5x speedup for add RDF via GUI; 25x speedup for SPARQL API writes. sameAs still needs fixing; will flunk tests.

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/api/SparqlUpdateApiController.java

@@ -19,6 +19,7 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.query.ReadWrite;
 import com.hp.hpl.jena.update.GraphStore;
 import com.hp.hpl.jena.update.GraphStoreFactory;
 import com.hp.hpl.jena.update.UpdateAction;
@@ -96,17 +97,26 @@ public class SparqlUpdateApiController extends VitroApiServlet {
 	}
 
 	private void executeUpdate(HttpServletRequest req, UpdateRequest parsed) {
-		ServletContext ctx = req.getSession().getServletContext();
 		VitroRequest vreq = new VitroRequest(req);
-
 		SearchIndexer indexer = ApplicationUtils.instance().getSearchIndexer();
-		indexer.pause();
+		Dataset ds = new RDFServiceDataset(vreq.getUnfilteredRDFService());
-		try {
+		GraphStore graphStore = GraphStoreFactory.create(ds);
-			Dataset ds = new RDFServiceDataset(vreq.getUnfilteredRDFService());
+	    try {
-			GraphStore graphStore = GraphStoreFactory.create(ds);
+	        if(indexer != null) {
+	            indexer.pause();
+	        }
+	        if(ds.supportsTransactions()) {
+			    ds.begin(ReadWrite.WRITE);
+	        }
 			UpdateAction.execute(parsed, graphStore);
 		} finally {
-			indexer.unpause();
+		    if(ds.supportsTransactions()) {
+                ds.commit();
+                ds.end();
+		    }
+			if(indexer != null) {
+			    indexer.unpause();
+			}
 		}
 	}
 

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

@@ -12,11 +12,14 @@ import org.apache.commons.logging.LogFactory;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelChangedListener;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
+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.shared.Lock;
+import com.hp.hpl.jena.vocabulary.OWL;
+import com.hp.hpl.jena.vocabulary.RDF;
 
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
-import edu.cornell.mannlib.vitro.webapp.servlet.setup.SimpleReasonerSetup;
 
 /**
  * A ChangeListener that forwards events to a Jena ModelChangedListener 
@@ -34,8 +37,10 @@ public class JenaChangeListener implements ChangeListener {
     
     public JenaChangeListener(ModelChangedListener listener) {
         this.listener = listener;
-        ignoredGraphs.add(SimpleReasonerSetup.JENA_INF_MODEL_REBUILD);
+        m.register(listener);
-        ignoredGraphs.add(SimpleReasonerSetup.JENA_INF_MODEL_SCRATCHPAD);
+        // these graphs no longer used
+//        ignoredGraphs.add(SimpleReasonerSetup.JENA_INF_MODEL_REBUILD);
+//        ignoredGraphs.add(SimpleReasonerSetup.JENA_INF_MODEL_SCRATCHPAD);
     }
     
     @Override
@@ -65,9 +70,11 @@ public class JenaChangeListener implements ChangeListener {
     // TODO avoid overhead of Model
     private Statement parseTriple(String serializedTriple) {
         try {
-            Model m = ModelFactory.createDefaultModel();
+            m.enterCriticalSection(Lock.WRITE);
+            m.removeAll();
+            // Model m = ModelFactory.createDefaultModel();
             m.read(new ByteArrayInputStream(
-                    serializedTriple.getBytes("UTF-8")), null, "N3");
+                    serializedTriple.getBytes("UTF-8")), null, "N-TRIPLE");
             StmtIterator sit = m.listStatements();
             if (!sit.hasNext()) {
                 throw new RuntimeException("no triple parsed from change event");
@@ -83,6 +90,8 @@ public class JenaChangeListener implements ChangeListener {
             throw riot;
         } catch (UnsupportedEncodingException uee) {
             throw new RuntimeException(uee);
+        } finally {
+            m.leaveCriticalSection();
         }
     }
 

