@Override
public List<Literal> getDataPropertyValuesForIndividualByProperty(
String subjectUri, String propertyUri) {
log.debug("Data property value query string:\n" + DATA_PROPERTY_VALUE_QUERY_STRING);
log.debug("Data property value:\n" + dataPropertyValueQuery);
QuerySolutionMap initialBindings = new QuerySolutionMap();
initialBindings.add("subject", ResourceFactory.createResource(subjectUri));
initialBindings.add("property", ResourceFactory.createResource(propertyUri));
// Run the SPARQL query to get the properties
List<Literal> values = new ArrayList<Literal>();
DatasetWrapper w = dwf.getDatasetWrapper();
Dataset dataset = w.getDataset();
dataset.getLock().enterCriticalSection(Lock.READ);
try {
QueryExecution qexec =
QueryExecutionFactory.create(dataPropertyValueQuery, dataset, initialBindings);
ResultSet results = qexec.execSelect();
while (results.hasNext()) {
QuerySolution soln = results.next();
RDFNode node = soln.get("value");
if (!node.isLiteral()) {
continue;
}
Literal value = soln.getLiteral("value");
values.add(value);
}
} finally {
dataset.getLock().leaveCriticalSection();
w.close();
}
return values;
}
private static boolean hasPermission(
String userPrefix, String username, String uri, Property[] permissions) {
Set<Property> permissionSet = new HashSet<Property>();
Resource resource = configModel.createResource(uri);
Resource user;
if (username == null) user = PERM.Public;
else user = configModel.createResource(userPrefix + username);
for (Property permission : permissions) {
if (configModel.contains(user, permission, resource)) return true;
permissionSet.add(permission);
}
StmtIterator stmts = user.listProperties();
while (stmts.hasNext()) {
Statement stmt = stmts.next();
if (!permissionSet.contains(stmt.getPredicate())) continue;
RDFNode resourceMatch = stmt.getObject();
if (!(resourceMatch.isResource()
&& configModel.contains((Resource) resourceMatch, RDF.type, PERM.ResourceMatch)))
continue;
RDFNode matchRegex = ((Resource) resourceMatch).getProperty(PERM.matchExpression).getObject();
if (matchRegex == null || !matchRegex.isLiteral()) continue;
try {
if (uri.matches(((Literal) matchRegex).getString())) return true;
} catch (PatternSyntaxException e) {
}
}
if (username != null) return hasPermission(userPrefix, null, uri, permissions);
else return false;
}
/**
* Query SPARQL endpoint with a SELECT query
*
* @param qExec QueryExecution encapsulating the query
* @return model retrieved by querying the endpoint
*/
private Model getSelectModel(QueryExecution qExec) {
Model model = ModelFactory.createDefaultModel();
Graph graph = model.getGraph();
ResultSet results = qExec.execSelect();
while (results.hasNext()) {
QuerySolution sol = results.next();
String subject;
String predicate;
RDFNode object;
try {
subject = sol.getResource("s").toString();
predicate = sol.getResource("p").toString();
object = sol.get("o");
} catch (NoSuchElementException e) {
logger.error("SELECT query does not return a (?s ?p ?o) Triple");
continue;
}
Node objNode;
if (object.isLiteral()) {
Literal obj = object.asLiteral();
objNode = NodeFactory.createLiteral(obj.getString(), obj.getDatatype());
} else {
objNode = NodeFactory.createLiteral(object.toString());
}
graph.add(
new Triple(NodeFactory.createURI(subject), NodeFactory.createURI(predicate), objNode));
}
return model;
}
private int getMaxRank(String objectUri, String subjectUri, VitroRequest vreq) {
int maxRank = 0; // default value
if (objectUri == null) { // adding new webpage
String queryStr = QueryUtils.subUriForQueryVar(MAX_RANK_QUERY, "subject", subjectUri);
log.debug("Query string is: " + queryStr);
try {
ResultSet results = QueryUtils.getQueryResults(queryStr, vreq);
if (results != null && results.hasNext()) { // there is at most one result
QuerySolution soln = results.next();
RDFNode node = soln.get("rank");
if (node != null && node.isLiteral()) {
// node.asLiteral().getInt() won't return an xsd:string that
// can be parsed as an int.
