eliminating Sesame dependencies

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/BaseResourceBean.java

@@ -112,6 +112,14 @@ public class BaseResourceBean implements ResourceBean {
 		}
 	}
 
+	public BaseResourceBean() {
+	    // default constructor
+	}
+	
+	public BaseResourceBean(String uri) {
+	    buildLocalAndNS(uri);
+	}
+	
     @Override
 	public boolean isAnonymous() {        
     	return (this.URI==null || VitroVocabulary.PSEUDO_BNODE_NS.equals(this.getNamespace()));

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/ObjectProperty.java

@@ -14,7 +14,6 @@ import java.util.List;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.joda.time.DateTime;
-import org.openrdf.model.impl.URIImpl;
 
 import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
 
@@ -184,7 +183,7 @@ public class ObjectProperty extends Property implements Comparable<ObjectPropert
             this.localNameInverse = null;
         } else {
             this.URIInverse = URIInverse;
-            URIImpl uriInverse = new URIImpl(URIInverse);
+            BaseResourceBean uriInverse = new BaseResourceBean(URIInverse);
             this.namespaceInverse = uriInverse.getNamespace();
             this.localNameInverse = uriInverse.getLocalName();
         }

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/VClass.java

@@ -6,8 +6,6 @@ import java.text.Collator;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.openrdf.model.impl.URIImpl;
-
 /**
  * A Java class representing an ontology ("Vitro") class
  *
@@ -124,14 +122,8 @@ public class VClass extends BaseResourceBean implements Comparable<VClass>
      */
     public VClass( String uriString )
     {
-        // The URIImpl class can be used to parse a URI string into its component parts
+        super(uriString);
-        URIImpl uri = new URIImpl(uriString);
+        myName = getLocalName();
-
-        // Use the URIImpl to obtain parts of this URI for local storage
-        myName = uri.getLocalName();
-        URI = uriString;
-        namespace = uri.getNamespace();
-        localName = uri.getLocalName();
     }
     
     /**

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/VClassGroup.java

@@ -12,7 +12,6 @@ import java.util.Map;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.openrdf.model.impl.URIImpl;
 
 public class VClassGroup extends LinkedList <VClass> implements Comparable<VClassGroup> {
 	
@@ -56,7 +55,7 @@ public class VClassGroup extends LinkedList <VClass> implements Comparable<VClas
     public VClassGroup(String uri, String name, int rank) {
         super();
         this.URI = uri;
-        URIImpl theURI = new URIImpl(uri);
+        BaseResourceBean theURI = new BaseResourceBean(uri);
         this.namespace = theURI.getNamespace();
         this.localName = theURI.getLocalName();
         this.displayRank = rank;

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/SparqlDataset.java

@@ -1,64 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao.jena;
-
-import java.util.ArrayList;
-import java.util.Iterator;
-
-import com.hp.hpl.jena.graph.Node;
-import com.hp.hpl.jena.query.Dataset;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.shared.Lock;
-import com.hp.hpl.jena.sparql.core.DatasetGraph;
-
-public class SparqlDataset implements Dataset {
-
-    private SparqlDatasetGraph g;
-    
-    public SparqlDataset(SparqlDatasetGraph g) {
-        this.g = g;
-    }
-    
-    @Override
-    public DatasetGraph asDatasetGraph() {
-        return g;
-    }
-
-    @Override
-    public void close() {
-        g.close();
-    }
-
-    @Override
-    public boolean containsNamedModel(String arg0) {
-        return g.containsGraph(Node.createURI(arg0));
-    }
-
-    @Override
-    public Model getDefaultModel() {
-        return ModelFactory.createModelForGraph(g.getDefaultGraph());
-    }
-
-    @Override
-    public Lock getLock() {
-        return g.getLock();
-    }
-
-    @Override
-    public Model getNamedModel(String arg0) {
-        return ModelFactory.createModelForGraph(g.getGraph(Node.createURI(arg0)));
-    }
-
-    @Override
-    public Iterator<String> listNames() {
-        ArrayList<String> nameList = new ArrayList<String>();
-        Iterator<Node> nodeIt = g.listGraphNodes();
-        while (nodeIt.hasNext()) {
-            Node n = nodeIt.next();
-            nameList.add(n.getURI());
-        }
-        return nameList.iterator();
-    }
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/SparqlDatasetGraph.java

