From a719e6b70658b5f7ddcd328094a139e20c0dea91 Mon Sep 17 00:00:00 2001
From: brianjlowe <bjl23@cornell.edu>
Date: Fri, 27 Sep 2013 14:17:38 -0400
Subject: [PATCH 01/10] minor data migration tweak

---
 .../ontology/update/KnowledgeBaseUpdater.java | 30 +++++++++++--------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java
index 6f46af050..2561f1f9d 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java
@@ -94,21 +94,25 @@ public class KnowledgeBaseUpdater {
 		
 		AtomicOntologyChangeLists changes = new AtomicOntologyChangeLists(rawChanges,settings.getNewTBoxModel(),settings.getOldTBoxModel());
 		
-        //process the TBox before the ABox
-		try {
-		    log.debug("\tupdating tbox annotations");
-	        updateTBoxAnnotations();
-		} catch (Exception e) {
-		    log.error(e,e);
+		// Only modify the TBox and migration metadata the first time
+		if(updateRequired(servletContext)) {
+            //process the TBox before the ABox
+    		try {
+    		    log.debug("\tupdating tbox annotations");
+    	        updateTBoxAnnotations();
+    		} catch (Exception e) {
+    		    log.error(e,e);
+    		}
+    	    
+    	    try {
+        	    migrateMigrationMetadata(servletContext);
+    		    logger.log("Migrated migration metadata");
+    	    } catch (Exception e) {
+    	    	log.error("unable to migrate migration metadata " + e.getMessage());
+    	    }
 		}
-	    
-	    try {
-    	    migrateMigrationMetadata(servletContext);
-		    logger.log("Migrated migration metadata");
-	    } catch (Exception e) {
-	    	log.error("unable to migrate migration metadata " + e.getMessage());
-	    }
 	        	
+		// update ABox data any time
     	log.info("performing SPARQL CONSTRUCT additions");
     	performSparqlConstructs(settings.getSparqlConstructAdditionsDir(), settings.getRDFService(), ADD);
     	

From 688b8586415ee2fdad70d116887a652d7a5d170d Mon Sep 17 00:00:00 2001
From: brianjlowe <bjl23@cornell.edu>
Date: Fri, 27 Sep 2013 15:42:43 -0400
Subject: [PATCH 02/10] VIVO-266 and VIVO-24 improvements to restriction
 editing

---
 .../edit/RestrictionRetryController.java      | 19 ++++++++++++++++---
 .../webapp/dao/jena/DataPropertyDaoJena.java  |  4 +++-
 .../dao/jena/ObjectPropertyDaoJena.java       |  6 ++++--
 3 files changed, 23 insertions(+), 6 deletions(-)

diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/RestrictionRetryController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/RestrictionRetryController.java
index e601aceac..a2d20d9f0 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/RestrictionRetryController.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/RestrictionRetryController.java
@@ -14,6 +14,7 @@ import javax.servlet.http.HttpServletResponse;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import com.hp.hpl.jena.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.RDFS;
 import com.ibm.icu.text.Collator;
 
@@ -63,7 +64,7 @@ public class RestrictionRetryController extends BaseEditController {
 			List<Option> onPropertyList = new LinkedList<Option>(); 
 			Collections.sort(pList, new PropSorter());
 			for (Property p: pList) {
-				onPropertyList.add( new Option(p.getURI(),p.getLocalNameWithPrefix()) );
+				onPropertyList.add( new Option(p.getURI(),p.getPickListName()));
 			}
 					
 			epo.setFormObject(new FormObject());
@@ -117,8 +118,20 @@ public class RestrictionRetryController extends BaseEditController {
 	private List<Option> getValueClassOptionList(VitroRequest request) {
 		List<Option> valueClassOptionList = new LinkedList<Option>();
 		VClassDao vcDao = request.getUnfilteredWebappDaoFactory().getVClassDao();
-		for (VClass vc: vcDao.getAllVclasses()) {
-			valueClassOptionList.add(new Option(vc.getURI(), vc.getLocalNameWithPrefix()));
+		List<VClass> vclasses = vcDao.getAllVclasses();
+        boolean addOwlThing = true;
+        for (VClass vclass : vclasses) {
+            if (OWL.Thing.getURI().equals(vclass.getURI())) {
+                addOwlThing = false;
+                break;
+            }
+        }
+        if(addOwlThing) {
+            vclasses.add(new VClass(OWL.Thing.getURI()));
+        }
+        Collections.sort(vclasses);
+		for (VClass vc: vclasses) {
+			valueClassOptionList.add(new Option(vc.getURI(), vc.getPickListName()));
 		}
 		return valueClassOptionList;
 	}
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyDaoJena.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyDaoJena.java
index 0d4d77a9b..053edbebc 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyDaoJena.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyDaoJena.java
@@ -183,9 +183,11 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
                 if (!VitroVocabulary.vitroURI.equals(dp.getNamespace())) {
                     log.debug("datapropFromOntProperty(): no ontology object found for the namespace "+dp.getNamespace());
                 }
+                dp.setLocalNameWithPrefix(dp.getLocalName());
+                dp.setPickListName(getLabelOrId(op));
             } else {
                 dp.setLocalNameWithPrefix(o.getPrefix()==null?(o.getName()==null?"unspec:"+dp.getLocalName():o.getName()+":"+dp.getLocalName()):o.getPrefix()+":"+dp.getLocalName());
-                dp.setPickListName(dp.getLocalName()+o.getPrefix()==null?(o.getName()==null?" (unspec:)":" ("+o.getName()+")"):" ("+o.getPrefix()+")");
+                dp.setPickListName(getLabelOrId(op)+o.getPrefix()==null?(o.getName()==null?" (unspec:)":" ("+o.getName()+")"):" ("+o.getPrefix()+")");
             }
             dp.setName(op.getLocalName());
             dp.setPublicName(getLabelOrId(op));
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ObjectPropertyDaoJena.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ObjectPropertyDaoJena.java
index 487d2a116..0a8ba5510 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ObjectPropertyDaoJena.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ObjectPropertyDaoJena.java
@@ -96,15 +96,17 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
             p.setLocalName(op.getLocalName());
             OntologyDao oDao=getWebappDaoFactory().getOntologyDao();
             Ontology o = oDao.getOntologyByURI(p.getNamespace());
-            if (o==null) {
+            if (o == null) {
                 if (!VitroVocabulary.vitroURI.equals(p.getNamespace())) {
                     log.debug("propertyFromOntProperty(): no ontology object found for the namespace "+p.getNamespace());
                 }
+                p.setLocalNameWithPrefix(p.getLocalName());
+                p.setPickListName(getLabelOrId(op));                
             } else {
                 String prefix = o.getPrefix()==null?(o.getName()==null?"unspec":o.getName()):o.getPrefix();
                 p.setLocalNameWithPrefix(prefix+":"+p.getLocalName());
                 //log.warn("setting pickListName to: "+p.getLocalName()+" ("+prefix+")");
-                p.setPickListName(p.getLocalName()+" ("+prefix+")");
+                p.setPickListName(getLabelOrId(op) + " ("+prefix+")");
             }
             String propertyName = getPropertyStringValue(op,PROPERTY_FULLPROPERTYNAMEANNOT);
             if (op.getLabel(null) != null)

