extras/indexingExample/src/main/java/RyaDirectExample.java

/*
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 *
 *   http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied.  See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */

import java.net.UnknownHostException;
import java.nio.charset.StandardCharsets;
import java.util.List;

import org.apache.accumulo.core.client.AccumuloException;
import org.apache.accumulo.core.client.AccumuloSecurityException;
import org.apache.accumulo.core.client.Connector;
import org.apache.accumulo.core.client.TableExistsException;
import org.apache.accumulo.core.client.TableNotFoundException;
import org.apache.accumulo.core.client.mock.MockInstance;
import org.apache.accumulo.core.client.security.tokens.PasswordToken;
import org.apache.commons.lang.Validate;
import org.apache.hadoop.conf.Configuration;
import org.apache.log4j.Logger;
import org.apache.rya.accumulo.AccumuloRdfConfiguration;
import org.apache.rya.api.persist.RyaDAOException;
import org.apache.rya.indexing.accumulo.AccumuloIndexingConfiguration;
import org.apache.rya.indexing.accumulo.ConfigUtils;
import org.apache.rya.indexing.external.PrecomputedJoinIndexerConfig;
import org.apache.rya.indexing.external.PrecomputedJoinIndexerConfig.PrecomputedJoinStorageType;
import org.apache.rya.indexing.pcj.storage.PcjException;
import org.apache.rya.indexing.pcj.storage.accumulo.PcjTables;
import org.apache.rya.rdftriplestore.inference.InferenceEngineException;
import org.apache.rya.sail.config.RyaSailFactory;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.model.vocabulary.RDF;
import org.eclipse.rdf4j.model.vocabulary.RDFS;
import org.eclipse.rdf4j.query.BindingSet;
import org.eclipse.rdf4j.query.MalformedQueryException;
import org.eclipse.rdf4j.query.QueryEvaluationException;
import org.eclipse.rdf4j.query.QueryLanguage;
import org.eclipse.rdf4j.query.QueryResultHandlerException;
import org.eclipse.rdf4j.query.TupleQuery;
import org.eclipse.rdf4j.query.TupleQueryResultHandler;
import org.eclipse.rdf4j.query.TupleQueryResultHandlerException;
import org.eclipse.rdf4j.query.Update;
import org.eclipse.rdf4j.query.UpdateExecutionException;
import org.eclipse.rdf4j.repository.RepositoryException;
import org.eclipse.rdf4j.repository.sail.SailRepository;
import org.eclipse.rdf4j.repository.sail.SailRepositoryConnection;
import org.eclipse.rdf4j.sail.Sail;
import org.eclipse.rdf4j.sail.SailException;

import com.google.common.base.Optional;

public class RyaDirectExample {
	private static final Logger log = Logger.getLogger(RyaDirectExample.class);

	//
	// Connection configuration parameters
	//

	private static final boolean USE_MOCK_INSTANCE = true;
	private static final boolean PRINT_QUERIES = true;
	private static final String INSTANCE = "instance";
	private static final String RYA_TABLE_PREFIX = "x_test_triplestore_";
	private static final String AUTHS = "U";

	public static void main(final String[] args) throws Exception {
		final Configuration conf = getConf();
		conf.set(PrecomputedJoinIndexerConfig.PCJ_STORAGE_TYPE, PrecomputedJoinStorageType.ACCUMULO.name());
		conf.setBoolean(ConfigUtils.DISPLAY_QUERY_PLAN, PRINT_QUERIES);

		log.info("Creating the tables as root.");

