eliminating Sesame dependencies
This commit is contained in:
brianjlowe
parent
a29b61d277
commit
710844a2fb
54 changed files with 84 additions and 608 deletions
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@ -112,6 +112,14 @@ public class BaseResourceBean implements ResourceBean {
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}
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}
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public BaseResourceBean() {
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// default constructor
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}
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public BaseResourceBean(String uri) {
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buildLocalAndNS(uri);
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}
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@Override
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public boolean isAnonymous() {
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return (this.URI==null || VitroVocabulary.PSEUDO_BNODE_NS.equals(this.getNamespace()));
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@ -14,7 +14,6 @@ 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 org.joda.time.DateTime;
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import org.openrdf.model.impl.URIImpl;
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import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
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@ -184,7 +183,7 @@ public class ObjectProperty extends Property implements Comparable<ObjectPropert
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this.localNameInverse = null;
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} else {
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this.URIInverse = URIInverse;
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URIImpl uriInverse = new URIImpl(URIInverse);
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BaseResourceBean uriInverse = new BaseResourceBean(URIInverse);
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this.namespaceInverse = uriInverse.getNamespace();
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this.localNameInverse = uriInverse.getLocalName();
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}
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@ -6,8 +6,6 @@ import java.text.Collator;
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import java.util.ArrayList;
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import java.util.List;
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import org.openrdf.model.impl.URIImpl;
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/**
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* A Java class representing an ontology ("Vitro") class
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*
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@ -124,14 +122,8 @@ public class VClass extends BaseResourceBean implements Comparable<VClass>
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*/
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public VClass( String uriString )
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{
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// The URIImpl class can be used to parse a URI string into its component parts
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URIImpl uri = new URIImpl(uriString);
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// Use the URIImpl to obtain parts of this URI for local storage
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myName = uri.getLocalName();
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URI = uriString;
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namespace = uri.getNamespace();
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localName = uri.getLocalName();
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super(uriString);
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myName = getLocalName();
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}
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/**
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@ -12,7 +12,6 @@ import java.util.Map;
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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 org.openrdf.model.impl.URIImpl;
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public class VClassGroup extends LinkedList <VClass> implements Comparable<VClassGroup> {
