NIHVIVO-3643 Jena graph implementation using RDFService
This commit is contained in:
brianjlowe
parent
525ad8d0fd
commit
1bd242a0e1
6 changed files with 1025 additions and 1 deletions
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package edu.cornell.mannlib.vitro.webapp.dao.jena;
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import java.util.ArrayList;
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import java.util.Iterator;
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import com.hp.hpl.jena.graph.Node;
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import com.hp.hpl.jena.query.Dataset;
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import com.hp.hpl.jena.rdf.model.Model;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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import com.hp.hpl.jena.shared.Lock;
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import com.hp.hpl.jena.sparql.core.DatasetGraph;
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public class RDFServiceDataset implements Dataset {
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private RDFServiceDatasetGraph g;
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public RDFServiceDataset(RDFServiceDatasetGraph g) {
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this.g = g;
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}
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@Override
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public DatasetGraph asDatasetGraph() {
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return g;
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}
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@Override
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public void close() {
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g.close();
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}
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@Override
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public boolean containsNamedModel(String arg0) {
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return g.containsGraph(Node.createURI(arg0));
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}
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@Override
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public Model getDefaultModel() {
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return ModelFactory.createModelForGraph(g.getDefaultGraph());
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}
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@Override
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public Lock getLock() {
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return g.getLock();
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}
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@Override
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public Model getNamedModel(String arg0) {
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return ModelFactory.createModelForGraph(g.getGraph(Node.createURI(arg0)));
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}
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@Override
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public Iterator<String> listNames() {
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ArrayList<String> nameList = new ArrayList<String>();
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Iterator<Node> nodeIt = g.listGraphNodes();
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while (nodeIt.hasNext()) {
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Node n = nodeIt.next();
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nameList.add(n.getURI());
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}
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return nameList.iterator();
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}
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}
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@ -0,0 +1,221 @@
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package edu.cornell.mannlib.vitro.webapp.dao.jena;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Iterator;
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import java.util.List;
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import com.hp.hpl.jena.graph.Graph;
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import com.hp.hpl.jena.graph.Node;
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import com.hp.hpl.jena.graph.Triple;
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import com.hp.hpl.jena.query.Query;
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import com.hp.hpl.jena.query.QueryExecution;
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import com.hp.hpl.jena.query.QueryExecutionFactory;
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import com.hp.hpl.jena.query.QueryFactory;
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import com.hp.hpl.jena.query.QuerySolution;
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import com.hp.hpl.jena.query.ResultSet;
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import com.hp.hpl.jena.shared.Lock;
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import com.hp.hpl.jena.shared.LockMRSW;
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import com.hp.hpl.jena.sparql.core.DatasetGraph;
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import com.hp.hpl.jena.sparql.core.Quad;
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import com.hp.hpl.jena.sparql.resultset.JSONInput;
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import com.hp.hpl.jena.sparql.resultset.ResultSetMem;
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import com.hp.hpl.jena.sparql.util.Context;
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import com.hp.hpl.jena.util.iterator.SingletonIterator;
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import com.hp.hpl.jena.util.iterator.WrappedIterator;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
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public class RDFServiceDatasetGraph implements DatasetGraph {
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private RDFService rdfService;
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private Lock lock = new LockMRSW();
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public RDFServiceDatasetGraph(RDFService rdfService) {
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this.rdfService = rdfService;
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}
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private Graph getGraphFor(Quad q) {
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return getGraphFor(q.getGraph());
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}
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private Graph getGraphFor(Node g) {
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return (g == Node.ANY)
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? new RDFServiceGraph(rdfService)
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: new RDFServiceGraph(rdfService, g.getURI());
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}
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@Override
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public void add(Quad arg0) {
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getGraphFor(arg0).add(new Triple(arg0.getSubject(), arg0.getPredicate(), arg0.getObject()));
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}
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@Override
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public void addGraph(Node arg0, Graph arg1) {
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// TODO Auto-generated method stub
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}
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@Override
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public void close() {
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// TODO Auto-generated method stub
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}
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@Override
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public boolean contains(Quad arg0) {
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return getGraphFor(arg0).contains(new Triple(arg0.getSubject(), arg0.getPredicate(), arg0.getObject()));
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}
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@Override
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public boolean contains(Node arg0, Node arg1, Node arg2, Node arg3) {
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return getGraphFor(arg0).contains(arg1, arg2, arg3);
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}
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@Override
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public boolean containsGraph(Node arg0) {
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// TODO Auto-generated method stub
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return true;
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}
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@Override
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public void delete(Quad arg0) {
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getGraphFor(arg0).delete(new Triple(arg0.getSubject(), arg0.getPredicate(), arg0.getObject()));
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}
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@Override
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public void deleteAny(Node arg0, Node arg1, Node arg2, Node arg3) {
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// TODO check this
