,
    // 1 row deleted, 1 new row added, 1 modified visibility, 1 deleted by child, 1 added by child).
    // There should be 5 rows in the child instance (4 which will be scanned over from the start time).
    ryaStatementUpdatedByChild.setObject(TestUtils.createRyaUri("football"));
    ryaStatementUpdatedByChild.setTimestamp(TODAY.getTime());
    ryaStatementVisibilityDifferent.setColumnVisibility(CHILD_COLUMN_VISIBILITY.getExpression());
    childDao.add(ryaStatementOutOfTimeRange);
    childDao.add(ryaStatementUpdatedByChild);
    childDao.add(ryaStatementUntouchedByChild);
    // Merging should add statement
    childDao.add(ryaStatementAddedByChild);
    childDao.add(ryaStatementVisibilityDifferent);
    childDao.add(ryaStatementParentDeletedAfter);
    // Merging should add statement
    childDao.add(ryaStatementChildAddedAfter);
    AccumuloRyaUtils.printTable(PARENT_TABLE_PREFIX + RdfCloudTripleStoreConstants.TBL_SPO_SUFFIX, parentConfig);
    AccumuloRyaUtils.printTable(CHILD_TABLE_PREFIX + RdfCloudTripleStoreConstants.TBL_SPO_SUFFIX, childConfig);
    log.info("Starting merge tool. Merging all data after the specified start time: " + YESTERDAY);
    mergeToolRun(YESTERDAY);
    for (final String tableSuffix : AccumuloInstanceDriver.TABLE_NAME_SUFFIXES) {
        AccumuloRyaUtils.printTable(PARENT_TABLE_PREFIX + tableSuffix, parentConfig);
    }
    final Scanner scanner = AccumuloRyaUtils.getScanner(PARENT_TABLE_PREFIX + RdfCloudTripleStoreConstants.TBL_SPO_SUFFIX, parentConfig);
    final Iterator<Entry<Key, Value>> iterator = scanner.iterator();
    int count = 0;
    while (iterator.hasNext()) {
        iterator.next();
        count++;
    }
    // Make sure we have all of them in the parent.
    assertEquals(7, count);
    assertStatementInParent("Parent missing statement that untouched by the child", 1, ryaStatementUntouchedByChild);
    assertStatementInParent("Parent missing statement that was out of time range", 1, ryaStatementOutOfTimeRange);
    assertStatementInParent("Parent missing statement that was updated by the child", 1, ryaStatementUpdatedByChild);
    assertStatementInParent("Parent missing statement that was added by the child", 1, ryaStatementAddedByChild);
    assertStatementInParent("Parent has statement that the child deleted", 0, ryaStatementDeletedByChild);
    // Check that it can be queried with parent's visibility
    assertStatementInParent("Parent missing statement with parent visibility", 1, ryaStatementVisibilityDifferent);
    // Check that it can be queried with child's visibility
    parentConfig.set(RdfCloudTripleStoreConfiguration.CONF_QUERY_AUTH, CHILD_AUTH);
    final Authorizations newParentAuths = AccumuloRyaUtils.addUserAuths(accumuloDualInstanceDriver.getParentUser(), accumuloDualInstanceDriver.getParentSecOps(), CHILD_AUTH);
    accumuloDualInstanceDriver.getParentSecOps().changeUserAuthorizations(accumuloDualInstanceDriver.getParentUser(), newParentAuths);
    assertStatementInParent("Parent missing statement with child visibility", 1, ryaStatementVisibilityDifferent);
    // Check that it can NOT be queried with some other visibility
    parentConfig.set(RdfCloudTripleStoreConfiguration.CONF_QUERY_AUTH, "bad_auth");
    final CloseableIteration<RyaStatement, RyaDAOException> iter = parentDao.getQueryEngine().query(ryaStatementVisibilityDifferent, parentConfig);
    count = 0;
    try {
        while (iter.hasNext()) {
            iter.next();
            count++;
        }
    } catch (final Exception e) {
        // Expected
        if (!(e.getCause() instanceof AccumuloSecurityException)) {
            fail();
        }
    }
    iter.close();
    assertEquals(0, count);
    // reset auth
    parentConfig.set(RdfCloudTripleStoreConfiguration.CONF_QUERY_AUTH, PARENT_AUTH);
    assertStatementInParent("Parent has statement it deleted later", 0, ryaStatementParentDeletedAfter);
    assertStatementInParent("Parent missing statement it added later", 1, ryaStatementParentAddedAfter);
    assertStatementInParent("Parent has statement child deleted later", 0, ryaStatementChildDeletedAfter);
    assertStatementInParent("Parent missing statement child added later", 1, ryaStatementChildAddedAfter);
    log.info("DONE");
}

