Merge branch 'maint-rel-1.7' into develop

Conflicts:
	webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/SpecialBulkUpdatingGraph.java

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

@@ -22,6 +22,7 @@ import org.mindswap.pellet.jena.vocabulary.SWRL;
 
 import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
 import com.hp.hpl.jena.graph.Node;
+import com.hp.hpl.jena.graph.NodeFactory;
 import com.hp.hpl.jena.ontology.DatatypeProperty;
 import com.hp.hpl.jena.ontology.ObjectProperty;
 import com.hp.hpl.jena.ontology.OntClass;
@@ -930,7 +931,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
     		if (vitroURIStr.indexOf(PSEUDO_BNODE_NS)==0) {
     			String idStr = vitroURIStr.split("#")[1];
     			log.debug("Trying to get bnode " + idStr);
-    			RDFNode rdfNode = ontModel.getRDFNode(Node.createAnon(AnonId.create(idStr)));
+    			RDFNode rdfNode = ontModel.getRDFNode(NodeFactory.createAnon(AnonId.create(idStr)));
     			if ( (rdfNode != null) && (rdfNode.canAs(OntClass.class)) ) {
     			    log.debug("found it");
     				cls = rdfNode.as(OntClass.class);
@@ -958,9 +959,9 @@ public class JenaBaseDao extends JenaBaseDaoCon {
 
     protected Node makeNodeForURI(String vitroURIStr) {
     	if (vitroURIStr.indexOf(PSEUDO_BNODE_NS)==0) {
-			return Node.createAnon(AnonId.create(vitroURIStr.split("#")[1]));
+			return NodeFactory.createAnon(AnonId.create(vitroURIStr.split("#")[1]));
     	} else {
-    		return Node.createURI(vitroURIStr);
+    		return NodeFactory.createURI(vitroURIStr);
     	}
     }
     

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

@@ -6,6 +6,7 @@ import java.util.ArrayList;
 import java.util.Iterator;
 
 import com.hp.hpl.jena.graph.Node;
+import com.hp.hpl.jena.graph.NodeFactory;
 import com.hp.hpl.jena.query.Dataset;
 import com.hp.hpl.jena.query.LabelExistsException;
 import com.hp.hpl.jena.query.ReadWrite;
@@ -40,7 +41,7 @@ public class RDFServiceDataset implements Dataset {
 
     @Override
     public boolean containsNamedModel(String arg0) {
-        return g.containsGraph(Node.createURI(arg0));
+        return g.containsGraph(NodeFactory.createURI(arg0));
     }
 
     @Override
@@ -55,7 +56,7 @@ public class RDFServiceDataset implements Dataset {
 
     @Override
     public Model getNamedModel(String arg0) {
-        return RDFServiceGraph.createRDFServiceModel(g.getGraph(Node.createURI(arg0)));
+        return RDFServiceGraph.createRDFServiceModel(g.getGraph(NodeFactory.createURI(arg0)));
     }
 
     @Override
@@ -80,7 +81,7 @@ public class RDFServiceDataset implements Dataset {
 						+ "': model already exists");
 			}
 		}
-		g.addGraph(Node.createURI(uri), model.getGraph());
+		g.addGraph(NodeFactory.createURI(uri), model.getGraph());
 	}
 
 	@Override
@@ -90,7 +91,7 @@ public class RDFServiceDataset implements Dataset {
 
 	@Override
 	public void removeNamedModel(String uri) {
-		g.removeGraph(Node.createURI(uri));
+		g.removeGraph(NodeFactory.createURI(uri));
 	}
 
 	@Override

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

@@ -9,6 +9,7 @@ import java.util.List;
 
 import com.hp.hpl.jena.graph.Graph;
 import com.hp.hpl.jena.graph.Node;
+import com.hp.hpl.jena.graph.NodeFactory;
 import com.hp.hpl.jena.graph.Triple;
 import com.hp.hpl.jena.query.QuerySolution;
 import com.hp.hpl.jena.query.ResultSet;
@@ -193,7 +194,7 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
         List<Node> graphNodeList = new ArrayList<Node>();
         try {
             for (String graphURI : rdfService.getGraphURIs()) {
-                graphNodeList.add(Node.createURI(graphURI));   
+                graphNodeList.add(NodeFactory.createURI(graphURI));   
             }
         } catch (RDFServiceException rdfse) {
             throw new RuntimeException(rdfse);