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getGraphFor(arg0).delete(new Triple(arg1, arg2, arg3));
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}
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@Override
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public Iterator<Quad> find() {
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return find(Node.ANY, Node.ANY, Node.ANY, Node.ANY);
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}
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@Override
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public Iterator<Quad> find(Quad arg0) {
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return find(arg0.getSubject(), arg0.getPredicate(), arg0.getObject(), arg0.getGraph());
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}
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@Override
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public Iterator<Quad> find(Node graph, Node subject, Node predicate, Node object) {
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if (!isVar(subject) && !isVar(predicate) && !isVar(object) &&!isVar(graph)) {
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if (contains(subject, predicate, object, graph)) {
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return new SingletonIterator(new Triple(subject, predicate, object));
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} else {
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return WrappedIterator.create(Collections.EMPTY_LIST.iterator());
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}
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}
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StringBuffer findQuery = new StringBuffer("SELECT * WHERE { \n");
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String graphURI = !isVar(graph) ? graph.getURI() : null;
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findQuery.append(" GRAPH ");
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if (graphURI != null) {
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findQuery.append(" <" + graphURI + ">");
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} else {
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findQuery.append("?g");
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}
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findQuery.append(" { ");
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findQuery.append(SparqlGraph.sparqlNode(subject, "?s"))
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.append(" ")
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.append(SparqlGraph.sparqlNode(predicate, "?p"))
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.append(" ")
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.append(SparqlGraph.sparqlNode(object, "?o"));
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findQuery.append(" } ");
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findQuery.append("\n}");
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//log.info(findQuery.toString());
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ResultSet rs = null;
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try {
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rs = JSONInput.fromJSON(rdfService.sparqlSelectQuery(
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findQuery.toString(), RDFService.ResultFormat.JSON));
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} catch (RDFServiceException rdfse) {
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throw new RuntimeException(rdfse);
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}
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List<Quad> quadlist = new ArrayList<Quad>();
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while (rs.hasNext()) {
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QuerySolution soln = rs.nextSolution();
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Quad q = new Quad(isVar(graph) ? soln.get("?g").asNode() : graph,
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isVar(subject) ? soln.get("?s").asNode() : subject,
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isVar(predicate) ? soln.get("?p").asNode() : predicate,
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isVar(object) ? soln.get("?o").asNode() : object);
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//log.info(t);
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quadlist.add(q);
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}
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//log.info(triplist.size() + " results");
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return WrappedIterator.create(quadlist.iterator()); }
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@Override
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public Iterator<Quad> findNG(Node arg0, Node arg1, Node arg2, Node arg3) {
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// TODO check this
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return find(arg0, arg1, arg2, arg3);
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}
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@Override
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public Context getContext() {
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// TODO Auto-generated method stub
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return null;
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}
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@Override
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public Graph getDefaultGraph() {
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return new RDFServiceGraph(rdfService);
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}
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@Override
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public Graph getGraph(Node arg0) {
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return new RDFServiceGraph(rdfService, arg0.getURI());
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}
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@Override
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public Lock getLock() {
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return lock;
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}
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@Override
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public boolean isEmpty() {
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// TODO Auto-generated method stub
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return false;
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}
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@Override
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public Iterator<Node> listGraphNodes() {
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List<Node> graphNodeList = new ArrayList<Node>();
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try {
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for (String graphURI : rdfService.getGraphURIs()) {
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graphNodeList.add(Node.createURI(graphURI));
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}
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} catch (RDFServiceException rdfse) {
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throw new RuntimeException(rdfse);
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}
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return graphNodeList.iterator();
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}
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@Override
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public void removeGraph(Node arg0) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setDefaultGraph(Graph arg0) {
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// TODO Auto-generated method stub
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}
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@Override
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public long size() {
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// TODO Auto-generated method stub
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return 0;
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}
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private boolean isVar(Node node) {
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return (node == null || node.isVariable() || node == Node.ANY);
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}
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}
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@ -0,0 +1,471 @@
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package edu.cornell.mannlib.vitro.webapp.dao.jena;
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import java.io.ByteArrayInputStream;
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import java.io.InputStream;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.List;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import com.hp.hpl.jena.graph.BulkUpdateHandler;
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import com.hp.hpl.jena.graph.Capabilities;
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import com.hp.hpl.jena.graph.Graph;
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import com.hp.hpl.jena.graph.GraphEventManager;
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import com.hp.hpl.jena.graph.GraphStatisticsHandler;
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import com.hp.hpl.jena.graph.Node;
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import com.hp.hpl.jena.graph.Reifier;
