Examples with InferenceEngine org.apache.rya.rdftriplestore.inference.InferenceEngine used on opensource projects

Example 1 with InferenceEngine

use of org.apache.rya.rdftriplestore.inference.InferenceEngine in project incubator-rya by apache.

the class QueryRuleset method setRules.

/**
 * Extract the rules from the query string, applying inference rules if configured to.
 * @throws QueryRulesetException if the parsed query can't be parsed and translated into valid rules.
 */
private void setRules() throws QueryRulesetException {
    final ParsedTupleQuery ptq;
    final TupleExpr te;
    try {
        ptq = QueryParserUtil.parseTupleQuery(QueryLanguage.SPARQL, query, null);
    } catch (UnsupportedQueryLanguageException | MalformedQueryException e) {
        throw new QueryRulesetException("Error parsing query:\n" + query, e);
    }
    te = ptq.getTupleExpr();
    // Before converting to rules (and renaming variables), validate that no statement patterns
    // consist of only variables (this would result in a rule  that matches every triple).
    // Needs to be done before inference, since inference rules may create such statement patterns
    // that are OK because they won'd be converted to rules directly.
    te.visit(new QueryModelVisitorBase<QueryRulesetException>() {

        @Override
        public void meet(final StatementPattern node) throws QueryRulesetException {
            if (!(node.getSubjectVar().hasValue() || node.getPredicateVar().hasValue() || node.getObjectVar().hasValue())) {
                throw new QueryRulesetException("Statement pattern with no constants would match every statement:\n" + node + "\nFrom parsed query:\n" + te);
            }
        }
    });
    // Apply inference, if applicable
    if (conf != null && conf.isInfer()) {
        RdfCloudTripleStore store = null;
        try {
            log.info("Applying inference rules");
            store = (RdfCloudTripleStore) RyaSailFactory.getInstance(conf);
            final InferenceEngine inferenceEngine = store.getInferenceEngine();
            // Apply in same order as query evaluation:
            te.visit(new TransitivePropertyVisitor(conf, inferenceEngine));
            te.visit(new SymmetricPropertyVisitor(conf, inferenceEngine));
            te.visit(new InverseOfVisitor(conf, inferenceEngine));
            te.visit(new SubPropertyOfVisitor(conf, inferenceEngine));
            te.visit(new SubClassOfVisitor(conf, inferenceEngine));
            te.visit(new SameAsVisitor(conf, inferenceEngine));
            log.info("Query after inference:\n");
            for (final String line : te.toString().split("\n")) {
                log.info("\t" + line);
            }
        } catch (final Exception e) {
            throw new QueryRulesetException("Error applying inference to parsed query:\n" + te, e);
        } finally {
            if (store != null) {
                try {
                    store.shutDown();
                } catch (final SailException e) {
                    log.error("Error shutting down Sail after applying inference", e);
                }
            }
        }
    }
    // Extract the StatementPatterns and Filters and turn them into rules:
    final RulesetVisitor rv = new RulesetVisitor();
    try {
        te.visit(rv);
        rv.addSchema();
    } catch (final QueryRulesetException e) {
        throw new QueryRulesetException("Error extracting rules from parsed query:\n" + te, e);
    }
    for (final CopyRule candidateRule : rv.rules) {
        boolean unique = true;
        for (final CopyRule otherRule : rv.rules) {
            if (!candidateRule.equals(otherRule) && otherRule.isGeneralizationOf(candidateRule)) {
                unique = false;
                break;
            }
        }
        if (unique) {
            rules.add(candidateRule);
        }
    }
}

Example 2 with InferenceEngine

use of org.apache.rya.rdftriplestore.inference.InferenceEngine in project incubator-rya by apache.

the class SparqlQueryPigEngine method init.

