misc. cleanup / minor fixes

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

@@ -12,14 +12,12 @@ import org.apache.commons.logging.LogFactory;
 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 edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapper;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ModelChange;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.ListeningGraph;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.RDFServiceJena;
 
 public class RDFServiceModel extends RDFServiceJena implements RDFService {

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

@@ -85,7 +85,6 @@ public class RDFServiceSDB extends RDFServiceJena implements RDFService {
 
         try {
             beginTransaction(sdbConn);
-        	startBulkUpdate();
         	notifyListenersOfPreChangeEvents(changeSet);
         	applyChangeSetToModel(changeSet, dataset);
             commitTransaction(sdbConn);
@@ -97,23 +96,10 @@ public class RDFServiceSDB extends RDFServiceJena implements RDFService {
             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();

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

@@ -16,10 +16,6 @@ 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;
@@ -60,7 +56,6 @@ 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;
@@ -68,10 +63,11 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ModelChange;
 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.impl.ChangeSetImpl;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceImpl;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.ListeningGraph;
+import edu.cornell.mannlib.vitro.webapp.utils.http.HttpClientFactory;
 import edu.cornell.mannlib.vitro.webapp.utils.sparql.ResultSetIterators.ResultSetQuadsIterator;
 import edu.cornell.mannlib.vitro.webapp.utils.sparql.ResultSetIterators.ResultSetTriplesIterator;
 

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

@@ -5,13 +5,11 @@ package edu.cornell.mannlib.vitro.webapp.reasoner;
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.InputStream;
-import java.util.ArrayDeque;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Queue;
@@ -164,6 +162,7 @@ public class ABoxRecomputer {
             return;
         }
         long start = System.currentTimeMillis();
+        int size = individuals.size();
         int numInds = 0;
         Model rebuildModel = ModelFactory.createDefaultModel();
         Model additionalInferences = ModelFactory.createDefaultModel();
@@ -185,7 +184,7 @@ public class ABoxRecomputer {
                 }
                 if (reportingInterval) {
                     log.info("Still recomputing inferences (" 
-                            + numInds + "/" + individuals.size() + " individuals)");
+                            + numInds + "/" + size + " individuals)");
                     log.info((System.currentTimeMillis() - start) / numInds + " ms per individual");
                 }
                 if (stopRequested) {
@@ -437,7 +436,7 @@ public class ABoxRecomputer {
      * Get the URIs for all individuals in the system
      */
     protected Queue<String> getAllIndividualURIs() {
-        Queue<String> individualURIs = new ArrayDeque<String>();
+        Queue<String> individualURIs = new IndividualURIQueue<String>();
         List<String> classList = new ArrayList<String>();
         tboxModel.enterCriticalSection(Lock.READ);
         try {

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

@@ -0,0 +1,141 @@
+package edu.cornell.mannlib.vitro.webapp.reasoner;
+
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.Queue;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ConcurrentLinkedQueue;
+
+public class IndividualURIQueue<E> implements Queue<E> {
+
+    private ConcurrentLinkedQueue<E> q = new ConcurrentLinkedQueue<E>();
+    private ConcurrentHashMap<E, Boolean> m = new ConcurrentHashMap<E, Boolean>();
+    
+    @Override
+    public synchronized 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 synchronized 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 synchronized boolean remove(Object o) {
+        m.remove(o);
+        return q.remove(o);
+    }
+    
+    @Override
+    public synchronized boolean removeAll(Collection<?> c) {
+        for (Object e : c) {
+            m.remove(e);
+        }
+        return q.removeAll(c);
+    }
+    
+    @Override
+    public synchronized 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 synchronized 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 synchronized E poll() {
+        E e =  q.poll();
+        m.remove(e);
+        return e;
+    }
+    
+    @Override
+    public synchronized E remove() {
+        E e = q.remove();
+        m.remove(e);
+        return e;
+    }
+    
+}

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

@@ -3,14 +3,11 @@
 package edu.cornell.mannlib.vitro.webapp.reasoner;
 