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import com.hp.hpl.jena.graph.TransactionHandler;
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import com.hp.hpl.jena.graph.Triple;
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import com.hp.hpl.jena.graph.TripleMatch;
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import com.hp.hpl.jena.graph.impl.GraphWithPerform;
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import com.hp.hpl.jena.graph.impl.SimpleEventManager;
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import com.hp.hpl.jena.graph.query.QueryHandler;
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import com.hp.hpl.jena.graph.query.SimpleQueryHandler;
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import com.hp.hpl.jena.query.QuerySolution;
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import com.hp.hpl.jena.query.ResultSet;
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import com.hp.hpl.jena.shared.AddDeniedException;
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import com.hp.hpl.jena.shared.DeleteDeniedException;
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import com.hp.hpl.jena.shared.PrefixMapping;
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import com.hp.hpl.jena.shared.impl.PrefixMappingImpl;
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import com.hp.hpl.jena.sparql.resultset.JSONInput;
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import com.hp.hpl.jena.util.iterator.ExtendedIterator;
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import com.hp.hpl.jena.util.iterator.SingletonIterator;
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import com.hp.hpl.jena.util.iterator.WrappedIterator;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
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public class RDFServiceGraph implements GraphWithPerform {
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private RDFService rdfService;
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private String graphURI;
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private static final Log log = LogFactory.getLog(SparqlGraph.class);
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private BulkUpdateHandler bulkUpdateHandler;
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private PrefixMapping prefixMapping = new PrefixMappingImpl();
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private GraphEventManager eventManager;
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private Reifier reifier = new EmptyReifier(this);
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private GraphStatisticsHandler graphStatisticsHandler;
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private TransactionHandler transactionHandler;
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private QueryHandler queryHandler;
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/**
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* Returns a SparqlGraph for the union of named graphs in a remote repository
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* @param endpointURI
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*/
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public RDFServiceGraph(RDFService rdfService) {
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this(rdfService, null);
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}
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/**
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* Returns a SparqlGraph for a particular named graph in a remote repository
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* @param endpointURI
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* @param graphURI
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*/
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public RDFServiceGraph(RDFService rdfService, String graphURI) {
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this.rdfService = rdfService;
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this.graphURI = graphURI;
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}
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public RDFService getRDFService() {
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return this.rdfService;
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}
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public String getGraphURI() {
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return graphURI;
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}
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@Override
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public void add(Triple arg0) throws AddDeniedException {
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performAdd(arg0);
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}
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// public void executeUpdate(String updateString) {
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// try {
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// RepositoryConnection conn = getConnection();
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// try {
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// Update u = conn.prepareUpdate(QueryLanguage.SPARQL, updateString);
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// u.execute();
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// } catch (MalformedQueryException e) {
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// throw new RuntimeException(e);
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// } catch (UpdateExecutionException e) {
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// log.error(e,e);
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// log.error("Update command: \n" + updateString);
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// throw new RuntimeException(e);
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// } finally {
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// conn.close();
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// }
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// } catch (RepositoryException re) {
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// throw new RuntimeException(re);
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// }
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// }
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private String serialize(Triple t) {
|
||||||
|
StringBuffer sb = new StringBuffer();
|
||||||
|
sb.append(sparqlNodeUpdate(t.getSubject(), "")).append(" ")
|
||||||
|
.append(sparqlNodeUpdate(t.getPredicate(), "")).append(" ")
|
||||||
|
.append(sparqlNodeUpdate(t.getObject(), "")).append(" .");
|
||||||
|
return sb.toString();
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void performAdd(Triple t) {
|
||||||
|
|
||||||
|
ChangeSet changeSet = rdfService.manufactureChangeSet();
|
||||||
|
try {
|
||||||
|
changeSet.addAddition(new ByteArrayInputStream(
|
||||||
|
serialize(t).getBytes()), RDFService.ModelSerializationFormat.N3, graphURI);
|
||||||
|
rdfService.changeSetUpdate(changeSet);
|
||||||
|
} catch (RDFServiceException rdfse) {
|
||||||
|
throw new RuntimeException(rdfse);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void performDelete(Triple t) {
|
||||||
|
ChangeSet changeSet = rdfService.manufactureChangeSet();
|
||||||
|
try {
|
||||||
|
changeSet.addRemoval(new ByteArrayInputStream(
|
||||||
|
serialize(t).getBytes()), RDFService.ModelSerializationFormat.N3, graphURI);
|
||||||
|
rdfService.changeSetUpdate(changeSet);
|
||||||
|
} catch (RDFServiceException rdfse) {
|
||||||
|
throw new RuntimeException(rdfse);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public void removeAll() {
|
||||||
|
// only to be used with a single graph
|
||||||
|
if (graphURI == null) {
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
String constructStr = "CONSTRUCT { ?s ?p ?o } WHERE { GRAPH <" + graphURI + "> { ?s ?p ?o } }";
|
||||||
|
try {
|
||||||
|
InputStream model = rdfService.sparqlConstructQuery(
|
||||||
|
constructStr, RDFService.ModelSerializationFormat.N3);
|
||||||
|
ChangeSet changeSet = rdfService.manufactureChangeSet();
|
||||||
|
changeSet.addRemoval(model, RDFService.ModelSerializationFormat.N3, graphURI);
|
||||||
|
rdfService.changeSetUpdate(changeSet);
|
||||||
|
} catch (RDFServiceException rdfse) {
|
||||||
|
throw new RuntimeException(rdfse);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void close() {
|
||||||
|
// can't close a remote endpoint
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public boolean contains(Triple arg0) {
|
||||||
|
return contains(arg0.getSubject(), arg0.getPredicate(), arg0.getObject());
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public boolean contains(Node subject, Node predicate, Node object) {
|
||||||
|
if (subject.isBlank() || predicate.isBlank() || object.isBlank()) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
StringBuffer containsQuery = new StringBuffer("ASK { \n");
|
||||||
|
if (graphURI != null) {
|
||||||
|
containsQuery.append(" GRAPH <" + graphURI + "> { ");
|
||||||
|
}
|
||||||
|
containsQuery.append(sparqlNode(subject, "?s"))
|
||||||
|
.append(" ")
|
||||||
|
.append(sparqlNode(predicate, "?p"))
|
||||||
|
.append(" ")
|
||||||
|
.append(sparqlNode(object, "?o"));
|
||||||
|
if (graphURI != null) {
|
||||||
|
containsQuery.append(" } \n");
|
||||||
|
}
|
||||||
|
containsQuery.append("\n}");
|
||||||
|
boolean result = execAsk(containsQuery.toString());
|
||||||
|
return result;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void delete(Triple arg0) throws DeleteDeniedException {
|
||||||
|
performDelete(arg0);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public boolean dependsOn(Graph arg0) {
|
||||||
|
return false; // who knows?
