public static String str(Triple t) {
return serialize(t.getSubject())
+ " "
+ serialize(t.getPredicate())
+ " "
+ serialize(t.getObject());
}
/**
* Returns a collection of RDFStatements that match the described subject
*
* @param subject Subject
* @return collection of RDFStatements
*/
public Collection<RDFStatement> getStatements(String subject) {
if (subject == null || subject.isEmpty()) {
return null;
}
List<RDFStatement> statement = null;
try {
// define a describe query
String query = String.format("DESCRIBE %s FROM < %s >", subject, this.graphName);
logger.debug("Query: \n{}", query);
Query sparqlQuery = QueryFactory.create(query);
VirtuosoQueryExecution vqe = VirtuosoQueryExecutionFactory.create(sparqlQuery, this.graph);
// execute the query and get the graph
Model model = vqe.execDescribe();
Graph queriedGraph = model.getGraph();
// itreate over the retrieved triples, and place them inside a list
ExtendedIterator<Triple> iter = queriedGraph.find(Node.ANY, Node.ANY, Node.ANY);
statement = new ArrayList<>();
while (iter.hasNext()) {
Triple t = (Triple) iter.next();
RDFStatement stmt =
new RDFStatement(
t.getSubject().toString(), t.getPredicate().toString(), t.getObject().toString());
statement.add(stmt);
}
} catch (Exception ex) {
logger.error("Exception occured while querying for statements", ex);
}
return statement;
}
@Override
public Op transform(OpQuadPattern quadPattern) {
Node gNode = quadPattern.getGraphNode();
Node g = substitute(gNode, binding);
BasicPattern triples = new BasicPattern();
for (Triple triple : quadPattern.getBasicPattern()) {
Node s = substitute(triple.getSubject(), binding);
Node p = substitute(triple.getPredicate(), binding);
Node o = substitute(triple.getObject(), binding);
Triple t = new Triple(s, p, o);
triples.add(t);
}
// Pure quading.
// for ( Iterator iter = quadPattern.getQuads().iterator() ;
// iter.hasNext() ; )
// {
// Quad quad = (Quad)iter.next() ;
// if ( ! quad.getGraph().equals(gNode) )
// throw new
// ARQInternalErrorException("Internal error: quads block is not uniform over the graph node")
// ;
// Node s = substitute(quad.getSubject(), binding) ;
// Node p = substitute(quad.getPredicate(), binding) ;
// Node o = substitute(quad.getObject(), binding) ;
// Triple t = new Triple(s, p, o) ;
// triples.add(t) ;
// }
return new OpQuadPattern(g, triples);
}
public static void outputPlain(IndentedWriter out, Triple triple, SerializationContext naming) {
// No tag
output(out, triple.getSubject(), naming);
out.print(" ");
output(out, triple.getPredicate(), naming);
out.print(" ");
output(out, triple.getObject(), naming);
}
@Override
public void addGraph(Node gn, Graph g) {
// Convert to quads.
// super.addGraph(gn, g) ;
ExtendedIterator<Triple> iter = g.find(Node.ANY, Node.ANY, Node.ANY);
for (; iter.hasNext(); ) {
Triple t = iter.next();
add(gn, t.getSubject(), t.getPredicate(), t.getObject());
}
}
protected static String sparqlTriple(Triple triple) {
StringBuffer serializedTriple = new StringBuffer();
serializedTriple.append(sparqlNodeUpdate(triple.getSubject(), ""));
serializedTriple.append(" ");
serializedTriple.append(sparqlNodeUpdate(triple.getPredicate(), ""));
serializedTriple.append(" ");
serializedTriple.append(sparqlNodeUpdate(triple.getObject(), ""));
serializedTriple.append(" .");
return serializedTriple.toString();
}
public DBPattern(Triple pat, Mapping varMap) {
pattern = pat;
sources = new ArrayList();
isBusy = false;
isConnected = false;
isStmt = isReif = false;
S = nodeToElement(pattern.getSubject(), varMap);