		SailRepository repository = null;
		SailRepositoryConnection conn = null;

		try {
			log.info("Creating PCJ Tables");
			createPCJ(conf);

			log.info("Connecting to Indexing Sail Repository.");
			final Sail extSail = RyaSailFactory.getInstance(conf);
			repository = new SailRepository(extSail);
			conn = repository.getConnection();

			final long start = System.currentTimeMillis();
			log.info("Running SPARQL Example: Add and Delete");
			testAddAndDelete(conn);
			log.info("Running SAIL/SPARQL Example: PCJ Search");
			testPCJSearch(conn);
			log.info("Running SAIL/SPARQL Example: Add and Temporal Search");
			testAddAndTemporalSearchWithPCJ(conn);
			log.info("Running SAIL/SPARQL Example: Add and Free Text Search with PCJ");
			testAddAndFreeTextSearchWithPCJ(conn);
//			log.info("Running SPARQL Example: Add Point and Geo Search with PCJ");
////			testAddPointAndWithinSearchWithPCJ(conn);
//			log.info("Running SPARQL Example: Temporal, Freetext, and Geo Search");
//			testTemporalFreeGeoSearch(conn);
//			log.info("Running SPARQL Example: Geo, Freetext, and PCJ Search");
//			testGeoFreetextWithPCJSearch(conn);
			log.info("Running SPARQL Example: Delete Temporal Data");
			testDeleteTemporalData(conn);
			log.info("Running SPARQL Example: Delete Free Text Data");
			testDeleteFreeTextData(conn);
//			log.info("Running SPARQL Example: Delete Geo Data");
//			testDeleteGeoData(conn);

			log.info("TIME: " + (System.currentTimeMillis() - start) / 1000.);
		} finally {
			log.info("Shutting down");
			closeQuietly(conn);
			closeQuietly(repository);
		}
	}

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

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

	private static Configuration getConf() {


		return AccumuloIndexingConfiguration.builder()
			.setUseMockAccumulo(USE_MOCK_INSTANCE)
			.setAuths(AUTHS)
			.setAccumuloUser("root")
			.setAccumuloPassword("")
			.setAccumuloInstance(INSTANCE)
			.setRyaPrefix(RYA_TABLE_PREFIX)
			.setUsePcj(true)
			.setUseAccumuloFreetextIndex(true)
			.setUseAccumuloTemporalIndex(true)
			.build();

	}

	public static void testAddAndDelete(final SailRepositoryConnection conn)
			throws MalformedQueryException, RepositoryException,
			UpdateExecutionException, QueryEvaluationException,
			TupleQueryResultHandlerException, AccumuloException,
			AccumuloSecurityException, TableNotFoundException {

		// Add data
		String query = "INSERT DATA\n"//
				+ "{ GRAPH <http://updated/test> {\n"//
				+ "  <http://acme.com/people/Mike> " //
				+ "       <http://acme.com/actions/likes> \"A new book\" ;\n"//
				+ "       <http://acme.com/actions/likes> \"Avocados\" .\n"
				+ "} }";

		log.info("Performing Query");

		Update update = conn.prepareUpdate(QueryLanguage.SPARQL, query);
		update.execute();

		query = "select ?p ?o { GRAPH <http://updated/test> {<http://acme.com/people/Mike> ?p ?o . }}";
		final CountingResultHandler resultHandler = new CountingResultHandler();
		TupleQuery tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL,
				query);
		tupleQuery.evaluate(resultHandler);
		log.info("Result count : " + resultHandler.getCount());

		Validate.isTrue(resultHandler.getCount() == 2);
		resultHandler.resetCount();

		// Delete Data
		query = "DELETE DATA\n" //
				+ "{ GRAPH <http://updated/test> {\n"
				+ "  <http://acme.com/people/Mike> <http://acme.com/actions/likes> \"A new book\" ;\n"
				+ "   <http://acme.com/actions/likes> \"Avocados\" .\n" + "}}";

		update = conn.prepareUpdate(QueryLanguage.SPARQL, query);
		update.execute();

		query = "select ?p ?o { GRAPH <http://updated/test> {<http://acme.com/people/Mike> ?p ?o . }}";
		tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, query);
		tupleQuery.evaluate(resultHandler);
		log.info("Result count : " + resultHandler.getCount());

		Validate.isTrue(resultHandler.getCount() == 0);
	}

	private static void testPCJSearch(final SailRepositoryConnection conn)
			throws Exception {

		String queryString;
		TupleQuery tupleQuery;
		CountingResultHandler tupleHandler;

