work on triple store independence including NIHVIVO-3751 NIHVIVO-3644 NIHVIVO-3743 and NIHVIVO-3745

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/Classes2ClassesOperationController.java

@@ -57,7 +57,7 @@ public class Classes2ClassesOperationController extends BaseEditController {
             return;
         }
 
-        VClassDao vcDao = request.getFullWebappDaoFactory().getVClassDao();
+        VClassDao vcDao = request.getAssertionsWebappDaoFactory().getVClassDao();
         
         String modeStr = request.getParameter("opMode");
         modeStr = (modeStr == null) ? "" : modeStr;

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/RestrictionOperationController.java

@@ -15,9 +15,12 @@ import com.hp.hpl.jena.datatypes.RDFDatatype;
 import com.hp.hpl.jena.datatypes.TypeMapper;
 import com.hp.hpl.jena.ontology.OntClass;
 import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.ontology.OntProperty;
 import com.hp.hpl.jena.ontology.Restriction;
 import com.hp.hpl.jena.rdf.model.Literal;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.shared.Lock;
 
@@ -59,16 +62,50 @@ public class RestrictionOperationController extends BaseEditController {
                 return;
             } 
                 
-            // TODO: I need to de-spaghettify this and remap this controller, now that I know what I'm doing 
-                
             if ( (request.getParameter("_cancel") == null ) ) {
+                processRestriction(request, epo, ontModel);   
+            }
                         
+            //if no page forwarder was set, just go back to referring page:
+            String referer = epo.getReferer();
+            if (referer == null) {
+                response.sendRedirect(defaultLandingPage);
+            } else {
+                response.sendRedirect(referer);
+            }
+		    
+	    } catch (Exception e) {
+	    	log.error(e, e);
+	    	try {
+	    		response.sendRedirect(defaultLandingPage);
+	    		return;
+	    	} catch (Exception f) {
+                log.error(f, f);
+                throw new RuntimeException(f);
+	    	}
+	    }
+	}
+	
+	private void processRestriction(VitroRequest request, EditProcessObject epo, OntModel ontModel) {
         ontModel.enterCriticalSection(Lock.WRITE);
         try {
             
             ontModel.getBaseModel().notifyEvent(new EditEvent(request.getFullWebappDaoFactory().getUserURI(),true));
             
-	            	if ( request.getParameter("_action") != null && request.getParameter("_action").equals("delete") ) {
+            if ("delete".equals(request.getParameter("_action"))) {
+                processDelete(request, ontModel);   
+            }  else {
+                processCreate(request, epo, ontModel);            
+            }
+            
+        } finally {
+            ontModel.getBaseModel().notifyEvent(new EditEvent(request.getFullWebappDaoFactory().getUserURI(),false));
+            ontModel.leaveCriticalSection();
+        }
+    
+    }
+
+    private void processDelete(VitroRequest request, OntModel ontModel) {
         
         String restId = request.getParameter("restrictionId");
         
@@ -94,13 +131,25 @@ public class RestrictionOperationController extends BaseEditController {
                 }   
             }
             
+            /**
+             * removing by graph subtraction so that statements with blank nodes
+             * stick together and are processed appropriately by the bulk update
+             * handler
+             */
             if ( rest != null ) {
-	            				rest.remove();
+                Model temp = ModelFactory.createDefaultModel();
+                temp.add(rest.listProperties());
+                ontModel.getBaseModel().remove(temp);                
             }
             
         }
+    }
     
-	            	} else {
+    private void processCreate(VitroRequest request, EditProcessObject epo, OntModel origModel) {
+        
+        Model temp = ModelFactory.createDefaultModel();
+        Model dynamicUnion = ModelFactory.createUnion(temp, origModel);
+        OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, dynamicUnion);
         
         OntProperty onProperty = ontModel.getOntProperty( (String) request.getParameter("onProperty") );
         
@@ -171,33 +220,7 @@ public class RestrictionOperationController extends BaseEditController {
             ontClass.addEquivalentClass(rest);
         }
         