int rank = Integer.parseInt(node.asLiteral().getLexicalForm());
if (rank > maxRank) {
log.debug("setting maxRank to " + rank);
maxRank = rank;
}
}
}
} catch (NumberFormatException e) {
log.error("Invalid rank returned from query: not an integer value.");
} catch (Exception e) {
log.error(e, e);
}
}
return maxRank;
}
@SuppressWarnings("unchecked")
private static List<RDFNode> getURIObjects() {
List<RDFNode> objectsURIs = new ArrayList<RDFNode>();
if (demo) { // Deserialize the results if exists (For Demo purpose)
if (useCache) {
try {
List<String> ser = new ArrayList<String>();
File file = new File("URIObjects.ser");
if (file.exists()) {
ObjectInputStream in;
in = new ObjectInputStream(new FileInputStream(file));
ser = (List<String>) in.readObject();
in.close();
// convert every object back from string
for (String n : ser) {
objectsURIs.add(ResourceFactory.createResource(n));
}
return objectsURIs;
}
} catch (Exception e) {
e.printStackTrace();
}
}
}
// create a query to retrieve URIs objects
String queryString =
"SELECT * "
+ "WHERE { ?s ?p ?o . FILTER (isURI(?o)) . "
+ "FILTER (STRSTARTS(STR(?o), \""
+ resourcePrefix
+ "\"))}";
Query query = QueryFactory.create(queryString);
QueryExecution exec = QueryExecutionFactory.create(query, localModel);
ResultSet rs = exec.execSelect();
while (rs.hasNext()) {
QuerySolution sol = rs.next();
RDFNode object = sol.get("?o");
objectsURIs.add(object);
}
if (demo) { // serialize the output (for Demo purpose)
try {
FileOutputStream fileOut = new FileOutputStream("URIObjects.ser");
ObjectOutputStream out = new ObjectOutputStream(fileOut);
// convert to Serializabe Strings
List<String> l = new ArrayList<String>();
for (RDFNode n : objectsURIs) {
l.add(n.toString());
}
out.writeObject(l);
out.close();
} catch (Exception e2) {
e2.printStackTrace();
}
}
return objectsURIs;
}
public static Map<String, RDFNode> solutionMap(QuerySolution qs, List<String> vars) {
Map<String, RDFNode> result = new HashMap<String, RDFNode>();
for (String var : vars) {
RDFNode val = qs.get(var);
result.put(var, val.isAnon() ? DUMMY_FOR_BNODE : val);
}
return result;
}
/**
* Answer the string described by the value of the unique optional <code>classProperty</code>
* property of <code>root</code>, or null if there's no such property. The value may be a URI, in
* which case it must be a <b>java:</b> URI with content the class name; or it may be a literal,
* in which case its lexical form is its class name; otherwise, BOOM.
