/**
* Create a QueryExecution that will access a SPARQL service over HTTP
*
* @param service URL of the remote service
* @param query Query to execute
* @param defaultGraph URI of the default graph
* @return QueryExecution
*/
public static QueryExecution sparqlService(String service, Query query, String defaultGraph) {
checkNotNull(service, "URL for service is null");
// checkNotNull(defaultGraph, "IRI for default graph is null") ;
checkArg(query);
QueryEngineHTTP qe = createServiceRequest(service, query);
qe.addDefaultGraph(defaultGraph);
return qe;
}
@Override
public QueryExecution execute(Query query) {
if (log.isDebugEnabled()) log.debug("Running query on " + sparqlEndpoint + ":\n" + query);
QueryEngineHTTP qe = new QueryEngineHTTP(sparqlEndpoint, query);
// System.err.println( ">> basic user: "******">> basic password: " + new String(basicPassword));
if (basicUser != null) qe.setBasicAuthentication(basicUser, basicPassword);
return qe;
}
/**
* Create a QueryExecution that will access a SPARQL service over HTTP
*
* @param service URL of the remote service
* @param query Query to execute
* @param defaultGraphURIs List of URIs to make up the default graph
* @param namedGraphURIs List of URIs to make up the named graphs
* @return QueryExecution
*/
public static QueryExecution sparqlService(
String service, Query query, List<String> defaultGraphURIs, List<String> namedGraphURIs) {
checkNotNull(service, "URL for service is null");
// checkNotNull(defaultGraphURIs, "List of default graph URIs is null") ;
// checkNotNull(namedGraphURIs, "List of named graph URIs is null") ;
checkArg(query);
QueryEngineHTTP qe = createServiceRequest(service, query);
if (defaultGraphURIs != null) qe.setDefaultGraphURIs(defaultGraphURIs);
if (namedGraphURIs != null) qe.setNamedGraphURIs(namedGraphURIs);
return qe;
}
@Override
public void processInput(Resource input, Resource output) {
final Model model = ModelFactory.createDefaultModel();
final List<Statement> tipURIs = input.listProperties(Vocab.has).toList();
final SublistIterator<Statement> tipsIterator =
new SublistIterator<Statement>(tipURIs, QUERY_CHUNK_SIZE);
while (tipsIterator.hasNext()) {
final List<String> ancestorQueryBlocks = new ArrayList<String>();
final List<String> parentQueryBlocks = new ArrayList<String>();
final List<Statement> tips = tipsIterator.next();
for (Statement statement : tips) {
final String tipURI =
statement.getResource().getProperty(DC.subject).getResource().getURI();
ancestorQueryBlocks.add(String.format(ancestorQueryBody, tipURI));
parentQueryBlocks.add(String.format(parentQueryBody, tipURI));
}
final String ancestorQuery =
String.format(ancestorQueryHead, StringUtils.join(ancestorQueryBlocks, " UNION "));
final String parentQuery =
String.format(parentQueryHead, StringUtils.join(parentQueryBlocks, ", "));
QueryEngineHTTP ancestorQE = new QueryEngineHTTP(endpoint, ancestorQuery);
QueryEngineHTTP parentQE = new QueryEngineHTTP(endpoint, parentQuery);
ancestorQE.execConstruct(model);
ancestorQE.close();
parentQE.execConstruct(model);
parentQE.close();
}
this.processNode(Vocab.TaxonomyRoot, model, output.getModel(), null, output);
output.getModel().setNsPrefix("cdao", "http://www.evolutionaryontology.org/cdao/1.0/cdao.owl#");
}