/**
* Create a JCR value from an RDF node with the given JCR type
*
* @param valueFactory
* @param data
* @param type
* @return
* @throws RepositoryException
*/
public Value createValue(final ValueFactory valueFactory, final RDFNode data, final int type)
throws RepositoryException {
assert (valueFactory != null);
if (data.isURIResource() && (type == REFERENCE || type == WEAKREFERENCE)) {
// reference to another node (by path)
final Node nodeFromGraphSubject =
session.getNode(graphSubjects.getPathFromSubject(data.asResource()));
return valueFactory.createValue(nodeFromGraphSubject, type == WEAKREFERENCE);
} else if (data.isURIResource() || type == URI) {
// some random opaque URI
return valueFactory.createValue(data.toString(), PropertyType.URI);
} else if (data.isResource()) {
// a non-URI resource (e.g. a blank node)
return valueFactory.createValue(data.toString(), UNDEFINED);
} else if (data.isLiteral() && type == UNDEFINED) {
// the JCR schema doesn't know what this should be; so introspect
// the RDF and try to figure it out
final Literal literal = data.asLiteral();
final RDFDatatype dataType = literal.getDatatype();
final Object rdfValue = literal.getValue();
if (rdfValue instanceof Boolean) {
return valueFactory.createValue((Boolean) rdfValue);
} else if (rdfValue instanceof Byte
|| (dataType != null && dataType.getJavaClass() == Byte.class)) {
return valueFactory.createValue(literal.getByte());
} else if (rdfValue instanceof Double) {
return valueFactory.createValue((Double) rdfValue);
} else if (rdfValue instanceof Float) {
return valueFactory.createValue((Float) rdfValue);
} else if (rdfValue instanceof Long
|| (dataType != null && dataType.getJavaClass() == Long.class)) {
return valueFactory.createValue(literal.getLong());
} else if (rdfValue instanceof Short
|| (dataType != null && dataType.getJavaClass() == Short.class)) {
return valueFactory.createValue(literal.getShort());
} else if (rdfValue instanceof Integer) {
return valueFactory.createValue((Integer) rdfValue);
} else if (rdfValue instanceof XSDDateTime) {
return valueFactory.createValue(((XSDDateTime) rdfValue).asCalendar());
} else {
return valueFactory.createValue(literal.getString(), STRING);
}
} else {
LOGGER.debug("Using default JCR value creation for RDF literal: {}", data);
return valueFactory.createValue(data.asLiteral().getString(), type);
}
}
/**
* Selects a triple by providing an RDFStatement object collection
*
* @param stmts
* @return Query result
*/
public List<RDFStatement> selectTriples(Collection<? extends RDFStatement> stmts) {
if (stmts == null || stmts.isEmpty()) {
return null;
}
RDFStatement rdfs = stmts.stream().findFirst().get();
String si = rdfs.getSubject(),
pi = rdfs.getPredicate(),
oi = rdfs.getObject(); // doesnt get value
StringBuilder sb = new StringBuilder();
stmts
.stream()
.forEach(
s -> {
s.setObject(RDFUtils.escapeString(s.getObject()));
sb.append(s.getSubject())
.append(" ")
.append(s.getPredicate())
.append(" ")
.append(s.getObject())
.append(" .\n");
});
String query =
String.format(
this.defaultPrefices + "SELECT * FROM <%s> WHERE { %s }",
this.graphName,
sb.toString());
Query sparqlQuery = QueryFactory.create(query);
VirtuosoQueryExecution vqe = VirtuosoQueryExecutionFactory.create(sparqlQuery, this.graph);
List<RDFStatement> stmtsList = new ArrayList<>();
ResultSet rs = vqe.execSelect();
while (rs.hasNext()) {
QuerySolution qs = rs.nextSolution();
RDFNode s = qs.get(si);
RDFNode p = qs.get(pi);
RDFNode o = qs.get(oi);
RDFStatement stmt =
new RDFStatement(
s != null ? s.toString() : "null",
p != null ? p.toString() : "null",
o != null ? RDFUtils.escapeString(o.toString()) : "null");
stmtsList.add(stmt);
logger.info("fetched: {}", stmt.toString());
}
return stmtsList;
}
/**
* 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;
}
@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;
}
@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);
}
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;
}
@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();
}
protected String getTextForRow(QuerySolution row, boolean addSpace) {
if (row == null) return "";
StringBuffer text = new StringBuffer();
Iterator<String> iter = row.varNames();
while (iter.hasNext()) {
String name = iter.next();
RDFNode node = row.get(name);
if (node != null) {
String value = (node.isLiteral()) ? node.asLiteral().getString() : node.toString();
if (StringUtils.isNotBlank(value)) {
if (addSpace) {
text.append(" ").append(value);
} else {
text.append(value);