@@ -1,266 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao.jena;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
-
-import org.openrdf.model.Resource;
-import org.openrdf.repository.Repository;
-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.Graph;
-import com.hp.hpl.jena.graph.Node;
-import com.hp.hpl.jena.graph.Triple;
-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.shared.Lock;
-import com.hp.hpl.jena.shared.LockMRSW;
-import com.hp.hpl.jena.sparql.core.DatasetGraph;
-import com.hp.hpl.jena.sparql.core.Quad;
-import com.hp.hpl.jena.sparql.resultset.ResultSetMem;
-import com.hp.hpl.jena.sparql.util.Context;
-import com.hp.hpl.jena.util.iterator.SingletonIterator;
-import com.hp.hpl.jena.util.iterator.WrappedIterator;
-
-public class SparqlDatasetGraph implements DatasetGraph {
-
-    private String endpointURI;
-    private Repository repository;
-    private Lock lock = new LockMRSW();
-    
-    public SparqlDatasetGraph(String endpointURI) {
-        this.endpointURI = endpointURI;
-        this.repository = new HTTPRepository(endpointURI);
-    }
-
-    private Graph getGraphFor(Quad q) {
-        return getGraphFor(q.getGraph());
-    }
-    
-    private Graph getGraphFor(Node g) {
-        return (g == Node.ANY) 
-                ? new SparqlGraph(endpointURI) 
-                : new SparqlGraph(endpointURI, g.getURI());
-    }
-    
-    @Override
-    public void add(Quad arg0) {
-        getGraphFor(arg0).add(new Triple(arg0.getSubject(), arg0.getPredicate(), arg0.getObject()));
-    }
-
-    @Override
-    public void addGraph(Node arg0, Graph arg1) {
-        // TODO Auto-generated method stub
-    }
-
-    @Override
-    public void close() {
-        // TODO Auto-generated method stub
-    }
-
-    @Override
-    public boolean contains(Quad arg0) {
-        return getGraphFor(arg0).contains(new Triple(arg0.getSubject(), arg0.getPredicate(), arg0.getObject()));
-    }
-
-    @Override
-    public boolean contains(Node arg0, Node arg1, Node arg2, Node arg3) {
-        return getGraphFor(arg0).contains(arg1, arg2, arg3);
-    }
-
-    @Override
-    public boolean containsGraph(Node arg0) {
-        // TODO Auto-generated method stub
-        return true;
-    }
-
-    @Override
-    public void delete(Quad arg0) {
-        getGraphFor(arg0).delete(new Triple(arg0.getSubject(), arg0.getPredicate(), arg0.getObject()));
-    }
-
-    @Override
-    public void deleteAny(Node arg0, Node arg1, Node arg2, Node arg3) {
-        // TODO check this
-        getGraphFor(arg0).delete(new Triple(arg1, arg2, arg3));
-    }
-
-    @Override
-    public Iterator<Quad> find() {
-        return find(Node.ANY, Node.ANY, Node.ANY, Node.ANY);
-    }
-
-    @Override
-    public Iterator<Quad> find(Quad arg0) {
-        return find(arg0.getSubject(), arg0.getPredicate(), arg0.getObject(), arg0.getGraph());
-    }
-
-    @Override
-    public Iterator<Quad> find(Node graph, Node subject, Node predicate, Node object) {
-        if (!isVar(subject) && !isVar(predicate)  && !isVar(object) &&!isVar(graph)) {
-            if (contains(subject, predicate, object, graph)) {
-                return new SingletonIterator(new Triple(subject, predicate, object));
-            } else {
-                return WrappedIterator.create(Collections.EMPTY_LIST.iterator());
-            }
-        }
-        StringBuffer findQuery = new StringBuffer("SELECT * WHERE { \n");
-        String graphURI = !isVar(graph) ? graph.getURI() : null;
-        findQuery.append("  GRAPH ");
-        if (graphURI != null) {
-            findQuery.append("  <" + graphURI + ">");
-        } else {
-            findQuery.append("?g");
-        }
-        findQuery.append(" { ");
-        findQuery.append(SparqlGraph.sparqlNode(subject, "?s"))
-        .append(" ")
-        .append(SparqlGraph.sparqlNode(predicate, "?p"))
-        .append(" ")
-        .append(SparqlGraph.sparqlNode(object, "?o"));
-        findQuery.append("  } ");
-        findQuery.append("\n}");
-        
-        //log.info(findQuery.toString());
-        ResultSet rs = execSelect(findQuery.toString());
-        //rs = execSelect(findQuery.toString());
-        //rs = execSelect(findQuery.toString());
-        
-        List<Quad> quadlist = new ArrayList<Quad>();
-        while (rs.hasNext()) {
-            QuerySolution soln = rs.nextSolution();
-            Quad q = new Quad(isVar(graph) ? soln.get("?g").asNode() : graph,
-                                  isVar(subject) ? soln.get("?s").asNode() : subject, 
-                                  isVar(predicate) ? soln.get("?p").asNode() : predicate, 
-                                  isVar(object) ? soln.get("?o").asNode() : object);
-            //log.info(t);
-            quadlist.add(q);
-        }
-        //log.info(triplist.size() + " results");
-        return WrappedIterator.create(quadlist.iterator());    }
-
-    @Override
-    public Iterator<Quad> findNG(Node arg0, Node arg1, Node arg2, Node arg3) {
-        // TODO check this
-        return find(arg0, arg1, arg2, arg3);
-    }
-
-    @Override
-    public Context getContext() {
-        // TODO Auto-generated method stub
-        return null;
-    }
-
-    @Override
-    public Graph getDefaultGraph() {
-        return new SparqlGraph(endpointURI);
-    }
-
-    @Override
-    public Graph getGraph(Node arg0) {
-        return new SparqlGraph(endpointURI, arg0.getURI());
-    }
-
-    @Override
-    public Lock getLock() {
-        return lock;
-    }
-
-    @Override
-    public boolean isEmpty() {
-        // TODO Auto-generated method stub
-        return false;
-    }
-
-    @Override
-    public Iterator<Node> listGraphNodes() {
-        List<Node> graphNodeList = new ArrayList<Node>();
-        try {
-            RepositoryConnection conn = getConnection();
-            try {
-                RepositoryResult<Resource> conResult = conn.getContextIDs();
-                while (conResult.hasNext()) {
-                    Resource con = conResult.next();
-                    graphNodeList.add(Node.createURI(con.stringValue()));   
-                }
-            } finally {
-                conn.close();
-            }
-        } catch (RepositoryException re) {
-            throw new RuntimeException(re);
-        }
-        return graphNodeList.iterator();
-    }
-    
-    private RepositoryConnection getConnection() {
-        try {
-            return this.repository.getConnection();
-        } catch (RepositoryException e) {
-            throw new RuntimeException(e);
-        }
-    }
-
-    @Override
-    public void removeGraph(Node arg0) {
-        // TODO Auto-generated method stub
-
-    }
-
-    @Override
-    public void setDefaultGraph(Graph arg0) {
-        // TODO Auto-generated method stub
-
-    }
-
-    @Override
-    public long size() {
-        // TODO Auto-generated method stub
-        return 0;
-    }
-    
-    private boolean isVar(Node node) {
-        return (node == null || node.isVariable() || node == Node.ANY);
-    }
-    
-    private ResultSet execSelect(String queryStr) {
-        
-//      long startTime1 = System.currentTimeMillis();
-//      try {
-//          
-//          RepositoryConnection conn = getConnection();
-//          try {
-//              GraphQuery q = conn.prepareGraphQuery(QueryLanguage.SPARQL, queryStr);
-//              q.evaluate();
-//          } 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");
-      
-      long startTime = System.currentTimeMillis();
-      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();
-      }
-  }
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/SparqlGraph.java