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

@@ -5,8 +5,13 @@ package edu.cornell.mannlib.vitro.webapp.dao.jena;
 import java.util.ArrayList;
 import java.util.Iterator;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import com.hp.hpl.jena.graph.Graph;
 import com.hp.hpl.jena.graph.Node;
 import com.hp.hpl.jena.graph.NodeFactory;
+import com.hp.hpl.jena.graph.TransactionHandler;
 import com.hp.hpl.jena.query.Dataset;
 import com.hp.hpl.jena.query.LabelExistsException;
 import com.hp.hpl.jena.query.ReadWrite;
@@ -21,6 +26,7 @@ import edu.cornell.mannlib.vitro.webapp.utils.logging.ToString;
 public class RDFServiceDataset implements Dataset {
 
     private RDFServiceDatasetGraph g;
+    private ReadWrite transactionMode;
     
     public RDFServiceDataset(RDFServiceDatasetGraph g) {
         this.g = g;
@@ -55,9 +61,13 @@ public class RDFServiceDataset implements Dataset {
         return g.getLock();
     }
 
+    private final static Log log = LogFactory.getLog(RDFServiceDataset.class);
+    
     @Override
     public Model getNamedModel(String arg0) {
-        return RDFServiceGraph.createRDFServiceModel(g.getGraph(NodeFactory.createURI(arg0)));
+        Model model = RDFServiceGraph.createRDFServiceModel(
+                g.getGraph(NodeFactory.createURI(arg0)));
+        return model;
     }
 
     @Override
@@ -108,36 +118,60 @@ public class RDFServiceDataset implements Dataset {
 
 	@Override
 	public boolean supportsTransactions() {
-		return false;
+		if (g.getDefaultGraph().getTransactionHandler() == null) {
+		    return false;
+		} else {
+		    return g.getDefaultGraph().getTransactionHandler().transactionsSupported();
+		}
 	}
 
 	@Override
 	public boolean isInTransaction() {
-		return false;
+		return (transactionMode != null);
 	}
 	
+    private boolean supportsTransactions(Graph graph) {
+        return (graph.getTransactionHandler() != null 
+                && graph.getTransactionHandler().transactionsSupported());
+    }
+
 	@Override
 	public void begin(ReadWrite arg0) {
-		throw new UnsupportedOperationException(this.getClass().getSimpleName()
+	    this.transactionMode = arg0;
-				+ " does not support transactions.");
+	    g.begin(arg0);
+	    for(String graphURI : g.getGraphCache().keySet()) {
+            Graph graph = g.getGraphCache().get(graphURI);
+            if (supportsTransactions(graph)) {
+                graph.getTransactionHandler().begin();
+            }
+        }
 	}
 
 	@Override
 	public void commit() {
-		throw new UnsupportedOperationException(this.getClass().getSimpleName()
+	    for(String graphURI : g.getGraphCache().keySet()) {
-				+ " does not support transactions.");
+            Graph graph = g.getGraphCache().get(graphURI);
+            if(supportsTransactions(graph)) {
+                graph.getTransactionHandler().commit();
+            }
+        }
 	}
 
 	@Override
 	public void abort() {
-		throw new UnsupportedOperationException(this.getClass().getSimpleName()
+	    for(String graphURI : g.getGraphCache().keySet()) {
-				+ " does not support transactions.");
+            Graph graph = g.getGraphCache().get(graphURI);
+            if(supportsTransactions(graph)) {
+                graph.getTransactionHandler().abort();
+            }
+        }
 	}
 
 	@Override
 	public void end() {
-		throw new UnsupportedOperationException(this.getClass().getSimpleName()
+	    // the Graph tranaction handlers don't seem to support .end()
-				+ " does not support transactions.");
+	    this.transactionMode = null;
+	    g.end();
 	}
 
 	@Override

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

@@ -6,18 +6,19 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
+import java.util.concurrent.ConcurrentHashMap;
 
 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;
+import com.hp.hpl.jena.query.ReadWrite;
 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.JSONInput;
 import com.hp.hpl.jena.sparql.util.Context;
 import com.hp.hpl.jena.util.iterator.SingletonIterator;
 import com.hp.hpl.jena.util.iterator.WrappedIterator;
@@ -32,11 +33,25 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
     private RDFService rdfService;
     private Lock lock = new LockMRSW();
     private Context context = new Context() ;
+    private Map<String, RDFServiceGraph> graphCache = new ConcurrentHashMap<String, RDFServiceGraph>();
+    private ReadWrite transactionMode;
     
     public RDFServiceDatasetGraph(RDFService rdfService) {
         this.rdfService = rdfService;
     }
 
+    public Map<String, RDFServiceGraph> getGraphCache() {
+        return graphCache;
+    }
+    
+    public void begin(ReadWrite mode) {
+        this.transactionMode = mode;
+    }
+    
+    public void end() {
+        this.transactionMode = null;
+    }
+    
     private Graph getGraphFor(Quad q) {
         return getGraphFor(q.getGraph());
     }
@@ -44,7 +59,7 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
     private Graph getGraphFor(Node g) {
         return (g == Node.ANY) 
                 ? new RDFServiceGraph(rdfService) 
-                : new RDFServiceGraph(rdfService, g.getURI());
+                : getGraph(g);
     }
     
