Java Code Examples for org.apache.jena.query.QuerySolution

private Model buildModel(QuerySolution results, JsonNode currentNode , HGQLSchema schema) {

        Model model = ModelFactory.createDefaultModel();

        FieldConfig propertyString = schema.getFields().get(currentNode.get("name").asText());
        TypeConfig targetTypeString = schema.getTypes().get(currentNode.get("targetName").asText());

        populateModel(results, currentNode, model, propertyString, targetTypeString);

        QueryFieldConfig queryField = schema.getQueryFields().get(currentNode.get("name").asText());

        if (queryField != null) {

            String typeName = (currentNode.get("alias").isNull()) ? currentNode.get("name").asText() : currentNode.get("alias").asText();
            Resource object = results.getResource(currentNode.get("nodeId").asText());
            Resource subject = model.createResource(HGQL_QUERY_URI);
            Property predicate = model.createProperty("", HGQL_QUERY_NAMESPACE + typeName);
            model.add(subject, predicate, object);
        }
        return model;
    }
 

private void parseResultSet(DataStore dataStore, MetaData dataStoreMeta, ResultSet resultSet) {
	List<String> columnNames = resultSet.getResultVars();
	for (; resultSet.hasNext();) {
		QuerySolution row = resultSet.nextSolution();
		IRecord record = new Record(dataStore);
		for (int i = 0; i < columnNames.size(); i++) {
			IFieldMetaData fieldMeta = dataStoreMeta.getFieldMeta(i);

			String columnName = columnNames.get(i);
			RDFNode rdfNode = row.get(columnName);
			getValue(rdfNode, record);
			getMetaData(rdfNode, fieldMeta);
		}
		dataStore.appendRecord(record);
	}
}
 

private Model buildModel(QuerySolution results, JsonNode currentNode , HGQLSchema schema) {

        Model model = ModelFactory.createDefaultModel();

        FieldConfig propertyString = schema.getFields().get(currentNode.get("name").asText());
        TypeConfig targetTypeString = schema.getTypes().get(currentNode.get("targetName").asText());

        populateModel(results, currentNode, model, propertyString, targetTypeString);

        QueryFieldConfig queryField = schema.getQueryFields().get(currentNode.get("name").asText());

        if (queryField != null) {

            String typeName = (currentNode.get("alias").isNull()) ? currentNode.get("name").asText() : currentNode.get("alias").asText();
            Resource object = results.getResource(currentNode.get("nodeId").asText());
            Resource subject = model.createResource(HGQL_QUERY_URI);
            Property predicate = model.createProperty("", HGQL_QUERY_NAMESPACE + typeName);
            model.add(subject, predicate, object);
        }
        return model;
    }
 

public Map<PubchemSynonymType, Set<String>> fetchPubchemSynonymsFromCID(String cid) {
  // The clone method has its own implementation in the SelectBuilder. Thus safe to use!
  SelectBuilder sb = PUBCHEM_SYNO_QUERY_TMPL.clone();
  sb.setVar(Var.alloc("compound"), String.format("compound:%s", cid));
  Query query = sb.build();
  LOGGER.debug("Executing SPARQL query: %s", query.toString());
  Map<PubchemSynonymType, Set<String>> map = new HashMap<>();

  try (QueryExecution queryExecution = QueryExecutionFactory.sparqlService(sparqlService, query)) {
    ResultSet results = queryExecution.execSelect();
    while(results.hasNext()) {
      QuerySolution solution = results.nextSolution();
      String cheminfId = solution.getResource("type").getLocalName();
      String synonym = solution.getLiteral("value").getString();
      LOGGER.debug("Found synonym %s with type %s", synonym, cheminfId);
      PubchemSynonymType synonymType = PubchemSynonymType.getByCheminfId(cheminfId);
      Set synonyms = map.get(synonymType);
      if (synonyms == null) {
        synonyms = new HashSet<>();
        map.put(synonymType, synonyms);
      }
      synonyms.add(synonym);
    }
  }
  return map;
}
 