From 9f2171c2a3a3e77aec614878d4fd9d90e888016c Mon Sep 17 00:00:00 2001
From: brianjlowe <bjl23@cornell.edu>
Date: Fri, 27 Sep 2013 16:16:25 -0400
Subject: [PATCH 03/10] Changing VClassRetryController to use context dao
 factory

---
 .../controller/edit/VclassRetryController.java  | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/VclassRetryController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/VclassRetryController.java
index 2e871b756..3b811f200 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/VclassRetryController.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/VclassRetryController.java
@@ -31,6 +31,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.edit.utils.RoleLevelOptionsSetup;
+import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
@@ -64,10 +65,12 @@ public class VclassRetryController extends BaseEditController {
             action = epo.getAction();
         }
 
-        VClassDao vcwDao = request.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
+        WebappDaoFactory wadf = ModelAccess.on(getServletContext()).getWebappDaoFactory();
+        
+        VClassDao vcwDao = wadf.getVClassDao();
         epo.setDataAccessObject(vcwDao);
-        VClassGroupDao cgDao = request.getUnfilteredWebappDaoFactory().getVClassGroupDao();
-        OntologyDao oDao = request.getUnfilteredWebappDaoFactory().getOntologyDao();
+        VClassGroupDao cgDao = wadf.getVClassGroupDao();
+        OntologyDao oDao = wadf.getOntologyDao();
 
         VClass vclassForEditing = null;
         if (!epo.getUseRecycledBean()){
@@ -82,18 +85,12 @@ public class VclassRetryController extends BaseEditController {
             } else {
                 vclassForEditing = new VClass();
                 if (request.getParameter("GroupId") != null) {
-                    try {
-                        vclassForEditing.setGroupURI(request.getParameter("GroupURI"));
-                    } catch (NumberFormatException e) {
-                        // too bad
-                    }
+                    vclassForEditing.setGroupURI(request.getParameter("GroupURI"));
                 }
             }
             epo.setOriginalBean(vclassForEditing);
         } else {
             vclassForEditing = (VClass) epo.getNewBean();
-            // action = "update";
-            // log.error("using newBean");
         }
 
         //make a simple mask for the class's id

From 9ef5e783a303b54f90a387656736cf5db3e7304d Mon Sep 17 00:00:00 2001
From: brianjlowe <bjl23@cornell.edu>
Date: Fri, 27 Sep 2013 16:40:34 -0400
Subject: [PATCH 04/10] fixing model used by RestrictionOperationController

---
 .../vedit/controller/BaseEditController.java  | 20 -------------------
 .../edit/RestrictionOperationController.java  |  6 +++++-
 2 files changed, 5 insertions(+), 21 deletions(-)

diff --git a/webapp/src/edu/cornell/mannlib/vedit/controller/BaseEditController.java b/webapp/src/edu/cornell/mannlib/vedit/controller/BaseEditController.java
index 9f1cc9c65..01b707451 100644
--- a/webapp/src/edu/cornell/mannlib/vedit/controller/BaseEditController.java
+++ b/webapp/src/edu/cornell/mannlib/vedit/controller/BaseEditController.java
@@ -155,26 +155,6 @@ public class BaseEditController extends VitroHttpServlet {
         }
     }
     
-    protected OntModel getOntModel( HttpServletRequest request, ServletContext ctx ) {
-
-    	// TODO: JB - This method gets the UNION FULL model from the session, if there is one, 
-    	// TODO and the BASE_TBOX model otherwise.
-    	OntModel ontModel = null;
-    	try {
-    		ontModel = ModelAccess.on(request.getSession()).getJenaOntModel();
-    	} catch (Exception e) {
-    	    // ignoring any problems here - we're not really expecting
-    	    // this attribute to be populated anyway
-    	}
-    	
-    	if ( ontModel == null ) {
-            ontModel = ModelAccess.on(ctx).getOntModel(ModelID.BASE_TBOX);
-    	}
-    	
-    	return ontModel;
-    	
-    }
-    
     protected WebappDaoFactory getWebappDaoFactory() {
     	return ModelAccess.on(getServletContext()).getBaseWebappDaoFactory();
     }
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/RestrictionOperationController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/RestrictionOperationController.java
index 6a4efe107..3bdb0142b 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/RestrictionOperationController.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/RestrictionOperationController.java
@@ -23,11 +23,14 @@ import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.shared.Lock;
+import com.hp.hpl.jena.vocabulary.DAML_OIL;
 
 import edu.cornell.mannlib.vedit.beans.EditProcessObject;
 import edu.cornell.mannlib.vedit.controller.BaseEditController;
 import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
+import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess.ModelID;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
 
 public class RestrictionOperationController extends BaseEditController {
@@ -44,7 +47,8 @@ public class RestrictionOperationController extends BaseEditController {
 		
 	    try {
 	    	
-	    	OntModel ontModel = getOntModel(request, getServletContext());
+	    	OntModel ontModel = ModelAccess.on(
+	    	        getServletContext()).getOntModel(ModelID.BASE_TBOX);
 		    
             HashMap epoHash = null;
             EditProcessObject epo = null;

From 4202f30ea780ee845c894dbaebba891f2058b524 Mon Sep 17 00:00:00 2001
From: brianjlowe <bjl23@cornell.edu>
Date: Fri, 27 Sep 2013 17:05:41 -0400
Subject: [PATCH 05/10] VIVO-237 changed "attach to TBox" function to "attach
 snapshot to ontology" using in-memory copies so older ingest examples should
 still work while avoiding a performance hit.

