Examples with ResultSet org.apache.jena.query.ResultSet used on opensource projects

Example 86 with ResultSet

use of org.apache.jena.query.ResultSet in project eol-globi-data by jhpoelen.

the class DatasetImporterForSaproxylic method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    try {
        final Model model = ModelFactory.createDefaultModel();
        NavigableSet<Triple<String, String, String>> triples = DBMaker.newTempTreeSet();
        Tripler add = triple -> {
            Resource resource = model.createResource("sx:" + triple.getLeft());
            Property property = model.createProperty("sx:" + triple.getMiddle());
            String obj = triple.getRight();
            if (StringUtils.startsWith(obj, "{")) {
                Resource food = model.createResource("sx:" + obj);
                model.add(resource, property, food);
            } else if (StringUtils.startsWith(obj, "http")) {
                model.add(resource, property, model.createResource(obj));
            } else if (StringUtils.isNotBlank(obj)) {
                model.add(resource, property, obj);
            }
        };
        parseReferences(add, getDataset().retrieve(URI.create("sx_txt/Reference.txt")));
        parseLocalities(add, getDataset().retrieve(URI.create("sx_txt/Locality.txt")));
        parseTaxa(add, getDataset().retrieve(URI.create("sx_txt/Taxon.txt")));
        parseTaxonRanks(add, getDataset().retrieve(URI.create("sx_txt/TaxonRank.txt")));
        parseOccurrences(add, getDataset().retrieve(URI.create("sx_txt/Occurrence.txt")));
        parseAssociations(add, getDataset().retrieve(URI.create("sx_txt/SX_Association.txt")));
        parseInteractionTypeMap(add, getDataset().retrieve(URI.create("interaction_type_map.tsv")));
        // associations -> occurrences, taxa, reference
        String queryString = "SELECT ?sourceTaxonName ?sourceLifeStage ?interactionTypeId ?targetTaxonName ?targetLifeStage ?referenceCitation ?localityName ?studyTitle " + "WHERE {" + "      ?interaction <sx:mentioned_by> ?studyTitle . " + "      ?studyTitle <sx:hasName> ?referenceCitation . " + "      ?sourceSpecimen <sx:participates_in> ?interaction . " + "      ?targetSpecimen <sx:participates_in> ?interaction . " + "      ?sourceSpecimen ?inter ?targetSpecimen . " + "      ?inter <sx:equivalentTo> ?interactionTypeId . " + "      ?sourceSpecimen <sx:classifiedAs> ?sourceTaxon . " + "      ?sourceTaxon <sx:hasName> ?sourceTaxonName . " + "      ?targetSpecimen <sx:classifiedAs> ?targetTaxon . " + "      ?targetTaxon <sx:hasName> ?targetTaxonName . " + "      ?sourceSpecimen <sx:inStage> ?sourceLifeStage . " + "      ?targetSpecimen <sx:inStage> ?targetLifeStage . " + "      ?targetSpecimen <sx:foundAt> ?locality . " + "      ?locality <sx:hasName> ?localityName . " + "}";
        Query query = QueryFactory.create(queryString);
        QueryExecution qe = QueryExecutionFactory.create(query, model);
        ResultSet results = qe.execSelect();
        toInteractions(results);
        qe.close();
    } catch (IOException e) {
        throw new StudyImporterException("failed to access resource", e);
    }
}

Example 87 with ResultSet

use of org.apache.jena.query.ResultSet in project jena by apache.

the class Service method exec.