		// ///////////// search for bob
		queryString = "SELECT ?e ?c ?l ?o " //
				+ "{" //
				+ "  ?e a ?c . "//
				+ "  ?e <http://www.w3.org/2000/01/rdf-schema#label> ?l . "//
				+ "  ?e <uri:talksTo> ?o . "//
				+ "}";//

		tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
		tupleHandler = new CountingResultHandler();
		tupleQuery.evaluate(tupleHandler);
		log.info("Result count : " + tupleHandler.getCount());
		Validate.isTrue(tupleHandler.getCount() == 1);

		// ///////////// search for bob
		queryString = "PREFIX fts: <http://rdf.useekm.com/fts#>  "//
				+ "SELECT ?e ?c ?l ?o " //
				+ "{" //
				+ "  ?c a ?e . "//
				+ "  ?e <http://www.w3.org/2000/01/rdf-schema#label> ?l . "//
				+ "  ?e <uri:talksTo> ?o . "//
				+ "}";//

		tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
		tupleHandler = new CountingResultHandler();
		tupleQuery.evaluate(tupleHandler);
		log.info("Result count : " + tupleHandler.getCount());
		Validate.isTrue(tupleHandler.getCount() == 2);

	}

	private static void testAddAndTemporalSearchWithPCJ(
			final SailRepositoryConnection conn) throws Exception {

		// create some resources and literals to make statements out of

		final String sparqlInsert = "PREFIX time: <http://www.w3.org/2006/time#>\n"
				+ "INSERT DATA {\n" //
				+ "_:eventz       a       time:Instant ;\n"
				+ "     time:inXSDDateTime '2001-01-01T01:01:01-08:00' ;\n" // one
																			// second
				+ "     time:inXSDDateTime '2001-01-01T04:01:02.000-05:00'^^<http://www.w3.org/2001/XMLSchema#dateTime> ;\n" // 2
																																// seconds
				+ "     time:inXSDDateTime \"2001-01-01T01:01:03-08:00\" ;\n" // 3
																				// seconds
				+ "     time:inXSDDateTime '2001-01-01T01:01:04-08:00' ;\n" // 4
																			// seconds
				+ "     time:inXSDDateTime '2001-01-01T09:01:05Z' ;\n"
				+ "     time:inXSDDateTime '2006-01-01' ;\n"
				+ "     time:inXSDDateTime '2007-01-01' ;\n"
				+ "     time:inXSDDateTime '2008-01-01' ; .\n" + "}";

		final Update update = conn.prepareUpdate(QueryLanguage.SPARQL,
				sparqlInsert);
		update.execute();

		// Find all stored dates.
		String queryString = "PREFIX time: <http://www.w3.org/2006/time#> \n"//
				+ "PREFIX tempo: <tag:rya-rdf.org,2015:temporal#> \n"//
				+ "SELECT ?event ?time \n" //
				+ "WHERE { \n"
				+ "  ?event time:inXSDDateTime ?time . \n"//
				+ "  FILTER(tempo:after(?time, '2001-01-01T01:01:03-08:00') ) \n"// after
																					// 3
																					// seconds
				+ "}";//

		TupleQuery tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL,
				queryString);
		CountingResultHandler tupleHandler = new CountingResultHandler();
		tupleQuery.evaluate(tupleHandler);
		log.info("Result count : " + tupleHandler.getCount());
		Validate.isTrue(tupleHandler.getCount() == 5);

		// Find all stored dates.
		queryString = "PREFIX time: <http://www.w3.org/2006/time#> \n"//
				+ "PREFIX tempo: <tag:rya-rdf.org,2015:temporal#> \n"//
				+ "SELECT ?event ?time \n" //
				+ "WHERE { \n"
				+ "  ?event time:inXSDDateTime ?time . \n"//
				+ "  ?event a  time:Instant . \n"//
				+ "  FILTER(tempo:after(?time, '2001-01-01T01:01:03-08:00') ) \n"// after
																					// 3
																					// seconds
				+ "}";//

		tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
		tupleHandler = new CountingResultHandler();
		tupleQuery.evaluate(tupleHandler);
		log.info("Result count : " + tupleHandler.getCount());
		Validate.isTrue(tupleHandler.getCount() == 5);