---
 .../webapp/controller/jena/JenaIngestController.java  | 11 +++--------
 webapp/web/jenaIngest/listModels.jsp                  |  4 ++--
 2 files changed, 5 insertions(+), 10 deletions(-)

diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java
index f21bfebd7..4eab56e4a 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java
@@ -822,13 +822,11 @@ public class JenaIngestController extends BaseEditController {
     
     private void doAttachModel(String modelName, ModelMaker modelMaker) {
         if (attachedModels.containsKey(modelName)) {
-            return;
+            doDetachModel(modelName, modelMaker);
         }
-        Model m = modelMaker.getModel(modelName);
-        ModelAccess.on(getServletContext()).getOntModel(ModelID.BASE_ABOX).addSubModel(m);
+        Model m = ModelFactory.createDefaultModel();
+        m.add(modelMaker.getModel(modelName));        
         ModelAccess.on(getServletContext()).getOntModel(ModelID.BASE_TBOX).addSubModel(m);
-        ModelAccess.on(getServletContext()).getOntModel(ModelID.UNION_ABOX).addSubModel(m);
-        ModelAccess.on(getServletContext()).getOntModel(ModelID.UNION_TBOX).addSubModel(m);
         attachedModels.put(modelName, m);
         log.info("Attached " + modelName + " (" + m.hashCode() + ") to webapp");
     }
@@ -838,10 +836,7 @@ public class JenaIngestController extends BaseEditController {
         if (m == null) {
             return;
         }
-        ModelAccess.on(getServletContext()).getOntModel(ModelID.BASE_ABOX).removeSubModel(m);
         ModelAccess.on(getServletContext()).getOntModel(ModelID.BASE_TBOX).removeSubModel(m);
-        ModelAccess.on(getServletContext()).getOntModel(ModelID.UNION_ABOX).removeSubModel(m);
-        ModelAccess.on(getServletContext()).getOntModel(ModelID.UNION_TBOX).removeSubModel(m);
         attachedModels.remove(modelName);
         log.info("Detached " + modelName + " (" + m.hashCode() + ") from webapp");
     }
diff --git a/webapp/web/jenaIngest/listModels.jsp b/webapp/web/jenaIngest/listModels.jsp
index 081168fb8..2b0f48343 100644
--- a/webapp/web/jenaIngest/listModels.jsp
+++ b/webapp/web/jenaIngest/listModels.jsp
@@ -96,7 +96,7 @@ function init(){
                 <input type="hidden" name="action" value="attachModel"/>
                 <input type="hidden" name="modelName" value="${modelName}"/>
                 <input type="hidden" name="modelType" value="${modelType}"/>
-                <input type="submit" name="submit" value="attach to TBox (ontology)"/>
+                <input type="submit" name="submit" value="attach snapshot to ontology"/>
             </form>
             </td>
             <td>
@@ -104,7 +104,7 @@ function init(){
                 <input type="hidden" name="action" value="detachModel"/>
                 <input type="hidden" name="modelName" value="${modelName}"/>
                 <input type="hidden" name="modelType" value="${modelType}"/>
-                <input type="submit" name="submit" value="detach from TBox (ontology)"/>
+                <input type="submit" name="submit" value="detach snapshot from ontology"/>
             </form>
             </td>
             <td>

From 4d5a567e36598a73838298e152b02abcc7817786 Mon Sep 17 00:00:00 2001
From: tworrall <tlw72@cornell.edu>
Date: Mon, 30 Sep 2013 09:29:19 -0400
Subject: [PATCH 06/10] VIVO-285: visualization updates for ISF

---
 .../individual/GroupedPropertyList.java        | 13 +++++++++++++
 .../freemarker/lib/lib-properties.ftl          | 18 ++++++++++++++++++
 2 files changed, 31 insertions(+)

diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/GroupedPropertyList.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/GroupedPropertyList.java
index 7c023e022..4ee0d14a7 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/GroupedPropertyList.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/GroupedPropertyList.java
@@ -476,6 +476,19 @@ public class GroupedPropertyList extends BaseTemplateModel {
         return null;
     }
 
+    public PropertyTemplateModel getProperty(String propertyUri, String rangeUri) {
+
+        for (PropertyGroupTemplateModel pgtm : groups) {
+            List<PropertyTemplateModel> properties = pgtm.getProperties();
+            for (PropertyTemplateModel ptm : properties) {
+                if (propertyUri.equals(ptm.getUri()) && rangeUri.equals(ptm.getRangeUri())) {
+                    return ptm;
+                }
+            }
+        }
+        return null;
+    }
+
     public PropertyTemplateModel pullProperty(String propertyUri) {
         return pullProperty(propertyUri, null);
     }
diff --git a/webapp/web/templates/freemarker/lib/lib-properties.ftl b/webapp/web/templates/freemarker/lib/lib-properties.ftl
index c54bd9b16..4925b61ca 100644
--- a/webapp/web/templates/freemarker/lib/lib-properties.ftl
+++ b/webapp/web/templates/freemarker/lib/lib-properties.ftl
@@ -22,6 +22,24 @@
     </#if>
 </#function>
 
+<#-- Return true iff there are statements for this property -->
+<#function hasVisualizationStatements propertyGroups propertyName rangeUri>
+
+    <#local property = propertyGroups.getProperty(propertyName, rangeUri)!>
+    
+        <#-- First ensure that the property is defined
+        (an unpopulated property while logged out is undefined) -->
+        <#if ! property?has_content>
+            <#return false>
+        </#if>
+    
+        <#if property.collatedBySubclass!false> <#-- collated object property-->
+            <#return property.subclasses?has_content>
+        <#else>
+            <#return property.statements?has_content> <#-- data property or uncollated object property -->
+        </#if>
+
+</#function>
 
 <#-----------------------------------------------------------------------------
     Macros for generating property lists

From 8671bf3c5d01e2005d2639140797155bb7199b9f Mon Sep 17 00:00:00 2001
From: brianjlowe <bjl23@cornell.edu>
Date: Mon, 30 Sep 2013 15:51:31 -0400
Subject: [PATCH 07/10] switching vitro:example and vitro:shortDef to new IAO
 properties, and adding escaping to JSON strings in site admin listing pages

---
 .../edit/DatapropRetryController.java         |  11 +-
 .../freemarker/ListClassGroupsController.java |  24 +--
 .../ListDatatypePropertiesController.java     |  23 +--
 .../ListPropertyGroupsController.java         |  22 +--
 .../ListPropertyWebappsController.java        |  41 ++--
 .../ListVClassWebappsController.java          | 161 +++++++---------
 .../ShowClassHierarchyController.java         | 180 +++++++++---------
 .../ShowDataPropertyHierarchyController.java  |  64 +++----
 ...ShowObjectPropertyHierarchyController.java |  65 ++++---
 .../vitro/webapp/dao/VitroVocabulary.java     |   5 +-
 10 files changed, 283 insertions(+), 313 deletions(-)

diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/DatapropRetryController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/DatapropRetryController.java
index ac443de7c..bc60934c8 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/DatapropRetryController.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/DatapropRetryController.java
@@ -34,8 +34,10 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.edit.utils.RoleLevelOptionsSetup;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
+import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 
 
 public class DatapropRetryController extends BaseEditController {
@@ -54,11 +56,12 @@ public class DatapropRetryController extends BaseEditController {
         