P = nodeToElement(pattern.getPredicate(), varMap);
O = nodeToElement(pattern.getObject(), varMap);
Scost = elementCost(S);
Pcost = elementCost(P);
Ocost = elementCost(O);
}
ReificationStatementMask(Triple t) {
mask = HasNada;
Node p = t.getPredicate();
if (p != null) {
if (p.equals(RDF.Nodes.subject)) mask = HasSubj;
else if (p.equals(RDF.Nodes.predicate)) mask = HasPred;
else if (p.equals(RDF.Nodes.object)) mask = HasObj;
else if (p.equals(RDF.Nodes.type)) {
Node o = t.getObject();
if (o.equals(RDF.Nodes.Statement)) mask = HasType;
}
}
}
public void testDeleteThenNextThrowsCME() {
TripleBunch b = getBunch();
b.add(Triple.create("a P b"));
b.add(Triple.create("c Q d"));
Iterator it = b.iterator();
it.next();
b.remove(Triple.create("a P b"));
try {
it.next();
fail("should have thrown ConcurrentModificationException");
} catch (ConcurrentModificationException e) {
pass();
}
}
public NTriplesFileLuceneSyntacticIndexCreator(
InputStream nTriplesStream, String indexPath, String searchField) throws IOException {
// setup the index
Directory directory = FSDirectory.open(new File(indexPath));
// setup the index analyzer
Analyzer analyzer = new StandardAnalyzer(Version.LUCENE_43);
IndexWriterConfig indexWriterConfig = new IndexWriterConfig(Version.LUCENE_43, analyzer);
indexWriterConfig.setRAMBufferSizeMB(1024.0);
indexWriterConfig.setOpenMode(OpenMode.CREATE);
IndexWriter writer = new IndexWriter(directory, indexWriterConfig);
System.out.println("Creating index ...");
// setup the index fields, here two fields, for URI and text
FieldType stringType = new FieldType(StringField.TYPE_STORED);
stringType.setStoreTermVectors(false);
FieldType textType = new FieldType(TextField.TYPE_STORED);
textType.setStoreTermVectors(false);
Set<Document> documents = new HashSet<Document>();
Iterator<Triple> iterator =
RiotReader.createIteratorTriples(nTriplesStream, Lang.NTRIPLES, null);
Triple triple;
String text;
String uri;
Document doc;
int i = 0;
while (iterator.hasNext()) {
triple = iterator.next();
uri = triple.getSubject().getURI();
text = triple.getObject().getLiteralLexicalForm();
doc = new Document();
doc.add(new Field("uri", uri, stringType));
doc.add(new Field(searchField, text, textType));
writer.addDocument(doc);
if (i++ % 10000 == 0) {
// writer.commit();
System.out.println(i);
}
}
writer.commit();
writer.close();
}
/* @see com.hp.hpl.jena.sparql.syntax.ElementVisitorBase#visit(com.hp.hpl.jena.sparql.syntax.ElementTriplesBlock) */
@Override
public void visit(final ElementTriplesBlock elementtriplesblock) {
for (final Triple t : elementtriplesblock.getPattern()) {
try {
if (t.getPredicate().isVariable())
throw new IllegalArgumentException(
"Variables cannot be used in predicate position in ABoxQuery");
Atom atom = null;
final String predURI = t.getPredicate().getURI();
if (RDF.type.getURI().equals(predURI)) {
if (t.getObject().isVariable())
throw new IllegalArgumentException(
"Variables cannot be used as objects of rdf:type triples in ABoxQuery");
final OWLClass c = owlModel.createClass(new URI(t.getObject().getURI()));
final SWRLIndividualObject arg = makeIndividalObject(t.getSubject());
atom = swrlFactory.createClassAtom(c, arg);
} else {
final OWLProperty p = owlModel.getProperty(new URI(predURI));
if (p == null)
throw new IllegalArgumentException(
predURI + " is unknown [Object|Datatype]Property in the backing OWL model.");
else if (p.isDatatypeProperty()) {
final OWLDataProperty dp = owlModel.createDataProperty(p.getURI());
final SWRLIndividualObject arg1 = makeIndividalObject(t.getSubject());
