public static Model exec(Model model, final Table table, Query query) throws IOException {
OntModel inferencedModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
ElementData tableElementData =
new ElementData() {
@Override
public Table getTable() {
return table;
}
};
for (Var var : table.getVars()) {
tableElementData.add(var);
}
ElementGroup elementGroup = new ElementGroup();
elementGroup.addElement(tableElementData);
if (query.getQueryPattern() instanceof ElementGroup) {
for (Element element : ((ElementGroup) query.getQueryPattern()).getElements()) {
elementGroup.addElement(element);
}
} else {
elementGroup.addElement(query.getQueryPattern());
}
query.setQueryPattern(elementGroup);
// QueryExecution ex = QueryExecutionFactory.create(query, model);
QueryExecution ex = ARQFactory.get().createQueryExecution(query, model);
if (query.isConstructType()) {
ex.execConstruct(inferencedModel);
} else {
inferencedModel.add(ex.execSelect().getResourceModel());
}
return inferencedModel;
}
private void generateSample() {
logger.info("Generating sample...");
sample = ModelFactory.createDefaultModel();
// we have to set up a new query execution factory working on our local model
qef = new QueryExecutionFactoryModel(sample);
reasoner = new SPARQLReasoner(qef);
// get the page size
// TODO put to base class
long pageSize = 10000; // PaginationUtils.adjustPageSize(globalQef, 10000);
ParameterizedSparqlString sampleQueryTemplate = getSampleQuery();
sampleQueryTemplate.setIri("p", entityToDescribe.toStringID());
Query query = sampleQueryTemplate.asQuery();
query.setLimit(pageSize);
boolean isEmpty = false;
int i = 0;
while (!isTimeout() && !isEmpty) {
// get next sample
logger.debug("Extending sample...");
query.setOffset(i++ * pageSize);
QueryExecution qe = ksQef.createQueryExecution(query);
Model tmp = qe.execConstruct();
sample.add(tmp);
// if last call returned empty model, we can leave loop
isEmpty = tmp.isEmpty();
}
logger.info("...done. Sample size: " + sample.size() + " triples");
}
private long doExecuteSparql(VitroRequest vreq) {
OntModel jenaOntModel = ModelAccess.on(getServletContext()).getOntModel();
OntModel source = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
String[] sourceModel = vreq.getParameterValues("sourceModelName");
for (int i = 0; i < sourceModel.length; i++) {
Model m = getModel(sourceModel[i], vreq);
source.addSubModel(m);
}
Model destination = getModel(vreq.getParameter("destinationModelName"), vreq);
String sparqlQueryStr = vreq.getParameter("sparqlQueryStr");
String savedQueryURIStr = vreq.getParameter("savedQuery");
String queryStr;
if (savedQueryURIStr.length() == 0) {
log.debug("Using entered query");
queryStr = sparqlQueryStr;
} else {
Property queryStrProp = ResourceFactory.createProperty(SPARQL_QUERYSTR_PROP);
jenaOntModel.enterCriticalSection(Lock.READ);
try {
Individual ind = jenaOntModel.getIndividual(savedQueryURIStr);
log.debug("Using query " + savedQueryURIStr);
queryStr = ((Literal) ind.getPropertyValue(queryStrProp)).getLexicalForm();
queryStr =
StringEscapeUtils.unescapeHtml(
queryStr); // !!! We need to turn off automatic HTML-escaping for data property
// editing.
} finally {
jenaOntModel.leaveCriticalSection();
}
}
Model tempModel = ModelFactory.createDefaultModel();
Query query = SparqlQueryUtils.create(queryStr);
QueryExecution qexec = QueryExecutionFactory.create(query, source);
try {
qexec.execConstruct(tempModel);
} catch (QueryExecException qee) {
qexec.execDescribe(tempModel);
}
destination.enterCriticalSection(Lock.WRITE);
try {
if (destination instanceof OntModel) {
((OntModel) destination).getBaseModel().notifyEvent(new EditEvent(null, true));
} else {
destination.notifyEvent(new EditEvent(null, true));
}
destination.add(tempModel);
} finally {
if (destination instanceof OntModel) {
((OntModel) destination).getBaseModel().notifyEvent(new EditEvent(null, false));
} else {
destination.notifyEvent(new EditEvent(null, false));
}
destination.leaveCriticalSection();
}
return tempModel.size();
}
/** @inheritDoc */
public Graph graphQuery(final String theQuery) throws QueryException {
assertConnected();
QueryExecution aQueryExec = query(theQuery);
try {
return JenaSesameUtils.asSesameGraph(aQueryExec.execConstruct());
} finally {
aQueryExec.close();
}
}
/**
* @see org.caboto.jena.db.Database#executeConstructQuery(com.hp.hpl.jena.query.Query,
* com.hp.hpl.jena.query.QuerySolution)
*/
public Model executeConstructQuery(Query query, QuerySolution initialBindings) {
try {
Data data = getData();
QueryExecution queryExec = getQueryExecution(query, initialBindings, data);
Model model = queryExec.execConstruct();
queryExec.close();
data.close();
return model;
} catch (DataException e) {
e.printStackTrace();
return null;
}
}
@Override
public void createSubModel() {