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@ -56,7 +55,7 @@ public class VClassGroup extends LinkedList <VClass> implements Comparable<VClas
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public VClassGroup(String uri, String name, int rank) {
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super();
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this.URI = uri;
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URIImpl theURI = new URIImpl(uri);
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BaseResourceBean theURI = new BaseResourceBean(uri);
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this.namespace = theURI.getNamespace();
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this.localName = theURI.getLocalName();
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this.displayRank = rank;
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@ -1,64 +0,0 @@
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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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 SparqlDataset implements Dataset {
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private SparqlDatasetGraph g;
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public SparqlDataset(SparqlDatasetGraph 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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@ -1,266 +0,0 @@
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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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 org.openrdf.model.Resource;
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import org.openrdf.repository.Repository;
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import org.openrdf.repository.RepositoryConnection;
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import org.openrdf.repository.RepositoryException;
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import org.openrdf.repository.RepositoryResult;
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import org.openrdf.repository.http.HTTPRepository;
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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.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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public class SparqlDatasetGraph implements DatasetGraph {
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private String endpointURI;
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private Repository repository;
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private Lock lock = new LockMRSW();
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public SparqlDatasetGraph(String endpointURI) {
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this.endpointURI = endpointURI;
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this.repository = new HTTPRepository(endpointURI);
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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 SparqlGraph(endpointURI)
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: new SparqlGraph(endpointURI, 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 = execSelect(findQuery.toString());
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//rs = execSelect(findQuery.toString());
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//rs = execSelect(findQuery.toString());
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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 SparqlGraph(endpointURI);
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}
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@Override
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public Graph getGraph(Node arg0) {
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return new SparqlGraph(endpointURI, 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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RepositoryConnection conn = getConnection();
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try {
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RepositoryResult<Resource> conResult = conn.getContextIDs();
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while (conResult.hasNext()) {
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Resource con = conResult.next();
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graphNodeList.add(Node.createURI(con.stringValue()));
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}
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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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return graphNodeList.iterator();