final SWRLDataObject arg2 = makeDataObject(t.getObject());
atom = swrlFactory.createDataPropertyAtom(dp, arg1, arg2);
} else if (p.isObjectProperty()) {
final OWLObjectProperty op = owlModel.createObjectProperty(p.getURI());
final SWRLIndividualObject arg1 = makeIndividalObject(t.getSubject());
final SWRLIndividualObject arg2 = makeIndividalObject(t.getObject());
atom = swrlFactory.createIndividualPropertyAtom(op, arg1, arg2);
}
// else it could be a annotation property, which are not relevant anyway
}
if (atom != null) atoms = atoms.cons(atom);
} catch (final URISyntaxException e) {
throw new IllegalArgumentException(
e.getInput() + " appearing in the query string is not a valid URI!");
}
}
}
@Override
public void remove(List<Statement> statements) {
Model graph = null;
GraphConnection graphConnection = null;
try {
graphConnection = openGraph();
graph = graphConnection.getGraph();
graph.enterCriticalSection(Lock.WRITE);
for (Statement nuxStmt : statements) {
com.hp.hpl.jena.graph.Node subject = getJenaNode(nuxStmt.getSubject());
com.hp.hpl.jena.graph.Node predicate = getJenaNode(nuxStmt.getPredicate());
com.hp.hpl.jena.graph.Node object = getJenaNode(nuxStmt.getObject());
Triple jenaTriple = Triple.create(subject, predicate, object);
com.hp.hpl.jena.rdf.model.Statement jenaStmt = graph.asStatement(jenaTriple);
graph.remove(jenaStmt);
// remove properties
RSIterator it = graph.listReifiedStatements(jenaStmt);
while (it.hasNext()) {
ReifiedStatement rs = it.nextRS();
rs.removeProperties();
}
// remove quadlets
graph.removeAllReifications(jenaStmt);
// graph.removeReification(reifiedStmt);
}
} finally {
if (graph != null) {
graph.leaveCriticalSection();
}
if (graphConnection != null) {
graphConnection.close();
}
}
}
public static String RenderTemplatePage(Bindings b, String templateName) throws IOException {
MediaType mt = MediaType.TEXT_HTML;
Resource config = model.createResource("eh:/root");
Mode prefixMode = Mode.PreferPrefixes;
ShortnameService sns = new StandardShortnameService();
List<Resource> noResults = CollectionUtils.list(root.inModel(model));
Graph resultGraph = graphModel.getGraph();
resultGraph.getPrefixMapping().setNsPrefix("api", API.NS);
resultGraph.add(Triple.create(root.asNode(), API.items.asNode(), RDF.nil.asNode()));
APIResultSet rs = new APIResultSet(resultGraph, noResults, true, true, "details", View.ALL);
VelocityRenderer vr = new VelocityRenderer(mt, null, config, prefixMode, sns);
VelocityRendering vx = new VelocityRendering(b, rs, vr);
VelocityEngine ve = vx.createVelocityEngine();
VelocityContext vc = vx.createVelocityContext(b);
ByteArrayOutputStream bos = new ByteArrayOutputStream();
Writer w = new OutputStreamWriter(bos, "UTF-8");
Template t = ve.getTemplate(templateName);
t.merge(vc, w);
w.close();
return bos.toString();
}
@Override
public void augmentBlock(
TripleCollector arg0, String annotationBodyVar, String annotationHeadVar) {
// This assumes subject indexing
arg0.addTriple(
Triple.create(Var.alloc(annotationBodyVar), TEXTMATCH, Node.createLiteral(searchTerm)));
}
private static int getIndex(Triple triple) {
String u = triple.getPredicate().getURI();
// Must be _nnn.
Matcher m = pattern.matcher(u);
if (!m.find()) return NOT_FOUND;
String index = m.group(1);
return Integer.parseInt(index);
}
/**
* Return an equivalent triple pattern with standardized variable names (?s, ?p, ?o). This
* method is needed to ensure that functionally equivalent triple patterns do not get assigned
* to different entries in the cache.
