Improvements to write performance

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

@@ -19,6 +19,7 @@
 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 @@ private UpdateRequest parseUpdateString(HttpServletRequest req)
 	}
 
 	private void executeUpdate(HttpServletRequest req, UpdateRequest parsed) {
-		ServletContext ctx = req.getSession().getServletContext();
 		VitroRequest vreq = new VitroRequest(req);
-
 		SearchIndexer indexer = ApplicationUtils.instance().getSearchIndexer();
-		indexer.pause();
-		try {
-			Dataset ds = new RDFServiceDataset(vreq.getUnfilteredRDFService());
-			GraphStore graphStore = GraphStoreFactory.create(ds);
+		Dataset ds = new RDFServiceDataset(vreq.getUnfilteredRDFService());
+		GraphStore graphStore = GraphStoreFactory.create(ds);
+	    try {
+	        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();
+			}
 		}
 	}
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java

@@ -73,6 +73,7 @@
 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.adapters.VitroModelFactory;
 import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils.MergeResult;
@@ -706,14 +707,13 @@ private void doRemoveModel(String modelName, ModelMaker modelMaker) {
 
     private void doClearModel(String modelName, ModelMaker modelMaker) {
         Model m = modelMaker.getModel(modelName);
-        OntModel o = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,m);
+        OntModel o = VitroModelFactory.createOntologyModel(m);
         o.enterCriticalSection(Lock.WRITE);
         try {
-            o.removeAll(null,null,null);
+            o.removeAll();
         } finally {
             o.leaveCriticalSection();
         }
-        // removeAll() doesn't work with the listeners!
     }
 
     private void doLoadRDFData(String modelName, String docLoc, String filePath, String language, ModelMaker modelMaker) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/jena/RDFUploadController.java

@@ -44,6 +44,7 @@
 import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess.WhichService;
+import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelNames;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
@@ -202,9 +203,20 @@ public void doPost(HttpServletRequest req,
             }
             if (aboxModel != null) {
                 aboxChangeModel = uploadModel.remove(tboxChangeModel);
-                aboxstmtCount = operateOnModel(request.getUnfilteredWebappDaoFactory(),
-                        aboxModel, aboxChangeModel, ontModelSelector, 
-                                remove, makeClassgroups, loginBean.getUserURI());
+                aboxstmtCount = aboxChangeModel.size();
+                ByteArrayOutputStream os = new ByteArrayOutputStream();
+                aboxChangeModel.write(os, "N3");
+                ByteArrayInputStream in = new ByteArrayInputStream(os.toByteArray());
+                if(!remove) {
+                    readIntoModel(in, "N3", request.getRDFService(), 
+                            ModelNames.ABOX_ASSERTIONS);
+                } else {
+                    removeFromModel(in, "N3", request.getRDFService(), 
+                            ModelNames.ABOX_ASSERTIONS);
+                }
+//                operateOnModel(request.getUnfilteredWebappDaoFactory(),
+//                        aboxModel, aboxChangeModel, ontModelSelector, 
+//                                remove, makeClassgroups, loginBean.getUserURI());
             }
             request.setAttribute("uploadDesc", uploadDesc + ". " + verb + " " + 
                     (tboxstmtCount + aboxstmtCount) + "  statements.");
@@ -225,9 +237,19 @@ public void doPost(HttpServletRequest req,
         }
     }
 
+    private static final boolean BEGIN = true;
+    private static final boolean END = !BEGIN;
+
+    private ChangeSet makeChangeSet(RDFService rdfService) {
+        ChangeSet cs = rdfService.manufactureChangeSet();
+        cs.addPreChangeEvent(new BulkUpdateEvent(null, BEGIN));
+        cs.addPostChangeEvent(new BulkUpdateEvent(null, END));
+        return cs;
+    }
+
     private void addUsingRDFService(InputStream in, String languageStr, 
             RDFService rdfService) {
-        ChangeSet changeSet = rdfService.manufactureChangeSet();
+        ChangeSet changeSet = makeChangeSet(rdfService);
         RDFService.ModelSerializationFormat format = 
                 ("RDF/XML".equals(languageStr) 
                         || "RDF/XML-ABBREV".equals(languageStr))
@@ -333,7 +355,7 @@ private long operateOnModel(WebappDaoFactory webappDaoFactory,
                     RDFService rdfService = new RDFServiceModel(mainModel);
                     ByteArrayOutputStream out = new ByteArrayOutputStream();
                     changesModel.write(out, "N-TRIPLE");
-                    ChangeSet cs = rdfService.manufactureChangeSet();
+                    ChangeSet cs = makeChangeSet(rdfService);
                     ByteArrayInputStream in = new ByteArrayInputStream(out.toByteArray());
                     cs.addRemoval(in, RDFService.ModelSerializationFormat.NTRIPLE, null);
                     try {
@@ -398,7 +420,7 @@ private void doLoadRDFData(String modelName,
 
     private void readIntoModel(InputStream in, String language, 
             RDFService rdfService, String modelName) {
-        ChangeSet cs = rdfService.manufactureChangeSet();
+        ChangeSet cs = makeChangeSet(rdfService);
         cs.addAddition(in, RDFServiceUtils.getSerializationFormatFromJenaString(
                         language), modelName);
         try {
@@ -408,6 +430,18 @@ private void readIntoModel(InputStream in, String language,
         }
     }
 
+    private void removeFromModel(InputStream in, String language, 
+            RDFService rdfService, String modelName) {
+        ChangeSet cs = makeChangeSet(rdfService);
+        cs.addRemoval(in, RDFServiceUtils.getSerializationFormatFromJenaString(
+                        language), modelName);
+        try {
+            rdfService.changeSetUpdate(cs);
+        } catch (RDFServiceException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
      private void forwardToFileUploadError( String errrorMsg , 
                                             HttpServletRequest req, 
                                             HttpServletResponse response) 

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

@@ -35,8 +35,7 @@ public class ModelContext {
 	public static void registerListenerForChanges(ServletContext ctx, ModelChangedListener ml){
 
         try {
-            RDFServiceUtils.getRDFServiceFactory(ctx).registerListener(
-                    new JenaChangeListener(ml));
+            RDFServiceUtils.getRDFServiceFactory(ctx).registerJenaModelChangedListener(ml);
         } catch (RDFServiceException e) {
             log.error(e,e);
         }