		// Find all stored dates.
		queryString = "PREFIX time: <http://www.w3.org/2006/time#> \n"//
				+ "PREFIX tempo: <tag:rya-rdf.org,2015:temporal#> \n"//
				+ "SELECT ?event ?time ?e ?c ?l ?o \n" //
				+ "WHERE { \n"
				+ "  ?e a ?c . \n"//
				+ "  ?e <http://www.w3.org/2000/01/rdf-schema#label> ?l . \n"//
				+ "  ?e <uri:talksTo> ?o . \n"//
				+ "  ?event a  time:Instant . \n"//
				+ "  ?event time:inXSDDateTime ?time . \n"//
				+ "  FILTER(tempo:after(?time, '2001-01-01T01:01:03-08:00') ) \n"// after
																					// 3
																					// seconds
				+ "}";//

		tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
		tupleHandler = new CountingResultHandler();
		tupleQuery.evaluate(tupleHandler);
		log.info("Result count : " + tupleHandler.getCount());
		Validate.isTrue(tupleHandler.getCount() == 5);
	}

	private static void testAddAndFreeTextSearchWithPCJ(
			final SailRepositoryConnection conn) throws Exception {
		// add data to the repository using the SailRepository add methods
		final ValueFactory f = conn.getValueFactory();
		final IRI person = f.createIRI("http://example.org/ontology/Person");

		String uuid;

		uuid = "urn:people:alice";
		conn.add(f.createIRI(uuid), RDF.TYPE, person);
		conn.add(f.createIRI(uuid), RDFS.LABEL,
				f.createLiteral("Alice Palace Hose", f.createIRI("xsd:string")));

		uuid = "urn:people:bob";
		conn.add(f.createIRI(uuid), RDF.TYPE, person);
		conn.add(f.createIRI(uuid), RDFS.LABEL,
				f.createLiteral("Bob Snob Hose", f.createIRI("xsd:string")));

		String queryString;
		TupleQuery tupleQuery;
		CountingResultHandler tupleHandler;

		// ///////////// search for alice
		queryString = "PREFIX fts: <http://rdf.useekm.com/fts#>  "//
				+ "SELECT ?person ?match ?e ?c ?l ?o " //
				+ "{" //
				+ "  ?person <http://www.w3.org/2000/01/rdf-schema#label> ?match . "//
				+ "  FILTER(fts:text(?match, \"pal*\")) " //
				+ "}";//
		tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
		tupleHandler = new CountingResultHandler();
		tupleQuery.evaluate(tupleHandler);
		log.info("Result count : " + tupleHandler.getCount());
		Validate.isTrue(tupleHandler.getCount() == 1);

		// ///////////// search for alice and bob
		queryString = "PREFIX fts: <http://rdf.useekm.com/fts#>  "//
				+ "SELECT ?person ?match " //
				+ "{" //
				+ "  ?person <http://www.w3.org/2000/01/rdf-schema#label> ?match . "//
				+ "  ?person a <http://example.org/ontology/Person> . "//
				+ "  FILTER(fts:text(?match, \"(alice | bob) *SE\")) " //
				+ "}";//
		tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
		tupleHandler = new CountingResultHandler();
		tupleQuery.evaluate(tupleHandler);
		log.info("Result count : " + tupleHandler.getCount());
		Validate.isTrue(tupleHandler.getCount() == 2);

		// ///////////// search for alice and bob
		queryString = "PREFIX fts: <http://rdf.useekm.com/fts#>  "//
				+ "SELECT ?person ?match " //
				+ "{" //
				+ "  ?person a <http://example.org/ontology/Person> . "//
				+ "  ?person <http://www.w3.org/2000/01/rdf-schema#label> ?match . "//
				+ "  FILTER(fts:text(?match, \"(alice | bob) *SE\")) " //
				+ "  FILTER(fts:text(?match, \"pal*\")) " //
				+ "}";//
		tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
		tupleHandler = new CountingResultHandler();
		tupleQuery.evaluate(tupleHandler);
		log.info("Result count : " + tupleHandler.getCount());
		Validate.isTrue(tupleHandler.getCount() == 1);

