Examples with BigdataSailRepositoryConnection com.bigdata.rdf.sail.BigdataSailRepositoryConnection used on opensource projects

Example 1 with BigdataSailRepositoryConnection

use of com.bigdata.rdf.sail.BigdataSailRepositoryConnection in project minerva by geneontology.

the class BlazegraphMolecularModelManager method loadModel.

@Override
public void loadModel(IRI modelId, boolean isOverride) throws OWLOntologyCreationException {
    if (modelMap.containsKey(modelId)) {
        if (!isOverride) {
            throw new OWLOntologyCreationException("Model already exists: " + modelId);
        }
        unlinkModel(modelId);
    }
    try {
        BigdataSailRepositoryConnection connection = repo.getReadOnlyConnection();
        try {
            RepositoryResult<Resource> graphs = connection.getContextIDs();
            if (!Iterations.asSet(graphs).contains(new URIImpl(modelId.toString()))) {
                throw new OWLOntologyCreationException("No such model in datastore: " + modelId);
            }
            graphs.close();
            RepositoryResult<Statement> statements = connection.getStatements(null, null, null, false, new URIImpl(modelId.toString()));
            // setting minimal = false will load the abox with the tbox ontology manager, allowing for OWL understanding of tbox content
            boolean minimal = false;
            OWLOntology abox = loadOntologyDocumentSource(new RioMemoryTripleSource(statements), minimal);
            statements.close();
            abox = postLoadFileFilter(abox);
            ModelContainer model = addModel(modelId, abox);
        } finally {
            connection.close();
        }
    } catch (RepositoryException e) {
        throw new OWLOntologyCreationException(e);
    }
}

Example 2 with BigdataSailRepositoryConnection

use of com.bigdata.rdf.sail.BigdataSailRepositoryConnection in project minerva by geneontology.

the class BlazegraphMolecularModelManager method executeSPARQLQueryWithoutPrefixManipulation.

public QueryResult executeSPARQLQueryWithoutPrefixManipulation(String queryText, int timeout) throws MalformedQueryException, QueryEvaluationException, RepositoryException {
    BigdataSailRepositoryConnection connection = repo.getReadOnlyConnection();
    try {
        Query query = connection.prepareQuery(QueryLanguage.SPARQL, queryText.toString());
        query.setMaxQueryTime(timeout);
        if (query instanceof TupleQuery) {
            TupleQuery tupleQuery = (TupleQuery) query;
            return tupleQuery.evaluate();
        } else if (query instanceof GraphQuery) {
            GraphQuery graphQuery = (GraphQuery) query;
            return graphQuery.evaluate();
        } else if (query instanceof BooleanQuery) {
            // FIXME
            throw new UnsupportedOperationException("Unsupported query type.");
        } else {
            throw new UnsupportedOperationException("Unsupported query type.");
        }
    } finally {
        connection.close();
    }
}

Example 3 with BigdataSailRepositoryConnection

use of com.bigdata.rdf.sail.BigdataSailRepositoryConnection in project minerva by geneontology.

the class BlazegraphMolecularModelManager method executeSPARQLQuery.

public QueryResult executeSPARQLQuery(String queryText, int timeout) throws MalformedQueryException, QueryEvaluationException, RepositoryException {
    BigdataSailRepositoryConnection connection = repo.getReadOnlyConnection();
    try {
        List<QueryPrologLexer.Token> tokens = QueryPrologLexer.lex(queryText);
        Set<String> declaredPrefixes = tokens.stream().filter(token -> token.getType().equals(QueryPrologLexer.TokenType.PREFIX)).map(token -> token.getStringValue()).collect(Collectors.toSet());
        StringBuffer queryWithDefaultPrefixes = new StringBuffer();
        for (Entry<String, String> entry : getCuriHandler().getMappings().entrySet()) {
            if (!declaredPrefixes.contains(entry.getKey())) {
                queryWithDefaultPrefixes.append("PREFIX " + entry.getKey() + ": <" + entry.getValue() + ">");
                queryWithDefaultPrefixes.append("\n");
            }
        }
        queryWithDefaultPrefixes.append(queryText);
        Query query = connection.prepareQuery(QueryLanguage.SPARQL, queryWithDefaultPrefixes.toString());
        query.setMaxQueryTime(timeout);
        if (query instanceof TupleQuery) {
            TupleQuery tupleQuery = (TupleQuery) query;
            return tupleQuery.evaluate();
        } else if (query instanceof GraphQuery) {
            GraphQuery graphQuery = (GraphQuery) query;
            return graphQuery.evaluate();
        } else if (query instanceof BooleanQuery) {
            // FIXME
            throw new UnsupportedOperationException("Unsupported query type.");
        } else {
            throw new UnsupportedOperationException("Unsupported query type.");
        }
    } finally {
        connection.close();
    }
}