 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;
 
 import org.apache.commons.logging.Log;
@@ -79,7 +76,6 @@ public class SimpleReasoner extends StatementListener
 			VitroModelFactory.createOntologyModel())
 				.createAnnotationProperty(mostSpecificTypePropertyURI);
 	
-	// Recomputer
 	private ABoxRecomputer recomputer = null;
 	private List<ReasonerPlugin> pluginList = new CopyOnWriteArrayList<ReasonerPlugin>();   
     private boolean doSameAs = true;
@@ -149,7 +145,6 @@ public class SimpleReasoner extends StatementListener
 		ds.addNamedModel(ModelNames.ABOX_ASSERTIONS, aboxModel);
 		ds.addNamedModel(ModelNames.ABOX_INFERENCES, inferenceModel);
 		ds.addNamedModel(ModelNames.TBOX_ASSERTIONS, tboxModel);	
-		
 		ds.setDefaultModel(ModelFactory.createUnion(fullModel, tboxModel));
 		recomputer = new ABoxRecomputer(tboxModel, aboxModel, new RDFServiceModel(ds), this, searchIndexer);
 	}
@@ -170,41 +165,6 @@ public class SimpleReasoner extends StatementListener
         return this.doSameAs;
     }
   
-    private void listenToStatement(Statement stmt) {
-        Queue<String> individualURIs = new IndividualURIQueue<String>();
-        listenToStatement(stmt, individualURIs);
-    }
-    
-    private void listenToStatement(Statement stmt, Queue<String> individualURIs) {
-        if(stmt.getSubject().isURIResource()) {
-            individualURIs.add(stmt.getSubject().getURI());
-        }
-        if(stmt.getObject().isURIResource() && !(RDF.type.equals(stmt.getPredicate()))) {
-            individualURIs.add(stmt.getObject().asResource().getURI());
-        }
-        recomputeIndividuals(individualURIs); 
-    }
-    
-    private void recomputeIndividuals(Queue<String> individualURIs) {
-        long start = System.currentTimeMillis();
-        int size = individualURIs.size();
-        recomputer.recompute(individualURIs);
-        if(size > 2) {
-            log.info((System.currentTimeMillis() - start) + " ms to recompute " 
-                    + size + " individuals");
-        }
-    }
-    
-    boolean isABoxInferenceGraph(String graphURI) {
-        return ModelNames.ABOX_INFERENCES.equals(graphURI);
-    }
-    
-    boolean isTBoxGraph(String graphURI) {
-        return ( ModelNames.TBOX_ASSERTIONS.equals(graphURI)
-                 || ModelNames.TBOX_INFERENCES.equals(graphURI)
-                 || (graphURI != null && graphURI.contains("tbox")) );
-    }
-    
     public void notifyModelChange(ModelChange modelChange) {
         if(isABoxInferenceGraph(modelChange.getGraphURI()) 
                 || isTBoxGraph(modelChange.getGraphURI())) {
@@ -230,24 +190,24 @@ public class SimpleReasoner extends StatementListener
         recomputeIndividuals(individualURIs);
     }
     
-	/*
+    /*
-	 * Performs incremental ABox reasoning based
+     * Performs incremental ABox reasoning based
-	 * on the addition of a new statement
+     * on the addition of a new statement
-	 *  (aka assertion) to the ABox.
+     *  (aka assertion) to the ABox.
-	 */
+     */
-	@Override
+    @Override
-	public void addedStatement(Statement stmt) {
+    public void addedStatement(Statement stmt) {
-	    doPlugins(ModelUpdate.Operation.ADD,stmt);
+        doPlugins(ModelUpdate.Operation.ADD,stmt);
-	    listenToStatement(stmt);	   
+        listenToStatement(stmt);       
-	}
+    }
     