		// ///////////// search for bob
		queryString = "PREFIX fts: <http://rdf.useekm.com/fts#>  "//
				+ "SELECT ?person ?match ?e ?c ?l ?o " //
				+ "{" //
				+ "  ?e a ?c . "//
				+ "  ?e <http://www.w3.org/2000/01/rdf-schema#label> ?l . "//
				+ "  ?e <uri:talksTo> ?o . "//
				+ "  ?person a <http://example.org/ontology/Person> . "//
				+ "  ?person <http://www.w3.org/2000/01/rdf-schema#label> ?match . "//
				+ "  FILTER(fts:text(?match, \"!alice & hose\")) " //
				+ "}";//

		tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
		tupleHandler = new CountingResultHandler();
		tupleQuery.evaluate(tupleHandler);
		log.info("Result count : " + tupleHandler.getCount());
		Validate.isTrue(tupleHandler.getCount() == 1);
	}

//	private static void testAddPointAndWithinSearchWithPCJ(
//			final SailRepositoryConnection conn) throws Exception {
//
//		final String update = "PREFIX geo: <http://www.opengis.net/ont/geosparql#>  "//
//				+ "INSERT DATA { " //
//				+ "  <urn:feature> a geo:Feature ; " //
//				+ "    geo:hasGeometry [ " //
//				+ "      a geo:Point ; " //
//				+ "      geo:asWKT \"Point(-77.03524 38.889468)\"^^geo:wktLiteral "//
//				+ "    ] . " //
//				+ "}";
//
//		final Update u = conn.prepareUpdate(QueryLanguage.SPARQL, update);
//		u.execute();
//
//		String queryString;
//		TupleQuery tupleQuery;
//		CountingResultHandler tupleHandler;
//
//		// point outside search ring
//		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 . "//
//				+ "  FILTER(geof:sfWithin(?wkt, \"POLYGON((-77 39, -76 39, -76 38, -77 38, -77 39))\"^^geo:wktLiteral)) " //
//				+ "}";//
//		tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
//		tupleHandler = new CountingResultHandler();
//		tupleQuery.evaluate(tupleHandler);
//		log.info("Result count : " + tupleHandler.getCount());
//		Validate.isTrue(tupleHandler.getCount() == 0);
//
//		// point inside search ring
//		queryString = "PREFIX geo: <http://www.opengis.net/ont/geosparql#>  "//
//				+ "PREFIX geof: <http://www.opengis.net/def/function/geosparql/>  "//
//				+ "SELECT ?feature ?point ?wkt ?e ?l ?o" //
//				+ "{" //
//				+ "  ?feature a ?e . "//
//				+ "  ?e <http://www.w3.org/2000/01/rdf-schema#label> ?l . "//
//				+ "  ?e <uri:talksTo> ?o . "//
//				+ "  ?feature a geo:Feature . "//
//				+ "  ?feature geo:hasGeometry ?point . "//
//				+ "  ?point a geo:Point . "//
//				+ "  ?point geo:asWKT ?wkt . "//
//				+ "  FILTER(geof:sfWithin(?wkt, \"POLYGON((-78 39, -77 39, -77 38, -78 38, -78 39))\"^^geo:wktLiteral)) " //
//				+ "}";//
//
//		tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
//		tupleHandler = new CountingResultHandler();
//		tupleQuery.evaluate(tupleHandler);
//		log.info("Result count : " + tupleHandler.getCount());
//		Validate.isTrue(tupleHandler.getCount() == 1);
//
//		// point inside search ring with Pre-Computed Join
//		queryString = "PREFIX geo: <http://www.opengis.net/ont/geosparql#>  "//
//				+ "PREFIX geof: <http://www.opengis.net/def/function/geosparql/>  "//