|
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}
|
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|
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private RepositoryConnection getConnection() {
|
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try {
|
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return this.repository.getConnection();
|
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} catch (RepositoryException e) {
|
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throw new RuntimeException(e);
|
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}
|
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}
|
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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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}
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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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|
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@Override
|
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public long size() {
|
||||
// TODO Auto-generated method stub
|
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return 0;
|
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}
|
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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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private ResultSet execSelect(String queryStr) {
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|
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// long startTime1 = System.currentTimeMillis();
|
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// try {
|
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//
|
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// RepositoryConnection conn = getConnection();
|
||||
// try {
|
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// GraphQuery q = conn.prepareGraphQuery(QueryLanguage.SPARQL, queryStr);
|
||||
// q.evaluate();
|
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// } catch (MalformedQueryException e) {
|
||||
// throw new RuntimeException(e);
|
||||
// } finally {
|
||||
// conn.close();
|
||||
// }
|
||||
// } catch (Exception re) {
|
||||
// //log.info(re,re);
|
||||
// }
|
||||
|
||||
// log.info((System.currentTimeMillis() - startTime1) + " to execute via sesame");
|
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|
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long startTime = System.currentTimeMillis();
|
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Query askQuery = QueryFactory.create(queryStr);
|
||||
QueryExecution qe = QueryExecutionFactory.sparqlService(endpointURI, askQuery);
|
||||
try {
|
||||
return new ResultSetMem(qe.execSelect());
|
||||
} finally {
|
||||
//log.info((System.currentTimeMillis() - startTime) + " to execute via Jena");
|
||||
qe.close();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -3,19 +3,12 @@
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package edu.cornell.mannlib.vitro.webapp.dao.jena;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.Collections;
|
||||
import java.util.List;
|
||||
|
||||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
import org.openrdf.query.MalformedQueryException;
|
||||
import org.openrdf.query.QueryLanguage;
|
||||
import org.openrdf.query.Update;
|
||||
import org.openrdf.query.UpdateExecutionException;
|
||||
import org.openrdf.repository.Repository;
|
||||
import org.openrdf.repository.RepositoryConnection;
|
||||
import org.openrdf.repository.RepositoryException;
|
||||
import org.openrdf.repository.http.HTTPRepository;
|
||||
|
||||
import com.hp.hpl.jena.graph.BulkUpdateHandler;
|
||||
import com.hp.hpl.jena.graph.Capabilities;
|
||||
|
|
@ -46,10 +39,23 @@ import com.hp.hpl.jena.util.iterator.ExtendedIterator;
|
|||
import com.hp.hpl.jena.util.iterator.SingletonIterator;
|
||||
import com.hp.hpl.jena.util.iterator.WrappedIterator;
|
||||
|
||||
import org.apache.http.client.entity.UrlEncodedFormEntity;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpGet;
|
||||
import org.apache.http.client.methods.HttpPost;
|
||||
import org.apache.http.client.utils.URIBuilder;
|
||||
import org.apache.http.impl.client.CloseableHttpClient;
|
||||
import org.apache.http.impl.client.HttpClients;
|
||||
import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
|
||||
import org.apache.http.message.BasicNameValuePair;
|
||||