}
}
} else {
log.debug(name + " is null");
}
}
return text.toString();
}
public static void main(String[] args) {
List<String> obj = new ArrayList<String>();
Scanner input = new Scanner(System.in);
System.out.print("Enter URI: ");
String userIn = input.nextLine();
// create an empty Model
Model model = ModelFactory.createDefaultModel();
// read the RDF/XML file
model.read(userIn);
// write it to standard out
// model.write(System.out);
// list the statements in the Model
StmtIterator iter = model.listStatements();
System.out.println();
// print out the predicate, subject and object of each statement
while (iter.hasNext()) {
Statement stmt = iter.nextStatement(); // get next statement
Resource subject = stmt.getSubject(); // get the subject
Property predicate = stmt.getPredicate(); // get the predicate
RDFNode object = stmt.getObject(); // get the object
System.out.print(subject.toString());
System.out.print(" -> " + predicate.toString() + " -> ");
if (object instanceof Resource) {
System.out.print(object.toString() + "\n");
} else {
// object is a literal
System.out.print(" \"" + object.toString() + "\"\n");
}
}
/* for(int i = 0; i < (obj.size()); i++){
String sparqlQueryString1=
"SELECT ?s ?o "+
"WHERE {"+
"?s ?p ?o ."+
"?o <bif:contains> \""+obj.get(i)+"\" ."+
"}"+
"limit 10";
Query query = QueryFactory.create(sparqlQueryString1);
QueryExecution qexec = QueryExecutionFactory.sparqlService("http://pubmed.bio2rdf.org/sparql", query);
ResultSet results = qexec.execSelect();
System.out.println("Query: "+obj.get(i));
ResultSetFormatter.out(System.out, results, query);
qexec.close() ;
} */
}
/**
* @return list of triples having URI-typed objects it queries the model for all its URI-typed
* objects as it check every object if it is a resource (URI). if so then add them to the
* list.
*/
@SuppressWarnings("unchecked")
private static List<Statement> getTriplesWithURIObjects() {
List<Statement> triplesWithURIObjects = new ArrayList<Statement>();
if (demo) { // Deserialize the results if exists (For Demo purpose)
if (useCache) {
try {
List<String> ser = new ArrayList<String>();
File file = new File("triplesWithURIObjects.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 st : ser) {
triplesWithURIObjects.add(
ResourceFactory.createStatement(
ResourceFactory.createResource(st.split(" ")[0]),
ResourceFactory.createProperty(st.split(" ")[1]),
ResourceFactory.createResource(st.split(" ")[2])));
}
return triplesWithURIObjects;
}
} 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 s = sol.get("?s");
RDFNode p = sol.get("?p");
RDFNode o = sol.get("?o");
Statement triple =
ResourceFactory.createStatement(
s.asResource(), ResourceFactory.createProperty(p.toString()), o);
triplesWithURIObjects.add(triple);
}
if (demo) { // serialize the output (for Demo purpose)
try {
FileOutputStream fileOut = new FileOutputStream("triplesWithURIObjects.ser");
ObjectOutputStream out = new ObjectOutputStream(fileOut);
List<String> l = new ArrayList<String>();
for (Statement s : triplesWithURIObjects) {
l.add(s.getSubject() + " " + s.getPredicate() + " " + s.getObject());
}
out.writeObject(l);
out.close();
} catch (Exception e2) {
e2.printStackTrace();
}
}
return triplesWithURIObjects;
}
private static void addAdditionalProperties() {
// Map <predicate,value> save each interesting predicate of the URI object
Map<Property, List<RDFNode>> resourceInterestingInfoExtension =
new HashMap<Property, List<RDFNode>>();
// Map<object,objectResourceData> to save each object with its related data resource and be
// retrieved whenever a URI object data needed to be added for extension
Map<RDFNode, Map<Property, List<RDFNode>>> objectWithInfoAttached =
new HashMap<RDFNode, Map<Property, List<RDFNode>>>();
// Get list of unique URI objects in the data source as http://dbpedia.org/resource/XXXX
List<RDFNode> urisObjects = getURIObjects();
// Get information for each single distinct objectURI according to interesting predicates
logger.info("Number of unique URI object to find extension: " + urisObjects.size());
if (urisObjects.size() > 0) {
// For each unique URI object, its predicate-value pairs are retrieved then add them attached
// to their object in a map
for (RDFNode uriObject : urisObjects) {
// Retrieve all interesting <predicate,object> info. for current URI object
resourceInterestingInfoExtension = getURIInfo(uriObject);
// Add retrieved predicate-value pair attached to the object in the map
objectWithInfoAttached.put(
uriObject, resourceInterestingInfoExtension); // enriched list of objects