//				+ "SELECT ?feature ?point ?wkt ?e ?l ?o" //
//				+ "{" //
//				+ "  ?feature a ?e . "//
//				+ "  ?e <http://www.w3.org/2000/01/rdf-schema#label> ?l . "//
//				+ "  ?e <uri:talksTo> ?o . "//
//				+ "  ?feature a geo:Feature . "//
//				+ "  ?feature geo:hasGeometry ?point . "//
//				+ "  ?point a geo:Point . "//
//				+ "  ?point geo:asWKT ?wkt . "//
//				+ "  FILTER(geof:sfWithin(?wkt, \"POLYGON((-78 39, -77 39, -77 38, -78 38, -78 39))\"^^geo:wktLiteral)) " //
//				+ "}";//
//
//		tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
//		tupleHandler = new CountingResultHandler();
//		tupleQuery.evaluate(tupleHandler);
//		log.info("Result count : " + tupleHandler.getCount());
//		Validate.isTrue(tupleHandler.getCount() >= 1); // may see points from
//														// during previous runs
//
//		// point outside search ring with PCJ
//		queryString = "PREFIX geo: <http://www.opengis.net/ont/geosparql#>  "//
//				+ "PREFIX geof: <http://www.opengis.net/def/function/geosparql/>  "//
//				+ "SELECT ?feature ?point ?wkt ?e ?l ?o " //
//				+ "{" //
//				+ "  ?feature a ?e . "//
//				+ "  ?e <http://www.w3.org/2000/01/rdf-schema#label> ?l . "//
//				+ "  ?e <uri:talksTo> ?o . "//
//				+ "  ?feature a geo:Feature . "//
//				+ "  ?feature geo:hasGeometry ?point . "//
//				+ "  ?point a geo:Point . "//
//				+ "  ?point geo:asWKT ?wkt . "//
//				+ "  FILTER(geof:sfWithin(?wkt, \"POLYGON((-77 39, -76 39, -76 38, -77 38, -77 39))\"^^geo:wktLiteral)) " //
//				+ "}";//
//		tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
//		tupleHandler = new CountingResultHandler();
//		tupleQuery.evaluate(tupleHandler);
//		log.info("Result count : " + tupleHandler.getCount());
//		Validate.isTrue(tupleHandler.getCount() == 0);
//
//		// point inside search ring with different Pre-Computed Join
//		queryString = "PREFIX geo: <http://www.opengis.net/ont/geosparql#>  "//
//				+ "PREFIX geof: <http://www.opengis.net/def/function/geosparql/>  "//
//				+ "SELECT ?feature ?point ?wkt ?e ?c ?l ?o " //
//				+ "{" //
//				+ "  ?e a ?c . "//
//				+ "  ?e <http://www.w3.org/2000/01/rdf-schema#label> ?l . "//
//				+ "  ?e <uri:talksTo> ?o . "//
//				+ "  ?feature a geo:Feature . "//
//				+ "  ?feature geo:hasGeometry ?point . "//
//				+ "  ?point a geo:Point . "//
//				+ "  ?point geo:asWKT ?wkt . "//
//				+ "  FILTER(geof:sfWithin(?wkt, \"POLYGON((-78 39, -77 39, -77 38, -78 38, -78 39))\"^^geo:wktLiteral)) " //
//				+ "}";//
//		tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
//		tupleHandler = new CountingResultHandler();
//		tupleQuery.evaluate(tupleHandler);
//		log.info("Result count : " + tupleHandler.getCount());
//		Validate.isTrue(tupleHandler.getCount() == 1);
//	}
//
//	private static void testTemporalFreeGeoSearch(
//			final SailRepositoryConnection conn)
//			throws MalformedQueryException, RepositoryException,
//			UpdateExecutionException, TupleQueryResultHandlerException,
//			QueryEvaluationException {
//
//		String queryString;