     @Override
@@ -175,7 +190,22 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
     
     @Override
     public RDFServiceGraph getGraph(Node arg0) {
-        return new RDFServiceGraph(rdfService, arg0.getURI());
+        String graphURI = arg0.getURI();
+        if(graphCache.containsKey(graphURI)) {
+            return graphCache.get(graphURI);
+        } else {
+            RDFServiceGraph graph = new RDFServiceGraph(rdfService, arg0.getURI());
+            graphCache.put(graphURI, graph);
+            if(transactionMode != null && supportsTransactions(graph)) {
+                graph.getTransactionHandler().begin();
+            }
+            return graph;
+        }
+    }
+    
+    private boolean supportsTransactions(Graph graph) {
+        return (graph.getTransactionHandler() != null 
+                && graph.getTransactionHandler().transactionsSupported());
     }
 
     @Override
@@ -205,13 +235,11 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
     @Override
     public void removeGraph(Node arg0) {
         // TODO Auto-generated method stub
-
     }
 
     @Override
     public void setDefaultGraph(Graph arg0) {
         // TODO Auto-generated method stub
-
     }
 
     @Override
@@ -229,4 +257,5 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
 		return "RDFServiceDatasetGraph[" + ToString.hashHex(this)
 				+ ", " + rdfService + "]";
 	}
+	
 }

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

@@ -6,8 +6,9 @@ import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.Queue;
+import java.util.concurrent.ConcurrentLinkedQueue;
 
-import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -23,14 +24,13 @@ import com.hp.hpl.jena.graph.TripleMatch;
 import com.hp.hpl.jena.graph.impl.GraphWithPerform;
 import com.hp.hpl.jena.graph.impl.SimpleEventManager;
 import com.hp.hpl.jena.query.QuerySolution;
-import com.hp.hpl.jena.query.ResultSet;
 import com.hp.hpl.jena.rdf.listeners.StatementListener;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.shared.AddDeniedException;
+import com.hp.hpl.jena.shared.Command;
 import com.hp.hpl.jena.shared.DeleteDeniedException;
 import com.hp.hpl.jena.shared.PrefixMapping;
 import com.hp.hpl.jena.shared.impl.PrefixMappingImpl;
-import com.hp.hpl.jena.sparql.resultset.JSONInput;
 import com.hp.hpl.jena.util.iterator.ExtendedIterator;
 import com.hp.hpl.jena.util.iterator.SingletonIterator;
 import com.hp.hpl.jena.util.iterator.WrappedIterator;
@@ -38,6 +38,7 @@ import com.hp.hpl.jena.util.iterator.WrappedIterator;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.VitroModelFactory;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.logging.ToString;
@@ -52,6 +53,11 @@ public class RDFServiceGraph implements GraphWithPerform {
     private PrefixMapping prefixMapping = new PrefixMappingImpl();
     private GraphEventManager eventManager;
     
+    private boolean queueWrites = false;
+    private ConcurrentLinkedQueue<Triple> addTripleQueue = new ConcurrentLinkedQueue<Triple>();
+    private ConcurrentLinkedQueue<Triple> removeTripleQueue = new ConcurrentLinkedQueue<Triple>();
+
+
     /**
      * Returns a SparqlGraph for the union of named graphs in a remote repository 
      * @param endpointURI
@@ -91,29 +97,47 @@ public class RDFServiceGraph implements GraphWithPerform {
         return sb.toString();
     }
         
-    @Override
+    public void flush() {
-    public void performAdd(Triple t) {
+        log.debug("Flushing a batch");                                
-        
         ChangeSet changeSet = rdfService.manufactureChangeSet();
         try {
-            changeSet.addAddition(RDFServiceUtils.toInputStream(serialize(t)), 
+            if(!removeTripleQueue.isEmpty()) {
-                    RDFService.ModelSerializationFormat.N3, graphURI);
+                String removals = serializeQueue(removeTripleQueue);
+                changeSet.addRemoval(RDFServiceUtils.toInputStream(removals), 
+                        RDFService.ModelSerializationFormat.N3, graphURI);
+            }
+            if(!addTripleQueue.isEmpty()) {
+                String additions = serializeQueue(addTripleQueue);
+                changeSet.addAddition(RDFServiceUtils.toInputStream(additions), 
+                        RDFService.ModelSerializationFormat.N3, graphURI);
+            }
             rdfService.changeSetUpdate(changeSet);
         } catch (RDFServiceException rdfse) {
             throw new RuntimeException(rdfse);
         }
+    }
     