public Map<MeshTermType, Set<String>> fetchMeshTermsFromCID(String cid) {
  // The clone method has its own implementation in the SelectBuilder. Thus safe to use!
  SelectBuilder sb = MESH_TERMS_QUERY_TMPL.clone();
  sb.setVar(Var.alloc("compound"), String.format("compound:%s", cid));
  Query query = sb.build();
  LOGGER.debug("Executing SPARQL query: %s", query.toString());
  Map<MeshTermType, Set<String>> map = new HashMap<>();

  try (QueryExecution queryExecution = QueryExecutionFactory.sparqlService(sparqlService, query)) {
    ResultSet results = queryExecution.execSelect();
    while(results.hasNext()) {
      QuerySolution solution = results.nextSolution();
      String conceptLabel = solution.getLiteral("concept_label").getString();
      String lexicalTag = solution.getLiteral("lexical_tag").getString();
      LOGGER.debug("Found term %s with tag %s", conceptLabel, lexicalTag);
      MeshTermType meshTermsType = MeshTermType.getByLexicalTag(lexicalTag);
      Set synonyms = map.get(meshTermsType);
      if (synonyms == null) {
        synonyms = new HashSet<>();
        map.put(meshTermsType, synonyms);
      }
      synonyms.add(conceptLabel);
    }
  }
  return map;
}
 

public void describe(Resource r) {
	// Default model.
	DB2Closure.closure(otherModel(r, dataset.getDefaultModel()), false, acc, resources);

	String query = "SELECT ?g { GRAPH ?g { <" + r.getURI() + "> ?p ?o } }";
	QueryExecution qExec = RdfStoreQueryExecutionFactory.create(query,
			dataset);

	ResultSet rs = qExec.execSelect();
	for (; rs.hasNext();) {
		QuerySolution qs = rs.next();
		String gName = qs.getResource("g").getURI(); // mdb for DB2
		Model model = dataset.getNamedModel(gName);
		Resource r2 = otherModel(r, model);
		DB2Closure.closure(r2, false, acc, resources);
	}

	qExec.close();
	
	DB2Closure.closure(r, false, acc, resources);
}
 

private static void updateGoldenAnswers(QueryExecutionFactory qef, IQuestion q) {
	Set<String> uris = new HashSet<>();
	if (null != q && null != q.getSparqlQuery() && !q.getSparqlQuery().contains("ASK")) {
		try (QueryExecution qe = qef.createQueryExecution(q.getSparqlQuery())) {
			ResultSet rs = qe.execSelect();
			while (rs.hasNext()) {
				QuerySolution qs = rs.next();

				RDFNode node = qs.get("uri");

				if (node != null && node.isResource()) {
					uris.add(node.asResource().getURI());
				}
			}
		}
		q.setGoldenAnswers(uris);
	} else {// TODO what happens if q is null?
	}

}
 

private List<List<NodeValue>> getListNodeValues(ResultSet result) {
	List<String> resultVars = result.getResultVars();
	List<List<NodeValue>> listNodeValues = new ArrayList<>();
	while (result.hasNext()) {
		List<NodeValue> nodeValues = new ArrayList<>();
		QuerySolution sol = result.next();
		for (String var : resultVars) {
			RDFNode rdfNode = sol.get(var);
			if (rdfNode != null) {
				NodeValue n = new NodeValueNode(rdfNode.asNode());
				nodeValues.add(n);
			} else {
				nodeValues.add(null);
			}
		}
		listNodeValues.add(nodeValues);
	}
	return listNodeValues;
}
 

private List<List<NodeValue>> getListNodeValues(ResultSet result) {
    List<String> resultVars = result.getResultVars();
    List<List<NodeValue>> listNodeValues = new ArrayList<>();
    while (result.hasNext()) {
        List<NodeValue> nodeValues = new ArrayList<>();
        QuerySolution sol = result.next();
        for (String var : resultVars) {
            RDFNode rdfNode = sol.get(var);
            if (rdfNode != null) {
                NodeValue n = new NodeValueNode(rdfNode.asNode());
                nodeValues.add(n);
            } else {
                nodeValues.add(null);
            }
        }
        listNodeValues.add(nodeValues);
    }
    return listNodeValues;
}
 