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

@@ -273,6 +273,7 @@ public class RDFServiceGraph implements GraphWithPerform {
     }
     
     @Override
+    @Deprecated
     public BulkUpdateHandler getBulkUpdateHandler() {
         if (this.bulkUpdateHandler == null) {
             this.bulkUpdateHandler = new RDFServiceGraphBulkUpdater(this);

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

@@ -40,6 +40,7 @@ public class RDFServiceGraphBulkUpdater implements BulkUpdateHandler {
     }
     
     @Override
+    @Deprecated
     public void add(Triple[] arg0) {
         Graph g = GraphFactory.createPlainGraph();
         for (int i = 0 ; i < arg0.length ; i++) {
@@ -49,6 +50,7 @@ public class RDFServiceGraphBulkUpdater implements BulkUpdateHandler {
     }
 
     @Override
+    @Deprecated
     public void add(List<Triple> arg0) {
         Graph g = GraphFactory.createPlainGraph();
         for (Triple t : arg0) {
@@ -58,6 +60,7 @@ public class RDFServiceGraphBulkUpdater implements BulkUpdateHandler {
     }
 
     @Override
+    @Deprecated
     public void add(Iterator<Triple> arg0) {
         Graph g = GraphFactory.createPlainGraph();
         while (arg0.hasNext()) {
@@ -68,11 +71,13 @@ public class RDFServiceGraphBulkUpdater implements BulkUpdateHandler {
     }
 
     @Override
+    @Deprecated
     public void add(Graph arg0) {
         add(arg0, false);
     }
 
     @Override
+    @Deprecated
     public void add(Graph g, boolean arg1) {
         Model[] model = separateStatementsWithBlankNodes(g);
         addModel(model[1] /* nonBlankNodeModel */);
@@ -108,6 +113,7 @@ public class RDFServiceGraphBulkUpdater implements BulkUpdateHandler {
     
 
 	@Override
+    @Deprecated
 	public void delete(Triple[] arg0) {
         Graph g = GraphFactory.createPlainGraph();
         for (int i = 0 ; i < arg0.length ; i++) {
@@ -117,6 +123,7 @@ public class RDFServiceGraphBulkUpdater implements BulkUpdateHandler {
 	}
 
 	@Override
+    @Deprecated
 	public void delete(List<Triple> arg0) {
         Graph g = GraphFactory.createPlainGraph();
         for (Triple t : arg0) {
@@ -126,6 +133,7 @@ public class RDFServiceGraphBulkUpdater implements BulkUpdateHandler {
 	}
 
 	@Override
+    @Deprecated
 	public void delete(Iterator<Triple> arg0) {
         Graph g = GraphFactory.createPlainGraph();
         while (arg0.hasNext()) {
@@ -136,11 +144,13 @@ public class RDFServiceGraphBulkUpdater implements BulkUpdateHandler {
 	}
 
     @Override 
+    @Deprecated
     public void delete(Graph g, boolean withReifications) {
         delete(g);
     }
     
     @Override 
+    @Deprecated
     public void delete(Graph g) {
         deleteModel(ModelFactory.createModelForGraph(g));
     }
@@ -174,6 +184,7 @@ public class RDFServiceGraphBulkUpdater implements BulkUpdateHandler {
     }    
 
     @Override 
+    @Deprecated
     public void removeAll() {
         removeAll(graph, null, null, null);
         notifyRemoveAll(); 
@@ -184,6 +195,7 @@ public class RDFServiceGraphBulkUpdater implements BulkUpdateHandler {
     }
 
     @Override
+    @Deprecated
     public void remove(Node s, Node p, Node o) {
         removeAll(graph, s, p, o);
         manager.notifyEvent(graph, GraphEvents.remove(s, p, o));

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

@@ -310,6 +310,7 @@ public class SparqlGraph implements GraphWithPerform {
     }
     
     @Override
+    @Deprecated
     public BulkUpdateHandler getBulkUpdateHandler() {
         if (this.bulkUpdateHandler == null) {
             this.bulkUpdateHandler = new SparqlGraphBulkUpdater(this);