public void init() throws Exception {
    Preconditions.checkNotNull(sparqlToPigTransformVisitor, "Sparql To Pig Transform Visitor must not be null");
    logger.info("Initializing Sparql Query Pig Engine");
    if (hadoopDir != null) {
        // set hadoop dir property
        System.setProperty("HADOOPDIR", hadoopDir);
    }
    if (pigServer == null) {
        pigServer = new PigServer(execType);
    }
    if (inference || stats) {
        final String instance = sparqlToPigTransformVisitor.getInstance();
        final String zoo = sparqlToPigTransformVisitor.getZk();
        final String user = sparqlToPigTransformVisitor.getUser();
        final String pass = sparqlToPigTransformVisitor.getPassword();
        final Connector connector = new ZooKeeperInstance(instance, zoo).getConnector(user, new PasswordToken(pass.getBytes(StandardCharsets.UTF_8)));
        final String tablePrefix = sparqlToPigTransformVisitor.getTablePrefix();
        conf.setTablePrefix(tablePrefix);
        if (inference) {
            logger.info("Using inference");
            inferenceEngine = new InferenceEngine();
            ryaDAO = new AccumuloRyaDAO();
            ryaDAO.setConf(conf);
            ryaDAO.setConnector(connector);
            ryaDAO.init();
            inferenceEngine.setRyaDAO(ryaDAO);
            inferenceEngine.setConf(conf);
            inferenceEngine.setSchedule(false);
            inferenceEngine.init();
        }
        if (stats) {
            logger.info("Using stats");
            rdfEvalStatsDAO = new AccumuloRdfEvalStatsDAO();
            rdfEvalStatsDAO.setConf(conf);
            rdfEvalStatsDAO.setConnector(connector);
            // rdfEvalStatsDAO.setEvalTable(tablePrefix + RdfCloudTripleStoreConstants.TBL_EVAL_SUFFIX);
            rdfEvalStatsDAO.init();
            rdfCloudTripleStoreEvaluationStatistics = new RdfCloudTripleStoreEvaluationStatistics<AccumuloRdfConfiguration>(conf, rdfEvalStatsDAO);
        }
    }
}

Example 3 with InferenceEngine

use of org.apache.rya.rdftriplestore.inference.InferenceEngine in project incubator-rya by apache.

the class SameAsTest method testGraphConfiguration.

@Test
public // This isn't a good test.  It's simply a cut-and-paste from a test that was failing in a different package in the SameAsVisitor.
void testGraphConfiguration() throws Exception {
    URI a = vf.createURI(namespace, "a");
    Statement statement = new StatementImpl(a, vf.createURI(namespace, "p"), vf.createLiteral("l"));
    Statement statement2 = new StatementImpl(a, vf.createURI(namespace, "p2"), vf.createLiteral("l"));
    ryaDAO.add(RdfToRyaConversions.convertStatement(statement));
    ryaDAO.add(RdfToRyaConversions.convertStatement(statement2));
    ryaDAO.add(RdfToRyaConversions.convertStatement(new StatementImpl(vf.createURI(namespace, "b"), vf.createURI(namespace, "p"), vf.createLiteral("l"))));
    ryaDAO.add(RdfToRyaConversions.convertStatement(new StatementImpl(vf.createURI(namespace, "c"), vf.createURI(namespace, "n"), vf.createLiteral("l"))));
    // build a connection
    RdfCloudTripleStore store = new RdfCloudTripleStore();
    store.setConf(conf);
    store.setRyaDAO(ryaDAO);
    InferenceEngine inferenceEngine = new InferenceEngine();
    inferenceEngine.setRyaDAO(ryaDAO);
    store.setInferenceEngine(inferenceEngine);
    store.initialize();
    System.out.println(Iterations.asList(store.getConnection().getStatements(a, vf.createURI(namespace, "p"), vf.createLiteral("l"), false, new Resource[0])).size());
}

Example 4 with InferenceEngine

use of org.apache.rya.rdftriplestore.inference.InferenceEngine in project incubator-rya by apache.

the class HasValueVisitorTest method testRewriteValuePattern.