Example 9 with RyaDAOException

use of org.apache.rya.api.persist.RyaDAOException in project incubator-rya by apache.

the class RyaDirectExample method createPCJ.

// private static void testDeleteGeoData(final SailRepositoryConnection conn)
// throws Exception {
// // Delete all stored points
// final String sparqlDelete = "PREFIX geo: <http://www.opengis.net/ont/geosparql#>  "//
// + "PREFIX geof: <http://www.opengis.net/def/function/geosparql/>  "//
// + "DELETE {\n" //
// + "  ?feature a geo:Feature . "//
// + "  ?feature geo:hasGeometry ?point . "//
// + "  ?point a geo:Point . "//
// + "  ?point geo:asWKT ?wkt . "//
// + "}\n" + "WHERE { \n" + "  ?feature a geo:Feature . "//
// + "  ?feature geo:hasGeometry ?point . "//
// + "  ?point a geo:Point . "//
// + "  ?point geo:asWKT ?wkt . "//
// + "}";//
// 
// final Update deleteUpdate = conn.prepareUpdate(QueryLanguage.SPARQL,
// sparqlDelete);
// deleteUpdate.execute();
// 
// String queryString;
// TupleQuery tupleQuery;
// CountingResultHandler tupleHandler;
// 
// // Find all stored points
// queryString = "PREFIX geo: <http://www.opengis.net/ont/geosparql#>  "//
// + "PREFIX geof: <http://www.opengis.net/def/function/geosparql/>  "//
// + "SELECT ?feature ?point ?wkt " //
// + "{" //
// + "  ?feature a geo:Feature . "//
// + "  ?feature geo:hasGeometry ?point . "//
// + "  ?point a geo:Point . "//
// + "  ?point geo:asWKT ?wkt . "//
// + "}";//
// tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
// tupleHandler = new CountingResultHandler();
// tupleQuery.evaluate(tupleHandler);
// log.info("Result count : " + tupleHandler.getCount());
// Validate.isTrue(tupleHandler.getCount() == 0);
// }
private static void createPCJ(final Configuration conf) throws RepositoryException, AccumuloException, AccumuloSecurityException, TableExistsException, PcjException, InferenceEngineException, NumberFormatException, UnknownHostException, SailException, TableNotFoundException {
    final Configuration config = new AccumuloRdfConfiguration(conf);
    config.set(ConfigUtils.USE_PCJ, "false");
    SailRepository repository = null;
    SailRepositoryConnection conn = null;
    try {
        final Sail extSail = RyaSailFactory.getInstance(config);
        repository = new SailRepository(extSail);
        conn = repository.getConnection();
        final String queryString1 = // 
        "" + // 
        "SELECT ?e ?c ?l ?o " + // 
        "{" + // 
        "  ?c a ?e . " + // 
        "  ?e <http://www.w3.org/2000/01/rdf-schema#label> ?l . " + // 
        "  ?e <uri:talksTo> ?o . " + // 
        "}";
        final String queryString2 = // 
        "" + // 
        "SELECT ?e ?c ?l ?o " + // 
        "{" + // 
        "  ?e a ?c . " + // 
        "  ?e <http://www.w3.org/2000/01/rdf-schema#label> ?l . " + // 
        "  ?e <uri:talksTo> ?o . " + // 
        "}";
        URI obj, subclass, talksTo;
        final URI person = new URIImpl("urn:people:alice");
        final URI feature = new URIImpl("urn:feature");
        final URI sub = new URIImpl("uri:entity");
        subclass = new URIImpl("uri:class");
        obj = new URIImpl("uri:obj");
        talksTo = new URIImpl("uri:talksTo");
        conn.add(person, RDF.TYPE, sub);
        conn.add(feature, RDF.TYPE, sub);
        conn.add(sub, RDF.TYPE, subclass);
        conn.add(sub, RDFS.LABEL, new LiteralImpl("label"));
        conn.add(sub, talksTo, obj);
        final String tablename1 = RYA_TABLE_PREFIX + "INDEX_1";
        final String tablename2 = RYA_TABLE_PREFIX + "INDEX_2";
        final Connector accCon = new MockInstance(INSTANCE).getConnector("root", new PasswordToken("".getBytes(StandardCharsets.UTF_8)));
        new PcjTables().createAndPopulatePcj(conn, accCon, tablename1, queryString1, new String[] { "e", "c", "l", "o" }, Optional.<PcjVarOrderFactory>absent());
        new PcjTables().createAndPopulatePcj(conn, accCon, tablename2, queryString2, new String[] { "e", "c", "l", "o" }, Optional.<PcjVarOrderFactory>absent());
    } catch (final RyaDAOException e) {
        throw new Error("While creating PCJ tables.", e);
    } finally {
        closeQuietly(conn);
        closeQuietly(repository);
    }
}