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public ExtendedIterator<Triple> find(TripleMatch arg0) {
|
||||||
|
//log.info("find(TripleMatch) " + arg0);
|
||||||
|
Triple t = arg0.asTriple();
|
||||||
|
return find(t.getSubject(), t.getPredicate(), t.getObject());
|
||||||
|
}
|
||||||
|
|
||||||
|
public static String sparqlNode(Node node, String varName) {
|
||||||
|
if (node == null || node.isVariable()) {
|
||||||
|
return varName;
|
||||||
|
} else if (node.isBlank()) {
|
||||||
|
return "<fake:blank>"; // or throw exception?
|
||||||
|
} else if (node.isURI()) {
|
||||||
|
StringBuffer uriBuff = new StringBuffer();
|
||||||
|
return uriBuff.append("<").append(node.getURI()).append(">").toString();
|
||||||
|
} else if (node.isLiteral()) {
|
||||||
|
StringBuffer literalBuff = new StringBuffer();
|
||||||
|
literalBuff.append("\"");
|
||||||
|
pyString(literalBuff, node.getLiteralLexicalForm());
|
||||||
|
literalBuff.append("\"");
|
||||||
|
if (node.getLiteralDatatypeURI() != null) {
|
||||||
|
literalBuff.append("^^<").append(node.getLiteralDatatypeURI()).append(">");
|
||||||
|
} else if (node.getLiteralLanguage() != null && node.getLiteralLanguage() != "") {
|
||||||
|
literalBuff.append("@").append(node.getLiteralLanguage());
|
||||||
|
}
|
||||||
|
return literalBuff.toString();
|
||||||
|
} else {
|
||||||
|
return varName;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public static String sparqlNodeUpdate(Node node, String varName) {
|
||||||
|
if (node.isBlank()) {
|
||||||
|
return "_:" + node.getBlankNodeLabel().replaceAll("\\W", "");
|
||||||
|
} else {
|
||||||
|
return sparqlNode(node, varName);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public static String sparqlNodeDelete(Node node, String varName) {
|
||||||
|
if (node.isBlank()) {
|
||||||
|
return "?" + node.getBlankNodeLabel().replaceAll("\\W", "");
|
||||||
|
} else {
|
||||||
|
return sparqlNode(node, varName);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public ExtendedIterator<Triple> find(Node subject, Node predicate, Node object) {
|
||||||
|
if (!isVar(subject) && !isVar(predicate) && !isVar(object)) {
|
||||||
|
if (contains(subject, predicate, object)) {
|
||||||
|
return new SingletonIterator(new Triple(subject, predicate, object));
|
||||||
|
} else {
|
||||||
|
return WrappedIterator.create(Collections.EMPTY_LIST.iterator());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
StringBuffer findQuery = new StringBuffer("SELECT * WHERE { \n");
|
||||||
|
if (graphURI != null) {
|
||||||
|
findQuery.append(" GRAPH <" + graphURI + "> { ");
|
||||||
|
}
|
||||||
|
findQuery.append(sparqlNode(subject, "?s"))
|
||||||
|
.append(" ")
|
||||||
|
.append(sparqlNode(predicate, "?p"))
|
||||||
|
.append(" ")
|
||||||
|
.append(sparqlNode(object, "?o"));
|
||||||
|
if (graphURI != null) {
|
||||||
|
findQuery.append(" } ");
|
||||||
|
}
|
||||||
|
findQuery.append("\n}");
|
||||||
|
|
||||||
|
String queryString = findQuery.toString();
|
||||||
|
//log.info(queryString);
|
||||||
|
|
||||||
|
// //TODO remove me
|
||||||
|
// if (queryString.contains("individual/AI") && queryString.contains("label")) {
|
||||||
|
// throw new RuntimeException("break!");
|
||||||
|
// }
|
||||||
|
|
||||||
|
ResultSet rs = execSelect(queryString);
|
||||||
|
//rs = execSelect(findQuery.toString());
|
||||||
|
//rs = execSelect(findQuery.toString());
|
||||||
|
|
||||||
|
List<Triple> triplist = new ArrayList<Triple>();
|
||||||
|
while (rs.hasNext()) {
|
||||||
|
QuerySolution soln = rs.nextSolution();
|
||||||
|
Triple t = new Triple(isVar(subject) ? soln.get("?s").asNode() : subject,
|
||||||
|
isVar(predicate) ? soln.get("?p").asNode() : predicate,
|
||||||
|
isVar(object) ? soln.get("?o").asNode() : object);
|
||||||
|
//log.info(t);
|
||||||
|
triplist.add(t);
|
||||||
|
}
|
||||||
|
//log.info(triplist.size() + " results");
|
||||||
|
return WrappedIterator.create(triplist.iterator());
|
||||||
|
}
|
||||||
|
|
||||||
|
private boolean isVar(Node node) {