-	            	}
+        origModel.add(temp);
-	            	
-	            } finally {
-	            	ontModel.getBaseModel().notifyEvent(new EditEvent(request.getFullWebappDaoFactory().getUserURI(),false));
-	            	ontModel.leaveCriticalSection();
-	            }
-            
-            }
-            
-            //if no page forwarder was set, just go back to referring page:
-            String referer = epo.getReferer();
-            if (referer == null) {
-                response.sendRedirect(defaultLandingPage);
-            } else {
-                response.sendRedirect(referer);
-            }
-		    
-	    } catch (Exception e) {
-	    	log.error(e, e);
-	    	try {
-	    		response.sendRedirect(defaultLandingPage);
-	    		return;
-	    	} catch (Exception f) {
-                log.error(f, f);
-                throw new RuntimeException(f);
-	    	}
-	    }
         
     }
     

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualResponseBuilder.java

@@ -176,7 +176,7 @@ class IndividualResponseBuilder {
     
 	private IndividualTemplateModel getIndividualTemplateModel(
 			Individual individual) {
-		individual.sortForDisplay();
+		//individual.sortForDisplay();
 		return new IndividualTemplateModel(individual, vreq);
 	}
 		

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

@@ -671,7 +671,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
     static {
         List<String> namespaceFilters = new ArrayList<String>();
         for (String namespace : EXCLUDED_NAMESPACES) {
-            namespaceFilters.add("( afn:namespace(?property) != \"" + namespace + "\" )");
+            namespaceFilters.add("( !regex(str(?property), \"^" + namespace + "\" ))");
         }
         PROPERTY_FILTERS = StringUtils.join(namespaceFilters, " && ");
     } 
@@ -683,11 +683,11 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
         "   ?property a owl:DatatypeProperty . \n" +
         "   FILTER ( \n" +
         "       isLiteral(?object) && \n" +
-        "       ( afn:namespace(?property) != \"" + VitroVocabulary.PUBLIC + "\" ) && \n" +
+        "       ( !regex(str(?property), \"^" + VitroVocabulary.PUBLIC + "\" )) && \n" +
-        "       ( afn:namespace(?property) != \"" + VitroVocabulary.OWL + "\" ) && \n" + 
+        "       ( !regex(str(?property), \"^" + VitroVocabulary.OWL + "\" )) && \n" + 
         // NIHVIVO-2790 vitro:moniker has been deprecated, but display existing values for editorial management (deletion is encouraged).
         // This property will be hidden from public display by default.
-        "       ( ?property = <" + VitroVocabulary.MONIKER + "> || afn:namespace(?property) != \"" + VitroVocabulary.vitroURI + "\" ) \n" +           
+        "       ( ?property = <" + VitroVocabulary.MONIKER + "> || !regex(str(?property), \"^" + VitroVocabulary.vitroURI + "\" )) \n" +           
         "   ) \n" +
         "}";
     

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

@@ -785,12 +785,12 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
     static {
         List<String> namespaceFilters = new ArrayList<String>();
         for (String namespace : EXCLUDED_NAMESPACES) {
-            namespaceFilters.add("( afn:namespace(?property) != \"" + namespace + "\" )");
+            namespaceFilters.add("( !regex(str(?property), \"^" + namespace + "\" ))");
         }
         // A hack to include the vitro:primaryLink and vitro:additionalLink properties in the list
         namespaceFilters.add("( ?property = vitro:primaryLink ||" +
                                "?property = vitro:additionalLink ||" +
-                               "afn:namespace(?property) != \"http://vitro.mannlib.cornell.edu/ns/vitro/0.7#\" )");
+                               "!regex(str(?property), \"^http://vitro.mannlib.cornell.edu/ns/vitro/0.7#\" ))");
         PROPERTY_FILTERS = StringUtils.join(namespaceFilters, " && ");
     }
     

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

@@ -1,59 +1,62 @@
 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 String endpointURI;
+    private SparqlDatasetGraph g;
     
-    public SparqlDataset(String endpointURI) {
+    public SparqlDataset(SparqlDatasetGraph g) {
-        this.endpointURI = endpointURI;
+        this.g = g;
     }
     
     @Override
     public DatasetGraph asDatasetGraph() {
-        // TODO Auto-generated method stub
+        return g;
-        return null;
     }
 
