merge changes from trunk to rdf api branch and fix issue with listeners notifying before triples are actually added/removed

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.util.HashSet;

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.util.Set;

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.util.ArrayList;

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.io.ByteArrayInputStream;

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.util.ArrayList;

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.util.ArrayList;

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.io.InputStream;

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.io.ByteArrayInputStream;
@@ -30,7 +32,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 
 public class RDFServiceGraphBulkUpdater extends SimpleBulkUpdateHandler {
 
-    private static final Log log = LogFactory.getLog(SparqlGraphBulkUpdater.class);
+    private static final Log log = LogFactory.getLog(RDFServiceGraphBulkUpdater.class);
     private RDFServiceGraph graph;
     
     public RDFServiceGraphBulkUpdater(RDFServiceGraph graph) {

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.util.ArrayList;

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.util.ArrayList;

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.util.ArrayList;

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.io.StringWriter;

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.util.ArrayList;

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

@@ -35,6 +35,7 @@ import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
 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.ModelContext;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlDataset;
@@ -90,7 +91,8 @@ public class WebappDaoFactorySDBPrep implements Filter {
             }
         }
 		
-        OntModelSelector oms = (OntModelSelector) _ctx.getAttribute("unionOntModelSelector");
+        OntModelSelector oms = ModelContext.getUnionOntModelSelector(_ctx);
+        OntModelSelector baseOms = ModelContext.getBaseOntModelSelector(_ctx);
         String defaultNamespace = (String) _ctx.getAttribute("defaultNamespace");
 		WebappDaoFactory wadf = null;
 		VitroRequest vreq = new VitroRequest((HttpServletRequest) request);
@@ -112,7 +114,7 @@ public class WebappDaoFactorySDBPrep implements Filter {
 		Dataset dataset = new RDFServiceDataset(rdfService);
 		wadf = new WebappDaoFactorySDB(rdfService, oms, config);
 	    WebappDaoFactory assertions = new WebappDaoFactorySDB(
-	            rdfService, oms, config, SDBDatasetMode.ASSERTIONS_ONLY);
+	            rdfService, baseOms, config, SDBDatasetMode.ASSERTIONS_ONLY);
 		vreq.setWebappDaoFactory(wadf);
 		vreq.setAssertionsWebappDaoFactory(assertions);
 		vreq.setFullWebappDaoFactory(wadf);

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.rdfservice;
 
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.rdfservice.impl;
 
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.rdfservice.impl;
 
 import java.io.ByteArrayInputStream;