*
* @param triplePattern
* @return a Triple that is equivalent to triplePattern, but with standard variable names
*/
protected Triple standardizeVarNames(Triple triplePattern) {
Node s = triplePattern.getSubject();
Node p = triplePattern.getPredicate();
Node o = triplePattern.getObject();
// make the key consistent, regardless of user's chosen variable names
if (s.isVariable()) {
s = NodeCreateUtils.create("?s");
}
if (p.isVariable()) {
p = NodeCreateUtils.create("?p");
}
if (o.isVariable()) {
o = NodeCreateUtils.create("?o");
}
return new Triple(s, p, o);
}
@Override
public void add(List<Statement> statements) {
Model graph = null;
GraphConnection graphConnection = null;
try {
graphConnection = openGraph();
graph = graphConnection.getGraph();
graph.enterCriticalSection(Lock.WRITE);
for (Statement nuxStmt : statements) {
com.hp.hpl.jena.graph.Node subject = getJenaNode(nuxStmt.getSubject());
com.hp.hpl.jena.graph.Node predicate = getJenaNode(nuxStmt.getPredicate());
com.hp.hpl.jena.graph.Node object = getJenaNode(nuxStmt.getObject());
Triple jenaTriple = Triple.create(subject, predicate, object);
com.hp.hpl.jena.rdf.model.Statement jenaStmt = graph.asStatement(jenaTriple);
// properties
Map<Resource, Node[]> properties = nuxStmt.getProperties();
if (properties == null || properties.isEmpty()) {
// no properties
graph.add(jenaStmt);
} else {
List<com.hp.hpl.jena.rdf.model.Statement> stmts =
new ArrayList<com.hp.hpl.jena.rdf.model.Statement>();
stmts.add(jenaStmt);
// create reified statement if it does not exist
com.hp.hpl.jena.graph.Node reifiedStmt = graph.getAnyReifiedStatement(jenaStmt).asNode();
for (Map.Entry<Resource, Node[]> property : properties.entrySet()) {
com.hp.hpl.jena.graph.Node prop = getJenaNode(property.getKey());
for (Node node : property.getValue()) {
com.hp.hpl.jena.graph.Node value = getJenaNode(node);
Triple propTriple = Triple.create(reifiedStmt, prop, value);
stmts.add(graph.asStatement(propTriple));
}
}
graph.add(stmts);
}
}
} finally {
if (graph != null) {
graph.leaveCriticalSection();
}
if (graphConnection != null) {
graphConnection.close();
}
}
}
public void testAddDuringAppThrowsCME() {
final TripleBunch b = getBunch();
b.add(Triple.create("a P b"));
b.add(Triple.create("c Q d"));
StageElement se =
new StageElement() {
public void run(Domain current) {
b.add(Triple.create("S P O"));
}
};
try {
b.app(new Domain(0), se, mob);
fail(" should throw CME");
} catch (ConcurrentModificationException e) {
pass();
}
}
@Override
public String toString() {
StringBuilder sb = new StringBuilder();
sb.append("Triple Bindings are: \n");
Set<Triple> triples = this.bindingMap.keySet();
for (Triple triple : triples) {
sb.append("* " + triple.toString() + "\n");
for (TripleMap tm : this.bindingMap.get(triple)) {
sb.append(" Triplemap: " + tm + "\n");
for (PO po : tm.getPos()) {
sb.append(
" PO:" + po.getPredicate().toString() + " " + po.getObject().toString() + "\n");
}
}
}
return sb.toString();
}
protected ElementGroup getWhereClauseWithBlankNodeFilter(Triple triplePattern) {
Node s = triplePattern.getSubject();
Node o = triplePattern.getObject();
ElementGroup whereClause = new ElementGroup();
whereClause.addTriplePattern(triplePattern);
if (s.isVariable()) {
whereClause.addElementFilter(
new ElementFilter(new E_LogicalNot(new E_IsBlank(new ExprVar(s)))));
}
if (o.isVariable()) {
whereClause.addElementFilter(
new ElementFilter(new E_LogicalNot(new E_IsBlank(new ExprVar(o)))));
}
return whereClause;
}
public static Triple substitute(Triple triple, Binding binding, int index) {
if (isNotNeeded(binding)) return triple;
Node s = triple.getSubject();
Node p = triple.getPredicate();
Node o = triple.getObject();
Node s1 = substitute(s, binding);
Node p1 = substitute(p, binding);
Node o1 = substitute(o, binding);
Triple t = triple;
s1 = generateCountableNode(index, s, s1);