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
|
||||
|
||||
public class SparqlGraph implements GraphWithPerform {
|
||||
|
||||
private String endpointURI;
|
||||
private String graphURI;
|
||||
private CloseableHttpClient httpClient;
|
||||
private static final Log log = LogFactory.getLog(SparqlGraph.class);
|
||||
|
||||
private BulkUpdateHandler bulkUpdateHandler;
|
||||
|
|
@ -60,8 +66,6 @@ public class SparqlGraph implements GraphWithPerform {
|
|||
private TransactionHandler transactionHandler;
|
||||
private QueryHandler queryHandler;
|
||||
|
||||
private Repository repository;
|
||||
|
||||
/**
|
||||
* Returns a SparqlGraph for the union of named graphs in a remote repository
|
||||
* @param endpointURI
|
||||
|
|
@ -78,7 +82,10 @@ public class SparqlGraph implements GraphWithPerform {
|
|||
public SparqlGraph(String endpointURI, String graphURI) {
|
||||
this.endpointURI = endpointURI;
|
||||
this.graphURI = graphURI;
|
||||
this.repository = new HTTPRepository(endpointURI);
|
||||
|
||||
PoolingHttpClientConnectionManager cm = new PoolingHttpClientConnectionManager();
|
||||
cm.setDefaultMaxPerRoute(50);
|
||||
this.httpClient = HttpClients.custom().setConnectionManager(cm).build();
|
||||
}
|
||||
|
||||
public String getEndpointURI() {
|
||||
|
|
@ -88,14 +95,6 @@ public class SparqlGraph implements GraphWithPerform {
|
|||
public String getGraphURI() {
|
||||
return graphURI;
|
||||
}
|
||||
|
||||
public RepositoryConnection getConnection() {
|
||||
try {
|
||||
return this.repository.getConnection();
|
||||
} catch (RepositoryException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void add(Triple arg0) throws AddDeniedException {
|
||||
|
|
@ -104,22 +103,24 @@ public class SparqlGraph implements GraphWithPerform {
|
|||
|
||||
public void executeUpdate(String updateString) {
|
||||
try {
|
||||
RepositoryConnection conn = getConnection();
|
||||
HttpPost meth = new HttpPost(endpointURI);
|
||||
meth.addHeader("Content-Type", "application/x-www-form-urlencoded");
|
||||
meth.setEntity(new UrlEncodedFormEntity(Arrays.asList(
|
||||
new BasicNameValuePair("update", updateString))));
|
||||
CloseableHttpResponse response = httpClient.execute(meth);
|
||||
try {
|
||||
Update u = conn.prepareUpdate(QueryLanguage.SPARQL, updateString);
|
||||
u.execute();
|
||||
} catch (MalformedQueryException e) {
|
||||
throw new RuntimeException(e);
|
||||
} catch (UpdateExecutionException e) {
|
||||
log.error(e,e);
|
||||
log.error("Update command: \n" + updateString);
|
||||
throw new RuntimeException(e);
|
||||
int statusCode = response.getStatusLine().getStatusCode();
|
||||
if (statusCode > 399) {
|
||||
log.error("response " + statusCode + " to update. \n");
|
||||
throw new RuntimeException("Unable to perform SPARQL UPDATE: \n"
|
||||
+ updateString);
|
||||
}
|
||||
} finally {
|
||||
conn.close();
|
||||
}
|
||||
} catch (RepositoryException re) {
|
||||
throw new RuntimeException(re);
|
||||
}
|
||||
response.close();
|
||||
}
|
||||
} catch (Exception e) {
|
||||
throw new RuntimeException("Unable to perform SPARQL UPDATE", e);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
|
|||
|
|
@ -14,9 +14,8 @@ import javax.servlet.http.HttpServletResponseWrapper;
|
|||
|
||||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
import org.openrdf.model.URI;
|
||||
import org.openrdf.model.impl.URIImpl;
|
||||
|
||||
import edu.cornell.mannlib.vitro.webapp.beans.IndividualImpl;
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
|
||||
import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapper;
|
||||
|
|
@ -136,7 +135,7 @@ public class URLRewritingHttpServletResponse extends HttpServletResponseWrapper/
|
|||
qpIndex++;
|
||||
if ( ("uri".equals(keyAndValue[0])) && (keyAndValue.length>1) && (keyAndValue[1] != null) ) {
|
||||
try {
|
||||
URI uri = new URIImpl(keyAndValue[1]);
|
||||
IndividualImpl uri = new IndividualImpl(keyAndValue[1]);
|
||||
String namespace = uri.getNamespace();
|
||||
String localName = uri.getLocalName();
|
||||
if ( (namespace != null) && (localName != null) ) {
|
||||
|
|
|
|||
|
|
@ -19,7 +19,6 @@ import javax.servlet.ServletContext;
|
|||
|
||||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
import org.openrdf.model.impl.URIImpl;
|
||||
|
||||
import com.hp.hpl.jena.iri.IRI;
|
||||
import com.hp.hpl.jena.iri.IRIFactory;
|
||||
|
|
|
|||
|
|
@ -26,11 +26,6 @@ import org.apache.http.impl.client.CloseableHttpClient;
|
|||
import org.apache.http.impl.client.HttpClients;
|
||||
import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
|
||||
import org.apache.http.message.BasicNameValuePair;