public QueryExecution createQueryExecution(Query query, Dataset dataset, QuerySolution initialBinding) {
		if(!query.getGraphURIs().isEmpty() || !query.getNamedGraphURIs().isEmpty()) {
			dataset = new FromDataset(dataset, query);
		}
		
		if ( LOG_QUERIES ) {
		    // And the data - can be long.
//    		System.err.println("~~ ~~");
//    		RDFDataMgr.write(System.err, dataset.getDefaultModel(), Lang.TTL);
    		System.err.println("~~ ~~");
    		System.err.println(initialBinding);
    		System.err.println(query);
		}
		
		QueryExecution qexec = QueryExecutionFactoryFilter.get().create(query, dataset, initialBinding);
		adjustQueryExecution(qexec);
		return qexec;
	}
 

/**
 * Turns a QuerySolution into a Binding. 
 * @param map  the input QuerySolution
 * @return a Binding or null if the input is null
 */
public static Binding asBinding(final QuerySolution map) {
	if(map != null) {
		BindingHashMap result = new BindingHashMap();
		Iterator<String> varNames = map.varNames();
		while(varNames.hasNext()) {
			String varName = varNames.next();
			RDFNode node = map.get(varName);
			if(node != null) {
				result.add(Var.alloc(varName), node.asNode());
			}
		}
		return result;
	}
	else {
		return null;
	}
}
 

/**
 * Calls a SPARQL expression and returns the result, using some initial bindings.
 *
 * @param expression     the expression to execute (must contain absolute URIs)
 * @param initialBinding the initial bindings for the unbound variables
 * @param dataset        the query Dataset or null for default
 * @return the result or null
 */
public static Node invokeExpression(String expression, QuerySolution initialBinding, Dataset dataset) {
    if (dataset == null) {
        dataset = ARQFactory.get().getDataset(ModelFactory.createDefaultModel());
    }
    Query query = ARQFactory.get().createExpressionQuery(expression);
    try(QueryExecution qexec = ARQFactory.get().createQueryExecution(query, dataset, initialBinding)) {
        ResultSet rs = qexec.execSelect();
        Node result = null;
        if (rs.hasNext()) {
            QuerySolution qs = rs.next();
            String firstVarName = rs.getResultVars().get(0);
            RDFNode rdfNode = qs.get(firstVarName);
            if (rdfNode != null) {
                result = rdfNode.asNode();
            }
        }
        return result;
    }
}
 

private void addDefaultMessages(ValidationEngine engine, Resource messageHolder, Resource fallback, Resource result, 
			QuerySolution bindings, QuerySolution solution) {
	boolean found = false;
	for(Statement s : messageHolder.listProperties(SH.message).toList()) {
		if(s.getObject().isLiteral()) {
			QuerySolutionMap map = new QuerySolutionMap();
			map.addAll(bindings);
			map.addAll(solution);
			engine.addResultMessage(result, s.getLiteral(), map);
			found = true;
		}
	}
	if(!found && fallback != null) {
		addDefaultMessages(engine, fallback, null, result, bindings, solution);
	}
}
 

@Override
   public NodeValue executeBody(Dataset dataset, Model defaultModel, QuerySolution bindings) {
    try( QueryExecution qexec = createQueryExecution(dataset, defaultModel, bindings) ) {
        if(arqQuery.isAskType()) {
            boolean result = qexec.execAsk();
            return NodeValue.makeBoolean(result);
        }
        else {
            ResultSet rs = qexec.execSelect();
            if(rs.hasNext()) {
                QuerySolution s = rs.nextSolution();
                List<String> resultVars = rs.getResultVars();
                String varName = resultVars.get(0);
                RDFNode resultNode = s.get(varName);
                if(resultNode != null) {
                    return NodeValue.makeNode(resultNode.asNode());
                }
            }
            throw new ExprEvalException("Empty result set for SHACL function");
        }
    }
}
 