*/
public static String getOptionalClassName(Resource root, Property classProperty) {
RDFNode classNode = getUnique(root, classProperty);
return classNode == null
? null
: classNode.isLiteral()
? classNode.asNode().getLiteralLexicalForm()
: classNode.isResource() ? mustBeJava(classNode.asNode().getURI()) : null;
}
@Override
public Country getCountryIdentifier() {
RDFNode countryIdentifier = getPropertyValue(mdrDatabase.getVocabulary().countryIdentifier);
if (countryIdentifier == null) {
logger.debug("LanguageIdentification does not have countryIdentifier");
return null;
}
return Country.getByValue(countryIdentifier.asLiteral().getString());
}
private void resolveChildren(ModelTreeNode modelTreeNode, String oldModelUrl) throws IOException {
ZdoModel model = modelTreeNode.getModel();
// If there is also a published version of this doc, find it, remove it and adopt all its
// children
if (oldModelUrl != null) {
// Change its children to be ours
String queryString =
"SELECT ?subject WHERE {\n"
+ " ?subject <"
+ DCTerms.isPartOf.getURI()
+ "> <"
+ oldModelUrl
+ ">.\n"
+ "}";
QueryExecution queryExecution =
QueryExecutionFactory.sparqlService(SPARQL_ENDPOINT, queryString);
ResultSet resultSet = queryExecution.execSelect();
while (resultSet.hasNext()) {
QuerySolution querySolution = resultSet.next();
RDFNode childNode = querySolution.get("subject");
String childToAdoptUrl = childNode.asResource().getURI();
ZdoModel childModel = store.get(childToAdoptUrl);
childModel.replaceValueOfProperty(
DCTerms.isPartOf, store.removeTransactionFromUrl(model.getUrl()));
// If this children was published
if (ZdoGroup.ZDO.name().equals(childModel.get(ZdoTerms.group))) {
// Is this children getting replaced by newer version?
if (modelTreeNodeKdrIndex.containsKey(childModel.get(ZdoTerms.kdrObject))) {
// Yes, unpublish it
ZdoModel childKdrObject = store.get(childModel.get(ZdoTerms.kdrObject));
markAsUnpublished(childModel, childKdrObject);
store.update(childKdrObject);
} else { // No, it should be added to our tree to solr
ModelTreeNode childModelTreeNode = new ModelTreeNode();
childModelTreeNode.setModel(childModel);
modelTreeNodeKdrIndex.put(childModel.get(ZdoTerms.kdrObject), childModelTreeNode);
modelTreeNodeIndex.put(
store.removeTransactionFromUrl(childModel.getUrl()), modelTreeNode);
modelTreeNode.getChildren().add(childModelTreeNode);
}
}
store.update(childModel);
}
}
// Recurse on children
for (ModelTreeNode childNode : modelTreeNode.getChildren()) {
// Get kdr version of this doc
ZdoModel kdrDoc = store.get(childNode.getModel().get(ZdoTerms.kdrObject));
resolveChildren(childNode, kdrDoc.get(ZdoTerms.newestPublished));
kdrDoc.replaceValueOfProperty(
ZdoTerms.newestPublished, store.removeTransactionFromUrl(childNode.getModel().getUrl()));
store.update(kdrDoc);
}
}
private boolean isAbstract(OntProperty p) {
List<RDFNode> list = p.listPropertyValues(RDF.type).toList();
for (RDFNode node : list) {
if (node.canAs(Resource.class)) {
Resource r = node.asResource();
if (BindVocabulary.AbstractProperty.getURI().equals(r.getURI())) return true;
}
}
return false;
}
@Override
public void processResults() {
String queryBegin =
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>"
+ "PREFIX mstr: <http://methodo-stat-tutor.com#>"
+ "SELECT ?NOTION "
+ "WHERE {";
String queryEnd = "}";
// create a query that asks for the color of the wine that
// would go with each meal course
String queryStr2 =
queryBegin
+ " ?EXO mstr:traiteNotion ?NOTION ."