         VitroRequest vreq = new VitroRequest(request);
 
-        DatatypeDao dDao = vreq.getUnfilteredWebappDaoFactory().getDatatypeDao();
-        DataPropertyDao dpDao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyDao();
+        WebappDaoFactory wadf = ModelAccess.on(getServletContext()).getWebappDaoFactory();
+        
+        DatatypeDao dDao = wadf.getDatatypeDao();
+        DataPropertyDao dpDao = wadf.getDataPropertyDao();
         epo.setDataAccessObject(dpDao);
-        OntologyDao ontDao = vreq.getUnfilteredWebappDaoFactory().getOntologyDao();
-        VClassDao vclassDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
+        OntologyDao ontDao = wadf.getOntologyDao();
 
         DataProperty objectForEditing = null;
         String action = null;
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListClassGroupsController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListClassGroupsController.java
index b87f93dfe..eb42252c3 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListClassGroupsController.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListClassGroupsController.java
@@ -2,17 +2,12 @@
 
 package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
 
-import java.net.URLEncoder;
-import java.util.ArrayList;
-import java.util.Collections;
 import java.util.HashMap;
-import java.util.Map;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 
-import javax.servlet.RequestDispatcher;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import net.sf.json.util.JSONUtils;
 
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
@@ -26,6 +21,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
+import edu.cornell.mannlib.vitro.webapp.web.URLEncoder;
 
 
 public class ListClassGroupsController extends FreemarkerHttpServlet {
@@ -64,12 +60,10 @@ public class ListClassGroupsController extends FreemarkerHttpServlet {
                     if ( StringUtils.isBlank(publicName) ) {
                         publicName = "(unnamed group)";
                     }           
-                    publicName = publicName.replace("\"","\\\"");
-                    publicName = publicName.replace("\'","\\\'");
                     try {
-                        json += "{ \"name\": \"<a href='./editForm?uri="+URLEncoder.encode(vcg.getURI(),"UTF-8")+"&amp;controller=Classgroup'>"+publicName+"</a>\", ";
+                        json += "{ \"name\": " + JSONUtils.quote("<a href='./editForm?uri="+URLEncoder.encode(vcg.getURI())+"&amp;controller=Classgroup'>"+publicName+"</a>") + ", ";
                     } catch (Exception e) {
-                        json += "{ \"name\": \"" + publicName + "\", ";
+                        json += "{ \"name\": " + JSONUtils.quote(publicName) + ", ";
                     }
                     Integer t;
                     
@@ -83,18 +77,16 @@ public class ListClassGroupsController extends FreemarkerHttpServlet {
                             VClass vcw = classIt.next();
                             if (vcw.getName() != null && vcw.getURI() != null) {
                                 try {
-                                    json += "{ \"name\": \"<a href='vclassEdit?uri="+URLEncoder.encode(vcw.getURI(),"UTF-8")+"'>"+vcw.getName()+"</a>\", ";
+                                    json += "{ \"name\": " + JSONUtils.quote("<a href='vclassEdit?uri="+URLEncoder.encode(vcw.getURI())+"'>"+vcw.getName()+"</a>") + ", ";
                                 } catch (Exception e) {
-                                    json += "\"" + vcw.getName() + "\", ";
+                                    json += "" + JSONUtils.quote(vcw.getName()) + ", ";
                                 }
                             } else {
                                 json += "\"\", ";
                             }
 
                             String shortDefStr = (vcw.getShortDef() == null) ? "" : vcw.getShortDef();
-                            shortDefStr = shortDefStr.replace("\"","\\\"");
-                            shortDefStr = shortDefStr.replace("\'","\\\'");
-                            json += "\"data\": { \"shortDef\": \"" + shortDefStr + "\"}, \"children\": [] ";
+                            json += "\"data\": { \"shortDef\": " + JSONUtils.quote(shortDefStr) + "}, \"children\": [] ";
                             if (classIt.hasNext())
                                 json += "} , ";
                             else 
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListDatatypePropertiesController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListDatatypePropertiesController.java
index cfa06ae55..56fc35a39 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListDatatypePropertiesController.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListDatatypePropertiesController.java
@@ -2,8 +2,6 @@
 
 package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
 
-import java.io.UnsupportedEncodingException;
-import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -13,8 +11,7 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import net.sf.json.util.JSONUtils;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -25,7 +22,6 @@ import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
 import edu.cornell.mannlib.vitro.webapp.beans.Datatype;
 import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
-import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
@@ -33,7 +29,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
-import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.web.URLEncoder;
 
 public class ListDatatypePropertiesController extends FreemarkerHttpServlet {
 
@@ -112,15 +108,14 @@ public class ListDatatypePropertiesController extends FreemarkerHttpServlet {
                         }
                         
                         String nameStr = prop.getPublicName()==null ? prop.getName()==null ? prop.getURI()==null ? "(no name)" : prop.getURI() : prop.getName() : prop.getPublicName();
-                        nameStr = nameStr.replace("\"","\\\"");
-                        nameStr = nameStr.replace("\'","\\\'");
+
                         try {
-                            json += "{ \"name\": \"<a href='datapropEdit?uri="+URLEncoder.encode(prop.getURI(),"UTF-8")+"'>" + nameStr + "</a>\", "; 
+                            json += "{ \"name\": " + JSONUtils.quote("<a href='datapropEdit?uri="+ URLEncoder.encode(prop.getURI())+"'>" + nameStr + "</a>") + ", "; 
                         } catch (Exception e) {
-                            json += "{ \"name\": \"" + nameStr + "\", ";
+                            json += "{ \"name\": " + JSONUtils.quote(nameStr) + ", ";
                         }
                         
-                        json += "\"data\": { \"internalName\": \"" + prop.getLocalNameWithPrefix() + "\", ";
+                        json += "\"data\": { \"internalName\": " + JSONUtils.quote(prop.getLocalNameWithPrefix()) + ", ";
                         
 /*                        VClass vc = null;
                         String domainStr="";
@@ -137,15 +132,15 @@ public class ListDatatypePropertiesController extends FreemarkerHttpServlet {
 */                        
                         VClass vc = (prop.getDomainClassURI() != null) ? vcDao.getVClassByURI(prop.getDomainClassURI()) : null;
                         String domainStr = (vc != null) ? vc.getLocalNameWithPrefix() : ""; 
-                        json += "\"domainVClass\": \"" + domainStr + "\", " ;
+                        json += "\"domainVClass\": " + JSONUtils.quote(domainStr) + ", " ;
 