}
} else { // Otherwise no URI objects to be extended
return;
}
List<Statement> triplesWithURIsObjects = getTriplesWithURIObjects();
logger.info("Starting model enriching");
if (triplesWithURIsObjects.size() > 0) {
// iterate over each triple to add each URI object information to its resource subject
for (Statement triple : triplesWithURIsObjects) {
// put a hand over the required subject
Resource enrichedResource = (Resource) triple.getObject();
// for the subject's related object in the enriched list get the related predicate-value
// pairs
Map<Property, List<RDFNode>> objectPredicateValuePairs =
objectWithInfoAttached.get(triple.getObject());
int i = 0;
for (Property predicate : objectPredicateValuePairs.keySet()) {
for (RDFNode value : objectPredicateValuePairs.get(predicate)) {
Property outputProperty =
(i < outputProperties.size()) ? outputProperties.get(i) : defaultOutputProperty;
if (value.isLiteral()) {
localModel.add(enrichedResource, outputProperty, value.asLiteral().toString());
logger.info(
"Triple found: <"
+ enrichedResource
+ "> <"
+ outputProperty
+ "> \""
+ value.toString()
+ "\"");
} else {
localModel.add(enrichedResource, outputProperty, value);
logger.info(
"Triple found: <"
+ enrichedResource
+ "> <"
+ outputProperty
+ "> <"
+ value
+ ">");
}
}
i++;
}
}
}
}
/**
* @param uri : the URI to be dereferenced
* @param predicates : targeted predicates to be added to enrich the model
* @return This method retrieves list of values for targeted predicates for a URI-typed object for
* each URI-typed object, through content negotiation an open connection is done retrieving
* its predicates/values. An iteration is made over targeted predicates. For each predicate
* list of statements with the targeted predicate is retrieved and extracting its value in
* order to be added to hashmap<predicate,Value>
*/
@SuppressWarnings("unchecked")
private static HashMap<Property, List<RDFNode>> getURIInfo(RDFNode p) {
String uri = p.asResource().getURI();
// to store each predicate and its value
HashMap<Property, List<RDFNode>> resourceFocusedInfo = new HashMap<Property, List<RDFNode>>();
if (demo) { // Deserialize the results if exists (For Demo purpose)
if (useCache) {
try {
HashMap<String, List<String>> ser = new HashMap<String, List<String>>();
File file = new File("resourceFocusedInfo.ser");
if (file.exists()) {
ObjectInputStream in = new ObjectInputStream(new FileInputStream(file));
ser = (HashMap<String, List<String>>) in.readObject();
in.close();
// convert every object back from string
for (String prop : ser.keySet()) {
List<String> l = ser.get(prop);
List<RDFNode> nodes = new ArrayList<RDFNode>();
for (String n : l) {
nodes.add(ResourceFactory.createResource(n));
}
resourceFocusedInfo.put(ResourceFactory.createProperty(prop), nodes);
}
return resourceFocusedInfo;
}
} catch (Exception e) {
e.printStackTrace();
}
}
}
// define local model to have the data of the URI and extract focused info through built sparql
// query
List<RDFNode> values = new ArrayList<RDFNode>();
try {
URLConnection conn = new URL(uri).openConnection();
conn.setRequestProperty("Accept", "application/rdf+xml");
conn.setRequestProperty("Accept-Language", "en");
Model model = ModelFactory.createDefaultModel();
InputStream in = conn.getInputStream();
model.read(in, null);
for (Property inputProperty : inputProperties) {
for (Statement st :
model.listStatements(model.getResource(uri), inputProperty, (RDFNode) null).toList()) {
RDFNode value = st.getObject();
if (value.isLiteral()) {
if (value.asLiteral().getLanguage().toLowerCase().equals("en")
|| value.asLiteral().getLanguage().toLowerCase().equals("")) {
values.add(value);
}
} else {
values.add(value);
}
}
resourceFocusedInfo.put(inputProperty, values);
values = new ArrayList<RDFNode>(); // create new list for new predicate
}
} catch (Exception e) {
e.printStackTrace();
}
if (demo) { // serialize the output (for Demo purpose)
try {
HashMap<String, List<String>> ser = new HashMap<String, List<String>>();
FileOutputStream fileOut = new FileOutputStream("resourceFocusedInfo.ser");
ObjectOutputStream out = new ObjectOutputStream(fileOut);
// convert to Serializabe Strings
for (Property prop : resourceFocusedInfo.keySet()) {
List<String> l = new ArrayList<String>();
for (RDFNode n : resourceFocusedInfo.get(prop)) {
l.add(n.toString());
}
ser.put(prop.toString(), l);
}
out.writeObject(ser);
out.close();
} catch (Exception e2) {
e2.printStackTrace();
}
}
return resourceFocusedInfo;
}