+ "FILTER (?EXO = mstr:"
+ this.exercise
+ ")\n"
+ queryEnd;
log.error(queryStr2);
Query query2 = QueryFactory.create(queryStr2);
ResultSet results = SparqlDLExecutionFactory.create(query2, ontModel).execSelect();
ArrayList<java.net.URI> needNotion = new ArrayList<java.net.URI>();
ArrayList<java.net.URI> giveNotion = new ArrayList<java.net.URI>();
while (results.hasNext()) {
RDFNode a = results.next().get("?NOTION");
giveNotion.add(java.net.URI.create(a.asLiteral().getString()));
needNotion.addAll(getSuperClassFromUri(a.asLiteral().getString()));
}
// remove duplicates from neednotion
Set<java.net.URI> hs = new HashSet<>();
hs.addAll(needNotion);
needNotion.clear();
needNotion.addAll(hs);
// end remove duplicate
this.needNotion = needNotion;
this.giveNotion = giveNotion;
// ajout des notions au modele
int i = 0;
while (i < needNotion.size()) {
log.error(needNotion.get(i).toString());
addStatementToOntModel("needNotion", needNotion.get(i).toString());
i++;
}
i = 0;
while (i < giveNotion.size()) {
log.error(giveNotion.get(i).toString());
addStatementToOntModel("giveNotion", giveNotion.get(i).toString());
i++;
}
}
public boolean doGet(
MappedResource resource,
Property property,
boolean isInverse,
HttpServletRequest request,
HttpServletResponse response,
Configuration config)
throws IOException {
Model descriptions = getAnonymousPropertyValues(resource, property, isInverse);
if (descriptions.size() == 0) {
return false;
}
Resource r = descriptions.getResource(resource.getWebURI());
List resourceDescriptions = new ArrayList();
StmtIterator it =
isInverse ? descriptions.listStatements(null, property, r) : r.listProperties(property);
while (it.hasNext()) {
Statement stmt = it.nextStatement();
RDFNode value = isInverse ? stmt.getSubject() : stmt.getObject();
if (!value.isAnon()) {
continue;
}
resourceDescriptions.add(
new ResourceDescription((Resource) value.as(Resource.class), descriptions, config));
}
Model description = getResourceDescription(resource);
ResourceDescription resourceDescription =
new ResourceDescription(resource, description, config);
String title =
resourceDescription.getLabel()
+ (isInverse ? " ? " : " ? ")
+ config.getPrefixes().getNsURIPrefix(property.getNameSpace())
+ ":"
+ property.getLocalName();
VelocityHelper template = new VelocityHelper(getServletContext(), response);
Context context = template.getVelocityContext();
context.put("project_name", config.getProjectName());
context.put("project_link", config.getProjectLink());
context.put("title", title);
context.put("server_base", config.getWebApplicationBaseURI());
context.put("sparql_endpoint", resource.getDataset().getDataSource().getEndpointURL());
context.put("back_uri", resource.getWebURI());
context.put("back_label", resourceDescription.getLabel());
context.put(
"rdf_link",
isInverse ? resource.getInversePathDataURL(property) : resource.getPathDataURL(property));
context.put("resources", resourceDescriptions);
template.renderXHTML("pathpage.vm");
return true;
}
private void handleSubpropertyOf(OntProperty p, OntProperty ancestor) {
List<RDFNode> list = ancestor.listPropertyValues(RDFS.subPropertyOf).toList();
for (RDFNode node : list) {
if (!node.canAs(OntProperty.class)) continue;
OntProperty superProperty = node.as(OntProperty.class);
if (superProperty.equals(ancestor)) continue;
addFields(p, superProperty);
handleSubpropertyOf(p, superProperty);
}
}
private static void doTypeString(StringBuffer json, RDFNode node) {
if (node.isURIResource()) {
json.append("uri");
return;
}
if (node.isAnon()) {
json.append("bnode");
return;
}
if (node.isLiteral()) {
json.append("literal");
}
}
protected static void addRangeTypes(Model result, Model schema) {
Model toAdd = ModelFactory.createDefaultModel();
for (StmtIterator it = schema.listStatements(ANY, RDFS.range, ANY); it.hasNext(); ) {
Statement s = it.nextStatement();
RDFNode type = s.getObject();
Property property = s.getSubject().as(Property.class);
for (StmtIterator x = result.listStatements(ANY, property, ANY); x.hasNext(); ) {
RDFNode ob = x.nextStatement().getObject();
if (ob.isResource()) toAdd.add((Resource) ob, RDF.type, type);
}
}
result.add(toAdd);
}
/**
* Checks if a given node is a Shape. Note this is just an approximation based on a couple of
* hard-coded properties. It should really rely on sh:defaultValueType.