|
||||
import org.openrdf.model.Resource;
|
||||
import org.openrdf.repository.RepositoryConnection;
|
||||
import org.openrdf.repository.RepositoryException;
|
||||
import org.openrdf.repository.RepositoryResult;
|
||||
import org.openrdf.repository.http.HTTPRepository;
|
||||
|
||||
import com.hp.hpl.jena.graph.Triple;
|
||||
import com.hp.hpl.jena.query.Query;
|
||||
|
|
@ -44,6 +39,7 @@ import com.hp.hpl.jena.query.ResultSetFormatter;
|
|||
import com.hp.hpl.jena.rdf.model.Model;
|
||||
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
||||
import com.hp.hpl.jena.rdf.model.RDFNode;
|
||||
import com.hp.hpl.jena.rdf.model.Resource;
|
||||
import com.hp.hpl.jena.rdf.model.Statement;
|
||||
import com.hp.hpl.jena.rdf.model.StmtIterator;
|
||||
|
||||
|
|
@ -67,10 +63,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
|
|||
private static final Log log = LogFactory.getLog(RDFServiceImpl.class);
|
||||
protected String readEndpointURI;
|
||||
protected String updateEndpointURI;
|
||||
private HTTPRepository readRepository;
|
||||
private HTTPRepository updateRepository;
|
||||
private CloseableHttpClient httpClient;
|
||||
private boolean useSesameContextQuery = true;
|
||||
// the number of triples to be
|
||||
private static final int CHUNK_SIZE = 1000; // added/removed in a single
|
||||
// SPARQL UPDATE
|
||||
|
|
@ -89,8 +82,6 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
|
|||
public RDFServiceSparql(String readEndpointURI, String updateEndpointURI, String defaultWriteGraphURI) {
|
||||
this.readEndpointURI = readEndpointURI;
|
||||
this.updateEndpointURI = updateEndpointURI;
|
||||
this.readRepository = new HTTPRepository(readEndpointURI);
|
||||
this.updateRepository = new HTTPRepository(updateEndpointURI);
|
||||
|
||||
PoolingHttpClientConnectionManager cm = new PoolingHttpClientConnectionManager();
|
||||
cm.setDefaultMaxPerRoute(50);
|
||||
|
|
@ -135,12 +126,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
|
|||
}
|
||||
|
||||
public void close() {
|
||||
try {
|
||||
this.readRepository.shutDown();
|
||||
this.updateRepository.shutDown();
|
||||
} catch (RepositoryException re) {
|
||||
log.error(re, re);
|
||||
}
|
||||
// nothing for now
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -234,6 +220,8 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
|
|||
|
||||
try {
|
||||
qe.execConstruct(model);
|
||||
} catch (Exception e) {
|
||||
log.error("Error executing CONSTRUCT against remote endpoint: " + queryStr);
|
||||
} finally {
|
||||
qe.close();
|
||||
}
|
||||
|
|
@ -359,47 +347,40 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
|
|||
*
|
||||
* @return List<String> - list of all the graph URIs in the RDF store
|
||||
*/
|
||||
//TODO - need to verify that the sesame getContextIDs method is implemented
|
||||
// in such a way that it works with all triple stores that support the
|
||||
// graph update API
|
||||
@Override
|
||||
public List<String> getGraphURIs() throws RDFServiceException {
|
||||
if (!this.useSesameContextQuery) {
|
||||
return getGraphURIsFromSparqlQuery();
|
||||
} else {
|
||||
try {
|
||||
return getGraphURIsFromSesameContexts();
|
||||
} catch (RepositoryException re) {
|
||||
this.useSesameContextQuery = false;
|
||||
return getGraphURIsFromSparqlQuery();
|
||||
}
|
||||
}
|
||||
return getGraphURIsFromSparqlQuery();
|
||||
}
|
||||
|
||||
private List<String> getGraphURIsFromSesameContexts() throws RepositoryException {
|
||||
List<String> graphURIs = new ArrayList<String>();
|
||||
RepositoryConnection conn = getReadConnection();
|
||||
try {
|
||||
RepositoryResult<Resource> conResult = conn.getContextIDs();
|
||||
while (conResult.hasNext()) {
|
||||
Resource res = conResult.next();
|
||||
graphURIs.add(res.stringValue());
|
||||
}
|
||||
} finally {
|
||||
conn.close();
|
||||
}
|
||||
return graphURIs;
|
||||
}
|
||||
|
||||
private List<String> getGraphURIsFromSparqlQuery() throws RDFServiceException {
|
||||
private List<String> getGraphURIsFromSparqlQuery() throws RDFServiceException {
|
||||
String fastJenaQuery = "SELECT DISTINCT ?g WHERE { GRAPH ?g {} } ORDER BY ?g";
|
||||
String standardQuery = "SELECT DISTINCT ?g WHERE { GRAPH ?g { ?s ?p ?o } } ORDER BY ?g";
|
||||
List<String> graphURIs = new ArrayList<String>();
|
||||
try {
|
||||
String graphURIString = "SELECT DISTINCT ?g WHERE { GRAPH ?g { ?s ?p ?o } } ORDER BY ?g";
|
||||
graphURIs = getGraphURIsFromSparqlQuery(fastJenaQuery);
|
||||
} catch (Exception e) {
|
||||
log.debug("Unable to use non-standard ARQ query for graph list", e);
|