@Override
public Object invokeFunction(String functionName, QuerySolution bindings) throws javax.script.ScriptException, java.lang.NoSuchMethodException {
	List<String> functionParams = getFunctionParameters(functionName);
	Object[] params = new Object[functionParams.size()];
	Iterator<String> varNames = bindings.varNames();
	while(varNames.hasNext()) {
		String varName = varNames.next();
		int index = functionParams.indexOf(varName);
		if(index < 0) {
			index = functionParams.indexOf("$" + varName);
		}
		if(index >= 0) {
			RDFNode value = bindings.get(varName);
			if(value != null) {
				params[index] = JSFactory.asJSTerm(value.asNode());
			}
		}
	}
	return invokeFunctionOrdered(functionName, params);
}
 

@SuppressWarnings("unchecked")
@Override
public Collection<TPatternMatch> evaluate() throws IOException {
	final List<TPatternMatch> matches = new ArrayList<>();

	try (QueryExecution queryExecution = QueryExecutionFactory.create(jenaQuery, driver.getModel())) {
		final ResultSet resultSet = queryExecution.execSelect();

		while (resultSet.hasNext()) {
			final QuerySolution qs = resultSet.next();
			final JenaMatch match = JenaMatch.createMatch(query, qs);
			matches.add((TPatternMatch) match);
		}
	}

	return matches;
}
 

@Test
public void componentStuff() throws Exception {
	Dataset dataset = annotations.annotationDatasetFor(component.getMainWorkflow());
	String query = "PREFIX comp: <http://purl.org/DP/components#> "
			+ "SELECT ?fits ?from ?to WHERE { "
			+ " GRAPH ?any { "
			+ "?w comp:fits ?fits ; "
			+ "   comp:migrates ?path . "
			+ "?path comp:fromMimetype ?from ; "
			+ "      comp:toMimetype ?to . "
			+ "  }"
			+ "}";
	
	ResultSet select = QueryExecutionFactory.create(query, dataset).execSelect();
	assertTrue(select.hasNext());
	QuerySolution solution = select.next();
	assertEquals("image/tiff", solution.getLiteral("from").toString());
	assertEquals("image/tiff", solution.getLiteral("to").toString());
	assertEquals("MigrationAction", solution.getResource("fits").getLocalName());
}
 

@Override
protected String getVarValueAsString(QuerySolution rBind, String varName) {
    final RDFNode obj = rBind.get(varName);

    if ( obj == null ) {
        return super.getVarValueAsString(rBind, varName);
    }
    else if ( obj.asNode() instanceof Node_Triple ) {
    	final Triple t = ( (Node_Triple) obj.asNode() ).get();
    	return getAsString(t);
    }
    else {
    	return FmtUtils.stringForRDFNode(obj, context);
    }
}
 

@Test
public void nested1() {
	final MyTextOutput o = new MyTextOutput( getPrefixMappingForTests() );
	
	final Node u = NodeFactory.createURI("http://example.com/i");
	final Node n1 = new Node_Triple(new Triple(u, u, u));
	final Node n2 = new Node_Triple(new Triple(n1, u, u));
	final QuerySolution s = createQuerySolution( "?t", n2 );		
	final String result = o.get(s, "?t");

	assertEquals("<< ex:i ex:i ex:i >> ex:i ex:i ", result);
}
 

@Test
public void nested2() {
	final MyTextOutput o = new MyTextOutput( getPrefixMappingForTests() );
	
	final Node u = NodeFactory.createURI("http://example.com/i");
	final Node n1 = new Node_Triple(new Triple(u, u, u));
	final Node n2 = new Node_Triple(new Triple(u, u, n1));
	final QuerySolution s = createQuerySolution( "?t", n2 );		
	final String result = o.get(s, "?t");

	assertEquals("ex:i ex:i << ex:i ex:i ex:i >> ", result);
}
 

@Override
public RDFNode getFocusNode(QuerySolution solution) {

    String focusVar = getVariableAnnotations().stream()
            .filter(ra -> ra.getAnnotationProperty().equals(SHACL.focusNode))
            .map(ResultAnnotation::getAnnotationVarName)
            .filter(Optional::isPresent)
            .map(Optional::get)
            .findFirst()
            .orElse(CommonNames.This);
    return solution.get(focusVar);
}
 