|
||||||
|
return (node == null || node.isVariable() || node == Node.ANY);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public BulkUpdateHandler getBulkUpdateHandler() {
|
||||||
|
if (this.bulkUpdateHandler == null) {
|
||||||
|
this.bulkUpdateHandler = new RDFServiceGraphBulkUpdater(this);
|
||||||
|
}
|
||||||
|
return this.bulkUpdateHandler;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public Capabilities getCapabilities() {
|
||||||
|
return capabilities;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public GraphEventManager getEventManager() {
|
||||||
|
if (eventManager == null) {
|
||||||
|
eventManager = new SimpleEventManager(this);
|
||||||
|
}
|
||||||
|
return eventManager;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public PrefixMapping getPrefixMapping() {
|
||||||
|
return prefixMapping;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public Reifier getReifier() {
|
||||||
|
//if (reifier == null) {
|
||||||
|
// reifier = new SimpleReifier(this, ReificationStyle.Standard);
|
||||||
|
//}
|
||||||
|
return reifier;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public GraphStatisticsHandler getStatisticsHandler() {
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public TransactionHandler getTransactionHandler() {
|
||||||
|
// TODO Auto-generated method stub
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public boolean isClosed() {
|
||||||
|
// TODO Auto-generated method stub
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public boolean isEmpty() {
|
||||||
|
return (size() == 0);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public boolean isIsomorphicWith(Graph arg0) {
|
||||||
|
log.info("Hey dummy!");
|
||||||
|
throw new UnsupportedOperationException("isIsomorphicWith() not supported " +
|
||||||
|
"by SPARQL graphs");
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public QueryHandler queryHandler() {
|
||||||
|
if (queryHandler == null) {
|
||||||
|
queryHandler = new SimpleQueryHandler(this);
|
||||||
|
}
|
||||||
|
return queryHandler;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public int size() {
|
||||||
|
int size = find(null, null, null).toList().size();
|
||||||
|
return size;
|
||||||
|
}
|
||||||
|
|
||||||
|
private final static Capabilities capabilities = new Capabilities() {
|
||||||
|
|
||||||
|
public boolean addAllowed() {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean addAllowed(boolean everyTriple) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean canBeEmpty() {
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean deleteAllowed() {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean deleteAllowed(boolean everyTriple) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean findContractSafe() {
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean handlesLiteralTyping() {
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean iteratorRemoveAllowed() {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean sizeAccurate() {
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
};
|
||||||
|
|
||||||
|
private boolean execAsk(String queryStr) {
|
||||||
|
try {
|
||||||
|
return rdfService.sparqlAskQuery(queryStr);
|
||||||
|
} catch (RDFServiceException rdfse) {
|
||||||
|
throw new RuntimeException(rdfse);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private ResultSet execSelect(String queryStr) {
|
||||||
|
try {
|
||||||
|
return JSONInput.fromJSON(rdfService.sparqlSelectQuery(
|
||||||
|
queryStr, RDFService.ResultFormat.JSON));
|
||||||
|
} catch (RDFServiceException rdfse) {
|
||||||
|
throw new RuntimeException(rdfse);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/*
|
||||||
|
*
|
||||||
|
* see http://www.python.org/doc/2.5.2/ref/strings.html
|
||||||
|
* or see jena's n3 grammar jena/src/com/hp/hpl/jena/n3/n3.g
|
||||||
|
*/
|
||||||
|
protected static void pyString(StringBuffer sbuff, String s)
|
||||||
|
{
|
||||||
|
for (int i = 0; i < s.length(); i++) {
|
||||||
|
char c = s.charAt(i);