+    private String serializeQueue(Queue<Triple> tripleQueue) {
+        String triples = "";
+        while(!tripleQueue.isEmpty()) {
+            triples += " \n" + serialize(tripleQueue.poll());
+        }
+        return triples;
+    }
+    
+    @Override
+    public void performAdd(Triple t) {
+        addTripleQueue.add(t);
+        if(!queueWrites) {
+            flush();
+        }
     }
     
     @Override
     public void performDelete(Triple t) {
-        ChangeSet changeSet = rdfService.manufactureChangeSet();
+        removeTripleQueue.add(t);
-        try {
+        if(!queueWrites) {
-            changeSet.addRemoval(RDFServiceUtils.toInputStream(serialize(t)), 
+            flush();
-                    RDFService.ModelSerializationFormat.N3, graphURI);
-            rdfService.changeSetUpdate(changeSet);
-        } catch (RDFServiceException rdfse) {
-            throw new RuntimeException(rdfse);
         }
     }
     
@@ -325,8 +349,7 @@ public class RDFServiceGraph implements GraphWithPerform {
       
     @Override
     public TransactionHandler getTransactionHandler() {
-        // TODO Auto-generated method stub
+        return transactionHandler;
-        return null;
     }
 
     @Override
@@ -403,6 +426,37 @@ public class RDFServiceGraph implements GraphWithPerform {
         public boolean sizeAccurate() {
             return true;
         }
+	};
+
+	private final TransactionHandler transactionHandler = new TransactionHandler() {
+	    @Override
+	    public void abort() {
+	        queueWrites = false;
+	        removeTripleQueue.clear();
+	        addTripleQueue.clear();
+	    }
+
+        @Override
+        public void begin() {
+            queueWrites = true;
+        }
+
+        @Override
+        public void commit() {
+            flush();
+            queueWrites = false;
+        }
+
+        @Override
+        public Object executeInTransaction(Command arg0) {
+            // TODO Auto-generated method stub
+            return null;
+        }
+
+        @Override
+        public boolean transactionsSupported() {
+            return true;
+        }  
     };
     
     private void execSelect(String queryStr, ResultSetConsumer consumer) {

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

@@ -16,6 +16,7 @@ import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.rdf.listeners.StatementListener;
+import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.shared.Lock;
@@ -33,6 +34,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.filtering.WebappDaoFactoryFiltering;
 import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.VitroFilterUtils;
 import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.VitroFilters;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.event.BulkUpdateEvent;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngine;
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngineException;
@@ -161,9 +163,28 @@ public class VClassGroupCache implements SearchIndexer.Listener {
         VclassMap = classMap;
     }
     
+    private boolean paused = false;
+    private boolean updateRequested = false;
+    
+    public void pause() {
+        this.paused = true;
+    }
+    
+    public void unpause() {
+        this.paused = false;
+        if(updateRequested) {
+            updateRequested = false;
+            requestCacheUpdate();
+        }
+    }
+    
     public void requestCacheUpdate() {
         log.debug("requesting update");
-        _cacheRebuildThread.informOfQueueChange();
+        if(paused) {
+            updateRequested = true;
+        } else {
+            _cacheRebuildThread.informOfQueueChange();
+        }
     }
     
     protected void requestStop() {
@@ -337,24 +358,25 @@ public class VClassGroupCache implements SearchIndexer.Listener {
         }        
     }
 
-    protected static boolean isClassNameChange(Statement stmt, OntModel jenaOntModel) {
+    protected static boolean isClassNameChange(Statement stmt, ServletContext context) {
         // Check if the stmt is a rdfs:label change and that the
         // subject is an owl:Class.
-        if( RDFS.label.equals( stmt.getPredicate() )) {                
+        if( !RDFS.label.equals( stmt.getPredicate() )) {
-            jenaOntModel.enterCriticalSection(Lock.READ);
-            try{                                                  
-                return jenaOntModel.contains(
-                        ResourceFactory.createStatement(
-                                ResourceFactory.createResource(stmt.getSubject().getURI()), 
-                                RDF.type, 
-                                OWL.Class));
-            }finally{
-                jenaOntModel.leaveCriticalSection();
-            }
-        }else{
             return false;
         } 
+        OntModel jenaOntModel = ModelAccess.on(context).getOntModelSelector().getTBoxModel();
+        jenaOntModel.enterCriticalSection(Lock.READ);
+        try{                                                  
+            return jenaOntModel.contains(
+                    ResourceFactory.createStatement(
+                            ResourceFactory.createResource(stmt.getSubject().getURI()), 
+                            RDF.type, 
+                            OWL.Class));
+        }finally{
+            jenaOntModel.leaveCriticalSection();
+        }
     }
+    
     /* ******************** RebuildGroupCacheThread **************** */
     
     protected class RebuildGroupCacheThread extends VitroBackgroundThread {
@@ -460,20 +482,26 @@ public class VClassGroupCache implements SearchIndexer.Listener {
                 log.debug("subject: " + stmt.getSubject().getURI());
                 log.debug("predicate: " + stmt.getPredicate().getURI());
             }
-            if (RDF.type.getURI().equals(stmt.getPredicate().getURI())) {
+            if (RDF.type.equals(stmt.getPredicate())) {
                 requestCacheUpdate();
             } else if (VitroVocabulary.IN_CLASSGROUP.equals(stmt.getPredicate().getURI())) {
                 requestCacheUpdate();
             } else if(VitroVocabulary.DISPLAY_RANK.equals(stmt.getPredicate().getURI())){
             	requestCacheUpdate();
-            } else {
+            } else if( isClassNameChange(stmt, context) ) {            
-                OntModel jenaOntModel = ModelAccess.on(context).getOntModel();
+                requestCacheUpdate();
-                if( isClassNameChange(stmt, jenaOntModel) ) {            
-                    requestCacheUpdate();
-                }
             }
         }       
         
+        public void notifyEvent(Model model, Object event) {
+            if (event instanceof BulkUpdateEvent) { 
+                if(((BulkUpdateEvent) event).getBegin()) {
+                    pause();
+                } else {
+                    unpause();
+                }
+            }
+        }
        
     }
     

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

@@ -2,10 +2,9 @@
 
 package edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.sdb;
 
+import java.io.IOException;
 import java.sql.Connection;
 import java.sql.SQLException;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 import javax.sql.DataSource;
 
@@ -23,6 +22,8 @@ import com.hp.hpl.jena.sdb.sql.SDBConnection;
 
 import edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapper;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.StaticDatasetFactory;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.event.BulkUpdateEvent;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
@@ -76,30 +77,43 @@ public class RDFServiceSDB extends RDFServiceJena implements RDFService {
             
         SDBConnection sdbConn = getSDBConnection();        
         Dataset dataset = getDataset(sdbConn);
+        try {
+            insureThatInputStreamsAreResettable(changeSet);
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
 
         try {
-        	insureThatInputStreamsAreResettable(changeSet);
+            beginTransaction(sdbConn);
-            
+        	startBulkUpdate();
-        	beginTransaction(sdbConn);
-
         	notifyListenersOfPreChangeEvents(changeSet);
-            applyChangeSetToModel(changeSet, dataset);
+        	applyChangeSetToModel(changeSet, dataset);
-            
             commitTransaction(sdbConn);
-            
             notifyListenersOfChanges(changeSet);
             notifyListenersOfPostChangeEvents(changeSet);            
-            
             return true;
         } catch (Exception e) {
             log.error(e, e);
             abortTransaction(sdbConn);
             throw new RDFServiceException(e);
         } finally {
+            endBulkUpdate();
             close(sdbConn);
         }
     }
     
+    private void startBulkUpdate() {
+        for (ChangeListener cl : this.getRegisteredListeners()) {
+            cl.notifyEvent(null, new BulkUpdateEvent(null, true));
+        }
+    }
+    
+    private void endBulkUpdate() {
+        for (ChangeListener cl : this.getRegisteredListeners()) {
+            cl.notifyEvent(null, new BulkUpdateEvent(null, false));
+        }
+    }
+    
 	private SDBConnection getSDBConnection() throws RDFServiceException  {
 		try {
 			Connection c = (conn != null) ? conn : ds.getConnection();
@@ -140,10 +154,6 @@ public class RDFServiceSDB extends RDFServiceJena implements RDFService {
 		}
 	}
 	    
-    private static final Pattern OPTIONAL_PATTERN = Pattern.compile("optional", Pattern.CASE_INSENSITIVE);
-    
-    private static final Pattern GRAPH_PATTERN = Pattern.compile("graph", Pattern.CASE_INSENSITIVE);
-    
     @Override
     protected QueryExecution createQueryExecution(String queryString, Query q, Dataset d) {
         return QueryExecutionFactory.create(q, d);

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

@@ -16,8 +16,10 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.concurrent.ConcurrentLinkedQueue;
 
+import edu.cornell.mannlib.vitro.webapp.modules.searchIndexer.SearchIndexer;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
 import edu.cornell.mannlib.vitro.webapp.utils.http.HttpClientFactory;
+
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -58,6 +60,7 @@ import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
 import com.hp.hpl.jena.sparql.core.Quad;
 
+import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraph;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
@@ -83,7 +86,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 	protected String readEndpointURI;
 	protected String updateEndpointURI;
 	// the number of triples to be
-	private static final int CHUNK_SIZE = 1000; // added/removed in a single
+	private static final int CHUNK_SIZE = 5000; // added/removed in a single
 	// SPARQL UPDATE
 
 	protected HttpClient httpClient;
@@ -170,12 +173,13 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 				&& !isPreconditionSatisfied(
 				changeSet.getPreconditionQuery(),
 				changeSet.getPreconditionQueryType())) {
-			return false;
+		    return false;
 		}
 
 		try {
-			for (Object o : changeSet.getPreChangeEvents()) {
+
-				this.notifyListenersOfEvent(o);
+		    for (Object o : changeSet.getPreChangeEvents()) {
+		        this.notifyListenersOfEvent(o);
 			}
 
 			Iterator<ModelChange> csIt = changeSet.getModelChanges().iterator();
@@ -196,10 +200,18 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 				modelChange.getSerializedModel().reset();
 				Model model = ModelFactory.createModelForGraph(
 						new ListeningGraph(modelChange.getGraphURI(), this));
+				long start = System.currentTimeMillis();
 				if (modelChange.getOperation() == ModelChange.Operation.ADD) {
-					model.read(modelChange.getSerializedModel(), null,
+				    Model temp = ModelFactory.createDefaultModel();
+					temp.read(modelChange.getSerializedModel(), null,
 							getSerializationFormatString(
 									modelChange.getSerializationFormat()));
+					StmtIterator sit = temp.listStatements();
+					while(sit.hasNext()) {
+					    Triple triple = sit.nextStatement().asTriple();
+					    this.notifyListeners(triple, ModelChange.Operation.ADD, modelChange.getGraphURI());
+					}
+					//model.add(temp);
 				} else if (modelChange.getOperation() == ModelChange.Operation.REMOVE){
 					Model temp = ModelFactory.createDefaultModel();
 					temp.read(modelChange.getSerializedModel(), null,
@@ -210,6 +222,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 					log.error("Unsupported model change type " +
 							modelChange.getOperation().getClass().getName());
 				}
+				log.info((System.currentTimeMillis() - start) + " ms to notify " + this.getRegisteredListeners().size() + " listeners");
 			}
 
 			for (Object o : changeSet.getPostChangeEvents()) {
@@ -468,7 +481,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 	 */
 	@Override
 	public void getGraphMetadata() throws RDFServiceException {
-
+	    throw new UnsupportedOperationException();
 	}
 
 	/**
@@ -549,7 +562,9 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 
 	public void addModel(Model model, String graphURI) throws RDFServiceException {
 		try {
+		    long start = System.currentTimeMillis();
 			verbModel(model, graphURI, "INSERT");
+			log.info((System.currentTimeMillis() - start) + " ms to insert " + model.size() + " triples");
 		} finally {
 			rebuildGraphURICache = true;
 		}

webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/ABoxRecomputer.java

@@ -64,7 +64,7 @@ public class ABoxRecomputer {
     private volatile boolean recomputing = false;
     private boolean stopRequested = false;
 
-    private final int BATCH_SIZE = 100;
+    private final int BATCH_SIZE = 500;
     private final int REPORTING_INTERVAL = 1000;
 
     /**
@@ -109,18 +109,24 @@ public class ABoxRecomputer {
                 recomputing = true;
             }
         }
+        boolean fullRecompute = (individualURIs == null);
+        boolean sizableRecompute = (!fullRecompute && individualURIs.size() > 2);
         try {
-            if  (searchIndexer != null) {
+            if(fullRecompute || sizableRecompute) { // if doing a full rebuild
-                searchIndexer.pause();
+                if (searchIndexer != null) {
-                // Register now that we want to rebuild the index when we unpause
+                    searchIndexer.pause();
-                // This allows the indexer to optimize behaviour whilst paused
+                    // Register now that we want to rebuild the index when we unpause
-                searchIndexer.rebuildIndex();
+                    // This allows the indexer to optimize behaviour whilst paused
+                    if(fullRecompute) {
+                        searchIndexer.rebuildIndex();
+                    }
+                }
             }
             // Create a type cache for this execution and pass it to the recompute function
             // Ensures that caches are only valid for the length of one recompute
             recomputeABox(individualURIs, new TypeCaches());
         } finally {
-            if  (searchIndexer != null) {
+            if  ((fullRecompute || sizableRecompute) && searchIndexer != null) {
                 searchIndexer.unpause();
             }
             synchronized (lock1) {
@@ -199,7 +205,7 @@ public class ABoxRecomputer {
             Model rebuildModel, TypeCaches caches) throws RDFServiceException {
         long start = System.currentTimeMillis();
         Model assertions = getAssertions(individualURI);
-        log.trace((System.currentTimeMillis() - start) + " ms to get assertions.");
+        log.debug((System.currentTimeMillis() - start) + " ms to get assertions.");
         Model additionalInferences = recomputeIndividual(
                 individualURI, null, assertions, rebuildModel, caches, RUN_PLUGINS);
 
@@ -588,7 +594,7 @@ public class ABoxRecomputer {
                 getSameAsIndividuals(indUri, sameAsInds);
             }
         } catch (RDFServiceException e) {
-
+            log.error(e,e);
         }
     }
 

webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java

@@ -2,14 +2,14 @@
 
 package edu.cornell.mannlib.vitro.webapp.reasoner;
 
-import static edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread.WorkLevel.WORKING;
-
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Queue;
 import java.util.Set;
+import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.ConcurrentLinkedQueue;
 import java.util.concurrent.CopyOnWriteArrayList;
 
@@ -50,7 +50,6 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.VitroModelFactory;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceModel;
-import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
 
 /**
  * Allows for real-time incremental materialization or retraction of RDFS-
@@ -77,7 +76,7 @@ public class SimpleReasoner extends StatementListener {
 			VitroModelFactory.createOntologyModel())
 				.createAnnotationProperty(mostSpecificTypePropertyURI);
 	
-	private Queue<String> individualURIqueue = new ConcurrentLinkedQueue<String>();
+	private Queue<String> individualURIqueue = new IndividualURIQueue<String>();
 	
 	// DeltaComputer
 	private CumulativeDeltaModeler aBoxDeltaModeler1 = null;
@@ -189,16 +188,12 @@ public class SimpleReasoner extends StatementListener {
   
     private void listenToStatement(Statement stmt) {
         if(stmt.getSubject().isURIResource()) {
-            if (!individualURIqueue.contains(stmt.getSubject().getURI())) {
+            individualURIqueue.add(stmt.getSubject().getURI());
-                individualURIqueue.add(stmt.getSubject().getURI());
-            }
         }
         if(stmt.getObject().isURIResource() && !(RDF.type.equals(stmt.getPredicate()))) {
-            if (!individualURIqueue.contains(stmt.getObject().asResource().getURI())) {
+            individualURIqueue.add(stmt.getObject().asResource().getURI());
-                individualURIqueue.add(stmt.getObject().asResource().getURI());
-            }
         }
-        if(!accumulateChanges || individualURIqueue.size() > SAFETY_VALVE) {
+        if(!accumulateChanges) {
             recomputeIndividuals(); 
         }
     }
@@ -206,8 +201,17 @@ public class SimpleReasoner extends StatementListener {
     private static final int SAFETY_VALVE = 1000000; // one million individuals
     
     private void recomputeIndividuals() {
+        if(recomputer.isRecomputing()) {
+            return;
+        }
+        long start = System.currentTimeMillis();
+        int size = individualURIqueue.size();
         recomputer.recompute(individualURIqueue);
-        individualURIqueue.clear();
+        //individualURIqueue.clear();
+        if(size > 2) {
+            log.info((System.currentTimeMillis() - start) + " ms to recompute " 
+                    + size + " individuals");
+        }
     }
     
     private boolean accumulateChanges = false;
@@ -220,8 +224,7 @@ public class SimpleReasoner extends StatementListener {
 	@Override
 	public void addedStatement(Statement stmt) {
 	    doPlugins(ModelUpdate.Operation.ADD,stmt);
-	    listenToStatement(stmt);
+	    listenToStatement(stmt);;	    
-	    
 //		try {
 //			if (stmt.getPredicate().equals(RDF.type)) {
 //			     addedABoxTypeAssertion(stmt, inferenceModel, new HashSet<String>()); 
@@ -1633,7 +1636,7 @@ public class SimpleReasoner extends StatementListener {
 	    	if (((BulkUpdateEvent) event).getBegin()) {	
 	    	    this.accumulateChanges = true;
 	    		
-	    		log.info("received a bulk update begin event");
+	    		//log.info("received a bulk update begin event");
 //	    		if (deltaComputerProcessing) {
 //	    			eventCount++;
 //	    			log.info("received a bulk update begin event while processing in asynchronous mode. Event count = " + eventCount);
@@ -1651,7 +1654,7 @@ public class SimpleReasoner extends StatementListener {
 //	    			log.info("initializing batch mode 1");
 //	    		}
 	    	} else {
-	    		log.info("received a bulk update end event");
+	    		//log.info("received a bulk update end event");
 	    		this.accumulateChanges = false;
 	    		recomputeIndividuals();
 //	    		if (!deltaComputerProcessing) {
@@ -1817,4 +1820,139 @@ public class SimpleReasoner extends StatementListener {
                                   : ((Resource)statement.getObject()).getURI() + " (Resource)") + "]";
     }  
     
+    private class IndividualURIQueue<E> implements Queue<E> {
+
+        private ConcurrentLinkedQueue<E> q = new ConcurrentLinkedQueue<E>();
+        private ConcurrentHashMap<E, Boolean> m = new ConcurrentHashMap<E, Boolean>();
+        
+        @Override
+        public boolean addAll(Collection<? extends E> c) {
+            boolean changed = false;
+            for (E e : c) {
+                if(!m.containsKey(e)) {
+                    m.put(e, Boolean.TRUE);
+                    q.add(e);
+                    changed = true;
+                }
+            }
+            return changed;
+        }
+        
+        @Override
+        public void clear() {
+            m.clear();
+            q.clear();
+        }
+        
+        @Override
+        public boolean contains(Object o) {
+            return m.contains(o);
+        }
+        
+        @Override
+        public boolean containsAll(Collection<?> c) {
+            boolean contains = true;
+            for(Object e : c) {
+                contains |= m.contains(e);
+            }
+            return contains;
+        }
+        
+        @Override
+        public boolean isEmpty() {
+            return q.isEmpty();
+        }
+        
+        @Override
+        public Iterator<E> iterator() {
+            return q.iterator();
+        }
+        
+        @Override
+        public boolean remove(Object o) {
+            m.remove(o);
+            return q.remove(o);
+        }
+        
+        @Override
+        public boolean removeAll(Collection<?> c) {
+            for (Object e : c) {
+                m.remove(e);
+            }
+            return q.removeAll(c);
+        }
+        
+        @Override
+        public boolean retainAll(Collection<?> c) {
+            boolean changed = false;
+            Iterator<E> it = m.keySet().iterator();
+            while(it.hasNext()) {
+                E e = it.next();
+                if(!c.contains(e)) {
+                   m.remove(e);
+                   q.remove(e);
+                   changed = true;
+                }
+            }
+            return changed;
+        }
+        
+        @Override
+        public int size() {
+            return m.size();
+        }
+        
+        @Override
+        public Object[] toArray() {
+            return q.toArray();
+        }
+        
+        @Override
+        public <T> T[] toArray(T[] a) {
+            return q.toArray(a);
+        }
+        
+        @Override
+        public boolean add(E e) {
+            if(m.containsKey(e)) {
+                return false;
+            } else {
+                m.put(e, Boolean.TRUE);
+                q.add(e);
+                return true;
+            }
+        }
+        
+        @Override
+        public E element() {
+            return q.element();
+        }
+        
+        @Override
+        public boolean offer(E e) {
+            return q.offer(e);
+        }
+        
+        @Override
+        public E peek() {
+            return q.peek();
+        }
+        
+        @Override
+        public E poll() {
+            E e =  q.poll();
+            m.remove(e);
+            return e;
+        }
+        
+        @Override
+        public E remove() {
+            E e = q.remove();
+            m.remove(e);
+            return e;
+        }
+        
+    }
+    
+
 }