*
* @param node the node to test
* @return true if node is a Shape
*/
public static boolean isShape(RDFNode node) {
if (node instanceof Resource) {
if (JenaUtil.hasIndirectType((Resource) node, SH.Shape)) {
return true;
} else if (node.isAnon() && !((Resource) node).hasProperty(RDF.type)) {
if (node.getModel().contains(null, SH.shape, node)
|| node.getModel().contains(null, SH.filterShape, node)) {
return true;
}
}
}
return false;
}
@Test(enabled = true)
public void selectAllNamedGraphs() {
List<String> namedGraphs = new ArrayList<String>();
String query = "SELECT DISTINCT(?g) WHERE { GRAPH ?g { ?s ?p ?o } }";
ResultSet results = Util.executeQuery(query, virtDataset);
while (results.hasNext()) {
QuerySolution sol = results.next();
RDFNode nodeVar = sol.get("g");
namedGraphs.add(nodeVar.toString());
}
System.out.println(namedGraphs);
}
private void createBackLinkViolation(String subjectURI, String resource) {
Model m = ModelFactory.createDefaultModel();
Resource subject = m.createResource(resource);
m.add(new StatementImpl(subject, QPRO.exceptionDescription, DQM.NoBackLink));
RDFNode violatedTriple = Commons.generateRDFBlankNode();
m.add(
new StatementImpl(violatedTriple.asResource(), RDF.subject, m.createResource(subjectURI)));
m.add(new StatementImpl(subject, DQM.hasViolatingTriple, violatedTriple));
this._problemList.add(m);
}
/**
* Attempts to find the most plausible RDF type for a given property.
*
* @param property the property to get the type of
* @return either owl:DatatypeProperty or owl:ObjectProperty
*/
private Resource getPropertyType(Resource property) {
StmtIterator it = model.listStatements(property, RDFS.range, (RDFNode) null);
if (it.hasNext()) {
while (it.hasNext()) {
Statement s = it.nextStatement();
RDFNode n = s.getObject();
if (n.canAs(Resource.class)
&& model.contains((Resource) n.as(Resource.class), RDF.type, OWL.Class)) {
return OWL.ObjectProperty;
}
}
}
return OWL.DatatypeProperty;
}
public static boolean isNativeScope(RDFNode node) {
if (node != null) {
if (node.isAnon()) {
if (((Resource) node).hasProperty(RDF.type, SH.NativeScope)) {
return true;
}
if (!((Resource) node).hasProperty(RDF.type)) {
return SH.NativeScope.equals(SHACLUtil.getDefaultTemplateType((Resource) node));
}
} else if (node.isURIResource()) {
return ((Resource) node).hasProperty(RDF.type, SH.NativeScope);
}
}
return false;
}
public Collection<URI> getSupportedFacets(URI needUri) throws NoSuchNeedException {
List<URI> ret = new LinkedList<URI>();
Need need = DataAccessUtils.loadNeed(needRepository, needUri);
Model content = rdfStorageService.loadContent(need);
if (content == null) return ret;
Resource baseRes = content.getResource(content.getNsPrefixURI(""));
StmtIterator stmtIterator = baseRes.listProperties(WON.HAS_FACET);
while (stmtIterator.hasNext()) {
RDFNode object = stmtIterator.nextStatement().getObject();
if (object.isURIResource()) {
ret.add(URI.create(object.toString()));
}
}
return ret;
}
protected Set<ValueFactory> getValueFactory(RDFNode valueNode, OntModel displayOntModel) {
// maybe use jenabean or owl2java for this?