                         Datatype rangeDatatype = dDao.getDatatypeByURI(prop.getRangeDatatypeURI());
                         String rangeDatatypeStr = (rangeDatatype==null)?prop.getRangeDatatypeURI():rangeDatatype.getName();
-                        json += "\"rangeVClass\": \"" + rangeDatatypeStr + "\", " ; 
+                        json += "\"rangeVClass\": " + JSONUtils.quote(rangeDatatypeStr) + ", " ; 
 
                         if (prop.getGroupURI() != null) {
                             PropertyGroup pGroup = pgDao.getGroupByURI(prop.getGroupURI());
-                            json += "\"group\": \"" + ((pGroup == null) ? "unknown group" : pGroup.getName()) + "\" } } " ; 
+                            json += "\"group\": " + JSONUtils.quote((pGroup == null) ? "unknown group" : pGroup.getName()) + " } } " ; 
                         } else {
                              json += "\"group\": \"unspecified\" } }" ;
                         }
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListPropertyGroupsController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListPropertyGroupsController.java
index 9eaf9cf47..468d57f76 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListPropertyGroupsController.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListPropertyGroupsController.java
@@ -3,29 +3,23 @@
 package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
 
 import java.net.URLEncoder;
-import java.util.ArrayList;
-import java.util.Collections;
 import java.util.HashMap;
-import java.util.Map;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 
-import javax.servlet.RequestDispatcher;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import net.sf.json.util.JSONUtils;
 
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
-import edu.cornell.mannlib.vedit.controller.BaseEditController;
 import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
 import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
 import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
-import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
@@ -70,12 +64,10 @@ public class ListPropertyGroupsController extends FreemarkerHttpServlet {
                         if ( StringUtils.isBlank(publicName) ) {
                             publicName = "(unnamed group)";
                         }           
-                        publicName = publicName.replace("\"","\\\"");
-                        publicName = publicName.replace("\'","\\\'");
                         try {
-                            json += "{ \"name\": \"<a href='./editForm?uri="+URLEncoder.encode(pg.getURI(),"UTF-8")+"&amp;controller=PropertyGroup'>" + publicName + "</a>\", ";
+                            json += "{ \"name\": " + JSONUtils.quote("<a href='./editForm?uri="+URLEncoder.encode(pg.getURI(),"UTF-8")+"&amp;controller=PropertyGroup'>" + publicName + "</a>") + ", ";
                         } catch (Exception e) {
-                            json += "{ \"name\": \"" + publicName + "\", ";
+                            json += "{ \"name\": " + JSONUtils.quote(publicName) + ", ";
                         }
                         Integer t;
 
@@ -100,10 +92,10 @@ public class ListPropertyGroupsController extends FreemarkerHttpServlet {
                                 }
                                 if (prop.getURI() != null) {
                                     try {
-                                        json += "{ \"name\": \"<a href='" + controllerStr 
-                                             + "?uri="+URLEncoder.encode(prop.getURI(),"UTF-8")+"'>"+ nameStr +"</a>\", ";
+                                        json += "{ \"name\": " + JSONUtils.quote("<a href='" + controllerStr 
+                                             + "?uri="+URLEncoder.encode(prop.getURI(),"UTF-8")+"'>"+ nameStr +"</a>") + ", ";
                                     } catch (Exception e) {
-                                        json += "\"" + nameStr + "\", ";
+                                        json += JSONUtils.quote(nameStr) + ", ";
                                     }
                                 } else {
                                     json += "\"\", ";
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListPropertyWebappsController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListPropertyWebappsController.java
index 81a12a4f0..df632a860 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListPropertyWebappsController.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListPropertyWebappsController.java
@@ -2,7 +2,6 @@
 
 package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
 
-import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -12,8 +11,7 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import net.sf.json.util.JSONUtils;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -25,7 +23,6 @@ import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
 import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
 import edu.cornell.mannlib.vitro.webapp.beans.PropertyInstance;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
-import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
@@ -35,6 +32,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyInstanceDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.web.URLEncoder;
 
 public class ListPropertyWebappsController extends FreemarkerHttpServlet {
     private static Log log = LogFactory.getLog( ListPropertyWebappsController.class );
@@ -67,7 +65,7 @@ public class ListPropertyWebappsController extends FreemarkerHttpServlet {
 
             String vclassURI = vreq.getParameter("vclassUri");
         
-            List props = new ArrayList();
+            List<ObjectProperty> props = new ArrayList<ObjectProperty>();
             if (vreq.getParameter("propsForClass") != null) {
                 noResultsMsgStr = "There are no object properties that apply to this class.";
             
@@ -87,8 +85,8 @@ public class ListPropertyWebappsController extends FreemarkerHttpServlet {
                 propInsts.addAll(propInstMap.values());
                 Collections.sort(propInsts);
             
-                Iterator propInstIt = propInsts.iterator();
-                HashSet propURIs = new HashSet();
+                Iterator<PropertyInstance> propInstIt = propInsts.iterator();
+                HashSet<String> propURIs = new HashSet<String>();
                 while (propInstIt.hasNext()) {
                     PropertyInstance pi = (PropertyInstance) propInstIt.next();
                     if (!(propURIs.contains(pi.getPropertyURI()))) {
@@ -108,13 +106,13 @@ public class ListPropertyWebappsController extends FreemarkerHttpServlet {
             OntologyDao oDao = vreq.getUnfilteredWebappDaoFactory().getOntologyDao();
             HashMap<String,String> ontologyHash = new HashMap<String,String>();
 
-            Iterator propIt = props.iterator();
-            List<ObjectProperty> scratch = new ArrayList();
+            Iterator<ObjectProperty> propIt = props.iterator();
+            List<ObjectProperty> scratch = new ArrayList<ObjectProperty>();
             while (propIt.hasNext()) {
-                ObjectProperty p = (ObjectProperty) propIt.next();
-                if (p.getNamespace()!=null) {
+                ObjectProperty p = propIt.next();
+                if (p.getNamespace() != null) {
                     if( !ontologyHash.containsKey( p.getNamespace() )){
-                        Ontology o = (Ontology)oDao.getOntologyByURI(p.getNamespace());
+                        Ontology o = oDao.getOntologyByURI(p.getNamespace());
                         if (o==null) {
                             if (!VitroVocabulary.vitroURI.equals(p.getNamespace())) {
                                 log.debug("doGet(): no ontology object found for the namespace "+p.getNamespace());
@@ -144,36 +142,35 @@ public class ListPropertyWebappsController extends FreemarkerHttpServlet {
                 if (props.size()==0) {
                     json = "{ \"name\": \"" + noResultsMsgStr + "\" }";
                 } else {
-                    Iterator propsIt = props.iterator();
+                    Iterator<ObjectProperty> propsIt = props.iterator();
                     while (propsIt.hasNext()) {
                         if ( counter > 0 ) {
                             json += ", ";
                         }
-                        ObjectProperty prop = (ObjectProperty) propsIt.next();
+                        ObjectProperty prop = propsIt.next();
                     