@Test
public void testRewriteValuePattern() throws Exception {
    // Configure a mock inference engine with an ontology:
    final InferenceEngine inferenceEngine = mock(InferenceEngine.class);
    Map<Resource, Set<Value>> typeToCharacteristic = new HashMap<>();
    Set<Value> chordateCharacteristics = new HashSet<>();
    Set<Value> vertebrateCharacteristics = new HashSet<>();
    chordateCharacteristics.add(notochord);
    vertebrateCharacteristics.addAll(chordateCharacteristics);
    vertebrateCharacteristics.add(skull);
    typeToCharacteristic.put(chordate, chordateCharacteristics);
    typeToCharacteristic.put(tunicate, chordateCharacteristics);
    typeToCharacteristic.put(vertebrate, vertebrateCharacteristics);
    typeToCharacteristic.put(mammal, vertebrateCharacteristics);
    when(inferenceEngine.getHasValueByProperty(hasCharacteristic)).thenReturn(typeToCharacteristic);
    // Query for a specific type and rewrite using the visitor:
    final Projection query = new Projection(new StatementPattern(new Var("s"), new Var("p", hasCharacteristic), new Var("o")), new ProjectionElemList(new ProjectionElem("s", "subject"), new ProjectionElem("o", "characteristic")));
    query.visit(new HasValueVisitor(conf, inferenceEngine));
    // Expected structure: Union(Join(FSP, SP), [original SP])
    Assert.assertTrue(query.getArg() instanceof Union);
    final Union union = (Union) query.getArg();
    final StatementPattern originalSP = new StatementPattern(new Var("s"), new Var("p", hasCharacteristic), new Var("o"));
    Join join;
    if (union.getLeftArg() instanceof Join) {
        join = (Join) union.getLeftArg();
        Assert.assertEquals(originalSP, union.getRightArg());
    } else {
        Assert.assertTrue(union.getRightArg() instanceof Join);
        join = (Join) union.getRightArg();
        Assert.assertEquals(originalSP, union.getLeftArg());
    }
    Assert.assertTrue(join.getLeftArg() instanceof FixedStatementPattern);
    Assert.assertTrue(join.getRightArg() instanceof StatementPattern);
    final FixedStatementPattern fsp = (FixedStatementPattern) join.getLeftArg();
    final StatementPattern sp = (StatementPattern) join.getRightArg();
    // Verify join: FSP{ ?t _ ?originalObjectVar } JOIN { ?originalSubjectVar rdf:type ?t }
    Assert.assertEquals(originalSP.getSubjectVar(), sp.getSubjectVar());
    Assert.assertEquals(RDF.TYPE, sp.getPredicateVar().getValue());
    Assert.assertEquals(fsp.getSubjectVar(), sp.getObjectVar());
    Assert.assertEquals(originalSP.getObjectVar(), fsp.getObjectVar());
    // Verify FSP: should provide (type, value) pairs
    final Set<Statement> expectedStatements = new HashSet<>();
    final URI fspPred = (URI) fsp.getPredicateVar().getValue();
    expectedStatements.add(vf.createStatement(chordate, fspPred, notochord));
    expectedStatements.add(vf.createStatement(tunicate, fspPred, notochord));
    expectedStatements.add(vf.createStatement(vertebrate, fspPred, notochord));
    expectedStatements.add(vf.createStatement(mammal, fspPred, notochord));
    expectedStatements.add(vf.createStatement(vertebrate, fspPred, skull));
    expectedStatements.add(vf.createStatement(mammal, fspPred, skull));
    final Set<Statement> actualStatements = new HashSet<>(fsp.statements);
    Assert.assertEquals(expectedStatements, actualStatements);
}

Example 5 with InferenceEngine

use of org.apache.rya.rdftriplestore.inference.InferenceEngine in project incubator-rya by apache.

the class GeoRyaSailFactory method getRyaSail.