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

@@ -33,6 +33,7 @@ public class SparqlGraphBulkUpdater extends SimpleBulkUpdateHandler {
     }
     
     @Override
+    @Deprecated
     public void add(Triple[] arg0) {
         Graph g = GraphFactory.createPlainGraph();
         for (int i = 0 ; i < arg0.length ; i++) {
@@ -42,6 +43,7 @@ public class SparqlGraphBulkUpdater extends SimpleBulkUpdateHandler {
     }
 
     @Override
+    @Deprecated
     public void add(List<Triple> arg0) {
         Graph g = GraphFactory.createPlainGraph();
         for (Triple t : arg0) {
@@ -51,6 +53,7 @@ public class SparqlGraphBulkUpdater extends SimpleBulkUpdateHandler {
     }
 
     @Override
+    @Deprecated
     public void add(Iterator<Triple> arg0) {
         Graph g = GraphFactory.createPlainGraph();
         while (arg0.hasNext()) {
@@ -61,11 +64,13 @@ public class SparqlGraphBulkUpdater extends SimpleBulkUpdateHandler {
     }
 
     @Override
+    @Deprecated
     public void add(Graph arg0) {
         add(arg0, false);
     }
 
     @Override
+    @Deprecated
     public void add(Graph g, boolean arg1) {
         log.info("adding graph");
         Model[] model = separateStatementsWithBlankNodes(g);
@@ -102,11 +107,13 @@ public class SparqlGraphBulkUpdater extends SimpleBulkUpdateHandler {
     
 
     @Override 
+    @Deprecated
     public void delete(Graph g, boolean withReifications) {
         delete(g);
     }
     
     @Override 
+    @Deprecated
     public void delete(Graph g) {
         Model[] model = separateStatementsWithBlankNodes(g);
         deleteModel(model[1] /*statements without blank nodes*/);
@@ -189,16 +196,20 @@ public class SparqlGraphBulkUpdater extends SimpleBulkUpdateHandler {
     
 
     @Override 
+    @Deprecated
     public void removeAll() {
         removeAll(graph);
         notifyRemoveAll(); 
     }
 
-    protected void notifyRemoveAll() { 
+    @Override
+    @Deprecated
+	protected void notifyRemoveAll() { 
         manager.notifyEvent(graph, GraphEvents.removeAll);
     }
 
     @Override
+    @Deprecated
     public void remove(Node s, Node p, Node o) {
         removeAll(graph, s, p, o);
         manager.notifyEvent(graph, GraphEvents.remove(s, p, o));

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

@@ -13,6 +13,7 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.graph.Node;
+import com.hp.hpl.jena.graph.NodeFactory;
 import com.hp.hpl.jena.graph.Triple;
 import com.hp.hpl.jena.graph.TripleMatch;
 import com.hp.hpl.jena.graph.impl.GraphWithPerform;
@@ -50,7 +51,7 @@ public class SparqlGraphMultilingual extends SparqlGraph implements GraphWithPer
                 && t.getObject().getLiteral().getDatatypeURI() == null) {
             log.info("adding language tag");
             super.performAdd(Triple.create(t.getSubject(), 
-                    t.getPredicate(), Node.createLiteral(
+                    t.getPredicate(), NodeFactory.createLiteral(
                             t.getObject().getLiteralLexicalForm(), langs.get(0), null)));
         } else {
             log.info("adding original triple " + t);

webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/AbstractModelDecorator.java

@@ -32,7 +32,6 @@ import com.hp.hpl.jena.rdf.model.RSIterator;
 import com.hp.hpl.jena.rdf.model.ReifiedStatement;
 import com.hp.hpl.jena.rdf.model.ResIterator;
 import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.ResourceF;
 import com.hp.hpl.jena.rdf.model.Selector;
 import com.hp.hpl.jena.rdf.model.Seq;
 import com.hp.hpl.jena.rdf.model.Statement;
@@ -40,7 +39,6 @@ import com.hp.hpl.jena.rdf.model.StmtIterator;
 import com.hp.hpl.jena.shared.Command;
 import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.shared.PrefixMapping;
-import com.hp.hpl.jena.shared.ReificationStyle;
 