                         String propNameStr = ShowObjectPropertyHierarchyController.getDisplayLabel(prop);
-                        propNameStr = propNameStr.replace("\"","\\\"");
-                        propNameStr = propNameStr.replace("\'","\\\'");
+
                         try {
-                            json += "{ \"name\": \"<a href='./propertyEdit?uri="+URLEncoder.encode(prop.getURI(),"UTF-8")+"'>" 
-                                 + propNameStr + "</a>\", "; 
+                            json += "{ \"name\": " + JSONUtils.quote("<a href='./propertyEdit?uri="+URLEncoder.encode(prop.getURI())+"'>" 
+                                 + propNameStr + "</a>") + ", "; 
                          } catch (Exception e) {
                              json += "{ \"name\": \"" + propNameStr + "\", "; 
                          }
                     
-                         json += "\"data\": { \"internalName\": \"" + prop.getLocalNameWithPrefix() + "\", "; 
+                         json += "\"data\": { \"internalName\": " + JSONUtils.quote(prop.getLocalNameWithPrefix()) + ", "; 
                     
                          VClass vc = (prop.getDomainVClassURI() != null) ? vcDao.getVClassByURI(prop.getDomainVClassURI()) : null;
                          String domainStr = (vc != null) ? vc.getLocalNameWithPrefix() : ""; 
-                         json += "\"domainVClass\": \"" + domainStr + "\", " ;
+                         json += "\"domainVClass\": " + JSONUtils.quote(domainStr) + ", " ;
                     
                          vc = (prop.getRangeVClassURI() != null) ? vcDao.getVClassByURI(prop.getRangeVClassURI()) : null;
                          String rangeStr = (vc != null) ? vc.getLocalNameWithPrefix() : ""; 
-                         json += "\"rangeVClass\": \"" + rangeStr + "\", " ; 
+                         json += "\"rangeVClass\": " + JSONUtils.quote(rangeStr) + ", " ; 
                     
                          if (prop.getGroupURI() != null) {
                              PropertyGroup pGroup = pgDao.getGroupByURI(prop.getGroupURI());
-                             json += "\"group\": \"" + ((pGroup == null) ? "unknown group" : pGroup.getName()) + "\" } } " ; 
+                             json += "\"group\": " + JSONUtils.quote((pGroup == null) ? "unknown group" : pGroup.getName()) + " } } " ; 
                          } else {
                              json += "\"group\": \"unspecified\" } }" ;
                          }
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListVClassWebappsController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListVClassWebappsController.java
index 5db89a942..d07ea6743 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListVClassWebappsController.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListVClassWebappsController.java
@@ -3,30 +3,22 @@
 package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
 
 import java.net.URLEncoder;
-import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
-import java.util.Map;
 import java.util.Iterator;
-import java.util.LinkedList;
 import java.util.List;
+import java.util.Map;
 
-import javax.servlet.RequestDispatcher;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import net.sf.json.util.JSONUtils;
 
-import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
-import com.hp.hpl.jena.vocabulary.OWL;
-
 import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
 import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup;
-import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
@@ -50,90 +42,83 @@ public class ListVClassWebappsController extends FreemarkerHttpServlet {
     
     @Override
     protected ResponseValues processRequest(VitroRequest vreq) {
-
+        
         Map<String, Object> body = new HashMap<String, Object>();
-        try {
 
-            body.put("displayOption", "all");
-            body.put("pageTitle", "All Classes");
-            
-            List<VClass> classes = null;
+        body.put("displayOption", "all");
+        body.put("pageTitle", "All Classes");
+        
+        List<VClass> classes = null;
 
-            if (vreq.getParameter("showPropertyRestrictions") != null) {
-            	PropertyDao pdao = vreq.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
-            	classes = pdao.getClassesWithRestrictionOnProperty(vreq.getParameter("propertyURI"));
-            } else {
-            	VClassDao vcdao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
+        if (vreq.getParameter("showPropertyRestrictions") != null) {
+        	PropertyDao pdao = vreq.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
+        	classes = pdao.getClassesWithRestrictionOnProperty(vreq.getParameter("propertyURI"));
+        } else {
+        	VClassDao vcdao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
 
-            	if (vreq.getParameter("iffRoot") != null) {
-                    classes = vcdao.getRootClasses();
-            	} else {
-            		classes = vcdao.getAllVclasses();
-            	}
+        	if (vreq.getParameter("iffRoot") != null) {
+                classes = vcdao.getRootClasses();
+        	} else {
+        		classes = vcdao.getAllVclasses();
+        	}
 
-            }
-            String json = new String();
-            int counter = 0;
-
-            String ontologyURI = vreq.getParameter("ontologyUri");
-
-            if (classes != null) {
-                Collections.sort(classes);
-                Iterator<VClass> classesIt = classes.iterator();
-                while (classesIt.hasNext()) {
-                    if ( counter > 0 ) {
-                        json += ", ";
-                    }
-                    VClass cls = (VClass) classesIt.next();
-                    if ( (ontologyURI==null) || ( (ontologyURI != null) && (cls.getNamespace()!=null) && (ontologyURI.equals(cls.getNamespace())) ) ) {
-    	                if (cls.getName() != null)
-    	                    try {
-    	                        json += "{ \"name\": \"<a href='./vclassEdit?uri="+URLEncoder.encode(cls.getURI(),"UTF-8")+"'>"+cls.getLocalNameWithPrefix()+"</a>\", ";
-    	                    } catch (Exception e) {
-    	                        json += "{ \"name\": \"" + cls.getLocalNameWithPrefix() + "\", ";
-    	                    }
-    	                else
-    	                    json += "{ \"name\": \"\"";
-    	                String shortDef = (cls.getShortDef()==null) ? "" : cls.getShortDef();
-    	                
-    	                json += "\"data\": { \"shortDef\": \"" + shortDef + "\", ";
-
-    	                // get group name
-    	                WebappDaoFactory wadf = vreq.getUnfilteredWebappDaoFactory();
-    	                VClassGroupDao groupDao= wadf.getVClassGroupDao();
-    	                String groupURI = cls.getGroupURI();                
-    	                String groupName = "";
-    	                VClassGroup classGroup = null;
-    	                if(groupURI != null) { 
-    	                	classGroup = groupDao.getGroupByURI(groupURI);
-    	                	if (classGroup!=null) {
-    	                	    groupName = classGroup.getPublicName();
-    	                	}
-    	                }
-                        
-                        json += "\"classGroup\": \"" + groupName + "\", ";
-
-    	                // get ontology name
-    	                OntologyDao ontDao = wadf.getOntologyDao();
-    	                String ontName = null;
-    	                try {
-    	                	Ontology ont = ontDao.getOntologyByURI(cls.getNamespace());
-    	                	ontName = ont.getName();
-    	                } catch (Exception e) {}
-    	                ontName = (ontName == null) ? "" : ontName;
-    	                
-    	                json += "\"ontology\": \"" + ontName + "\"} }";
-    	                
-    	                counter += 1;
-
-                   }
-                }
-                body.put("jsonTree",json);
-            }
-
-        } catch (Throwable t) {
-                t.printStackTrace();
         }
+        String json = new String();
+        int counter = 0;
+
+        String ontologyURI = vreq.getParameter("ontologyUri");
+
+        if (classes != null) {
+            Collections.sort(classes);
+            Iterator<VClass> classesIt = classes.iterator();
+            while (classesIt.hasNext()) {
+                if ( counter > 0 ) {
+                    json += ", ";
+                }
+                VClass cls = (VClass) classesIt.next();
+                if ( (ontologyURI==null) || ( (ontologyURI != null) && (cls.getNamespace()!=null) && (ontologyURI.equals(cls.getNamespace())) ) ) {
+	                if (cls.getName() != null)
+	                    try {
+	                        json += "{ \"name\": " + JSONUtils.quote("<a href='./vclassEdit?uri="+URLEncoder.encode(cls.getURI(),"UTF-8")+"'>"+cls.getLocalNameWithPrefix()+"</a>") + ", ";
+	                    } catch (Exception e) {
+	                        json += "{ \"name\": " + JSONUtils.quote(cls.getLocalNameWithPrefix()) + ", ";
+	                    }
+	                else
+	                    json += "{ \"name\": \"\"";
+	                String shortDef = (cls.getShortDef() == null) ? "" : cls.getShortDef();
+	                
+	                json += "\"data\": { \"shortDef\": " + JSONUtils.quote(shortDef) + ", ";
+
+	                // get group name
+	                WebappDaoFactory wadf = vreq.getUnfilteredWebappDaoFactory();
+	                VClassGroupDao groupDao= wadf.getVClassGroupDao();
+	                String groupURI = cls.getGroupURI();                
+	                String groupName = "";
+	                VClassGroup classGroup = null;
+	                if(groupURI != null) { 
+	                	classGroup = groupDao.getGroupByURI(groupURI);
+	                	if (classGroup!=null) {
+	                	    groupName = classGroup.getPublicName();
+	                	}
+	                }
+                    
+                    json += "\"classGroup\": " + JSONUtils.quote(groupName) + ", ";
+
+	                // get ontology name
+	                OntologyDao ontDao = wadf.getOntologyDao();
+	                String ontName = cls.getNamespace();
+	                Ontology ont = ontDao.getOntologyByURI(ontName);
+	                if (ont != null && ont.getName() != null) {
+	                    ontName = ont.getName();
+	                }
+	                json += "\"ontology\": " + JSONUtils.quote(ontName) + "} }";
+	                
+	                counter++;
+
+               }
+            }
+            body.put("jsonTree",json);
+        }      
         
         return new TemplateResponseValues(TEMPLATE_NAME, body);
     }
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowClassHierarchyController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowClassHierarchyController.java
index d06861ab7..f703b4318 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowClassHierarchyController.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowClassHierarchyController.java
@@ -11,6 +11,8 @@ import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 
+import net.sf.json.util.JSONUtils;
+
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -50,77 +52,73 @@ public class ShowClassHierarchyController extends FreemarkerHttpServlet {
     protected ResponseValues processRequest(VitroRequest vreq) {
 
         Map<String, Object> body = new HashMap<String, Object>();
-        try {
-            String displayOption = "";
-            
-            if ( vreq.getParameter("displayOption") != null ) {
-                displayOption = vreq.getParameter("displayOption");
-            }
-            else {
-                displayOption = "asserted";
-            }
-
-            body.put("displayOption", displayOption);
-            boolean inferred = ( displayOption.equals("inferred") );
-            if ( inferred ) {
-                body.put("pageTitle", "Inferred Class Hierarchy");
-            }
-            else {
-                body.put("pageTitle", "Asserted Class Hierarchy");
-            }
-
-            if (!inferred) {
-            	vcDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
-            } else {
-            	vcDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
-            }
-            String json = new String();
-
-            String ontologyUri = vreq.getParameter("ontologyUri");
-            String startClassUri = vreq.getParameter("vclassUri");
-
-            List<VClass> roots = null;
-
-            if (ontologyUri != null) {
-                roots = vcDao.getOntologyRootClasses(ontologyUri);
-            } else if (startClassUri != null) {
-            	roots = new LinkedList<VClass>();
-            	roots.add(vcDao.getVClassByURI(startClassUri));
-            } else {    	
-           		roots = vcDao.getRootClasses();
-            }
-
-            if (roots.isEmpty()) {
-            	roots = new LinkedList<VClass>();
-            	roots.add(vreq.getUnfilteredWebappDaoFactory().getVClassDao()
-            			.getTopConcept());
-            }
-            Collections.sort(roots);
-            int counter = 0;
-
-            Iterator rootIt = roots.iterator();
-            if (!rootIt.hasNext()) {
-                VClass vcw = new VClass();
-                vcw.setName("<strong>No classes found.</strong>");
-                json += addVClassDataToResultsList(vreq.getUnfilteredWebappDaoFactory(), vcw,0,ontologyUri,counter);
-            } else {
-                while (rootIt.hasNext()) {
-                    VClass root = (VClass) rootIt.next();
-    	            if (root != null) {
-    	                json += addChildren(vreq.getUnfilteredWebappDaoFactory(), root, 0, ontologyUri,counter);
-    	                counter += 1;
-                    }
-                }
-                int length = json.length();
-                if ( length > 0 ) {
-                    json += " }"; 
-                }
-            }
-            body.put("jsonTree",json);
- 
-        } catch (Throwable t) {
-                t.printStackTrace();
+        
+        String displayOption = "";
+        
+        if ( vreq.getParameter("displayOption") != null ) {
+            displayOption = vreq.getParameter("displayOption");
         }
+        else {
+            displayOption = "asserted";
+        }
+
+        body.put("displayOption", displayOption);
+        boolean inferred = ( displayOption.equals("inferred") );
+        if ( inferred ) {
+            body.put("pageTitle", "Inferred Class Hierarchy");
+        }
+        else {
+            body.put("pageTitle", "Asserted Class Hierarchy");
+        }
+
+        if (!inferred) {
+        	vcDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
+        } else {
+        	vcDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
+        }
+        String json = new String();
+
+        String ontologyUri = vreq.getParameter("ontologyUri");
+        String startClassUri = vreq.getParameter("vclassUri");
+
+        List<VClass> roots = null;
+
+        if (ontologyUri != null) {
+            roots = vcDao.getOntologyRootClasses(ontologyUri);
+        } else if (startClassUri != null) {
+        	roots = new LinkedList<VClass>();
+        	roots.add(vcDao.getVClassByURI(startClassUri));
+        } else {    	
+       		roots = vcDao.getRootClasses();
+        }
+
+        if (roots.isEmpty()) {
+        	roots = new LinkedList<VClass>();
+        	roots.add(vreq.getUnfilteredWebappDaoFactory().getVClassDao()
+        			.getTopConcept());
+        }
+        Collections.sort(roots);
+        int counter = 0;
+
+        Iterator<VClass> rootIt = roots.iterator();
+        if (!rootIt.hasNext()) {
+            VClass vcw = new VClass();
+            vcw.setName("<strong>No classes found.</strong>");
+            json += addVClassDataToResultsList(vreq.getUnfilteredWebappDaoFactory(), vcw,0,ontologyUri,counter);
+        } else {
+            while (rootIt.hasNext()) {
+                VClass root = (VClass) rootIt.next();
+	            if (root != null) {
+	                json += addChildren(vreq.getUnfilteredWebappDaoFactory(), root, 0, ontologyUri,counter);
+	                counter += 1;
+                }
+            }
+            int length = json.length();
+            if ( length > 0 ) {
+                json += " }"; 
+            }
+        }
+        body.put("jsonTree",json);
         