ConnectTDB.dataset.begin(ReadWrite.WRITE);
String queryBegin =
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n"
+ "PREFIX mstr: <http://methodo-stat-tutor.com#>\n"
+ "\r\n"
+ "CONSTRUCT { "
+ "?EXO a mstr:Exercice .\n"
+ "?Q a mstr:Question .\n"
+ "?PZ a mstr:PubliZone .\n"
+ "?T a mstr:Tag .\n"
+ "?CZ a mstr:ChoiceZone .\n"
+ "?EXO mstr:hasQuestion ?Q .\n"
+ "?Q mstr:hasChoiceZone ?CZ .\n"
+ "?CZ mstr:hasPubliZone ?PZ .\n"
+ "?PZ mstr:hasTag ?T .\n"
+ "?T mstr:uri ?URI .\n"
+ "?EXO mstr:needNotion ?NN .\n"
+ "?EXO mstr:giveNotion ?GN .\n"
+ "} "
+ "WHERE {";
String queryEnd = "}";
String queryStudent =
queryBegin
+ "?EXO a mstr:Exercice .\n"
+ "OPTIONAL {?EXO mstr:needNotion ?NN} .\n"
+ "OPTIONAL {?EXO mstr:giveNotion ?GN} .\n"
+ "?Q a mstr:Question .\n"
+ "?PZ a mstr:PubliZone .\n"
+ "?T a mstr:Tag .\n"
+ "?CZ a mstr:ChoiceZone .\n"
+ "?EXO mstr:hasQuestion ?Q .\n"
+ "?Q mstr:hasChoiceZone ?CZ .\n"
+ "?CZ mstr:hasPubliZone ?PZ .\n"
+ "?PZ mstr:hasTag ?T .\n"
+ "?T mstr:uri ?URI .\n"
+ "FILTER (?EXO = mstr:"
+ this.exercise
+ ")\n"
+ queryEnd;
QueryExecution q1 = QueryExecutionFactory.create(queryStudent, ConnectTDB.dataset);
Model modelStudent = q1.execConstruct();
mergeModelsInSubModel(modelStudent);
ConnectTDB.dataset.end();
}
public static void main(String[] args) {
try {
String request = FileUtils.readFileToString(new File("src/test/requete.rq"));
Model trace = ModelFactory.createDefaultModel();
trace.read(new FileInputStream("src/test/@obsels.rdf"), "", KtbsConstants.JENA_RDF_XML);
Query query = QueryFactory.create(request, Syntax.syntaxARQ);
// Execute the query and obtain results
QueryExecution qe = QueryExecutionFactory.create(query, trace);
Model resultModel = qe.execConstruct();
resultModel.write(System.out, KtbsConstants.JENA_TURTLE, null);
} catch (IOException e) {
e.printStackTrace();
}
}
protected Model executeConstructQuery(String query) {
logger.trace("Sending query\n{} ...", query);
QueryExecution qe = qef.createQueryExecution(query);
try {
Model model = qe.execConstruct();
timeout = false;
if (model.size() == 0) {
fullDataLoaded = true;
}
logger.debug("Got " + model.size() + " triples.");
return model;
} catch (QueryExceptionHTTP e) {
if (e.getCause() instanceof SocketTimeoutException) {
logger.warn("Got timeout");
} else {
logger.error("Exception executing query", e);
}
return ModelFactory.createDefaultModel();
}
}
private IRI executeRule(final Rule r, final IRI inputIRI) {
try {
PelletOptions.USE_ANNOTATION_SUPPORT = true;
PelletOptions.TREAT_ALL_VARS_DISTINGUISHED = controller.isTreatAllVariablesDistinguished();
QueryEngineType type = (QueryEngineType) controller.getQueryEngineType();
final QueryExecution qe;
final ByteArrayOutputStream w = new ByteArrayOutputStream();
final Query qSelect = getSelectExampleQuery(r.getQuery());
if (type.toPellet() != null) {
final OWLOntology queryOntology = getInputOntologyForRule(inputIRI);
final PelletReasoner reasoner =
PelletReasonerFactory.getInstance().createReasoner(queryOntology);
log.info("Ontology size: " + reasoner.getKB().getInfo());
final Dataset ds = kb2ds(reasoner.getKB());
final QueryExecution qeSelect =
SparqlDLExecutionFactory.create(qSelect, ds, null, type.toPellet());
final ResultSet rs = qeSelect.execSelect();
controller.setSelect(r, rs.getResultVars(), ResultSetFormatter.toList(rs));
qe =
SparqlDLExecutionFactory.create(
r.getQuery(), kb2ds(reasoner.getKB()), null, type.toPellet());
qe.execConstruct().write(w);
} else {
final ByteArrayOutputStream w2 = new ByteArrayOutputStream();
final Model model = ModelFactory.createDefaultModel();
try {
controller
.getOWLOntologyManager()
.saveOntology(queryOntology, new TurtleOntologyFormat(), w2);
model.read(new ByteArrayInputStream(w2.toByteArray()), "", "TURTLE");
final QueryExecution qeSelect = QueryExecutionFactory.create(qSelect, model);
final ResultSet rs = qeSelect.execSelect();
controller.setSelect(r, rs.getResultVars(), ResultSetFormatter.toList(rs));
qe = QueryExecutionFactory.create(r.getQuery(), model);
qe.execConstruct().write(w);
} catch (OWLOntologyStorageException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
final IRI outputIRI = getOntologyIRIForRuleName(r.getName());
// loaded generated ontology
final OWLOntology generatedOntology =
controller
.getOWLOntologyManager()
.loadOntologyFromOntologyDocument(new ByteArrayInputStream(w.toByteArray()));
controller.updateOntology(
generatedOntology,
outputIRI,
inputIRI,
controller.getRuleSpec().getResultFile(r).toURI());
controller.setStatus("Rule " + r.getName() + " successfully executed");
return outputIRI;
} catch (OWLOntologyCreationException e1) {
controller.setStatus(e1.getMessage());
return null;
}
}
void runTestConstruct(Query query, QueryExecution qe) throws Exception {
// Do the query!