-	/*
+    /*
-	 * Performs incremental ABox reasoning based
+     * Performs incremental ABox reasoning based
-	 * on the retraction of a statement (aka assertion)
+     * on the retraction of a statement (aka assertion)
-	 * from the ABox. 
+     * from the ABox. 
-	 */
+     */
-	@Override
+    @Override
-	public void removedStatement(Statement stmt) {	
+    public void removedStatement(Statement stmt) {  
         doPlugins(ModelUpdate.Operation.RETRACT,stmt);
         Queue<String> individualURIs = new IndividualURIQueue<String>();
         if(doSameAs && OWL.sameAs.equals(stmt.getPredicate())) {
@@ -260,8 +220,33 @@ public class SimpleReasoner extends StatementListener
                         stmt.getObject().asResource().getURI()));
             }
         }
-	    listenToStatement(stmt, individualURIs);
+        listenToStatement(stmt, individualURIs);
-	}	
+    }   
+    
+    private void listenToStatement(Statement stmt) {
+        Queue<String> individualURIs = new IndividualURIQueue<String>();
+        listenToStatement(stmt, individualURIs);
+    }
+    
+    private void listenToStatement(Statement stmt, Queue<String> individualURIs) {
+        if(stmt.getSubject().isURIResource()) {
+            individualURIs.add(stmt.getSubject().getURI());
+        }
+        if(stmt.getObject().isURIResource() && !(RDF.type.equals(stmt.getPredicate()))) {
+            individualURIs.add(stmt.getObject().asResource().getURI());
+        }
+        recomputeIndividuals(individualURIs); 
+    }
+
+    private void recomputeIndividuals(Queue<String> individualURIs) {
+        long start = System.currentTimeMillis();
+        int size = individualURIs.size();
+        recomputer.recompute(individualURIs);
+        if(size > 2) {
+            log.info((System.currentTimeMillis() - start) + " ms to recompute " 
+                    + size + " individuals");
+        }
+    }
     
     /**
 	 * Performs incremental ABox reasoning based
@@ -1158,12 +1143,23 @@ public class SimpleReasoner extends StatementListener
 	}
 	  
 	/**
-	 * Asynchronous reasoning mode (DeltaComputer) no longer used in the case of batch removals. 
+	 * Asynchronous reasoning mode (DeltaComputer) no longer used 
+	 * in the case of batch removals. 
 	 */
 	public boolean isABoxReasoningAsynchronous() {
          return false;
 	}
 	
+    boolean isABoxInferenceGraph(String graphURI) {
+        return ModelNames.ABOX_INFERENCES.equals(graphURI);
+    }
+    
+    boolean isTBoxGraph(String graphURI) {
+        return ( ModelNames.TBOX_ASSERTIONS.equals(graphURI)
+                 || ModelNames.TBOX_INFERENCES.equals(graphURI)
+                 || (graphURI != null && graphURI.contains("tbox")) );
+    }
+    
 	@Override 
 	public void notifyEvent(String string, Object event) {
 	    // don't care
@@ -1171,24 +1167,9 @@ public class SimpleReasoner extends StatementListener
 	
 	@Override
 	public void notifyEvent(Model model, Object event) {	    
-//	    if (event instanceof BulkUpdateEvent) {	
+	    // don't care
-//	    	handleBulkUpdateEvent(event);
-//	    }
 	}
 	
-//	public synchronized void handleBulkUpdateEvent(Object event) {
-//	    
-//	    if (event instanceof BulkUpdateEvent) {	
-//	    	if (((BulkUpdateEvent) event).getBegin()) {	
-//	    	    this.accumulateChanges = true;
-//	    	} else {
-//	    		log.debug("received a bulk update end event");
-//	    		this.accumulateChanges = false;
-//	    		recomputeIndividuals();
-//	    	}
-//	    }
-//	}
-	
 	/**
 	 * Utility method for logging
 	 */
@@ -1200,138 +1181,4 @@ 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 synchronized 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 synchronized 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 synchronized boolean remove(Object o) {
-            m.remove(o);
-            return q.remove(o);
-        }
-        
-        @Override
-        public synchronized boolean removeAll(Collection<?> c) {
-            for (Object e : c) {
-                m.remove(e);
-            }
-            return q.removeAll(c);
-        }
-        
-        @Override
-        public synchronized 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 synchronized 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 synchronized E poll() {
-            E e =  q.poll();
-            m.remove(e);
-            return e;
-        }
-        
-        @Override
-        public synchronized E remove() {
-            E e = q.remove();
-            m.remove(e);
-            return e;
-        }
-        
-    }
-    
 }