Example 10 with RyaDAOException

use of org.apache.rya.api.persist.RyaDAOException in project incubator-rya by apache.

the class MongoExecuteSparqlQuery method executeSparqlQuery.

@Override
public String executeSparqlQuery(final String ryaInstanceName, final String sparqlQuery) throws InstanceDoesNotExistException, RyaClientException {
    requireNonNull(ryaInstanceName);
    requireNonNull(sparqlQuery);
    // Ensure the Rya Instance exists.
    if (!instanceExists.exists(ryaInstanceName)) {
        throw new InstanceDoesNotExistException(String.format("There is no Rya instance named '%s'.", ryaInstanceName));
    }
    Sail sail = null;
    SailRepositoryConnection sailRepoConn = null;
    try {
        // Get a Sail object that is connected to the Rya instance.
        final MongoDBRdfConfiguration ryaConf = connectionDetails.build(ryaInstanceName);
        sail = RyaSailFactory.getInstance(ryaConf);
        final SailRepository sailRepo = new SailRepository(sail);
        sailRepoConn = sailRepo.getConnection();
        // Execute the query.
        final long start = System.currentTimeMillis();
        final TupleQuery tupleQuery = sailRepoConn.prepareTupleQuery(QueryLanguage.SPARQL, sparqlQuery);
        final ByteArrayOutputStream baos = new ByteArrayOutputStream();
        final CountingSPARQLResultsCSVWriter handler = new CountingSPARQLResultsCSVWriter(baos);
        tupleQuery.evaluate(handler);
        final long end = System.currentTimeMillis();
        // Format and return the result of the query.
        final String queryResult = new String(baos.toByteArray(), StandardCharsets.UTF_8);
        final String queryDuration = new DecimalFormat("0.0##").format((end - start) / 1000.0);
        return "Query Result:\n" + queryResult + "Retrieved " + handler.getCount() + " results in " + queryDuration + " seconds.";
    } catch (SailException | RyaDAOException | InferenceEngineException | AccumuloException | AccumuloSecurityException e) {
        throw new RyaClientException("Could not create the Sail object used to query the RYA instance.", e);
    } catch (final MalformedQueryException | QueryEvaluationException | TupleQueryResultHandlerException | RepositoryException e) {
        throw new RyaClientException("Could not execute the SPARQL query.", e);
    } finally {
        // Close the resources that were opened.
        if (sailRepoConn != null) {
            try {
                sailRepoConn.close();
            } catch (final RepositoryException e) {
                log.error("Couldn't close the SailRepositoryConnection object.", e);
            }
        }
        if (sail != null) {
            try {
                sail.shutDown();
            } catch (final SailException e) {
                log.error("Couldn't close the Sail object.", e);
            }
        }
    }
}