|
||||||
|
|
||||||
|
// Escape escapes and quotes
|
||||||
|
if (c == '\\' || c == '"' )
|
||||||
|
{
|
||||||
|
sbuff.append('\\') ;
|
||||||
|
sbuff.append(c) ;
|
||||||
|
continue ;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Whitespace
|
||||||
|
if (c == '\n'){ sbuff.append("\\n");continue; }
|
||||||
|
if (c == '\t'){ sbuff.append("\\t");continue; }
|
||||||
|
if (c == '\r'){ sbuff.append("\\r");continue; }
|
||||||
|
if (c == '\f'){ sbuff.append("\\f");continue; }
|
||||||
|
if (c == '\b'){ sbuff.append("\\b");continue; }
|
||||||
|
if( c == 7 ) { sbuff.append("\\a");continue; }
|
||||||
|
|
||||||
|
// Output as is (subject to UTF-8 encoding on output that is)
|
||||||
|
sbuff.append(c) ;
|
||||||
|
|
||||||
|
// // Unicode escapes
|
||||||
|
// // c < 32, c >= 127, not whitespace or other specials
|
||||||
|
// String hexstr = Integer.toHexString(c).toUpperCase();
|
||||||
|
// int pad = 4 - hexstr.length();
|
||||||
|
// sbuff.append("\\u");
|
||||||
|
// for (; pad > 0; pad--)
|
||||||
|
// sbuff.append("0");
|
||||||
|
// sbuff.append(hexstr);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,211 @@
|
||||||
|
package edu.cornell.mannlib.vitro.webapp.dao.jena;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.io.PipedInputStream;
|
||||||
|
import java.io.PipedOutputStream;
|
||||||
|
import java.util.Iterator;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
import org.apache.commons.logging.Log;
|
||||||
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
|
||||||
|
import com.hp.hpl.jena.graph.Graph;
|
||||||
|
import com.hp.hpl.jena.graph.GraphEvents;
|
||||||
|
import com.hp.hpl.jena.graph.GraphUtil;
|
||||||
|
import com.hp.hpl.jena.graph.Node;
|
||||||
|
import com.hp.hpl.jena.graph.Triple;
|
||||||
|
import com.hp.hpl.jena.graph.impl.SimpleBulkUpdateHandler;
|
||||||
|
import com.hp.hpl.jena.rdf.model.Model;
|
||||||
|
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
||||||
|
import com.hp.hpl.jena.rdf.model.Statement;
|
||||||
|
import com.hp.hpl.jena.rdf.model.StmtIterator;
|
||||||
|
import com.hp.hpl.jena.sparql.util.graph.GraphFactory;
|
||||||
|
import com.hp.hpl.jena.util.iterator.ExtendedIterator;
|
||||||
|
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
|
||||||
|
|
||||||
|
public class RDFServiceGraphBulkUpdater extends SimpleBulkUpdateHandler {
|
||||||
|
|
||||||
|
private static final Log log = LogFactory.getLog(SparqlGraphBulkUpdater.class);
|
||||||
|
private RDFServiceGraph graph;
|
||||||
|
|
||||||
|
public RDFServiceGraphBulkUpdater(RDFServiceGraph graph) {
|
||||||
|
super(graph);
|
||||||
|
this.graph = graph;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void add(Triple[] arg0) {
|
||||||
|
Graph g = GraphFactory.createPlainGraph();
|
||||||
|
for (int i = 0 ; i < arg0.length ; i++) {
|
||||||
|
g.add(arg0[i]);
|
||||||
|
}
|
||||||
|
add(g);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void add(List<Triple> arg0) {
|
||||||
|
Graph g = GraphFactory.createPlainGraph();
|
||||||
|
for (Triple t : arg0) {
|
||||||
|
g.add(t);
|
||||||
|
}
|
||||||
|
add(g);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void add(Iterator<Triple> arg0) {
|
||||||
|
Graph g = GraphFactory.createPlainGraph();
|
||||||
|
while (arg0.hasNext()) {
|
||||||
|
Triple t = arg0.next();
|
||||||
|
g.add(t);
|
||||||
|
}
|
||||||
|
add(g);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void add(Graph arg0) {
|
||||||
|
add(arg0, false);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void add(Graph g, boolean arg1) {
|
||||||
|
log.info("adding graph");
|
||||||
|
Model[] model = separateStatementsWithBlankNodes(g);
|
||||||
|
addModel(model[1] /* nonBlankNodeModel */);
|
||||||
|
// replace following call with different method
|
||||||
|
addModel(model[0] /*blankNodeModel*/);
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Returns a pair of models. The first contains any statement containing at
|
||||||
|
* least one blank node. The second contains all remaining statements.
|
||||||
|
* @param g
|
||||||
|
* @return
|
||||||
|
*/
|
||||||
|
|
||||||
|
private Model[] separateStatementsWithBlankNodes(Graph g) {
|
||||||
|
Model gm = ModelFactory.createModelForGraph(g);
|
||||||
|
Model blankNodeModel = ModelFactory.createDefaultModel();
|
||||||
|
Model nonBlankNodeModel = ModelFactory.createDefaultModel();
|
||||||
|
StmtIterator sit = gm.listStatements();
|
||||||
|
while (sit.hasNext()) {
|
||||||
|
Statement stmt = sit.nextStatement();
|
||||||
|
if (!stmt.getSubject().isAnon() && !stmt.getObject().isAnon()) {
|
||||||
|
nonBlankNodeModel.add(stmt);
|
||||||
|
} else {
|
||||||
|
blankNodeModel.add(stmt);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
Model[] result = new Model[2];
|
||||||
|
result[0] = blankNodeModel;
|
||||||
|
result[1] = nonBlankNodeModel;
|
||||||
|
return result;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void delete(Graph g, boolean withReifications) {
|
||||||
|
delete(g);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void delete(Graph g) {
|
||||||
|
ChangeSet changeSet = graph.getRDFService().manufactureChangeSet();
|
||||||
|
Model m = ModelFactory.createModelForGraph(g);
|
||||||
|
PipedOutputStream out = new PipedOutputStream();
|
||||||
|
m.write(out, "N-TRIPLE");
|
||||||
|
try {
|
||||||
|
changeSet.addRemoval(new PipedInputStream(
|
||||||
|
out), RDFService.ModelSerializationFormat.N3, graph.getGraphURI());
|
||||||
|
graph.getRDFService().changeSetUpdate(changeSet);
|
||||||
|
} catch (IOException ioe) {
|
||||||
|
throw new RuntimeException(ioe);
|
||||||
|
} catch (RDFServiceException rdfse) {
|
||||||
|
throw new RuntimeException(rdfse);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public void addModel(Model model) {
|
||||||
|
ChangeSet changeSet = graph.getRDFService().manufactureChangeSet();
|
||||||
|
PipedOutputStream out = new PipedOutputStream();
|
||||||
|
model.write(out, "N-TRIPLE");
|
||||||
|
try {
|
||||||
|
changeSet.addAddition(new PipedInputStream(
|
||||||
|
out), RDFService.ModelSerializationFormat.N3, graph.getGraphURI());
|
||||||
|
graph.getRDFService().changeSetUpdate(changeSet);
|
||||||
|
} catch (IOException ioe) {
|
||||||
|
throw new RuntimeException(ioe);
|
||||||
|
} catch (RDFServiceException rdfse) {
|
||||||
|
throw new RuntimeException(rdfse);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public void deleteModel(Model model) {
|
||||||
|
ChangeSet changeSet = graph.getRDFService().manufactureChangeSet();
|
||||||
|
PipedOutputStream out = new PipedOutputStream();
|
||||||
|
model.write(out, "N-TRIPLE");
|
||||||
|
try {
|
||||||
|
changeSet.addRemoval(new PipedInputStream(
|
||||||
|
out), RDFService.ModelSerializationFormat.N3, graph.getGraphURI());
|
||||||
|
graph.getRDFService().changeSetUpdate(changeSet);
|
||||||
|
} catch (IOException ioe) {
|
||||||
|
throw new RuntimeException(ioe);
|
||||||
|
} catch (RDFServiceException rdfse) {
|
||||||
|
throw new RuntimeException(rdfse);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void removeAll() {
|
||||||
|
removeAll(graph);
|
||||||
|
notifyRemoveAll();
|
||||||
|
}
|
||||||
|
|
||||||
|
protected void notifyRemoveAll() {
|
||||||
|
manager.notifyEvent(graph, GraphEvents.removeAll);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void remove(Node s, Node p, Node o) {
|
||||||
|
removeAll(graph, s, p, o);
|
||||||
|
manager.notifyEvent(graph, GraphEvents.remove(s, p, o));
|
||||||
|
}
|
||||||
|
|
||||||
|
public static void removeAll(Graph g, Node s, Node p, Node o)
|
||||||
|
{
|
||||||
|
ExtendedIterator<Triple> it = g.find( s, p, o );
|
||||||
|
try {
|
||||||
|
while (it.hasNext()) {
|
||||||
|
Triple t = it.next();
|
||||||
|
g.delete(t);
|
||||||
|
it.remove();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
finally {
|
||||||
|
it.close();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public static void removeAll( Graph g )
|
||||||
|
{
|
||||||
|
ExtendedIterator<Triple> it = GraphUtil.findAll(g);
|
||||||
|
try {
|
||||||
|
while (it.hasNext()) {
|
||||||
|
Triple t = it.next();
|
||||||
|
g.delete(t);
|
||||||
|
it.remove();
|
||||||
|
}
|
||||||
|
} finally {
|
||||||
|
it.close();
|
||||||
|
}
|
||||||
|
|
||||||
|
// get rid of remaining blank nodes using a SPARQL DELETE
|
||||||
|
if (g instanceof SparqlGraph) {
|
||||||
|
((SparqlGraph) g).removeAll();
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -12,6 +12,7 @@ import org.apache.commons.dbcp.BasicDataSource;
|
||||||
import org.apache.commons.logging.Log;