Model resultsActual = qe.execConstruct();
compareGraphResults(resultsActual, query);
}
/**
* Query SPARQL endpoint with a CONSTRUCT query
*
* @param qExec QueryExecution encapsulating the query
* @return model retrieved by querying the endpoint
*/
private Model getConstructModel(QueryExecution qExec) {
return qExec.execConstruct(ModelFactory.createDefaultModel());
}
/**
* Starts a harvester with predefined queries to synchronize with the changes from the SPARQL
* endpoint
*/
public boolean sync() {
logger.info("Sync resources newer than {}", startTime);
String rdfQueryTemplate =
"PREFIX xsd:<http://www.w3.org/2001/XMLSchema#> "
+ "SELECT DISTINCT ?resource WHERE { "
+ " GRAPH ?graph { %s }"
+ " ?graph <%s> ?time . %s "
+ " FILTER (?time > xsd:dateTime(\"%s\")) }";
String queryStr =
String.format(
rdfQueryTemplate, syncConditions, syncTimeProp, graphSyncConditions, startTime);
Set<String> syncUris = executeSyncQuery(queryStr, "resource");
if (syncUris == null) {
logger.error("Errors occurred during sync procedure. Aborting!");
return false;
}
/**
* If desired, query for old data that has the sync conditions modified
*
* <p>This option is useful in the case in which the application indexes resources that match
* some conditions. In this case, if they are modified and no longer match the initial
* conditions, they will not be synchronized. When syncOldData is True, the modified resources
* that no longer match the conditions are deleted.
*/
int deleted = 0;
int count = 0;
if (this.syncOldData) {
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss");
queryStr =
String.format(
rdfQueryTemplate,
syncConditions,
syncTimeProp,
graphSyncConditions,
sdf.format(new Date(0)));
HashSet<String> allIndexURIs = executeSyncQuery(queryStr, "resource");
if (allIndexURIs == null) {
logger.error("Errors occurred during modified content sync query. Aborting!");
return false;
}
deleted = removeMissingUris(allIndexURIs);
}
/* Prepare a series of bulk uris to be described so we can make
* a smaller number of calls to the SPARQL endpoint. */
ArrayList<ArrayList<String>> bulks = new ArrayList<ArrayList<String>>();
ArrayList<String> currentBulk = new ArrayList<String>();
for (String uri : syncUris) {
currentBulk.add(uri);
if (currentBulk.size() == EEASettings.DEFAULT_BULK_SIZE) {
bulks.add(currentBulk);
currentBulk = new ArrayList<String>();
}
}
if (currentBulk.size() > 0) {
bulks.add(currentBulk);
}
/* Execute RDF queries for the resources in each bulk */
for (ArrayList<String> bulk : bulks) {
String syncQuery = getSyncQueryStr(bulk);
try {
Query query = QueryFactory.create(syncQuery);
QueryExecution qExec = QueryExecutionFactory.sparqlService(rdfEndpoint, query);
try {
Model constructModel = ModelFactory.createDefaultModel();
qExec.execConstruct(constructModel);
BulkRequestBuilder bulkRequest = client.prepareBulk();
/**
* When adding the model to ES do not use toDescribeURIs as the query already returned the
* correct labels.
*/
addModelToES(constructModel, bulkRequest, false);
count += bulk.size();
} catch (Exception e) {
logger.error("Error while querying for modified content. {}", e.getLocalizedMessage());
return false;
} finally {
qExec.close();
}
} catch (QueryParseException qpe) {
logger.warn(
"Could not parse Sync query. Please provide a relevant query. {}",
qpe.getLocalizedMessage());
return false;
}
}
logger.info(
"Finished synchronisation: Deleted {}, Updated {}/{}", deleted, count, syncUris.size());
return true;
}