if (valueNode.isResource()) {
Resource res = (Resource) valueNode.as(Resource.class);
Statement stmt = res.getProperty(DisplayVocabulary.JAVA_CLASS_NAME);
if (stmt == null || !stmt.getObject().isLiteral()) {
log.debug("Cannot build value factory: java class was " + stmt.getObject());
return Collections.emptySet();
}
String javaClassName = ((Literal) stmt.getObject().as(Literal.class)).getLexicalForm();
if (javaClassName == null || javaClassName.length() == 0) {
log.debug("Cannot build value factory: no java class was set.");
return Collections.emptySet();
}
Class<?> clazz;
Object newObj;
try {
clazz = Class.forName(javaClassName);
} catch (ClassNotFoundException e) {
log.debug("Cannot build value factory: no class found for " + javaClassName);
return Collections.emptySet();
}
try {
newObj = clazz.newInstance();
} catch (Exception e) {
log.debug(
"Cannot build value factory: exception while creating object of java class "
+ javaClassName
+ " "
+ e.getMessage());
return Collections.emptySet();
}
if (newObj instanceof ValueFactory) {
ValueFactory valueFactory = (ValueFactory) newObj;
return Collections.singleton(valueFactory);
} else {
log.debug(
"Cannot build value factory: "
+ javaClassName
+ " does not implement "
+ ValueFactory.class.getName());
return Collections.emptySet();
}
} else {
log.debug("Cannot build value factory for " + valueNode);
return Collections.emptySet();
}
}
@Override
public QueryResult query(String queryString, String language, String baseURI) {
Model graph = null;
GraphConnection graphConnection = null;
QueryResult res = null;
QueryExecution qe = null;
try {
graphConnection = openGraph();
graph = graphConnection.getGraph();
graph.enterCriticalSection(Lock.READ);
log.debug(String.format("Running query %s", queryString));
// XXX AT: ignore language for now
if (language != null && !language.equals("sparql")) {
log.warn(String.format("Unknown language %s for query, using SPARQL", language));
}
Query query = QueryFactory.create(queryString);
query.setBaseURI(baseURI);
qe = QueryExecutionFactory.create(query, graph);
res = new QueryResultImpl(0, new ArrayList<String>(), new ArrayList<Map<String, Node>>());
ResultSet jenaResults = qe.execSelect();
Integer count = 0;
List<String> variableNames = jenaResults.getResultVars();
List<Map<String, Node>> nuxResults = new ArrayList<Map<String, Node>>();
while (jenaResults.hasNext()) {
QuerySolution soln = jenaResults.nextSolution();
Map<String, Node> nuxSol = new HashMap<String, Node>();
for (String varName : variableNames) {
RDFNode x = soln.get(varName);
nuxSol.put(varName, getNXRelationsNode(x.asNode()));
}
nuxResults.add(nuxSol);
count++;
}
res = new QueryResultImpl(count, variableNames, nuxResults);
} finally {
if (qe != null) {
// Important - free up resources used running the query
qe.close();
}
if (graph != null) {
graph.leaveCriticalSection();
}
if (graphConnection != null) {
graphConnection.close();
}
}
return res;
}
@Override
protected Object readObject(final int columnOrdinal) throws SQLException {
checkPosition();
checkColumn(columnOrdinal);
final QuerySolution soln = (QuerySolution) getRowObject();
final String colName = query.getProjectVars().get(columnOrdinal - 1).getName();
final RDFNode node = soln.get(colName);
if (node == null) {
return null;
}
if (node.isLiteral()) {
return TypeConverter.getJavaValue(node.asLiteral());
}
return node.toString();
}
private void writeNode(RDFNode node) throws IOException {
Node n = node.asNode();
if (n.isURI()) {
write(" <uri>" + escape(n.getURI()) + "</uri>\n");
return;
}
if (n.isBlank()) {