 /**
  * The base class for a delegating model decorator.
@@ -48,7 +46,6 @@ import com.hp.hpl.jena.shared.ReificationStyle;
  * As implemented, all methods simply delegate to the inner model. Subclasses
  * should override selected methods to provide functionality.
  */
-@SuppressWarnings("deprecation")
 public abstract class AbstractModelDecorator implements Model {
 	private final Model inner;
 
@@ -60,7 +57,8 @@ public abstract class AbstractModelDecorator implements Model {
 	}
 
 	@Override
-	public Resource getResource(String uri, ResourceF f) {
+	@Deprecated
+	public Resource getResource(String uri, com.hp.hpl.jena.rdf.model.ResourceF f) {
 		return inner.getResource(uri, f);
 	}
 
@@ -115,12 +113,14 @@ public abstract class AbstractModelDecorator implements Model {
 	}
 
 	@Override
-	public Resource createResource(ResourceF f) {
+	@Deprecated
+	public Resource createResource(com.hp.hpl.jena.rdf.model.ResourceF f) {
 		return inner.createResource(f);
 	}
 
 	@Override
-	public Resource createResource(String uri, ResourceF f) {
+	@Deprecated
+	public Resource createResource(String uri, com.hp.hpl.jena.rdf.model.ResourceF f) {
 		return inner.createResource(uri, f);
 	}
 
@@ -422,6 +422,7 @@ public abstract class AbstractModelDecorator implements Model {
 	}
 
 	@Override
+	@Deprecated
 	public Model addLiteral(Resource s, Property p, Object o) {
 		return inner.addLiteral(s, p, o);
 	}
@@ -467,6 +468,7 @@ public abstract class AbstractModelDecorator implements Model {
 	}
 
 	@Override
+	@Deprecated
 	public Model remove(Model m, boolean suppressReifications) {
 		return m.remove(m, suppressReifications);
 	}
@@ -739,6 +741,7 @@ public abstract class AbstractModelDecorator implements Model {
 	}
 
 	@Override
+	@Deprecated
 	public Model add(Model m, boolean suppressReifications) {
 		return m.add(m, suppressReifications);
 	}
@@ -954,7 +957,8 @@ public abstract class AbstractModelDecorator implements Model {
 	}
 
 	@Override
-	public ReificationStyle getReificationStyle() {
+	@Deprecated
+	public com.hp.hpl.jena.shared.ReificationStyle getReificationStyle() {
 		return inner.getReificationStyle();
 	}
 

webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/AbstractOntModelDecorator.java

@@ -67,7 +67,6 @@ import com.hp.hpl.jena.rdf.model.RSIterator;
 import com.hp.hpl.jena.rdf.model.ReifiedStatement;
 import com.hp.hpl.jena.rdf.model.ResIterator;
 import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.ResourceF;
 import com.hp.hpl.jena.rdf.model.Selector;
 import com.hp.hpl.jena.rdf.model.Seq;
 import com.hp.hpl.jena.rdf.model.Statement;
@@ -78,7 +77,6 @@ import com.hp.hpl.jena.reasoner.ValidityReport;
 import com.hp.hpl.jena.shared.Command;
 import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.shared.PrefixMapping;
-import com.hp.hpl.jena.shared.ReificationStyle;
 import com.hp.hpl.jena.util.iterator.ExtendedIterator;
 
 /**
@@ -87,7 +85,6 @@ import com.hp.hpl.jena.util.iterator.ExtendedIterator;
  * As implemented, all methods simply delegate to the inner model. Subclasses
  * should override selected methods to provide functionality.
  */
-@SuppressWarnings("deprecation")
 public abstract class AbstractOntModelDecorator implements OntModel {
 	private final OntModel inner;
 
@@ -99,7 +96,8 @@ public abstract class AbstractOntModelDecorator implements OntModel {
 	}
 
 	@Override
-	public Resource getResource(String uri, ResourceF f) {
+	@Deprecated
+	public Resource getResource(String uri, com.hp.hpl.jena.rdf.model.ResourceF f) {
 		return inner.getResource(uri, f);
 	}
 