||||
}
|
||||
if (graphURIs.isEmpty()) {
|
||||
graphURIs = getGraphURIsFromSparqlQuery(standardQuery);
|
||||
}
|
||||
return graphURIs;
|
||||
}
|
||||
|
||||
private List<String> getGraphURIsFromSparqlQuery(String queryString) throws RDFServiceException {
|
||||
List<String> graphURIs = new ArrayList<String>();
|
||||
try {
|
||||
|
||||
ResultSet rs = ResultSetFactory.fromJSON(
|
||||
sparqlSelectQuery(graphURIString, RDFService.ResultFormat.JSON));
|
||||
sparqlSelectQuery(queryString, RDFService.ResultFormat.JSON));
|
||||
while (rs.hasNext()) {
|
||||
QuerySolution qs = rs.nextSolution();
|
||||
graphURIs.add(qs.getResource("g").getURI());
|
||||
if (qs != null) { // no idea how this happens, but it seems to
|
||||
RDFNode n = qs.getResource("g");
|
||||
if (n != null && n.isResource()) {
|
||||
graphURIs.add(((Resource) n).getURI());
|
||||
}
|
||||
}
|
||||
}
|
||||
} catch (Exception e) {
|
||||
throw new RDFServiceException("Unable to list graph URIs", e);
|
||||
|
|
@ -470,22 +451,6 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
|
|||
return updateEndpointURI;
|
||||
}
|
||||
|
||||
protected RepositoryConnection getReadConnection() {
|
||||
try {
|
||||
return this.readRepository.getConnection();
|
||||
} catch (RepositoryException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
protected RepositoryConnection getWriteConnection() {
|
||||
try {
|
||||
return this.updateRepository.getConnection();
|
||||
} catch (RepositoryException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
protected void executeUpdate(String updateString) throws RDFServiceException {
|
||||
try {
|
||||
HttpPost meth = new HttpPost(updateEndpointURI);
|
||||
|
|
|
|||
|
|
@ -15,9 +15,9 @@ import javax.servlet.http.HttpServletResponse;
|
|||
|
||||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
import org.openrdf.model.vocabulary.OWL;
|
||||
import org.openrdf.model.vocabulary.RDF;
|
||||
|
||||
import com.hp.hpl.jena.vocabulary.OWL;
|
||||
import com.hp.hpl.jena.vocabulary.RDF;
|
||||
import com.hp.hpl.jena.vocabulary.RDFS;
|
||||
import com.hp.hpl.jena.vocabulary.XSD;
|
||||
|
||||
|
|
@ -99,8 +99,8 @@ public class GetAllPrefix extends BaseEditController {
|
|||
}
|
||||
|
||||
// add standard namespaces
|
||||
addPrefixIfNecessary("owl", OWL.NAMESPACE, prefixMap);
|
||||
addPrefixIfNecessary("rdf", RDF.NAMESPACE, prefixMap);
|
||||
addPrefixIfNecessary("owl", OWL.getURI(), prefixMap);
|
||||
addPrefixIfNecessary("rdf", RDF.getURI(), prefixMap);
|
||||
addPrefixIfNecessary("rdfs", RDFS.getURI(), prefixMap);
|
||||
addPrefixIfNecessary("swrl", "http://www.w3.org/2003/11/swrl#", prefixMap);
|
||||
addPrefixIfNecessary("swrlb", "http://www.w3.org/2003/11/swrlb#", prefixMap);
|
||||
|
|
|
|||
|
|
@ -1,156 +0,0 @@
|
|||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
||||
|
||||
package edu.cornell.mannlib.vitro.webapp.utils.jena;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.io.OutputStream;
|
||||
import java.io.PipedInputStream;
|
||||
import java.io.PipedOutputStream;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
import org.openrdf.model.Resource;
|
||||
import org.openrdf.model.impl.URIImpl;
|
||||
import org.openrdf.repository.Repository;
|
||||
import org.openrdf.repository.RepositoryConnection;
|
||||
import org.openrdf.repository.RepositoryException;
|
||||
import org.openrdf.repository.http.HTTPRepository;
|
||||
import org.openrdf.rio.RDFFormat;
|
||||
import org.openrdf.rio.RDFParseException;
|
||||
|
||||
import com.hp.hpl.jena.query.Query;
|
||||
import com.hp.hpl.jena.query.QueryExecution;
|
||||
import com.hp.hpl.jena.query.QueryExecutionFactory;
|
||||
import com.hp.hpl.jena.query.QueryFactory;
|
||||
import com.hp.hpl.jena.query.QuerySolution;
|
||||
import com.hp.hpl.jena.query.ResultSet;
|
||||
import com.hp.hpl.jena.rdf.model.Model;
|
||||
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
||||
import com.hp.hpl.jena.rdf.model.RDFNode;
|
||||
import com.hp.hpl.jena.vocabulary.OWL;
|
||||
|
||||
public class SesameSyncUtils {
|
||||
|
||||
private static final Log log = LogFactory.getLog(SesameSyncUtils.class);
|
||||
|
||||
public void writeModelToSesameContext
|
||||
(Model jenaModel, String serverURI, String repositoryId, String contextId)
|
||||
throws RepositoryException, IOException, RDFParseException {
|
||||
Repository myRepository = new HTTPRepository(serverURI, repositoryId);
|
||||
myRepository.initialize();
|
||||
RepositoryConnection myConn = myRepository.getConnection();
|
||||
|
||||
myConn.setAutoCommit(false);
|
||||
try {
|
||||
|
||||