/**
 * Similarly to {@link #getCyNode(Resource, String, String)}, uses a binding (i.e., row) from a 
 * {@link CyRelationLoadingHandler#getRelationTypesSparql() relation type query} and creates a new {@link CyRelation}
 * with the RDF mapped data.
 */
public CyRelation getCyRelation ( QuerySolution relRow )
{		
	Resource relRes = relRow.get ( "iri" ).asResource ();
	CyRelation cyRelation = new CyRelation ( relRes.getURI () );
	
	cyRelation.setType ( this.getCypherId ( relRow.get ( "type" ), this.getCyRelationTypeIdConverter () ) );

	cyRelation.setFromIri ( relRow.get ( "fromIri" ).asResource ().getURI () );
	cyRelation.setToIri ( relRow.get ( "toIri" ).asResource ().getURI () );
			
	return cyRelation;
}
 

/**
 * If sparql is null, just doesn't do anything. This is useful in the rdf2neo context, since there are configured
 * queries that are optional. 
 */
@Override
public long processSelect ( String logPrefix, String sparql, Consumer<QuerySolution> action )
{
	if ( sparql == null ) {
		log.debug ( "null SPARQL for {}, skipping", logPrefix );
		return 0;
	}
	
	return super.processSelect ( logPrefix, sparql, action );
}
 

/**
 * This takes the relations mapped via {@link CyRelationLoadingHandler#getRelationTypesSparql()} and creates
 * sets of {@link QuerySolution}s that are sent to {@link CyRelationLoadingHandler} tasks.
 */
public void process ( RdfDataManager rdfMgr, Object...opts )
{
	log.info ( "Starting Cypher Relations Loading" );
	
	CyRelationLoadingHandler handler = this.getBatchJob ();

	// processNodeIris() passes the IRIs obtained from SPARQL to the IRI consumer set by the BatchProcessor. The latter
	// pushes each IRI into a batch and submits a filled-up batch to the parallel executor.
	Consumer<Consumer<QuerySolution>> relIriProcessor = 
		solProc -> rdfMgr.processRelationIris ( handler.getRelationTypesSparql (), solProc );
	
	super.process ( relIriProcessor );
	log.info ( "Cypher Relations Loading ended" );
}
 

public static void execQuery(String sparqlQueryString, Dataset dataset)
{
    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() ; }
}
 

public List<String> getSubscribeUri() {
	List<String> result = new ArrayList<String>();
	String query = this.makeQueryString();
	String serviceURI = Utils.getSdaProperty("com.pineone.icbms.sda.knowledgebase.sparql.endpoint");
	String baseuri = Utils.getSdaProperty("com.pineone.icbms.sda.knowledgebase.uri");
	QueryExecution queryExec = QueryExecutionFactory.sparqlService(serviceURI, query);
	ResultSet rs = queryExec.execSelect();
	for (; rs.hasNext();) {
		QuerySolution qs = rs.nextSolution();
		result.add(getProperContainerType(
				new String(qs.get("uri").toString().replaceAll(baseuri, ""))));
	}
	return result;
}
 

/***
 * Queries the DBpedia SPARQL endpoint for the range of the given property.
 * @param property
 * @return range of the property
 */
private String queryRange(String property) {	
	String q = "PREFIX rdfs:   <http://www.w3.org/2000/01/rdf-schema#> SELECT ?x {<" + property + "> rdfs:range ?x.  }";	
	QueryExecution qe = QueryExecutionFactory.sparqlService(SERVICE, q);
	ResultSet rs = qe.execSelect();	
	if(rs.hasNext()) {
		QuerySolution solution = rs.nextSolution();			
		RDFNode node = solution.get("?x");	
		return node.toString();
	}	
	return "Misc";
}
 

/**
 * Executes a select query for the given endpoint and query. Returns the answer as an {@link Results} object.
 * @param query
 * @param endpoint
 * @return
 */
public static Results executeSelect(final String query, final String endpoint) {
	QueryExecutionFactory qef = new QueryExecutionFactoryHttp(endpoint);
	QueryExecution qe = qef.createQueryExecution(query);

	ResultSet rs = qe.execSelect();	
	
	Results res = new Results();
	res.header.addAll(rs.getResultVars());

	while(rs.hasNext()) {
		QuerySolution sol = rs.nextSolution();
		res.table.add(new ArrayList<String>());
		for(String head: res.header) {
			String answer = "";
			
			if(sol.get(head).isResource()) {
				answer = sol.getResource(head).toString();
			} else {
				String temp = sol.get(head).toString();
				if(temp.contains("@")) {
					answer = "\"" + temp.substring(0, temp.indexOf("@")) + "\"" + temp.substring(temp.indexOf("@"));
				} else if (temp.contains("^^")){
					answer = "\"" + temp.substring(0, temp.indexOf("^")) + "\"^^<" + temp.substring(temp.indexOf("^")+2) + ">";
				} else {
					answer = temp;
				}
			}
			res.table.get(res.table.size()-1).add(answer);
		}
	}		
	closeExecFactory(qef);
	return res;
}
 

public static void main(String[] args) throws IOException, InterruptedException {

		PROPERTY_SURFACE_FORMS = DIRECTORY + "property_surface_forms.ttl";

		// create an empty model
		Model inputModel = ModelFactory.createDefaultModel();

		// use the FileManager to find the input file
		InputStream in = FileManager.get().open(DBPEDIA_PROPERTY_FILE);
		if (in == null) {
			throw new IllegalArgumentException("File: " + DBPEDIA_PROPERTY_FILE + " not found");
		}

		// read the RDF/XML file
		inputModel.read(in, null, "N-TRIPLE");
		inputModel.write(System.out);

		Model outputModel = ModelFactory.createDefaultModel();
		QueryExecution qExec = QueryExecutionFactory
				.create("SELECT ?s  ?label WHERE{?s a <http://www.w3.org/1999/02/22-rdf-syntax-ns#Property>."
						+ " ?s <http://www.w3.org/2000/01/rdf-schema#label> ?label. }", inputModel);
		ResultSet rs = qExec.execSelect();
		System.out.println(qExec);
		while (rs.hasNext()) {
			QuerySolution qs = rs.next();
			Resource uri = qs.get("?s").asResource();
			RDFNode label = qs.get("?label");
			StatementImpl s = new StatementImpl(uri, RDFS.label, label);
			outputModel.add(s);

		}

		qExec.close();

		FileOutputStream outputFile = new FileOutputStream(PROPERTY_SURFACE_FORMS);
		RDFDataMgr.write(outputFile, outputModel, RDFFormat.NTRIPLES);
	}
 

public static void main(String[] args) throws IOException, InterruptedException {

		CLASS_SURFACE_FORMS = DIRECTORY + "class_surface_forms.ttl";

		// create an empty model
		Model inputModel = ModelFactory.createDefaultModel();

		// use the FileManager to find the input file
		InputStream in = FileManager.get().open(DBPEDIA_CLASSE_FILE);
		if (in == null) {
			throw new IllegalArgumentException("File: " + DBPEDIA_CLASSE_FILE + " not found");
		}

		// read the RDF/XML file
		inputModel.read(in, null, "N-TRIPLE");

		Model outputModel = ModelFactory.createDefaultModel();
		QueryExecution qExec = QueryExecutionFactory
				.create("SELECT ?s ?label WHERE{?s a <http://www.w3.org/2002/07/owl#Class>."
						+ " ?s <http://www.w3.org/2000/01/rdf-schema#label> ?label. "
						+ "FILTER (lang(?label) = \"en\")}", inputModel);
		ResultSet rs = qExec.execSelect();
		while (rs.hasNext()) {
			QuerySolution qs = rs.next();
			Resource uri = qs.get("?s").asResource();
			RDFNode label = qs.get("?label");
			StatementImpl s = new StatementImpl(uri, RDFS.label, label);
			outputModel.add(s);

		}

		qExec.close();

		FileOutputStream outputFile = new FileOutputStream(CLASS_SURFACE_FORMS);
		RDFDataMgr.write(outputFile, outputModel, RDFFormat.NTRIPLES);

	}