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

@@ -0,0 +1,217 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.rdfservice.impl.sdb;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+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.impl.GraphWithPerform;
+import com.hp.hpl.jena.graph.impl.SimpleBulkUpdateHandler;
+import com.hp.hpl.jena.graph.impl.SimpleEventManager;
+import com.hp.hpl.jena.graph.query.QueryHandler;
+import com.hp.hpl.jena.graph.query.SimpleQueryHandler;
+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.shared.impl.PrefixMappingImpl;
+import com.hp.hpl.jena.util.iterator.ExtendedIterator;
+import com.hp.hpl.jena.util.iterator.WrappedIterator;
+
+import edu.cornell.mannlib.vitro.webapp.dao.jena.EmptyReifier;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.ModelChange;
+
+public class ListeningGraph implements GraphWithPerform {
+    
+    private static final Log log = LogFactory.getLog(ListeningGraph.class);
+    
+    private RDFServiceSDB rdfServiceSDB;
+    private String graphURI;
+    
+    private BulkUpdateHandler bulkUpdateHandler;
+    private GraphEventManager eventManager;
+    private PrefixMapping prefixMapping = new PrefixMappingImpl();
+    private Reifier reifier = new EmptyReifier(this);
+    private QueryHandler queryHandler;
+    
+    public ListeningGraph(String graphURI, RDFServiceSDB rdfServiceSDB) {
+        this.graphURI = graphURI;
+        this.rdfServiceSDB = rdfServiceSDB;
+    }
+    
+    @Override
+    public void add(Triple triple) throws AddDeniedException {
+        performAdd(triple);
+    }
+
+    @Override
+    public void performAdd(Triple triple) throws AddDeniedException {
+        this.rdfServiceSDB.notifyListeners(triple, ModelChange.Operation.ADD, graphURI);
+    }
+
+    @Override
+    public void delete(Triple triple) throws DeleteDeniedException {
+        performDelete(triple);
+    }
+    
+    @Override 
+    public void performDelete(Triple triple) throws DeleteDeniedException {
+        this.rdfServiceSDB.notifyListeners(triple, ModelChange.Operation.REMOVE, graphURI);
+    }    
+      
+    @Override
+    public void close() {
+    }
+
+    @Override
+    public boolean contains(Triple arg0) {
+       return contains(arg0.getSubject(), arg0.getPredicate(), arg0.getObject());
+    }
+
+    @Override
+    public boolean contains(Node subject, Node predicate, Node object) {
+        return false;
+    }
+
+    @Override
+    public boolean dependsOn(Graph arg0) {
+        return false; // who knows?
+    }
+
+    @Override
+    public ExtendedIterator<Triple> find(TripleMatch arg0) {
+        Triple t = arg0.asTriple();
+        return find(t.getSubject(), t.getPredicate(), t.getObject());
+    }
+  
+    @Override
+    public ExtendedIterator<Triple> find(Node subject, Node predicate, Node object) {
+        List<Triple> triplist = new ArrayList<Triple>();
+        return WrappedIterator.create(triplist.iterator());
+    }
+    
+    @Override
+    public BulkUpdateHandler getBulkUpdateHandler() {
+        if (this.bulkUpdateHandler == null) {
+            this.bulkUpdateHandler = new SimpleBulkUpdateHandler(this);
+        }
+        return this.bulkUpdateHandler;
+    }
+
+    @Override
+    public Capabilities getCapabilities() {
+        return capabilities;
+    }
+
+    @Override
+    public GraphEventManager getEventManager() {
+        if (eventManager == null) {
+            eventManager = new SimpleEventManager(this);
+        }
+        return eventManager;
+    }
+
+    @Override
+    public PrefixMapping getPrefixMapping() {
+        return prefixMapping;
+    }
+
+    @Override
+    public Reifier getReifier() {
+        return reifier;
+    }
+
+    @Override
+    public GraphStatisticsHandler getStatisticsHandler() {
+        return null;
+    }
+
+    @Override
+    public TransactionHandler getTransactionHandler() {
+        // TODO Auto-generated method stub
+        return null;
+    }
+
+    @Override
+    public boolean isClosed() {
+        // TODO Auto-generated method stub
+        return false;
+    }
+
+    @Override
+    public boolean isEmpty() {
+        return (size() == 0);
+    }
+
+    @Override
+    public boolean isIsomorphicWith(Graph arg0) {
+        throw new UnsupportedOperationException("isIsomorphicWith() not supported " +
+                "by SPARQL graphs");
+    }
+
+    @Override
+    public QueryHandler queryHandler() {
+        if (queryHandler == null) {
+            queryHandler = new SimpleQueryHandler(this);
+        }
+        return queryHandler;
+    }
+
+    @Override
+    public int size() {
+        int size = find(null, null, null).toList().size();
+        return size;
+    }
+    
+    private final static Capabilities capabilities = new Capabilities() {
+        
+        public boolean addAllowed() {
+            return false;
+        }
+        
+        public boolean addAllowed(boolean everyTriple) {
+            return false;
+        }
+        
+        public boolean canBeEmpty() {
+            return true;
+        }
+        
+        public boolean deleteAllowed() {
+            return false;
+        }
+        
+        public boolean deleteAllowed(boolean everyTriple) {
+            return false;
+        }
+        
+        public boolean findContractSafe() {
+            return true;
+        }
+        
+        public boolean handlesLiteralTyping() {
+            return true;
+        }
+        
+        public boolean iteratorRemoveAllowed() {
+            return false;
+        }
+        
+        public boolean sizeAccurate() {
+            return true;
+        }
+    };
+    
+}

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.rdfservice.impl.sdb;
 
 import org.apache.commons.dbcp.BasicDataSource;

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 package edu.cornell.mannlib.vitro.webapp.rdfservice.impl.sdb;
 
 import java.io.ByteArrayInputStream;
@@ -35,6 +37,7 @@ import com.hp.hpl.jena.sdb.Store;
 import com.hp.hpl.jena.sdb.StoreDesc;
 import com.hp.hpl.jena.sdb.sql.SDBConnection;
 import com.hp.hpl.jena.shared.Lock;
+import com.hp.hpl.jena.vocabulary.OWL;
 
 import edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapper;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraph;
@@ -82,9 +85,7 @@ public class RDFServiceSDB extends RDFServiceImpl implements RDFService {
                                 changeSet.getPreconditionQueryType())) {
             return false;
         }
-        
-        Iterator<ModelChange> csIt = changeSet.getModelChanges().iterator();
-        
+            
         SDBConnection conn = null;
         try {
             conn = new SDBConnection(bds.getConnection());
@@ -96,47 +97,47 @@ public class RDFServiceSDB extends RDFServiceImpl implements RDFService {
         Dataset dataset = getDataset(conn);
         boolean transaction = conn.getTransactionHandler().transactionsSupported();
         