p1 = generateCountableNode(index, p, p1);
o1 = generateCountableNode(index, o, o1);
t = new Triple(s1, p1, o1);
return t;
}
public static Collection<Node> containerMembers(Graph graph, Node container, Node containerType) {
if (!isContainer(graph, container, containerType)) return null;
ExtendedIterator<Triple> iter = graph.find(container, Node.ANY, Node.ANY);
SortedMap<Integer, Node> triples = new TreeMap<Integer, Node>(order);
try {
for (; iter.hasNext(); ) {
Triple t = iter.next();
int index = getIndex(t);
if (index == NOT_FOUND) continue;
// Insert
triples.put(new Integer(index), t.getObject());
}
} finally {
iter.close();
}
return triples.values();
}
public OntModel applyRenamings() {
OntModel result = ModelFactory.createMem();
Graph graph = result.getGraph();
Iterator it = model.getGraph().find(Triple.ANY);
while (it.hasNext()) {
Triple t = (Triple) it.next();
Node s = t.getSubject().isURI() ? rename(t.getSubject()) : null;
Node o = t.getObject().isURI() ? rename(t.getObject()) : null;
if (s != null || o != null)
t =
Triple.create(
s != null ? s : t.getSubject(), t.getPredicate(), o != null ? o : t.getObject());
graph.add(t);
}
return result;
}
public SPDXChecksum(Model spdxModel, Node checksumNode) throws InvalidSPDXAnalysisException {
this.model = spdxModel;
this.checksumNode = checksumNode;
if (checksumNode.isBlank()) {
checksumResource = model.createResource(checksumNode.getBlankNodeId());
} else if (checksumNode.isURI()) {
checksumResource = model.createResource(checksumNode.getURI());
} else {
throw (new InvalidSPDXAnalysisException("Checksum node can not be a literal"));
}
// Algorithm
Node p =
spdxModel
.getProperty(SpdxRdfConstants.SPDX_NAMESPACE, SpdxRdfConstants.PROP_CHECKSUM_ALGORITHM)
.asNode();
Triple m = Triple.createMatch(checksumNode, p, null);
ExtendedIterator<Triple> tripleIter = spdxModel.getGraph().find(m);
while (tripleIter.hasNext()) {
Triple t = tripleIter.next();
if (t.getObject().isLiteral()) {
// The following is for compatibility with rdf generated with older
// versions of the tool
this.algorithm = t.getObject().toString(false);
} else if (t.getObject().isURI()) {
this.algorithm = URI_TO_ALGORITHM.get(t.getObject().getURI());
if (this.algorithm == null) {
this.algorithm = "UNKNOWN";
}
} else {
throw (new InvalidSPDXAnalysisException(
"Invalid checksum algorithm - must be one of the defined algorithms supported by SPDX."));
}
}
// value
p =
spdxModel
.getProperty(SpdxRdfConstants.SPDX_NAMESPACE, SpdxRdfConstants.PROP_CHECKSUM_VALUE)
.asNode();
m = Triple.createMatch(checksumNode, p, null);
tripleIter = spdxModel.getGraph().find(m);
while (tripleIter.hasNext()) {
Triple t = tripleIter.next();
this.value = t.getObject().toString(false);
}
}
private static RdfStream getRdfStreamFromResource(final String resourcePath, final Lang lang) {
final Model model = createDefaultModel();
RDFDataMgr.read(model, WebACRolesProviderTest.class.getResourceAsStream(resourcePath), lang);
final List<Triple> triples = new ArrayList<>();
model
.listStatements()
.forEachRemaining(
x -> {
final Triple t = x.asTriple();
if (t.getObject().isURI() && t.getObject().getURI().startsWith(FEDORA_URI_PREFIX)) {
triples.add(
new Triple(
t.getSubject(),
t.getPredicate(),
createURI(
FEDORA_PREFIX
+ t.getObject().getURI().substring(FEDORA_URI_PREFIX.length()))));
} else {
triples.add(t);
}
});
return new RdfStream(triples);
}
@Override
public void delete(Graph g) {
Model[] model = separateStatementsWithBlankNodes(g);
deleteModel(model[1] /*statements without blank nodes*/);
// replace blank nodes in remaining statements with variables
StringBuffer patternBuff = new StringBuffer();
Iterator<Triple> tripIt = g.find(null, null, null);
while (tripIt.hasNext()) {
Triple t = tripIt.next();
patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getSubject(), null));
patternBuff.append(" ");
patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getPredicate(), null));
patternBuff.append(" ");
patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getObject(), null));
patternBuff.append(" .\n");
}
StringBuffer queryBuff = new StringBuffer();
String graphURI = graph.getGraphURI();
queryBuff.append(
"DELETE { " + ((graphURI != null) ? "GRAPH <" + graphURI + "> { " : "") + " \n");
queryBuff.append(patternBuff);
if (graphURI != null) {
queryBuff.append(" } \n");
}
queryBuff.append("} WHERE { \n");
if (graphURI != null) {
queryBuff.append(" GRAPH <" + graphURI + "> { \n");
}
queryBuff.append(patternBuff);
if (graphURI != null) {
queryBuff.append(" } \n");
}
queryBuff.append("} \n");
log.debug(queryBuff.toString());
graph.executeUpdate(queryBuff.toString());
}
private static int countContainerMember(
Graph graph, Node container, Node containerType, Node member, boolean stopEarly) {
if (graph == null) {
Log.warn(GraphContainerUtils.class, "containerMember called with null graph");
return 0;
}
if (container == null) {
Log.warn(GraphContainerUtils.class, "containerMember called with null list");
return 0;
}
if (member == null) {
Log.warn(GraphContainerUtils.class, "containerMember called with null member");
return 0;
}
if (!isContainer(graph, container, containerType)) return 0;
int count = 0;
ExtendedIterator<Triple> iter = graph.find(container, Node.ANY, member);
try {
for (; iter.hasNext(); ) {
Triple t = iter.next();
Node p = t.getPredicate();
String u = p.getURI();
if (u.matches(membershipPattern)) {
count++;
if (stopEarly) return count;
}
}
} finally {
iter.close();
}
return count;
}
public SPhraseSpec getNLForTriple(Triple t) {
SPhraseSpec p = nlgFactory.createClause();
// process predicate then return subject is related to
if (t.getPredicate().isVariable()) {
if (t.getSubject().isVariable()) {
p.setSubject(t.getSubject().toString());
} else {
p.setSubject(getNPPhrase(t.getSubject().toString(), false));
}
p.setVerb("be related via " + t.getPredicate().toString() + " to");
if (t.getObject().isVariable()) {
p.setObject(t.getObject().toString());
} else {
p.setObject(getNPPhrase(t.getObject().toString(), false));
}
} else {
NLGElement subj;
if (t.getSubject().isVariable()) {
subj = nlgFactory.createWord(t.getSubject().toString(), LexicalCategory.NOUN);
} else {
subj =
nlgFactory.createWord(
uriConverter.convert(t.getSubject().toString()), LexicalCategory.NOUN);
}
// subj.setFeature(Feature.POSSESSIVE, true);
// PhraseElement np = nlgFactory.createNounPhrase(subj,
// getEnglishLabel(t.getPredicate().toString()));
p.setSubject(
realiser.realise(subj) + "\'s " + uriConverter.convert(t.getPredicate().toString()));
p.setVerb("be");
if (t.getObject().isVariable()) {
p.setObject(t.getObject().toString());
} else if (t.getObject().isLiteral()) {
p.setObject(t.getObject().getLiteralLexicalForm());
} else {
p.setObject(getNPPhrase(t.getObject().toString(), false));
}
}
p.setFeature(Feature.TENSE, Tense.PRESENT);
return p;
}
public SPhraseSpec getNLForTriple2(Triple t) {
SPhraseSpec p = nlgFactory.createClause();
// process subject
if (t.getSubject().isVariable()) {
p.setSubject(t.getSubject().toString());
} else {
p.setSubject(getNPPhrase(t.getSubject().toString(), false));
}
// process predicate
if (t.getPredicate().isVariable()) {
p.setVerb("be related via " + t.getPredicate().toString() + " to");
} else {
p.setVerb(getVerbFrom(t.getPredicate()));
}
// process object
if (t.getObject().isVariable()) {
p.setObject(t.getObject().toString());
} else if (t.getObject().isLiteral()) {
p.setObject(t.getObject().getLiteralLexicalForm());
} else {
p.setObject(getNPPhrase(t.getObject().toString(), false));
}
p.setFeature(Feature.TENSE, Tense.PRESENT);
return p;
}
public static void addVarsFromTriple(Collection<Var> acc, Triple t) {
addVar(acc, t.getSubject());
addVar(acc, t.getPredicate());
addVar(acc, t.getObject());
}