private static Sail getRyaSail(final Configuration config) throws InferenceEngineException, RyaDAOException, AccumuloException, AccumuloSecurityException, SailException {
    final RdfCloudTripleStore store = new RdfCloudTripleStore();
    final RyaDAO<?> dao;
    final RdfCloudTripleStoreConfiguration rdfConfig;
    final String user;
    final String pswd;
    // XXX Should(?) be MongoDBRdfConfiguration.MONGO_COLLECTION_PREFIX inside the if below. RYA-135
    final String ryaInstance = config.get(RdfCloudTripleStoreConfiguration.CONF_TBL_PREFIX);
    Objects.requireNonNull(ryaInstance, "RyaInstance or table prefix is missing from configuration." + RdfCloudTripleStoreConfiguration.CONF_TBL_PREFIX);
    if (ConfigUtils.getUseMongo(config)) {
        // Get a reference to a Mongo DB configuration object.
        final MongoDBRdfConfiguration mongoConfig = (config instanceof MongoDBRdfConfiguration) ? (MongoDBRdfConfiguration) config : new MongoDBRdfConfiguration(config);
        // Create the MongoClient that will be used by the Sail object's components.
        final MongoClient client = createMongoClient(mongoConfig);
        // Add the Indexer and Optimizer names to the configuration object that are configured to be used.
        OptionalConfigUtils.setIndexers(mongoConfig);
        // Populate the configuration using previously stored Rya Details if this instance uses them.
        try {
            final MongoRyaInstanceDetailsRepository ryaDetailsRepo = new MongoRyaInstanceDetailsRepository(client, mongoConfig.getRyaInstanceName());
            RyaDetailsToConfiguration.addRyaDetailsToConfiguration(ryaDetailsRepo.getRyaInstanceDetails(), mongoConfig);
        } catch (final RyaDetailsRepositoryException e) {
            LOG.info("Instance does not have a rya details collection, skipping.");
        }
        // Set the configuration to the stateful configuration that is used to pass the constructed objects around.
        final StatefulMongoDBRdfConfiguration statefulConfig = new StatefulMongoDBRdfConfiguration(mongoConfig, client);
        final List<MongoSecondaryIndex> indexers = statefulConfig.getInstances(AccumuloRdfConfiguration.CONF_ADDITIONAL_INDEXERS, MongoSecondaryIndex.class);
        statefulConfig.setIndexers(indexers);
        rdfConfig = statefulConfig;
        // Create the DAO that is able to interact with MongoDB.
        final MongoDBRyaDAO mongoDao = new MongoDBRyaDAO();
        mongoDao.setConf(statefulConfig);
        mongoDao.init();
        dao = mongoDao;
    } else {
        rdfConfig = new AccumuloRdfConfiguration(config);
        user = rdfConfig.get(ConfigUtils.CLOUDBASE_USER);
        pswd = rdfConfig.get(ConfigUtils.CLOUDBASE_PASSWORD);
        Objects.requireNonNull(user, "Accumulo user name is missing from configuration." + ConfigUtils.CLOUDBASE_USER);
        Objects.requireNonNull(pswd, "Accumulo user password is missing from configuration." + ConfigUtils.CLOUDBASE_PASSWORD);
        rdfConfig.setTableLayoutStrategy(new TablePrefixLayoutStrategy(ryaInstance));
        RyaSailFactory.updateAccumuloConfig((AccumuloRdfConfiguration) rdfConfig, user, pswd, ryaInstance);
        dao = getAccumuloDAO((AccumuloRdfConfiguration) rdfConfig);
    }
    store.setRyaDAO(dao);
    rdfConfig.setTablePrefix(ryaInstance);
    if (rdfConfig.isInfer()) {
        final InferenceEngine inferenceEngine = new InferenceEngine();
        inferenceEngine.setConf(rdfConfig);
        inferenceEngine.setRyaDAO(dao);
        inferenceEngine.init();
        store.setInferenceEngine(inferenceEngine);
    }
    store.initialize();
    return store;
}