     @Override
     public void close() {
-        // TODO Auto-generated method stub
+        g.close();
-
     }
 
     @Override
     public boolean containsNamedModel(String arg0) {
-        return true;
+        return g.containsGraph(Node.createURI(arg0));
     }
 
     @Override
     public Model getDefaultModel() {
-        // TODO Auto-generated method stub
+        return ModelFactory.createModelForGraph(g.getDefaultGraph());
-        return null;
     }
 
     @Override
     public Lock getLock() {
-        // TODO Auto-generated method stub
+        return g.getLock();
-        return null;
     }
 
     @Override
     public Model getNamedModel(String arg0) {
-        // TODO Auto-generated method stub
+        return ModelFactory.createModelForGraph(g.getGraph(Node.createURI(arg0)));
-        return null;
     }
 
     @Override
     public Iterator<String> listNames() {
-        // TODO Auto-generated method stub
+        ArrayList<String> nameList = new ArrayList<String>();
-        return null;
+        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/SparqlGraph.java

@@ -131,7 +131,11 @@ public class SparqlGraph implements GraphWithPerform {
                 + sparqlNodeUpdate(t.getObject(), "") + " } " 
                 + ((graphURI != null) ? " } " : "");
         
-        //log.info(updateString);
+        
+        if (graphURI != null) {
+            log.info("=====> update to graph " + graphURI);
+        }
+        log.info(updateString);
         
         executeUpdate(updateString);
                 
@@ -195,7 +199,6 @@ public class SparqlGraph implements GraphWithPerform {
 
     @Override
     public void delete(Triple arg0) throws DeleteDeniedException {
-        //log.info("********************** DELETE!!!!!! ************************");
         performDelete(arg0);
     }
 
@@ -228,7 +231,7 @@ public class SparqlGraph implements GraphWithPerform {
                 literalBuff.append("^^<").append(node.getLiteralDatatypeURI()).append(">");
             } else if (node.getLiteralLanguage() != null && node.getLiteralLanguage() != "") {
                 literalBuff.append("@").append(node.getLiteralLanguage());
-;            }
+            }
             return literalBuff.toString();
         } else {
             return varName;
@@ -243,6 +246,14 @@ public class SparqlGraph implements GraphWithPerform {
         }
     }
     
+    public static String sparqlNodeDelete(Node node, String varName) {
+        if (node.isBlank()) {
+            return "?" + node.getBlankNodeLabel().replaceAll("\\W", "");
+        } else {
+            return sparqlNode(node, varName);
+        }
+    }
+    
     @Override
     public ExtendedIterator<Triple> find(Node subject, Node predicate, Node object) {
         if (!isVar(subject) && !isVar(predicate)  && !isVar(object)) {
@@ -265,7 +276,16 @@ public class SparqlGraph implements GraphWithPerform {
             findQuery.append("  } ");
         }
         findQuery.append("\n}");
-        ResultSet rs = execSelect(findQuery.toString());
+        
+        String queryString = findQuery.toString();
+        //log.info(queryString);
+        
+//        //TODO remove me
+//        if (queryString.contains("individual/AI") && queryString.contains("label")) {
+//            throw new RuntimeException("break!");
+//        }
+        
+        ResultSet rs = execSelect(queryString);
         //rs = execSelect(findQuery.toString());
         //rs = execSelect(findQuery.toString());
         

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

@@ -65,6 +65,21 @@ public class SparqlGraphBulkUpdater extends SimpleBulkUpdateHandler {
 
