VIVO-898 Call removedStatements.add(), not removedStatements.remove()

Also, in RefactorOperationController, edit events must be fired against the base model, not against the ontModel itself.
Also, add some debugging statements.

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/RefactorOperationController.java

@@ -238,10 +238,10 @@ public class RefactorOperationController extends BaseEditController {
     			Model model = null;
     			
     			if (TBOX_ASSERTIONS.equals(graphURI)) {
-    				model = ModelAccess.on(getServletContext()).getOntModel(TBOX_ASSERTIONS);
+    				model = ModelAccess.on(getServletContext()).getOntModel(TBOX_ASSERTIONS).getBaseModel();
     				doNotify = true;
     			} else if (ABOX_ASSERTIONS.equals(graphURI)) {
-					model = ModelAccess.on(getServletContext()).getOntModel(ABOX_ASSERTIONS);
+					model = ModelAccess.on(getServletContext()).getOntModel(ABOX_ASSERTIONS).getBaseModel();
 					doNotify = true;
     			} else {
     			    model = dataset.getNamedModel(graphURI);

webapp/src/edu/cornell/mannlib/vitro/webapp/tboxreasoner/ConfiguredReasonerListener.java

@@ -173,10 +173,17 @@ public class ConfiguredReasonerListener implements ModelChangedListener {
 
 	@Override
 	public void notifyEvent(Model m, Object event) {
+		log.debug("Notified of event.");
 		if (event instanceof EditEvent) {
 			EditEvent ee = (EditEvent) event;
 			if (!ee.getBegin()) {
+				log.debug("Notified of ending EditEvent.");
+
 				TBoxChanges changes = changeSet.getAndSet(new TBoxChanges());
+				if (log.isDebugEnabled()) {
+					log.debug("Change set: " + changes);
+				}
+				
 				this.reasonerDriver.runSynchronizer(changes);
 			}
 		}
@@ -190,6 +197,10 @@ public class ConfiguredReasonerListener implements ModelChangedListener {
 	// ----------------------------------------------------------------------
 
 	public void tryAdd(Statement stmt) {
+		if (log.isDebugEnabled()) {
+			log.debug("try to add statement: " + stmt);
+		}
+
 		if (suspended.get()) {
 			return;
 		}
@@ -215,6 +226,10 @@ public class ConfiguredReasonerListener implements ModelChangedListener {
 	}
 
 	public void tryRemove(Statement stmt) {
+		if (log.isDebugEnabled()) {
+			log.debug("try to remove statement: " + stmt);
+		}
+
 		if (suspended.get()) {
 			return;
 		}

webapp/src/edu/cornell/mannlib/vitro/webapp/tboxreasoner/TBoxChanges.java

@@ -36,7 +36,7 @@ public class TBoxChanges {
 	}
 
 	public void removeStatement(Statement stmt) {
-		removedStatements.remove(stmt);
+		removedStatements.add(stmt);
 	}
 
 	public void deleteDataProperty(Statement stmt) {
@@ -80,4 +80,13 @@ public class TBoxChanges {
 		return deletedObjectPropertyUris;
 	}
 
+	@Override
+	public String toString() {
+		return "TBoxChanges[addedStatements=" + addedStatements
+				+ ", removedStatements=" + removedStatements
+				+ ", deletedDataPropertyUris=" + deletedDataPropertyUris
+				+ ", deletedObjectPropertyUris=" + deletedObjectPropertyUris
+				+ "]";
+	}
+
 }