@@ -3,19 +3,12 @@
 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);
+                int statusCode = response.getStatusLine().getStatusCode();
-                u.execute();
+                if (statusCode > 399) {
-            } catch (MalformedQueryException e) {
+                    log.error("response " + statusCode + " to update. \n");
-                throw new RuntimeException(e);
+                    throw new RuntimeException("Unable to perform SPARQL UPDATE: \n"
-            } catch (UpdateExecutionException e) {
+                        + updateString);
-                log.error(e,e);
+                }
-                log.error("Update command: \n" + updateString);
-                throw new RuntimeException(e);
             } finally {
-                conn.close();
+                response.close();
-            }
+            } 
-        } catch (RepositoryException re) {
+        } catch (Exception e) {
-            throw new RuntimeException(re);
+            throw new RuntimeException("Unable to perform SPARQL UPDATE", e);
-        }
+        } 
     }
     
     @Override

webapp/src/edu/cornell/mannlib/vitro/webapp/filters/URLRewritingHttpServletResponse.java

@@ -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) ) { 

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java

@@ -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;

webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/sparql/RDFServiceSparql.java

@@ -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 {
+        // nothing for now
-            this.readRepository.shutDown();
-            this.updateRepository.shutDown();
-        } catch (RepositoryException re) {
-            log.error(re, re);
-        }
     }
     
 	/**
@@ -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();
-            return getGraphURIsFromSparqlQuery();
-        } else {
-            try {
-                return getGraphURIsFromSesameContexts();
-            } catch (RepositoryException re) {
-                this.useSesameContextQuery = false;
-                return getGraphURIsFromSparqlQuery();
-            }
-        } 
 	}
 	
-	private List<String> getGraphURIsFromSesameContexts() throws RepositoryException {
+	private List<String> getGraphURIsFromSparqlQuery() throws RDFServiceException {	    
-	    List<String> graphURIs = new ArrayList<String>();
+	    String fastJenaQuery = "SELECT DISTINCT ?g WHERE { GRAPH ?g {} } ORDER BY ?g";
-	    RepositoryConnection conn = getReadConnection();
+	    String standardQuery = "SELECT DISTINCT ?g WHERE { GRAPH ?g { ?s ?p ?o } } ORDER BY ?g";
-        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 {
 	    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);

webapp/src/edu/cornell/mannlib/vitro/webapp/sparql/GetAllPrefix.java

@@ -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("owl", OWL.getURI(), prefixMap);
-	    addPrefixIfNecessary("rdf", RDF.NAMESPACE, 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);

webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/SesameSyncUtils.java

@@ -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();
-				}
-			}
-		}
-		
-	}
-	
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/NameStatementTemplateModel.java

@@ -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 {