|
import org.apache.commons.logging.Log;
|
||||||
import org.apache.commons.logging.LogFactory;
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
|
||||||
|
import com.hp.hpl.jena.graph.Triple;
|
||||||
import com.hp.hpl.jena.query.Dataset;
|
import com.hp.hpl.jena.query.Dataset;
|
||||||
import com.hp.hpl.jena.query.Query;
|
import com.hp.hpl.jena.query.Query;
|
||||||
import com.hp.hpl.jena.query.QueryExecution;
|
import com.hp.hpl.jena.query.QueryExecution;
|
||||||
|
|
@ -23,11 +24,18 @@ import com.hp.hpl.jena.rdf.listeners.StatementListener;
|
||||||
import com.hp.hpl.jena.rdf.model.Model;
|
import com.hp.hpl.jena.rdf.model.Model;
|
||||||
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
||||||
import com.hp.hpl.jena.rdf.model.Statement;
|
import com.hp.hpl.jena.rdf.model.Statement;
|
||||||
|
import com.hp.hpl.jena.rdf.model.StmtIterator;
|
||||||
import com.hp.hpl.jena.sdb.SDBFactory;
|
import com.hp.hpl.jena.sdb.SDBFactory;
|
||||||
import com.hp.hpl.jena.sdb.StoreDesc;
|
import com.hp.hpl.jena.sdb.StoreDesc;
|
||||||
import com.hp.hpl.jena.sdb.sql.SDBConnection;
|
import com.hp.hpl.jena.sdb.sql.SDBConnection;
|
||||||
|
import com.hp.hpl.jena.update.GraphStore;
|
||||||
|
import com.hp.hpl.jena.update.GraphStoreFactory;
|
||||||
|
import com.hp.hpl.jena.update.UpdateAction;
|
||||||
|
import com.hp.hpl.jena.update.UpdateFactory;
|
||||||
|
import com.hp.hpl.jena.update.UpdateRequest;
|
||||||
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapper;
|
import edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapper;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraph;
|
||||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
|
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
|
||||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.ModelChange;
|
import edu.cornell.mannlib.vitro.webapp.rdfservice.ModelChange;
|
||||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
|
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
|
||||||
|
|
@ -93,6 +101,7 @@ public class RDFServiceSDB extends RDFServiceImpl implements RDFService {
|
||||||
model.add(parseModel(modelChange));
|
model.add(parseModel(modelChange));
|
||||||
} else if (modelChange.getOperation() == ModelChange.Operation.REMOVE) {
|
} else if (modelChange.getOperation() == ModelChange.Operation.REMOVE) {
|
||||||
model.remove(parseModel(modelChange));
|
model.remove(parseModel(modelChange));
|
||||||
|
removeBlankNodesWithSparqlUpdate(dataset, model, modelChange.getGraphURI());
|
||||||
} else {
|
} else {
|
||||||
log.error("unrecognized operation type");
|
log.error("unrecognized operation type");
|
||||||
}
|
}
|
||||||
|
|
@ -112,6 +121,56 @@ public class RDFServiceSDB extends RDFServiceImpl implements RDFService {
|
||||||
return true;
|
return true;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
private void removeBlankNodesWithSparqlUpdate(Dataset dataset, Model model, String graphURI) {
|
||||||
|
Model blankNodeModel = ModelFactory.createDefaultModel();
|
||||||
|
StmtIterator stmtIt = model.listStatements();
|
||||||
|
while (stmtIt.hasNext()) {
|
||||||
|
Statement stmt = stmtIt.nextStatement();
|
||||||
|
if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
|
||||||
|
blankNodeModel.add(stmt);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
removeUsingSparqlUpdate(dataset, blankNodeModel, graphURI);
|
||||||
|
}
|
||||||
|
|
||||||
|
private void removeUsingSparqlUpdate(Dataset dataset, Model model, String graphURI) {
|
||||||
|
|
||||||
|
StringBuffer patternBuff = new StringBuffer();
|
||||||
|
StmtIterator stmtIt = model.listStatements();
|
||||||
|
while(stmtIt.hasNext()) {
|
||||||
|
Triple t = stmtIt.next().asTriple();
|
||||||
|
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();
|
||||||
|
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());
|
||||||
|
|
||||||
|
GraphStore graphStore = GraphStoreFactory.create(dataset);
|
||||||
|
UpdateRequest request = UpdateFactory.create();
|
||||||
|
request.add(queryBuff.toString());
|
||||||
|
UpdateAction.execute(request, graphStore);
|
||||||
|
}
|
||||||
|
|
||||||
private Model parseModel(ModelChange modelChange) {
|
private Model parseModel(ModelChange modelChange) {
|
||||||
Model model = ModelFactory.createDefaultModel();
|
Model model = ModelFactory.createDefaultModel();
|
||||||
model.read(modelChange.getSerializedModel(),
|
model.read(modelChange.getSerializedModel(),
|
||||||
|
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue