Merge branch 'writePerformance-1.8' into writePerformance

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

@@ -5,9 +5,8 @@ package edu.cornell.mannlib.vitro.webapp.dao.jena;
 import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.Collections;
+import java.util.Iterator;
 import java.util.List;
-import java.util.Queue;
-import java.util.concurrent.ConcurrentLinkedQueue;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -26,6 +25,8 @@ import com.hp.hpl.jena.graph.impl.SimpleEventManager;
 import com.hp.hpl.jena.query.QuerySolution;
 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.rdf.model.StmtIterator;
 import com.hp.hpl.jena.shared.AddDeniedException;
 import com.hp.hpl.jena.shared.Command;
 import com.hp.hpl.jena.shared.DeleteDeniedException;
@@ -53,10 +54,9 @@ public class RDFServiceGraph implements GraphWithPerform {
     private PrefixMapping prefixMapping = new PrefixMappingImpl();
     private GraphEventManager eventManager;
     
-    private boolean queueWrites = false;
+    private boolean inTransaction = false;
-    private ConcurrentLinkedQueue<Triple> addTripleQueue = new ConcurrentLinkedQueue<Triple>();
+    private Graph additionsGraph = ModelFactory.createDefaultModel().getGraph();
-    private ConcurrentLinkedQueue<Triple> removeTripleQueue = new ConcurrentLinkedQueue<Triple>();
+    private Graph removalsGraph = ModelFactory.createDefaultModel().getGraph();
-
 
     /**
      * Returns a SparqlGraph for the union of named graphs in a remote repository 
@@ -97,19 +97,20 @@ public class RDFServiceGraph implements GraphWithPerform {
         return sb.toString();
     }
         
-    public void flush() {
+    private synchronized void flush() {                                
-        log.debug("Flushing a batch");                                
         ChangeSet changeSet = rdfService.manufactureChangeSet();
         try {
-            if(!removeTripleQueue.isEmpty()) {
+            if(!removalsGraph.isEmpty()) {
-                String removals = serializeQueue(removeTripleQueue);
+                String removals = serializeGraph(removalsGraph);
                 changeSet.addRemoval(RDFServiceUtils.toInputStream(removals), 
                         RDFService.ModelSerializationFormat.N3, graphURI);
+                removalsGraph.clear();
             }
-            if(!addTripleQueue.isEmpty()) {
+            if(!additionsGraph.isEmpty()) {
-                String additions = serializeQueue(addTripleQueue);
+                String additions = serializeGraph(additionsGraph);
                 changeSet.addAddition(RDFServiceUtils.toInputStream(additions), 
                         RDFService.ModelSerializationFormat.N3, graphURI);
+                additionsGraph.clear();
             }
             rdfService.changeSetUpdate(changeSet);
         } catch (RDFServiceException rdfse) {
@@ -117,27 +118,60 @@ public class RDFServiceGraph implements GraphWithPerform {
         }
     }
     
-    private String serializeQueue(Queue<Triple> tripleQueue) {
+    private synchronized String serializeGraph(Graph graph) {
         String triples = "";
-        while(!tripleQueue.isEmpty()) {
+        Iterator<Triple> tripIt = graph.find(null, null, null);
-            triples += " \n" + serialize(tripleQueue.poll());
+        while(tripIt.hasNext()) {
+            triples += " \n" + serialize(tripIt.next());
         }
         return triples;
     }
     
     @Override
     public void performAdd(Triple t) {
-        addTripleQueue.add(t);
+        if(inTransaction) {
-        if(!queueWrites) {
+            stageAddition(t);
-            flush();
+        } else {
+            ChangeSet changeSet = rdfService.manufactureChangeSet();
+            try {
+                changeSet.addAddition(RDFServiceUtils.toInputStream(serialize(t)),
+                        RDFService.ModelSerializationFormat.N3, graphURI);
+                rdfService.changeSetUpdate(changeSet);
+            } catch (RDFServiceException rdfse) {
+                throw new RuntimeException(rdfse);
+            }
+        }
+    }
+    
+    private void stageAddition(Triple t) {
+        if(removalsGraph.contains(t)) {
+            removalsGraph.remove(t.getSubject(), t.getPredicate(), t.getObject());
+        } else {
+            additionsGraph.add(t);
         }
     }
     
     @Override
     public void performDelete(Triple t) {
-        removeTripleQueue.add(t);
+        if(inTransaction) {
-        if(!queueWrites) {
+            stageDeletion(t);
-            flush();
+        } else {
+            ChangeSet changeSet = rdfService.manufactureChangeSet();
+            try {
+                changeSet.addRemoval(RDFServiceUtils.toInputStream(serialize(t)),
+                        RDFService.ModelSerializationFormat.N3, graphURI);
+                rdfService.changeSetUpdate(changeSet);
+            } catch (RDFServiceException rdfse) {
+                throw new RuntimeException(rdfse);
+            }
+        }
+    }
+    
+    private synchronized void stageDeletion(Triple t) {
+        if(additionsGraph.contains(t)) {
+            additionsGraph.remove(t.getSubject(), t.getPredicate(), t.getObject());
+        } else {
+            removalsGraph.add(t);
         }
     }
     
@@ -148,16 +182,30 @@ public class RDFServiceGraph implements GraphWithPerform {
         }
         String constructStr = "CONSTRUCT { ?s ?p ?o } WHERE { GRAPH <" + graphURI + "> { ?s ?p ?o } }";
         try {
-            InputStream model = rdfService.sparqlConstructQuery(
+            if(inTransaction) {
-                    constructStr, RDFService.ModelSerializationFormat.N3);
+                Model model = ModelFactory.createDefaultModel();
-            ChangeSet changeSet = rdfService.manufactureChangeSet();
+                rdfService.sparqlConstructQuery(constructStr, model);
-            changeSet.addRemoval(model, RDFService.ModelSerializationFormat.N3, graphURI);
+                stageRemoveAll(model);
-            rdfService.changeSetUpdate(changeSet);
+            } else {
+                InputStream model = rdfService.sparqlConstructQuery(
+                        constructStr, RDFService.ModelSerializationFormat.N3);
+                ChangeSet changeSet = rdfService.manufactureChangeSet();
+                changeSet.addRemoval(model, RDFService.ModelSerializationFormat.N3, graphURI);
+                rdfService.changeSetUpdate(changeSet);
+            }
         } catch (RDFServiceException rdfse) {
             throw new RuntimeException(rdfse);
         }
     }
     
+    private void stageRemoveAll(Model removals) {
+        StmtIterator sit = removals.listStatements();
+        while (sit.hasNext()) {
+            Triple t = sit.nextStatement().asTriple();
+            stageDeletion(t);
+        }
+    }
+    
     @Override
     public void close() {
         // can't close a remote endpoint
@@ -191,7 +239,22 @@ public class RDFServiceGraph implements GraphWithPerform {
 
         ResultSetConsumer.HasResult consumer = new ResultSetConsumer.HasResult();
         execSelect(containsQuery.toString(), consumer);
-        return consumer.hasResult();
+        boolean initialResult = consumer.hasResult();
+        if(!inTransaction) {
+            return initialResult;
+        } else {
+            Triple t = Triple.create(subject, predicate, object);
+            return (initialResult || additionsGraphContains(t)) 
+                    && !removalsGraphContains(t);
+        } 
+    }
+    
+    private synchronized boolean additionsGraphContains(Triple t) {
+        return additionsGraph.contains(t);
+    }
+    
+    private synchronized boolean removalsGraphContains(Triple t) {
+        return removalsGraph.contains(t);
     }
 
     @Override
@@ -284,6 +347,10 @@ public class RDFServiceGraph implements GraphWithPerform {
         String queryString = findQuery.toString();
 
         final List<Triple> triplist = new ArrayList<Triple>();
+        if(inTransaction) {
+            addAdditions(triplist, additionsGraph.find(subject, predicate, object));
+            subtractRemovals(triplist, removalsGraph.find(subject, predicate, object));
+        }
         
         execSelect(queryString, new ResultSetConsumer() {
             @Override
@@ -311,6 +378,24 @@ public class RDFServiceGraph implements GraphWithPerform {
         return WrappedIterator.create(triplist.iterator());
     }
 