Example 4 with BigdataSailRepositoryConnection

use of com.bigdata.rdf.sail.BigdataSailRepositoryConnection in project minerva by geneontology.

the class BlazegraphMolecularModelManager method getAllModelAnnotations.

public Map<IRI, Set<OWLAnnotation>> getAllModelAnnotations() throws IOException {
    Map<IRI, Set<OWLAnnotation>> annotations = new HashMap<>();
    // First get annotations from all the stored ontologies
    try {
        BigdataSailRepositoryConnection connection = repo.getReadOnlyConnection();
        try {
            String query = "PREFIX owl: <http://www.w3.org/2002/07/owl#> " + "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " + "SELECT ?model ?p ?o " + "WHERE { " + "?model a owl:Ontology . " + "?model ?p ?o . " + "FILTER(?p NOT IN (owl:imports, rdf:type, <http://geneontology.org/lego/json-model>)) " + "} ";
            TupleQuery tupleQuery = connection.prepareTupleQuery(QueryLanguage.SPARQL, query);
            TupleQueryResult result = tupleQuery.evaluate();
            OWLDataFactory factory = OWLManager.getOWLDataFactory();
            while (result.hasNext()) {
                BindingSet binding = result.next();
                Value model = binding.getValue("model");
                Value predicate = binding.getValue("p");
                String value = binding.getValue("o").stringValue();
                if ((model instanceof URI) && (predicate instanceof URI)) {
                    IRI modelId = IRI.create(((URI) model).toString());
                    OWLAnnotationProperty property = factory.getOWLAnnotationProperty(IRI.create(((URI) predicate).toString()));
                    OWLAnnotation annotation = factory.getOWLAnnotation(property, factory.getOWLLiteral(value));
                    Set<OWLAnnotation> modelAnnotations = annotations.getOrDefault(modelId, new HashSet<>());
                    modelAnnotations.add(annotation);
                    annotations.put(modelId, modelAnnotations);
                }
            }
        } catch (MalformedQueryException e) {
            throw new IOException(e);
        } catch (QueryEvaluationException e) {
            throw new IOException(e);
        } finally {
            connection.close();
        }
    } catch (RepositoryException e) {
        throw new IOException(e);
    }
    // Next get annotations from ontologies that may not be stored, replacing any stored annotations
    modelMap.values().stream().filter(mc -> mc.isModified()).forEach(mc -> {
        annotations.put(mc.getModelId(), mc.getAboxOntology().getAnnotations());
    });
    return annotations;
}

Example 5 with BigdataSailRepositoryConnection

use of com.bigdata.rdf.sail.BigdataSailRepositoryConnection in project minerva by geneontology.

the class BlazegraphOntologyManager method buildRegulationMap.

private Map<IRI, Set<IRI>> buildRegulationMap() throws IOException {
    String regulationTargetsQuery = IOUtils.toString(BlazegraphOntologyManager.class.getResourceAsStream("regulation_targets.rq"), StandardCharsets.UTF_8);
    try {
        BigdataSailRepositoryConnection connection = go_lego_repo.getReadOnlyConnection();
        try {
            TupleQuery tupleQuery = connection.prepareTupleQuery(QueryLanguage.SPARQL, regulationTargetsQuery);
            TupleQueryResult result = tupleQuery.evaluate();
            Map<IRI, Set<IRI>> regulators = new HashMap<>();
            while (result.hasNext()) {
                BindingSet binding = result.next();
                IRI regulator = IRI.create(binding.getValue("subjectDown").stringValue());
                IRI regulated = IRI.create(binding.getValue("fillerUp").stringValue());
                if (!regulators.containsKey(regulator)) {
                    regulators.put(regulator, new HashSet<>());
                }
                regulators.get(regulator).add(regulated);
            }
            return regulators;
        } catch (MalformedQueryException e) {
            throw new IOException(e);
        } catch (QueryEvaluationException e) {
            throw new IOException(e);
        } finally {
            connection.close();
        }
    } catch (RepositoryException e) {
        throw new IOException(e);
    }
}