//		TupleQuery tupleQuery;
//		CountingResultHandler tupleHandler;
//
//		// ring containing point
//		queryString = "PREFIX geo: <http://www.opengis.net/ont/geosparql#>  "//
//				+ "PREFIX geof: <http://www.opengis.net/def/function/geosparql/>  "//
//				+ "PREFIX time: <http://www.w3.org/2006/time#> "//
//				+ "PREFIX tempo: <tag:rya-rdf.org,2015:temporal#> "//
//				+ "PREFIX fts: <http://rdf.useekm.com/fts#>  "//
//				+ "SELECT ?feature ?point ?wkt ?event ?time ?person ?match" //
//				+ "{" //
//				+ "  ?event a  time:Instant . \n"//
//				+ "  ?event time:inXSDDateTime ?time . \n"//
//				+ "  FILTER(tempo:after(?time, '2001-01-01T01:01:03-08:00') ) \n"// after
//																					// 3
//																					// seconds
//				+ "  ?feature a geo:Feature . "//
//				+ "  ?feature geo:hasGeometry ?point . "//
//				+ "  ?point a geo:Point . "//
//				+ "  ?point geo:asWKT ?wkt . "//
//				+ "  FILTER(geof:sfWithin(?wkt, \"POLYGON((-78 39, -77 39, -77 38, -78 38, -78 39))\"^^geo:wktLiteral)). " //
//				+ "  ?person a <http://example.org/ontology/Person> . "//
//				+ "  ?person <http://www.w3.org/2000/01/rdf-schema#label> ?match . "//
//				+ "  FILTER(fts:text(?match, \"pal*\")) " //
//				+ "}";//
//
//		tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
//
//		tupleHandler = new CountingResultHandler();
//		tupleQuery.evaluate(tupleHandler);
//		log.info("Result count : " + tupleHandler.getCount());
//		Validate.isTrue(tupleHandler.getCount() == 5);
//
//	}
//
//	private static void testGeoFreetextWithPCJSearch(
//			final SailRepositoryConnection conn)
//			throws MalformedQueryException, RepositoryException,
//			TupleQueryResultHandlerException, QueryEvaluationException {
//		// ring outside point
//		final String queryString = "PREFIX geo: <http://www.opengis.net/ont/geosparql#>  "//
//				+ "PREFIX fts: <http://rdf.useekm.com/fts#>  "//
//				+ "PREFIX geof: <http://www.opengis.net/def/function/geosparql/>  "//
//				+ "SELECT ?feature ?point ?wkt ?e ?c ?l ?o ?person ?match " //
//				+ "{" //
//				+ "  ?person a <http://example.org/ontology/Person> . "//
//				+ "  ?person <http://www.w3.org/2000/01/rdf-schema#label> ?match . "//
//				+ "  FILTER(fts:text(?match, \"!alice & hose\")) " //
//				+ "  ?e a ?c . "//
//				+ "  ?e <http://www.w3.org/2000/01/rdf-schema#label> ?l . "//
//				+ "  ?e <uri:talksTo> ?o . "//
//				+ "  ?feature a geo:Feature . "//
//				+ "  ?feature geo:hasGeometry ?point . "//
//				+ "  ?point a geo:Point . "//
//				+ "  ?point geo:asWKT ?wkt . "//
//				+ "  FILTER(geof:sfWithin(?wkt, \"POLYGON((-78 39, -77 39, -77 38, -78 38, -78 39))\"^^geo:wktLiteral)) " //
//				+ "}";//
//		final TupleQuery tupleQuery = conn.prepareTupleQuery(
//				QueryLanguage.SPARQL, queryString);
//		final CountingResultHandler tupleHandler = new CountingResultHandler();
//		tupleQuery.evaluate(tupleHandler);
//		log.info("Result count : " + tupleHandler.getCount());
//		Validate.isTrue(tupleHandler.getCount() == 1);
//	}