+    private void addAdditions(List<Triple> tripList, ExtendedIterator<Triple> tripIt) {
+        while(tripIt.hasNext()) {
+            Triple t = tripIt.next();
+            if(!tripList.contains(t)) {
+                tripList.add(t);
+            }
+         }
+    }
+    
+    private void subtractRemovals(List<Triple> tripList, ExtendedIterator<Triple> tripIt) {
+        while(tripIt.hasNext()) {
+            Triple t = tripIt.next();
+            if(tripList.contains(t)) {
+                tripList.remove(t);
+            }
+         }
+    }
+    
     private boolean isVar(Node node) {
         return (node == null || node.isVariable() || node == Node.ANY);
     }
@@ -430,21 +515,21 @@ public class RDFServiceGraph implements GraphWithPerform {
 
 	private final TransactionHandler transactionHandler = new TransactionHandler() {
 	    @Override
-	    public void abort() {
+	    public synchronized void abort() {
-	        queueWrites = false;
+	        inTransaction = false;
-	        removeTripleQueue.clear();
+	        removalsGraph.clear();
-	        addTripleQueue.clear();
+	        additionsGraph.clear();
 	    }
 
         @Override
-        public void begin() {
+        public synchronized void begin() {
-            queueWrites = true;
+            inTransaction = true;
         }
 
         @Override
-        public void commit() {
+        public synchronized void commit() {
             flush();
-            queueWrites = false;
+            inTransaction = false;
         }
 
         @Override

webapp/test/edu/cornell/mannlib/vitro/webapp/controller/api/SparqlUpdateApiTest.java

@@ -0,0 +1,90 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.controller.api;
+
+import static org.junit.Assert.*;
+
+import java.io.StringReader;
+
+import junit.framework.Assert;
+
+import org.junit.Before;
+import org.junit.Test;
+
+import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.query.DatasetFactory;
+import com.hp.hpl.jena.query.ReadWrite;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.update.GraphStore;
+import com.hp.hpl.jena.update.GraphStoreFactory;
+import com.hp.hpl.jena.update.UpdateAction;
+import com.hp.hpl.jena.update.UpdateFactory;
+
+import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceModel;
+
+/**
+ * Test that the SparqlQueryApiExecutor can handle all query types and all
+ * formats.
+ */
+public class SparqlUpdateApiTest extends AbstractTestClass {
+
+    private final String GRAPH_URI = "http://example.org/graph"; 
+    
+    private final String updateStr1 = 
+        "INSERT DATA { GRAPH <" + GRAPH_URI + "> { \n" +
+        "    <http://here.edu/n1> a <http://here.edu/Class1> . \n" +        
+        "} } ; \n" +
+        "INSERT { GRAPH <" + GRAPH_URI + "> { \n " +
+        "     ?x a <http://here.edu/Class2> . \n " +  
+        "} } WHERE { \n" +
+        "    GRAPH <" + GRAPH_URI + "> { ?x a <http://here.edu/Class1> } \n " + 
+        "}";
+
+    private final String result1 = 
+        "<http://here.edu/n1> a <http://here.edu/Class1> . \n" +
+        "<http://here.edu/n1> a <http://here.edu/Class2> ." ;
+    
+    // look at how the SimpleReasoner is set up.
+    
+    private Model model;
+    private RDFService rdfService;
+
+    @Before
+    public void setup() {
+        model = ModelFactory.createDefaultModel();
+        Dataset ds = DatasetFactory.createMem();
+        ds.addNamedModel(GRAPH_URI, model);
+        rdfService = new RDFServiceModel(ds);
+    }
+
+    // ----------------------------------------------------------------------
+    // Tests
+    // ----------------------------------------------------------------------
+
+    @Test
+    public void nullRdfService() throws Exception {
+        model.removeAll();
+        Model desiredResults = ModelFactory.createDefaultModel();
+        desiredResults.read(new StringReader(result1), null, "N3");
+        Dataset ds = new RDFServiceDataset(rdfService);
+        GraphStore graphStore = GraphStoreFactory.create(ds);
+        try {
+            if(ds.supportsTransactions()) {
+                ds.begin(ReadWrite.WRITE);
+                System.out.println("yep");
+            }
+            UpdateAction.execute(UpdateFactory.create(updateStr1), graphStore);
+        } finally {
+            if(ds.supportsTransactions()) {
+                ds.commit();
+                ds.end();
+            }
+        }
+        assertEquals("updateStr1 yields result1", desiredResults.toString(), model.toString());
+    }
+
+}