write(" <id>" + escape(n.getBlankNodeId().toString()) + "</id>\n");
return;
}
if (!n.isLiteral()) {
throw new JenaException("Don't know how to serialize node " + n);
}
if (n.getLiteral().getDatatypeURI() != null) {
write(
" <typedLiteral datatype=\""
+ escape(n.getLiteral().getDatatypeURI())
+ "\">"
+ escape(n.getLiteral().getLexicalForm())
+ "</typedLiteral>\n");
return;
}
if (n.getLiteral().language() == null || "".equals(n.getLiteral().language())) {
write(" <plainLiteral>" + escape(n.getLiteral().getLexicalForm()) + "</plainLiteral>\n");
return;
}
write(
" <plainLiteral xml:lang=\""
+ n.getLiteral().language()
+ "\">"
+ escape(n.getLiteral().getLexicalForm())
+ "</plainLiteral>\n");
}
private void createViolatingTriple(Statement stmt, String resource) {
Model m = ModelFactory.createDefaultModel();
Resource subject = m.createResource(resource);
m.add(new StatementImpl(subject, QPRO.exceptionDescription, DQM.ViolatingTriple));
RDFNode violatedTriple = Commons.generateRDFBlankNode();
m.add(new StatementImpl(violatedTriple.asResource(), RDF.type, RDF.Statement));
m.add(new StatementImpl(violatedTriple.asResource(), RDF.subject, stmt.getSubject()));
m.add(new StatementImpl(violatedTriple.asResource(), RDF.predicate, stmt.getPredicate()));
m.add(new StatementImpl(violatedTriple.asResource(), RDF.object, stmt.getObject()));
m.add(new StatementImpl(subject, DQM.hasViolatingTriple, violatedTriple));
this._problemList.add(m);
}
protected boolean populateKeyValue(Text key, Triple value) {
Resource subject;
Property predicate = null;
RDFNode object;
inErr = false;
skipWhiteSpace();
if (in.eof()) {
return false;
}
subject = readResource();
if (inErr) return false;
skipWhiteSpace();
try {
predicate = model.createProperty(readResource().getURI());
} catch (Exception e1) {
e1.printStackTrace();
errorHandler.fatalError(e1);
}
if (inErr) return false;
skipWhiteSpace();
object = readNode();
if (inErr) return false;
skipWhiteSpace();
if (badEOF()) return false;
if (!expect(".")) return false;
try {
key.set(getCurrentFileName());
value.setTriple(subject.asNode(), predicate.asNode(), object.asNode());
recordCounter++;
// System.out.println("Triple value:"+value);
return true;
} catch (Exception e2) {
e2.printStackTrace();
errorHandler.fatalError(e2);
}
return false;
}
/**
* Create a ResearchObject from given zip as input stream.
*
* @param id Research Object id
* @param input The content of the zip aggreagated ResearchObject
* @return a instance of ResearchObject
*/
@SuppressWarnings("resource")
public static ResearchObjectSerializable toResearchObject(URI id, InputStream input) {
File tmpZipFile = null;
ZipFile zipFile = null;
try {
tmpZipFile = File.createTempFile("zipInput", ".zip");
IOUtils.copy(input, new FileOutputStream(tmpZipFile));
zipFile = new ZipFile(tmpZipFile);
} catch (IOException e) {
LOGGER.error("Can't create a tmpFile for a RO " + id + " given from dArceo", e);
return null;
}
Enumeration<? extends ZipEntry> entries = zipFile.entries();
// first get Manifest build Jena and parese it
ResearchObject researchObject = new ResearchObject(id);
while (entries.hasMoreElements()) {
ZipEntry entry = entries.nextElement();
if (entry.getName().equals("content/.ro/manifest.rdf")) {
OntModel model = ModelFactory.createOntologyModel();
try {
model.read(zipFile.getInputStream(entry), id.toString() + ".ro/");
Individual roIndividual = model.getResource(id.toString()).as(Individual.class);
for (RDFNode node : roIndividual.listPropertyValues(ORE.aggregates).toList()) {
if (node.isURIResource()) {
URI resourceUri = URI.create(node.asResource().getURI());