Resource contextRes = (contextId != null)
|
||||
? new URIImpl(contextId) : null ;
|
||||
|
||||
if (contextRes != null) {
|
||||
myConn.clear(contextRes);
|
||||
} else {
|
||||
myConn.clear();
|
||||
}
|
||||
|
||||
PipedInputStream in = new PipedInputStream();
|
||||
PipedOutputStream out = new PipedOutputStream(in);
|
||||
|
||||
|
||||
|
||||
try {
|
||||
|
||||
new Thread(new JenaOutputter(jenaModel, out, myConn), "SesameSyncUtilities.JenaOutputter").start();
|
||||
|
||||
if (contextRes != null) {
|
||||
myConn.add(in,"http://example.org/base/", RDFFormat.NTRIPLES, contextRes);
|
||||
} else {
|
||||
myConn.add(in,"http://example.org/base/", RDFFormat.NTRIPLES);
|
||||
}
|
||||
} finally {
|
||||
in.close();
|
||||
}
|
||||
|
||||
myConn.commit();
|
||||
|
||||
} catch (Throwable e) {
|
||||
myConn.rollback();
|
||||
e.printStackTrace();
|
||||
log.error("Error writing to Sesame repository", e);
|
||||
throw new RuntimeException("Error writing to Sesame repository", e);
|
||||
} finally {
|
||||
myConn.close();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private List<String> getIndividualURIs(Model model) {
|
||||
List<String> individualURIs = new ArrayList<String>();
|
||||
String queryStr = "SELECT DISTINCT ?s WHERE { \n" +
|
||||
" ?s a <" + OWL.Thing.getURI() + "> \n" +
|
||||
"}";
|
||||
Query query = QueryFactory.create(queryStr);
|
||||
QueryExecution qe = QueryExecutionFactory.create(query, model);
|
||||
try {
|
||||
ResultSet rs = qe.execSelect();
|
||||
while (rs.hasNext()) {
|
||||
QuerySolution qsoln = rs.nextSolution();
|
||||
String individualURI = qsoln.getResource("s").getURI();
|
||||
if (individualURI != null) {
|
||||
individualURIs.add(individualURI);
|
||||
}
|
||||
}
|
||||
} finally {
|
||||
qe.close();
|
||||
}
|
||||
return individualURIs;
|
||||
}
|
||||
|
||||
private class JenaOutputter implements Runnable {
|
||||
|
||||
private Model model;
|
||||
private OutputStream out;
|
||||
private RepositoryConnection rconn;
|
||||
|
||||
public JenaOutputter(Model model, OutputStream out, RepositoryConnection rconn) {
|
||||
this.model = model;
|
||||
this.out = out;
|
||||
this.rconn = rconn;
|
||||
}
|
||||
|
||||
public void run() {
|
||||
Model t = ModelFactory.createDefaultModel();
|
||||
try {
|
||||
List<String> individualURIs = getIndividualURIs(model);
|
||||
log.info(individualURIs.size() + " individuals to send to Sesame");
|
||||
int i = 0;
|
||||
for (String individualURI : individualURIs) {
|
||||
t.removeAll();
|
||||
t.add(model.listStatements(
|
||||
model.getResource(
|
||||
individualURI), null, (RDFNode) null));
|
||||
t.write(out, "N-TRIPLE");
|
||||
i++;
|
||||
if (i % 100 == 0) {
|
||||
try {
|
||||
rconn.commit();
|
||||
} catch (Throwable e) {
|
||||
log.error(e, e);
|
||||
}
|
||||
log.info(i + " individuals sent to Sesame");
|
||||
}
|
||||
}
|
||||
} finally {
|
||||
try {
|
||||
out.flush();
|
||||
out.close();
|
||||
} catch (IOException ioe) {
|
||||
ioe.printStackTrace();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -4,8 +4,6 @@ package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
|
|||
|
||||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
import org.openrdf.model.URI;
|
||||
import org.openrdf.model.impl.URIImpl;
|
||||
|
||||
import com.hp.hpl.jena.rdf.model.Literal;
|
||||
|
||||
|
|
@ -14,6 +12,8 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.RequestedAction;
|
|||
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditDataPropertyStatement;
|
||||
import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
|
||||
import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatementImpl;
|
||||
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
|
||||
import edu.cornell.mannlib.vitro.webapp.beans.IndividualImpl;
|
||||
import edu.cornell.mannlib.vitro.webapp.beans.Property;
|
||||
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
|
||||
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
|
||||
|
|
@ -51,7 +51,7 @@ public class NameStatementTemplateModel extends PropertyStatementTemplateModel {
|
|||
// If the individual has no rdfs:label, use the local name. It will not be editable. (This replicates previous behavior;
|
||||
// perhaps we would want to allow a label to be added. But such individuals do not usually have their profiles viewed or
|
||||
// edited directly.)
|
||||
URI uri = new URIImpl(subjectUri);
|
||||
Individual uri = new IndividualImpl(subjectUri);
|
||||
this.stringValue = uri.getLocalName();
|
||||
this.editUrl = "";
|
||||
} else {
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue