event notification for RDF API and change to model setup for SimpleReasoner

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

@@ -0,0 +1,136 @@
+package edu.cornell.mannlib.vitro.webapp.dao.jena;
+
+import java.util.Set;
+
+import com.hp.hpl.jena.graph.BulkUpdateHandler;
+import com.hp.hpl.jena.graph.Capabilities;
+import com.hp.hpl.jena.graph.Graph;
+import com.hp.hpl.jena.graph.GraphEventManager;
+import com.hp.hpl.jena.graph.GraphStatisticsHandler;
+import com.hp.hpl.jena.graph.Node;
+import com.hp.hpl.jena.graph.Reifier;
+import com.hp.hpl.jena.graph.TransactionHandler;
+import com.hp.hpl.jena.graph.Triple;
+import com.hp.hpl.jena.graph.TripleMatch;
+import com.hp.hpl.jena.graph.query.QueryHandler;
+import com.hp.hpl.jena.shared.AddDeniedException;
+import com.hp.hpl.jena.shared.DeleteDeniedException;
+import com.hp.hpl.jena.shared.PrefixMapping;
+import com.hp.hpl.jena.util.iterator.ExtendedIterator;
+import com.hp.hpl.jena.util.iterator.WrappedIterator;
+
+public class DifferenceGraph implements Graph {
+
+    private Graph g;
+    private Graph subtract;
+    
+    public DifferenceGraph(Graph g, Graph subtract) {    
+        this.g = g;
+        this.subtract = subtract;
+    }
+    
+    @Override
+    public void close() {
+        // not clear what the best behavior here is
+    }
+
+    @Override
+    public boolean contains(Triple arg0) {
+        return g.contains(arg0) && !subtract.contains(arg0);
+    }
+
+    @Override
+    public boolean contains(Node arg0, Node arg1, Node arg2) {
+        return g.contains(arg0, arg1, arg2) && !subtract.contains(arg0, arg1, arg2);
+    }
+
+    @Override
+    public void delete(Triple arg0) throws DeleteDeniedException {
+        g.delete(arg0);
+    }
+
+    @Override
+    public boolean dependsOn(Graph arg0) {
+        return g.dependsOn(arg0);
+    }
+
+    @Override
+    public ExtendedIterator<Triple> find(TripleMatch arg0) {
+        Set<Triple> tripSet = g.find(arg0).toSet();
+        tripSet.removeAll(subtract.find(arg0).toSet());
+        return WrappedIterator.create(tripSet.iterator());
+    }
+
+    @Override
+    public ExtendedIterator<Triple> find(Node arg0, Node arg1, Node arg2) {
+        Set<Triple> tripSet = g.find(arg0, arg1, arg2).toSet();
+        tripSet.removeAll(subtract.find(arg0, arg1, arg2).toSet());
+        return WrappedIterator.create(tripSet.iterator());
+    }
+
+    @Override
+    public BulkUpdateHandler getBulkUpdateHandler() {
+        return g.getBulkUpdateHandler();
+    }
+
+    @Override
+    public Capabilities getCapabilities() {
+        return g.getCapabilities();
+    }
+
+    @Override
+    public GraphEventManager getEventManager() {
+        return g.getEventManager();
+    }
+
+    @Override
+    public PrefixMapping getPrefixMapping() {
+        return g.getPrefixMapping();
+    }
+
+    @Override
+    public Reifier getReifier() {
+        return g.getReifier();
+    }
+
+    @Override
+    public GraphStatisticsHandler getStatisticsHandler() {
+        return g.getStatisticsHandler();
+    }
+
+    @Override
+    public TransactionHandler getTransactionHandler() {
+        return g.getTransactionHandler();
+    }
+
+    @Override
+    public boolean isClosed() {
+        return g.isClosed();
+    }
+
+    @Override
+    public boolean isEmpty() {
+        return g.isEmpty();
+    }
+
+    @Override
+    public boolean isIsomorphicWith(Graph arg0) {
+        return g.isIsomorphicWith(arg0);
+    }
+
+    @Override
+    public QueryHandler queryHandler() {
+        return g.queryHandler();
+    }
+
+    @Override
+    public int size() {
+        return g.size() - subtract.size();
+    }
+
+    @Override
+    public void add(Triple arg0) throws AddDeniedException {
+        g.add(arg0);
+    }
+
+}

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

@@ -109,7 +109,8 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
     public void removeVClass(String individualURI, String vclassURI) {
     	OntModel ontModel = getOntModelSelector().getABoxModel();
         ontModel.enterCriticalSection(Lock.WRITE);
-        ontModel.getBaseModel().notifyEvent(new IndividualUpdateEvent(getWebappDaoFactory().getUserURI(),true,individualURI));
+        Object event = new IndividualUpdateEvent(getWebappDaoFactory().getUserURI(),true,individualURI);
+        ontModel.getBaseModel().notifyEvent(event);
         try {
             Resource indRes = ontModel.getResource(individualURI);
             getOntModel().remove(indRes, RDF.type, ontModel.getResource(vclassURI));

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

@@ -42,6 +42,7 @@ public class JenaChangeListener implements ChangeListener {
 
     @Override
     public void notifyEvent(String graphURI, Object event) {
+        log.debug("event: " + event.getClass());
         listener.notifyEvent(m, event);
     }
     

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

@@ -41,7 +41,7 @@ public class RDFServiceDataset implements Dataset {
 
     @Override
     public Model getDefaultModel() {
-        return ModelFactory.createModelForGraph(g.getDefaultGraph());
+        return RDFServiceGraph.createRDFServiceModel(g.getDefaultGraph());
     }
 
     @Override
@@ -51,7 +51,7 @@ public class RDFServiceDataset implements Dataset {
 
     @Override
     public Model getNamedModel(String arg0) {
-        return ModelFactory.createModelForGraph(g.getGraph(Node.createURI(arg0)));
+        return RDFServiceGraph.createRDFServiceModel(g.getGraph(Node.createURI(arg0)));
     }
 
     @Override

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

@@ -161,12 +161,12 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
     }
 
     @Override
-    public Graph getDefaultGraph() {
+    public RDFServiceGraph getDefaultGraph() {
         return new RDFServiceGraph(rdfService);
     }
 
     @Override
-    public Graph getGraph(Node arg0) {
+    public RDFServiceGraph getGraph(Node arg0) {
         return new RDFServiceGraph(rdfService, arg0.getURI());
     }
 

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

@@ -24,6 +24,9 @@ import com.hp.hpl.jena.graph.query.QueryHandler;
 import com.hp.hpl.jena.graph.query.SimpleQueryHandler;
 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.rdf.model.ModelFactory;
 import com.hp.hpl.jena.shared.AddDeniedException;
 import com.hp.hpl.jena.shared.DeleteDeniedException;
 import com.hp.hpl.jena.shared.PrefixMapping;
@@ -434,4 +437,22 @@ public class RDFServiceGraph implements GraphWithPerform {
         }
     }
     
+    public static Model createRDFServiceModel(final RDFServiceGraph g) {
+        Model m = ModelFactory.createModelForGraph(g);
+        m.register(new StatementListener() {
+            @Override 
+            public void notifyEvent(Model m, Object event) {
+                ChangeSet changeSet = g.getRDFService().manufactureChangeSet();
+                changeSet.addPreChangeEvent(event);
+                try {
+                    g.getRDFService().changeSetUpdate(changeSet);
+                } catch (RDFServiceException e) {
+                    throw new RuntimeException(e);
+                }
+            }
+            
+        });
+        return m;
+    }
+    
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/ChangeSet.java

@@ -86,4 +86,34 @@ public interface ChangeSet {
                                               RDFService.ModelSerializationFormat serializationFormat,
                                               ModelChange.Operation operation,
                                               String graphURI);
+	
+	/**
+	 * Add an event that will be be passed to any change listeners in advance of
+	 * the change set additions and retractions being performed.  The event
+	 * will only be fired if the precondition (if any) is met.
+	 * @param event
+	 */
+	public void addPreChangeEvent(Object event);
+	    
+    /**
+     * Add an event that will be be passed to any change listeners after all of
+     * the change set additions and retractions are performed.
+     * @param event
+     */
+    public void addPostChangeEvent(Object event);
+
+    /**
+     * Return a list of events to pass to any change listeners in 
+     * advance of the change set additions and retractions being performed.
+     * @return
+     */
+	public List<Object> getPreChangeEvents();
+	
+    /**
+     * Return a list of events to pass to any change listeners after 
+     * the change set additions and retractions are performed.
+     * @return
+     */
+    public List<Object> getPostChangeEvents();
+    
 }

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

@@ -23,8 +23,10 @@ public class ChangeSetImpl implements ChangeSet {
 	
 	private String preconditionQuery;
 	private RDFService.SPARQLQueryType queryType;
-	private ArrayList<ModelChange> modelChanges;
+	private ArrayList<ModelChange> modelChanges = new ArrayList<ModelChange>();
-	
+	private ArrayList<Object> preChangeEvents = new ArrayList<Object>();
+	private ArrayList<Object> postChangeEvents = new ArrayList<Object>();
+ 	
 	/**   
 	 * Getter for the precondition query
 	 * 
@@ -122,4 +124,25 @@ public class ChangeSetImpl implements ChangeSet {
                                               String graphURI) {
 		return new ModelChangeImpl(serializedModel, serializationFormat, operation, graphURI); 
 	}
+	
+	@Override 
+	public void addPreChangeEvent(Object o) {
+	    this.preChangeEvents.add(o);
+	}
+	
+	@Override 
+    public void addPostChangeEvent(Object o) {
+        this.postChangeEvents.add(o);
+    }
+	
+	@Override
+	public List<Object> getPreChangeEvents() {
+	    return this.preChangeEvents;
+	}
+	
+	@Override
+    public List<Object> getPostChangeEvents() {
+        return this.postChangeEvents;
+    }
+	
 }

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

@@ -143,6 +143,17 @@ public abstract class RDFServiceImpl implements RDFService {
                 listener.removedStatement(sparqlTriple(triple).toString(), graphURI);   			
             }
         }
+    }
+    
+    public synchronized void notifyListenersOfEvent(Object event) {
+        
+        Iterator<ChangeListener> iter = registeredListeners.iterator();
+
+        while (iter.hasNext()) {
+            ChangeListener listener = iter.next();
+            // TODO what is the graphURI parameter for?
+            listener.notifyEvent(null, event);
+        }
     }    
     
     protected boolean isPreconditionSatisfied(String query, 

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

@@ -124,9 +124,15 @@ public class RDFServiceSDB extends RDFServiceImpl implements RDFService {
                     dataset.getLock().leaveCriticalSection();
                 }
             }
+            for (Object o : changeSet.getPreChangeEvents()) {
+                this.notifyListenersOfEvent(o);
+            }
             if (transaction) {
                 conn.getTransactionHandler().commit();
             }
+            for (Object o : changeSet.getPostChangeEvents()) {
+                this.notifyListenersOfEvent(o);
+            }
         } catch (Exception e) {
             log.error(e, e);
             if (transaction) {
@@ -404,10 +410,12 @@ public class RDFServiceSDB extends RDFServiceImpl implements RDFService {
         }
         
         public void addedStatement(Statement stmt) {
+            log.debug("adding " + stmt + " to " + graphURI);
             s.notifyListeners(stmt.asTriple(), ModelChange.Operation.ADD, graphURI);
         }
         
         public void removedStatement(Statement stmt) {
+            log.debug("removing " + stmt + " from " + graphURI);
             s.notifyListeners(stmt.asTriple(), ModelChange.Operation.REMOVE, graphURI);
         }
         

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

@@ -41,6 +41,7 @@ import com.hp.hpl.jena.vocabulary.RDFS;
 
 import edu.cornell.mannlib.vitro.webapp.dao.jena.ABoxJenaChangeListener;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.CumulativeDeltaModeler;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.DifferenceGraph;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.event.BulkUpdateEvent;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
@@ -89,7 +90,7 @@ public class SimpleReasoner extends StatementListener {
 		this.tboxModel = tboxModel;
         this.aboxModel = ModelFactory.createOntologyModel(
                 OntModelSpec.OWL_MEM, ModelFactory.createModelForGraph(
-                        new RDFServiceGraph(rdfService))); 
+                        new DifferenceGraph(new RDFServiceGraph(rdfService), inferenceModel.getGraph()))); 
 		this.inferenceModel = inferenceModel;
 		this.inferenceRebuildModel = inferenceRebuildModel;
 		this.scratchpadModel = scratchpadModel;	
@@ -187,8 +188,7 @@ public class SimpleReasoner extends StatementListener {
 	 * Synchronized part of removedStatement. Interacts
 	 * with DeltaComputer.
 	 */
-	protected synchronized void handleRemovedStatement(Statement stmt) {
+	protected synchronized void handleRemovedStatement(Statement stmt) {    
-		
 		if (batchMode1) {
 			 aBoxDeltaModeler1.removedStatement(stmt);
 		} else if (batchMode2) {
@@ -753,7 +753,7 @@ public class SimpleReasoner extends StatementListener {
 					Iterator<OntClass> parentIt = parents.iterator();
 					
 					while (parentIt.hasNext()) {
-						OntClass parentClass = parentIt.next();
+							OntClass parentClass = parentIt.next();
 						
 						// VIVO doesn't materialize statements that assert anonymous types
 						// for individuals. Also, sharing an identical anonymous node is
@@ -770,7 +770,7 @@ public class SimpleReasoner extends StatementListener {
 						inferenceModel.enterCriticalSection(Lock.WRITE);
 						try {
 							if (inferenceModel.contains(infStmt)) {
-								inferenceModel.remove(infStmt);
+	     						inferenceModel.remove(infStmt);
 							}
 						} finally {
 							inferenceModel.leaveCriticalSection();
@@ -1745,7 +1745,7 @@ public class SimpleReasoner extends StatementListener {
     
 	@Override
 	public synchronized void notifyEvent(Model model, Object event) {
-		
+	    
 	    if (event instanceof BulkUpdateEvent) {	
 	    	if (((BulkUpdateEvent) event).getBegin()) {	
 	    		

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

@@ -135,7 +135,7 @@ public class RDFServiceSetup extends JenaDataSourceSetupBase
         RDFServiceFactory rdfServiceFactory = new RDFServiceFactorySingle(rdfService);
         RDFServiceUtils.setRDFServiceFactory(ctx, rdfServiceFactory);
         
-        Graph g = new RDFServiceGraph(rdfService);
+//        Graph g = new RDFServiceGraph(rdfService);
         
         Dataset dataset = new RDFServiceDataset(rdfService);
         setStartupDataset(dataset, ctx);