From c8172a49ea974d168da3fce7293bd0e6a3620e4f Mon Sep 17 00:00:00 2001
From: bjl23 <bjl23@440791e1-c2bf-4c1e-ad7c-caf3f8b0ebe8>
Date: Mon, 5 Apr 2010 12:37:40 +0000
Subject: [PATCH] bugfixes for NIHVIVO-177 and NIHVIVO-205

---
 .../ontology/update/OntologyUpdater.java      |  4 ++--
 .../servlet/setup/UpdateKnowledgeBase.java    | 23 +++++++++++--------
 2 files changed, 16 insertions(+), 11 deletions(-)

diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyUpdater.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyUpdater.java
index f98302293..0eac83462 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyUpdater.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyUpdater.java
@@ -159,8 +159,8 @@ public class OntologyUpdater {
 		aboxModel.enterCriticalSection(Lock.WRITE);
 		try {
 			JenaIngestUtils jiu = new JenaIngestUtils();
-			jiu.renameBNodes(anonModel, settings.getDefaultNamespace() + "n", 
-					aboxModel);
+			aboxModel.add(jiu.renameBNodes(anonModel, settings.getDefaultNamespace() + "n", 
+					aboxModel));
 		} finally {
 			aboxModel.leaveCriticalSection();
 		}
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
index 3427d248d..944e2387c 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
@@ -132,21 +132,26 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 		    OntModel applicationMetadataModel = oms.getApplicationMetadataModel();
 		    FileInputStream fis = new FileInputStream(new File(filename));
 		    replacementValues.read(fis, null);
+		    Model retractions = ModelFactory.createDefaultModel();
+		    Model additions = ModelFactory.createDefaultModel();
 		    StmtIterator replaceIt = replacementValues.listStatements();
 		    while (replaceIt.hasNext()) {
 		    	Statement replacement = replaceIt.nextStatement();
 		    	applicationMetadataModel.enterCriticalSection(Lock.WRITE);
 		    	try {
-		    		Iterator<Resource> resIt = 
-		    			    applicationMetadataModel.listSubjectsWithProperty(
-		    				replacement.getPredicate(), replacement.getObject());
-		    		while (resIt.hasNext()) {
-		    			Resource subj = resIt.next();
-		    			applicationMetadataModel.removeAll(
-		    					subj, replacement.getPredicate(), (RDFNode) null);
-		    			applicationMetadataModel.add(
-		    					subj, replacement.getPredicate(), replacement.getObject());
+		    		StmtIterator stmtIt = 
+		    			    applicationMetadataModel.listStatements( 
+		    			    		(Resource) null, replacement.getPredicate(),
+		    			    		(RDFNode) null);
+		    		while (stmtIt.hasNext()) {
+		    			Statement stmt = stmtIt.nextStatement();
+		    			retractions.add(stmt);
+		    			additions.add(stmt.getSubject(),
+		    					replacement.getPredicate(), 
+		    					replacement.getObject());
 		    		}
+		    		applicationMetadataModel.remove(retractions);
+		    		applicationMetadataModel.add(additions);
 		    	} finally {
 		    		applicationMetadataModel.leaveCriticalSection();
 		    	}