URI entryName =
URI.create("content/")
.resolve(id.relativize(URI.create(node.asResource().getURI())).toString());
InputStream entryInput = zipFile.getInputStream(new ZipEntry(entryName.toString()));
researchObject.addSerializable(new ResearchObjectComponent(resourceUri, entryInput));
}
}
// add manifest
InputStream entryInput = zipFile.getInputStream(new ZipEntry("content/.ro/manifest.rdf"));
researchObject.addSerializable(
new ResearchObjectComponent(id.resolve(".ro/manifest.rdf"), entryInput));
break;
} catch (IOException e) {
LOGGER.error("can't load the manifest from zip for RO " + id, e);
tmpZipFile.delete();
return researchObject;
}
}
}
tmpZipFile.delete();
return researchObject;
}
private Node walkTree(
Model model,
Dataset oldDataset,
Node node,
Node predicate,
Query query,
QuerySolution initialBinding,
Set<Node> reached) {
QuerySolutionMap localBinding = new QuerySolutionMap();
localBinding.addAll(initialBinding);
localBinding.add("arg1", model.asRDFNode(node));
Dataset dataset = new DatasetWithDifferentDefaultModel(model, oldDataset);
QueryExecution qexec = ARQFactory.get().createQueryExecution(query, dataset, localBinding);
ResultSet rs = qexec.execSelect();
try {
if (rs.hasNext()) {
List<String> resultVars = rs.getResultVars();
String varName = resultVars.get(0);
RDFNode resultNode = rs.next().get(varName);
if (resultNode != null) {
return resultNode.asNode();
}
}
} finally {
qexec.close();
}
// Recurse into parents
ExtendedIterator<Triple> it = createIterator(model.getGraph(), node, predicate);
try {
while (it.hasNext()) {
Node next = getNext(it.next());
if ((next.isBlank() || next.isURI()) && !reached.contains(next)) {
reached.add(next);
Node nextResult =
walkTree(model, oldDataset, next, predicate, query, initialBinding, reached);
if (nextResult != null) {
return nextResult;
}
}
}
} finally {
it.close();
}
return null;
}
public static void main(String[] args) throws IOException {
Model model = ModelFactory.createDefaultModel();
try (InputStream is =
new BZip2CompressorInputStream(new URL(DBPEDIA_SCHEMA_DOWNLOAD_URL).openStream())) {
// model = FileManager.get().loadModel("input/dbpedia_3.9.owl");
model.read(is, null, "RDF/XML");
}
System.out.println(model.size() + " triples loaded.");
Set<Resource> classes = subjects(model, RDF.type, OWL.Class);
Set<Resource> objectProperties = subjects(model, RDF.type, OWL.ObjectProperty);
Set<Resource> dataProperties = subjects(model, RDF.type, OWL.DatatypeProperty);
Map<Set<Resource>, String> setToName = new HashMap<>();
setToName.put(classes, "classes");
setToName.put(objectProperties, "objectproperties");
setToName.put(dataProperties, "dataproperties");
FieldType stringType = new FieldType(StringField.TYPE_STORED);
stringType.setStoreTermVectors(false);
FieldType textType = new FieldType(TextField.TYPE_STORED);
textType.setStoreTermVectors(false);
for (Set<Resource> set : setToName.keySet()) {
IndexWriter writer = createWriter(setToName.get(set));
Set<Document> documents = new HashSet<>();
for (Resource resource : set) {
for (RDFNode object : model.listObjectsOfProperty(resource, RDFS.label).toSet()) {
String label = object.asLiteral().getLexicalForm();
Document luceneDocument = new Document();
luceneDocument.add(new Field("uri", resource.getURI(), stringType));
// luceneDocument.add(new Field("dbpediaUri", indexDocument.getCanonicalDBpediaUri(),
// stringType));
luceneDocument.add(new Field("label", label, textType));
// documents.add(luceneDocument);
writer.addDocument(luceneDocument);
}
}
writer.addDocuments(documents);
writer.commit();
writer.close();
}
}
