From f25ffeffafd1d56fc693d02ae5822425b08364d2 Mon Sep 17 00:00:00 2001
From: stellamit <stellamit@440791e1-c2bf-4c1e-ad7c-caf3f8b0ebe8>
Date: Wed, 2 Nov 2011 21:21:24 +0000
Subject: [PATCH] updates for NIHVIVO-3271 and NIHVIVO-3207

---
 .../vitro/webapp/dao/DisplayVocabulary.java   |  2 --
 .../webapp/ontology/update/ABoxUpdater.java   | 27 +++++--------------
 .../vitro/webapp/reasoner/SimpleReasoner.java |  4 +--
 3 files changed, 8 insertions(+), 25 deletions(-)

diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/DisplayVocabulary.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/DisplayVocabulary.java
index 1ba46e224..6684e9af6 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/DisplayVocabulary.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/DisplayVocabulary.java
@@ -8,9 +8,7 @@ import com.hp.hpl.jena.ontology.OntClass;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
 
 
 public class DisplayVocabulary {
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java
index 16a19f4d1..fa651d5a1 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java
@@ -146,48 +146,33 @@ public class ABoxUpdater {
 		   
 		   StmtIterator iter = aboxModel.listStatements(oldClass, (Property) null, (RDFNode) null);
 
-		   int renameCount = 0;
 		   int removeCount = 0;
 		   while (iter.hasNext()) {
 			   Statement oldStatement = iter.next();
-			   if (newTBoxAnnotationsModel.contains(oldStatement)) {
-				   continue; 
-				   // if this statement was loaded from the new annotations,
-				   // don't attempt to remove it.
-				   // This happens in cases where a class hasn't really
-				   // been removed, but we just want to map any ABox
-				   // data using it to use a different class instead.
-			   } else {
-				   removeCount++;
-				   retractions.add(oldStatement);
-			   }
-			   //logChange(oldStatement, false);
-			   //logChange(newStatement,true);
+			   removeCount++;
+			   retractions.add(oldStatement);
 		   }
 		   
 		   //log summary of changes
-		   if (renameCount > 0) {
-			   logger.log("Changed " + renameCount + " subject reference" + ((renameCount > 1) ? "s" : "") + " from type"  + oldClass.getURI() + " to type " + newClass.getURI());
-		   }
 		   if (removeCount > 0) {
 			   logger.log("Removed " + removeCount + " subject reference" + ((removeCount > 1) ? "s" : "") + " to the "  + oldClass.getURI() + " class");
 		   }
 
 		   // Change class references in the objects of rdf:type statements
-		   iter = aboxModel.listStatements((Resource) null, (Property) null, oldClass);
+		   iter = aboxModel.listStatements((Resource) null, RDF.type, oldClass);
 
-		   renameCount = 0;
+		   int renameCount = 0;
 		   while (iter.hasNext()) {
 			   renameCount++;
 			   Statement oldStatement = iter.next();
-			   Statement newStatement = ResourceFactory.createStatement(oldStatement.getSubject(), oldStatement.getPredicate(), newClass);
+			   Statement newStatement = ResourceFactory.createStatement(oldStatement.getSubject(), RDF.type, newClass);
 			   retractions.add(oldStatement);
 			   additions.add(newStatement);
 		   }
 		   
 		   //log summary of changes
 		   if (renameCount > 0) {
-			   logger.log("Renamed " + renameCount + " object reference" + ((renameCount > 1) ? "s" : "") + " from type "  + oldClass.getURI() + " to type " + newClass.getURI());
+			   logger.log("Retyped " + renameCount + " individual" + ((renameCount > 1) ? "s" : "") + " from type "  + oldClass.getURI() + " to type " + newClass.getURI());
 		   }
 		   
 		   aboxModel.remove(retractions);
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
index 456699436..8cbe88543 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
@@ -1024,7 +1024,7 @@ public class SimpleReasoner extends StatementListener {
 	 * then reconciled with the inference graph used by the
 	 * application. The model reconciliation must be done
 	 * without reading the whole inference models into 
-	 * memory since we are supporting very large ABox 
+	 * memory in order to support very large ABox 
 	 * inference models.	  
 	 */
 	public synchronized void recomputeABox() {
@@ -1390,7 +1390,7 @@ public class SimpleReasoner extends StatementListener {
 	    		log.info("received BulkUpdateEvent(begin)");
 	    		
 	    		if (batchMode1 || batchMode2) {
-	    			log.info("received a BulkUpdateEvent(begin) while already in batch update mode; this event will be ignored.");
+	    			log.info("received a BulkUpdateEvent(begin) while already in batch update mode; this event will be ignored (and processing in batch mode will continue until there are no pending updates)");
 	    			return;  
 	    		} else {
 	    			batchMode1 = true;