@@ -154,12 +152,14 @@ public abstract class AbstractOntModelDecorator implements OntModel {
 	}
 
 	@Override
-	public Resource createResource(ResourceF f) {
+	@Deprecated
+	public Resource createResource(com.hp.hpl.jena.rdf.model.ResourceF f) {
 		return inner.createResource(f);
 	}
 
 	@Override
-	public Resource createResource(String uri, ResourceF f) {
+	@Deprecated
+	public Resource createResource(String uri, com.hp.hpl.jena.rdf.model.ResourceF f) {
 		return inner.createResource(uri, f);
 	}
 
@@ -461,6 +461,7 @@ public abstract class AbstractOntModelDecorator implements OntModel {
 	}
 
 	@Override
+	@Deprecated
 	public Model addLiteral(Resource s, Property p, Object o) {
 		return inner.addLiteral(s, p, o);
 	}
@@ -506,6 +507,7 @@ public abstract class AbstractOntModelDecorator implements OntModel {
 	}
 
 	@Override
+	@Deprecated
 	public Model remove(Model m, boolean suppressReifications) {
 		return m.remove(m, suppressReifications);
 	}
@@ -778,6 +780,7 @@ public abstract class AbstractOntModelDecorator implements OntModel {
 	}
 
 	@Override
+	@Deprecated
 	public Model add(Model m, boolean suppressReifications) {
 		return m.add(m, suppressReifications);
 	}
@@ -993,7 +996,8 @@ public abstract class AbstractOntModelDecorator implements OntModel {
 	}
 
 	@Override
-	public ReificationStyle getReificationStyle() {
+	@Deprecated
+	public com.hp.hpl.jena.shared.ReificationStyle getReificationStyle() {
 		return inner.getReificationStyle();
 	}
 
@@ -1630,6 +1634,7 @@ public abstract class AbstractOntModelDecorator implements OntModel {
 	}
 
 	@Override
+	@Deprecated
 	public ModelMaker getModelMaker() {
 		return inner.getModelMaker();
 	}
@@ -1645,6 +1650,7 @@ public abstract class AbstractOntModelDecorator implements OntModel {
 	}
 
 	@Override
+	@Deprecated
 	public ExtendedIterator<OntModel> listImportedModels() {
 		return inner.listImportedModels();
 	}

webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/RDFServiceImpl.java

@@ -13,6 +13,7 @@ import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.graph.Graph;
 import com.hp.hpl.jena.graph.Node;
+import com.hp.hpl.jena.graph.NodeFactory;
 import com.hp.hpl.jena.graph.Triple;
 import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryFactory;
@@ -69,7 +70,7 @@ public abstract class RDFServiceImpl implements RDFService {
        if (sparqlAskQuery(containsQuery.toString())) {
             throw new RDFServiceException("individual already exists");
        } else {
-            Triple triple = new Triple(Node.createURI(individualURI), RDF.type.asNode(), Node.createURI(individualTypeURI));
+            Triple triple = new Triple(NodeFactory.createURI(individualURI), RDF.type.asNode(), NodeFactory.createURI(individualTypeURI));
             //addTriple(triple, graphURI);
             ChangeSet cs = this.manufactureChangeSet();
             cs.addAddition(new ByteArrayInputStream(

webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/ListeningGraph.java

@@ -119,6 +119,7 @@ public class ListeningGraph implements GraphWithPerform {
 	}
 
     @Override
+    @Deprecated
     public BulkUpdateHandler getBulkUpdateHandler() {
         if (this.bulkUpdateHandler == null) {
             this.bulkUpdateHandler = new SimpleBulkUpdateHandler(this);

webapp/src/edu/cornell/mannlib/vitro/webapp/searchengine/solr/SolrConversionUtils.java

@@ -92,6 +92,7 @@ public class SolrConversionUtils {
 	 * Convert from a SearchQuery to a SolrQuery, so the Solr server may execute
 	 * it.
 	 */
+	@SuppressWarnings("deprecation")
 	static SolrQuery convertToSolrQuery(SearchQuery query) {
 		SolrQuery solrQuery = new SolrQuery(query.getQuery());
 		solrQuery.setStart(query.getStart());