-        try {
+        try {       
+            
             if (transaction) {
                 conn.getTransactionHandler().begin();
-            } else {
-                for (Object o : changeSet.getPreChangeEvents()) {
-                    this.notifyListenersOfEvent(o);
-                }
             }
+            
+            for (Object o : changeSet.getPreChangeEvents()) {
+                this.notifyListenersOfEvent(o);
+            }
+
+            Iterator<ModelChange> csIt = changeSet.getModelChanges().iterator();
             while (csIt.hasNext()) {
                 ModelChange modelChange = csIt.next();
+                modelChange.getSerializedModel().mark(Integer.MAX_VALUE);
                 dataset.getLock().enterCriticalSection(Lock.WRITE);
                 try {
                     Model model = dataset.getNamedModel(modelChange.getGraphURI());
-                    model.enterCriticalSection(Lock.WRITE);
-                    try {
-                        model.register(new ModelListener(modelChange.getGraphURI(), this));
-                        if (modelChange.getOperation() == ModelChange.Operation.ADD) {
-                            model.read(modelChange.getSerializedModel(), null,
-                                    getSerializationFormatString(modelChange.getSerializationFormat()));  
-                        } else if (modelChange.getOperation() == ModelChange.Operation.REMOVE) {
-                            model.remove(parseModel(modelChange));
-                            removeBlankNodesWithSparqlUpdate(dataset, model, modelChange.getGraphURI());
-                        } else {
-                            log.error("unrecognized operation type");
-                        } 
-                    } finally {
-                        model.leaveCriticalSection();
-                    }
+                    operateOnModel(model, modelChange, dataset);
                 } finally {
                     dataset.getLock().leaveCriticalSection();
                 }
             }
+            
             if (transaction) {
-                for (Object o : changeSet.getPreChangeEvents()) {
-                    this.notifyListenersOfEvent(o);
-                }
                 conn.getTransactionHandler().commit();
             }
+            
+            // notify listeners of triple changes
+            csIt = changeSet.getModelChanges().iterator();
+            while (csIt.hasNext()) {
+                ModelChange modelChange = csIt.next();
+                modelChange.getSerializedModel().reset();
+                Model model = ModelFactory.createModelForGraph(
+                        new ListeningGraph(modelChange.getGraphURI(), this));
+                operateOnModel(model, modelChange, null);
+            }
+            
             for (Object o : changeSet.getPostChangeEvents()) {
                 this.notifyListenersOfEvent(o);
             }
+            
         } catch (Exception e) {
             log.error(e, e);
             if (transaction) {
@@ -150,6 +151,25 @@ public class RDFServiceSDB extends RDFServiceImpl implements RDFService {
         return true;
     }
     
+    private void operateOnModel(Model model, ModelChange modelChange, Dataset dataset) {
+        model.enterCriticalSection(Lock.WRITE);
+        try {
+            if (modelChange.getOperation() == ModelChange.Operation.ADD) {
+                model.read(modelChange.getSerializedModel(), null,
+                        getSerializationFormatString(modelChange.getSerializationFormat()));  
+            } else if (modelChange.getOperation() == ModelChange.Operation.REMOVE) {
+                model.remove(parseModel(modelChange));
+                if (dataset != null) {
+                    removeBlankNodesWithSparqlUpdate(dataset, model, modelChange.getGraphURI());
+                }
+            } else {
+                log.error("unrecognized operation type");
+            } 
+        } finally {
+            model.leaveCriticalSection();
+        }
+    }
+    
     private void removeBlankNodesWithSparqlUpdate(Dataset dataset, Model model, String graphURI) {
         
         Model blankNodeModel = ModelFactory.createDefaultModel();
@@ -414,12 +434,10 @@ 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/ReasonerPlugin.java

@@ -22,4 +22,7 @@ public interface ReasonerPlugin {
 			                       Model aboxInferencesModel, 
 			                       OntModel TBoxInferencesModel);
 	
+	public void setSimpleReasoner(SimpleReasoner simpleReasoner);
+	
+	public SimpleReasoner getSimpleReasoner();
 }

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

@@ -49,12 +49,14 @@ public class SimpleReasonerTBoxListener extends StatementListener {
 	
 	@Override
 	public void addedStatement(Statement statement) {
+		
 		ModelUpdate mu = new ModelUpdate(statement, ModelUpdate.Operation.ADD, JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
 		processUpdate(mu);
 	}
 
 	@Override
 	public void removedStatement(Statement statement) {
+		
 		ModelUpdate mu = new ModelUpdate(statement, ModelUpdate.Operation.RETRACT, JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);	
 		processUpdate(mu);
 	}

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

@@ -115,6 +115,7 @@ public class SimpleReasonerSetup implements ServletContextListener {
                 try {
                     ReasonerPlugin plugin = (ReasonerPlugin) Class.forName(
                             classname).getConstructors()[0].newInstance();
+                    plugin.setSimpleReasoner(simpleReasoner);
                     pluginList.add(plugin);
                 } catch(Throwable t) {              
                     ss.info(this, "Could not instantiate reasoner plugin " + classname);