	private static void testDeleteTemporalData(
			final SailRepositoryConnection conn) throws Exception {
		// Delete all stored dates
		final String sparqlDelete = "PREFIX time: <http://www.w3.org/2006/time#>\n"
				+ "PREFIX tempo: <tag:rya-rdf.org,2015:temporal#> \n"//
				+ "DELETE {\n" //
				+ "  ?event time:inXSDDateTime ?time . \n"
				+ "}\n"
				+ "WHERE { \n" + "  ?event time:inXSDDateTime ?time . \n"//
				+ "}";//

		final Update deleteUpdate = conn.prepareUpdate(QueryLanguage.SPARQL,
				sparqlDelete);
		deleteUpdate.execute();

		// Find all stored dates.
		final String queryString = "PREFIX time: <http://www.w3.org/2006/time#> \n"//
				+ "PREFIX tempo: <tag:rya-rdf.org,2015:temporal#> \n"//
				+ "SELECT ?event ?time \n" //
				+ "WHERE { \n"
				+ "  ?event time:inXSDDateTime ?time . \n"//
				+ "  FILTER(tempo:after(?time, '2001-01-01T01:01:03-08:00') ) \n"// after
																					// 3
																					// seconds
				+ "}";//

		final CountingResultHandler tupleHandler = new CountingResultHandler();
		final TupleQuery tupleQuery = conn.prepareTupleQuery(
				QueryLanguage.SPARQL, queryString);
		tupleQuery.evaluate(tupleHandler);
		log.info("Result count : " + tupleHandler.getCount());
		Validate.isTrue(tupleHandler.getCount() == 0);
	}

	private static void testDeleteFreeTextData(
			final SailRepositoryConnection conn) throws Exception {
		// Delete data from the repository using the SailRepository remove
		// methods
		final ValueFactory f = conn.getValueFactory();
		final IRI person = f.createIRI("http://example.org/ontology/Person");

		String uuid;

		uuid = "urn:people:alice";
		conn.remove(f.createIRI(uuid), RDF.TYPE, person);
		conn.remove(f.createIRI(uuid), RDFS.LABEL,
				f.createLiteral("Alice Palace Hose", f.createIRI("xsd:string")));

		uuid = "urn:people:bob";
		conn.remove(f.createIRI(uuid), RDF.TYPE, person);
		conn.remove(f.createIRI(uuid), RDFS.LABEL,
				f.createLiteral("Bob Snob Hose", f.createIRI("xsd:string")));

		conn.remove(person, RDFS.LABEL, f.createLiteral("label", f.createIRI("xsd:string")));

		String queryString;
		TupleQuery tupleQuery;
		CountingResultHandler tupleHandler;

		// Find all
		queryString = "PREFIX fts: <http://rdf.useekm.com/fts#>  "//
				+ "SELECT ?person ?match " //
				+ "{" //
				+ "  ?person <http://www.w3.org/2000/01/rdf-schema#label> ?match . "//
				+ "  ?person a <http://example.org/ontology/Person> . "//
				+ "}";//
		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 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 . "//
					+ "}";//

			ValueFactory vf = SimpleValueFactory.getInstance();
			IRI obj, subclass, talksTo;
			final IRI person = vf.createIRI("urn:people:alice");
			final IRI feature = vf.createIRI("urn:feature");
			final IRI sub = vf.createIRI("uri:entity");
			subclass = vf.createIRI("uri:class");
			obj = vf.createIRI("uri:obj");
			talksTo = vf.createIRI("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, vf.createLiteral("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.absent());

			new PcjTables().createAndPopulatePcj(conn, accCon, tablename2,
					queryString2, new String[] { "e", "c", "l", "o" },
					Optional.absent());

		} catch (final RyaDAOException e) {
			throw new Error("While creating PCJ tables.",e);
		} finally {
			closeQuietly(conn);
			closeQuietly(repository);
		}

	}

	private static class CountingResultHandler implements
			TupleQueryResultHandler {
		private int count = 0;

		public int getCount() {
			return count;
		}

		public void resetCount() {
			count = 0;
		}

		@Override
		public void startQueryResult(final List<String> arg0)
				throws TupleQueryResultHandlerException {
		}

		@Override
		public void handleSolution(final BindingSet arg0)
				throws TupleQueryResultHandlerException {
			count++;
			System.out.println(arg0);
		}

		@Override
		public void endQueryResult() throws TupleQueryResultHandlerException {
		}

		@Override
		public void handleBoolean(final boolean arg0)
				throws QueryResultHandlerException {
		}

		@Override
		public void handleLinks(final List<String> arg0)
				throws QueryResultHandlerException {
		}
	}
}