     @Override
     public void add(Graph g, boolean arg1) {
+        log.info("adding graph");
+        Model[] model = separateStatementsWithBlankNodes(g);
+        addModel(model[1] /* nonBlankNodeModel */);
+        // replace following call with different method
+        addModel(model[0] /*blankNodeModel*/);
+    }
+    
+    /**
+     * Returns a pair of models.  The first contains any statement containing at 
+     * least one blank node.  The second contains all remaining statements.
+     * @param g
+     * @return
+     */
+    
+    private Model[] separateStatementsWithBlankNodes(Graph g) {
         Model gm = ModelFactory.createModelForGraph(g);
         Model blankNodeModel = ModelFactory.createDefaultModel();
         Model nonBlankNodeModel = ModelFactory.createDefaultModel();
@@ -77,12 +92,68 @@ public class SparqlGraphBulkUpdater extends SimpleBulkUpdateHandler {
                 blankNodeModel.add(stmt);
             }
         }
-        addModel(nonBlankNodeModel);
+        Model[] result = new Model[2];
-        // replace following call with different method
+        result[0] = blankNodeModel;
-        addModel(blankNodeModel);
+        result[1] = nonBlankNodeModel;
+        return result;
+    }
+    
+
+    @Override 
+    public void delete(Graph g, boolean withReifications) {
+        delete(g);
+    }
+    
+    @Override 
+    public void delete(Graph g) {
+        Model[] model = separateStatementsWithBlankNodes(g);
+        deleteModel(model[1] /*statements without blank nodes*/);
+        // replace blank nodes in remaining statements with variables
+        
+        StringBuffer patternBuff = new StringBuffer();
+        Iterator<Triple> tripIt = g.find(null, null, null);
+        while(tripIt.hasNext()) {
+            Triple t = tripIt.next();
+            patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getSubject(), null));
+            patternBuff.append(" ");
+            patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getPredicate(), null));
+            patternBuff.append(" ");
+            patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getObject(), null));
+            patternBuff.append(" .\n");
+        }
+        
+        StringBuffer queryBuff = new StringBuffer();
+        String graphURI = graph.getGraphURI();
+        queryBuff.append("DELETE { " + ((graphURI != null) ? "GRAPH <" + graphURI + "> { " : "" ) + " \n");
+        queryBuff.append(patternBuff);
+        if (graphURI != null) {
+            queryBuff.append("    } \n");
+        }
+        queryBuff.append("} WHERE { \n");
+        if (graphURI != null) {
+            queryBuff.append("    GRAPH <" + graphURI + "> { \n");
+        }
+        queryBuff.append(patternBuff);
+        if (graphURI != null) {
+            queryBuff.append("    } \n");
+        }
+        queryBuff.append("} \n");
+        
+        log.debug(queryBuff.toString());
+        
+        graph.executeUpdate(queryBuff.toString());
+        
     }
     
     public void addModel(Model model) {
+        verbModel(model, "INSERT");
+    }
+    
+    public void deleteModel(Model model) {
+        verbModel(model, "DELETE");
+    }
+    
+    private void verbModel(Model model, String verb) {
         Model m = ModelFactory.createDefaultModel();
         int testLimit = 1000;
         StmtIterator stmtIt = model.listStatements();
@@ -96,7 +167,7 @@ public class SparqlGraphBulkUpdater extends SimpleBulkUpdateHandler {
                     m.write(sw, "N-TRIPLE");
                     StringBuffer updateStringBuff = new StringBuffer();
                     String graphURI = graph.getGraphURI();
-                    updateStringBuff.append("INSERT DATA { " + ((graphURI != null) ? "GRAPH <" + graphURI + "> { " : "" ));
+                    updateStringBuff.append(verb + " DATA { " + ((graphURI != null) ? "GRAPH <" + graphURI + "> { " : "" ));
                     updateStringBuff.append(sw);
                     updateStringBuff.append(((graphURI != null) ? " } " : "") + " }");
                     
@@ -133,10 +204,6 @@ public class SparqlGraphBulkUpdater extends SimpleBulkUpdateHandler {
 
     public static void removeAll(Graph g, Node s, Node p, Node o)
     {        
-        // OK, so the strategy here should be to remove all triples without blank nodes first
-        // Then, feel the entire remaining part of the graph as a DELETE WHERE 
-        // with the blank nodes as variables?
-        
         ExtendedIterator<Triple> it = g.find( s, p, o );
         try { 
             while (it.hasNext()) {