/**
     * Executes a service operator
     * 
     * @param op
     *            Service
     * @param context
     *            Context
     * @return Query iterator of service results
     */
public static QueryIterator exec(OpService op, Context context) {
    if (context != null && context.isFalse(serviceAllowed))
        throw new QueryExecException("SERVICE execution disabled");
    if (!op.getService().isURI())
        throw new QueryExecException("Service URI not bound: " + op.getService());
    // This relies on the observation that the query was originally correct,
    // so reversing the scope renaming is safe (it merely restores the
    // algebra expression).
    // Any variables that reappear should be internal ones that were hidden
    // by renaming in the first place.
    // Any substitution is also safe because it replaced variables by
    // values.
    Op opRemote = Rename.reverseVarRename(op.getSubOp(), true);
    // JENA-494 There is a bug here that the renaming means that if this is
    // deeply nested and joined to other things at the same level of you end
    // up with the variables being disjoint and the same results
    // The naive fix for this is to map the variables visible in the inner
    // operator to those visible in the rewritten operator
    // There may be some cases where the re-mapping is incorrect due to
    // deeply nested SERVICE clauses
    Map<Var, Var> varMapping = new HashMap<>();
    Set<Var> originalVars = OpVars.visibleVars(op);
    Set<Var> remoteVars = OpVars.visibleVars(opRemote);
    boolean requiresRemapping = false;
    for (Var v : originalVars) {
        if (v.getName().contains("/")) {
            // A variable which was scope renamed so has a different name
            String origName = v.getName().substring(v.getName().lastIndexOf('/') + 1);
            Var remoteVar = Var.alloc(origName);
            if (remoteVars.contains(remoteVar)) {
                varMapping.put(remoteVar, v);
                requiresRemapping = true;
            }
        } else {
            // A variable which does not have a different name
            if (remoteVars.contains(v))
                varMapping.put(v, v);
        }
    }
    // Explain.explain("HTTP", opRemote, context) ;
    Query query;
    //@formatter:off
    // Comment (for the future?)
    //        if ( false )
    //        {
    //            // ***** Interacts with substitution.
    //            Element el = op.getServiceElement().getElement() ;
    //            if ( el instanceof ElementSubQuery )
    //                query = ((ElementSubQuery)el).getQuery() ;
    //            else
    //            {
    //                query = QueryFactory.create() ;
    //                query.setQueryPattern(el) ;
    //                query.setResultVars() ;
    //            }
    //        }
    //        else
    //@formatter:on
    query = OpAsQuery.asQuery(opRemote);
    Explain.explain("HTTP", query, context);
    String uri = op.getService().getURI();
    HttpQuery httpQuery = configureQuery(uri, context, query);
    InputStream in = httpQuery.exec();
    // Read the whole of the results now.
    // Avoids the problems with calling back into the same system e.g.
    // Fuseki+SERVICE <http://localhost:3030/...>
    ResultSet rs = ResultSetFactory.fromXML(in);
    QueryIterator qIter = QueryIter.materialize(new QueryIteratorResultSet(rs));
    // And close connection now, not when qIter is closed.
    IO.close(in);
    // nested SERVICE clauses
    if (requiresRemapping) {
        qIter = QueryIter.map(qIter, varMapping);
    }
    return qIter;
}

Example 88 with ResultSet

use of org.apache.jena.query.ResultSet in project jena by apache.

the class StoreUtils method storeGraphNames.

public static Iterator<Node> storeGraphNames(Store store) {
    List<Node> x = new ArrayList<Node>();
    String qs = "SELECT ?g { GRAPH ?g { }}";
    QueryExecution qExec = QueryExecutionFactory.create(qs, SDBFactory.connectDataset(store));
    ResultSet rs = qExec.execSelect();
    Var var_g = Var.alloc("g");
    while (rs.hasNext()) {
        Node n = rs.nextBinding().get(var_g);
        x.add(n);
    }
    return x.iterator();
}

Example 89 with ResultSet

use of org.apache.jena.query.ResultSet in project jena by apache.

the class ExTDB5 method main.

public static void main(String... argv) {
    // Direct way: Make a TDB-back Jena model in the named directory.
    String directory = "MyDatabases/DB1";
    Dataset dataset = TDBFactory.createDataset(directory);
    // Potentially expensive query.
    String sparqlQueryString = "SELECT (count(*) AS ?count) { ?s ?p ?o }";
    // See http://incubator.apache.org/jena/documentation/query/app_api.html
    Query query = QueryFactory.create(sparqlQueryString);
    QueryExecution qexec = QueryExecutionFactory.create(query, dataset);
    try {
        ResultSet results = qexec.execSelect();
        for (; results.hasNext(); ) {
            QuerySolution soln = results.nextSolution();
            int count = soln.getLiteral("count").getInt();
            System.out.println("count = " + count);
        }
    } finally {
        qexec.close();
    }
    // Close the dataset.
    dataset.close();
}

Example 90 with ResultSet

use of org.apache.jena.query.ResultSet in project jena by apache.

the class TestResultSet method test_RS_9.

@Test
public void test_RS_9() {
    ResultSet rs = ResultSetFactory.load("testing/ResultSet/output.srx");
    test_RS_fmt(rs, ResultsFormat.FMT_RDF_XML, false);
}