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

@@ -38,6 +38,7 @@ import com.hp.hpl.jena.query.ResultSet;
 import com.hp.hpl.jena.query.Syntax;
 import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.rdf.model.ResourceFactory;
@@ -620,9 +621,13 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
                 supURIs.add(getClassURIStr(cls));
             }
         } catch (Exception e) {
-            //TODO make this attempt respect the direct argument
+            log.debug(e,e);
-            // we'll try this again using a different method that doesn't try to convert to OntClass
+            // we'll try this again using a different method 
-            List<Resource> supList = this.listDirectObjectPropertyValues(getOntModel().getResource(classURI), RDFS.subClassOf);
+            // that doesn't try to convert to OntClass
+            supURIs.clear();
+            List<Resource> supList = (direct) 
+                    ? listDirectObjectPropertyValues(subClass, RDFS.subClassOf)
+                    : listObjectPropertyValues(subClass, RDFS.subClassOf);
             for (Resource res : supList) {
                 supURIs.add(getClassURIStr(res));
             }
@@ -630,6 +635,18 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
         return supURIs;
     }
 
+    private List<Resource> listObjectPropertyValues(Resource res, Property prop) {
+        List<Resource> values = new ArrayList<Resource>();
+        StmtIterator stmtIt = res.listProperties(prop);
+        while (stmtIt.hasNext()) {
+            Statement s = stmtIt.nextStatement();
+            if (s.getObject().isResource()) {
+                values.add(s.getObject().asResource());
+            }
+        }
+        return values;
+    }
+    
     public VClass getTopConcept() {
         VClass top = new VClass();
         if (getOntModel().getProfile().NAMESPACE().equals(RDFS.getURI())) {

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

@@ -28,9 +28,7 @@ import org.apache.commons.logging.LogFactory;
 import com.hp.hpl.jena.graph.Graph;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
-import com.hp.hpl.jena.query.DataSource;
 import com.hp.hpl.jena.query.Dataset;
-import com.hp.hpl.jena.query.DatasetFactory;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.sdb.SDBFactory;
@@ -43,10 +41,9 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
-import edu.cornell.mannlib.vitro.webapp.dao.jena.SingleContentOntModelSelector;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlDataset;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlDatasetGraph;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraphMultilingual;
-import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactoryJena;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
 import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 
@@ -198,7 +195,7 @@ public class WebappDaoFactorySDBPrep implements Filter {
         OntModel om = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, m);
         //oms = new SingleContentOntModelSelector(om, oms.getDisplayModel(), oms.getUserAccountsModel());
                         
-        Dataset dataset = DatasetFactory.create(new SparqlDatasetGraph(endpointURI));
+        Dataset dataset = new SparqlDataset(new SparqlDatasetGraph(endpointURI));
         
         //DataSource datasource = DatasetFactory.create();
         //datasource.addNamedModel("fake:fake", m);

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetupSparql2.java

@@ -19,7 +19,6 @@ import com.hp.hpl.jena.graph.Graph;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.query.Dataset;
-import com.hp.hpl.jena.query.DatasetFactory;
 import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
@@ -32,7 +31,6 @@ import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
-import com.hp.hpl.jena.sdb.SDB;
 import com.hp.hpl.jena.sdb.SDBFactory;
 import com.hp.hpl.jena.sdb.Store;
 import com.hp.hpl.jena.sdb.StoreDesc;
@@ -54,6 +52,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelectorImpl;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlDataset;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlDatasetGraph;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraph;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
@@ -129,7 +128,7 @@ public class JenaDataSourceSetupSparql2 extends JenaDataSourceSetupBase
                 ctx).getProperty("VitroConnection.DataSource.endpointURI");
         
         Graph g = new SparqlGraph(endpointURI);
-        Dataset dataset = DatasetFactory.create(new SparqlDatasetGraph(endpointURI));
+        Dataset dataset = new SparqlDataset(new SparqlDatasetGraph(endpointURI));
         setStartupDataset(dataset, ctx);
         
 //        setStartupDataset(SDBFactory.connectDataset(store), ctx);
@@ -191,6 +190,7 @@ public class JenaDataSourceSetupSparql2 extends JenaDataSourceSetupBase
 
             tboxAssertions.getBaseModel().register(new ModelSynchronizer(
                     tboxAssertionsDB));
+                        
             baseOms.setTBoxModel(tboxAssertions);
         } catch (Throwable e) {
             log.error("Unable to load tbox assertion cache from DB", e);