         return new TemplateResponseValues(TEMPLATE_NAME, body);
     }
@@ -131,21 +129,21 @@ public class ShowClassHierarchyController extends FreemarkerHttpServlet {
         int length = rowElts.length();
         String leaves = "";
         leaves += rowElts;
-        List childURIstrs = vcDao.getSubClassURIs(parent.getURI());
+        List<String> childURIstrs = vcDao.getSubClassURIs(parent.getURI());
         if ((childURIstrs.size()>0) && position<MAXDEPTH) {
-            List childClasses = new ArrayList();
-            Iterator childURIstrIt = childURIstrs.iterator();
+            List<VClass> childClasses = new ArrayList<VClass>();
+            Iterator<String> childURIstrIt = childURIstrs.iterator();
             while (childURIstrIt.hasNext()) {
-                String URIstr = (String) childURIstrIt.next();
+                String URIstr = childURIstrIt.next();
                 try {
-                    VClass child = (VClass) vcDao.getVClassByURI(URIstr);
+                    VClass child = vcDao.getVClassByURI(URIstr);
                     if (!child.getURI().equals(OWL.Nothing.getURI())) {
                     	childClasses.add(child);
                     }
                 } catch (Exception e) {}
             }
             Collections.sort(childClasses);
-            Iterator childClassIt = childClasses.iterator();
+            Iterator<VClass> childClassIt = childClasses.iterator();
             while (childClassIt.hasNext()) {
                 VClass child = (VClass) childClassIt.next();
                 leaves += addChildren(wadf, child, position + childShift, ontologyUri, counter);
@@ -197,15 +195,16 @@ public class ShowClassHierarchyController extends FreemarkerHttpServlet {
                 tempString += "}, { \"name\": ";
             }
             try {
-                tempString +=  "\"<a href='vclassEdit?uri="+URLEncoder.encode(vcw.getURI(),"UTF-8")+"'>"+ vcw.getLocalNameWithPrefix() +"</a>\", ";
+                tempString += JSONUtils.quote("<a href='vclassEdit?uri=" + 
+                        URLEncoder.encode(vcw.getURI(),"UTF-8") + "'>" + 
+                        vcw.getLocalNameWithPrefix() + "</a>") +", ";
             } catch (Exception e) {
-                 tempString += "\" " + ((vcw.getLocalNameWithPrefix() == null) ? "" : vcw.getLocalNameWithPrefix()) + "\", ";
+                 tempString += JSONUtils.quote(((vcw.getLocalNameWithPrefix() == null) 
+                         ? "" : vcw.getLocalNameWithPrefix())) + ", ";
             }
 
             String shortDef = ((vcw.getShortDef() == null) ? "" : vcw.getShortDef()) ;
-            shortDef = shortDef.replace("\"","\\\"");
-            shortDef = shortDef.replace("\'","\\\'");
-            tempString += "\"data\": { \"shortDef\": \"" + shortDef + "\", ";
+            tempString += "\"data\": { \"shortDef\": " + JSONUtils.quote(shortDef) + ", ";
 
             // Get group name if it exists
             VClassGroupDao groupDao= wadf.getVClassGroupDao();
@@ -218,16 +217,17 @@ public class ShowClassHierarchyController extends FreemarkerHttpServlet {
             		groupName = classGroup.getPublicName();
             	}
             }
-            tempString += "\"classGroup\": \"" + ((groupName == null) ? "" : groupName) + "\", ";
+            tempString += "\"classGroup\": " + JSONUtils.quote(
+                    (groupName == null) ? "" : groupName) + ", ";
             // Get ontology name
-			String ontName = null;
-			try {
-            	OntologyDao ontDao = wadf.getOntologyDao();
-            	Ontology ont = ontDao.getOntologyByURI(vcw.getNamespace());
-            	ontName = ont.getName();
-			} catch (Exception e) {}
-
-            tempString += "\"ontology\": \"" + ((ontName == null) ? "" : ontName) + "\"}, \"children\": [";
+            OntologyDao ontDao = wadf.getOntologyDao();
+            String ontName = vcw.getNamespace();
+            Ontology ont = ontDao.getOntologyByURI(ontName);
+            if (ont != null && ont.getName() != null) {
+                ontName = ont.getName();
+            }
+            tempString += "\"ontology\": " + JSONUtils.quote(
+                    (ontName == null) ? "" : ontName) + "}, \"children\": [";
 
             previous_posn = position;
         }
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowDataPropertyHierarchyController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowDataPropertyHierarchyController.java
index 586ec5c73..7c5dcf90a 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowDataPropertyHierarchyController.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowDataPropertyHierarchyController.java
@@ -2,19 +2,17 @@
 
 package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
 
-import java.net.URLEncoder;
 import java.text.Collator;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashMap;
-import java.util.Map;
 import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Map;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import net.sf.json.util.JSONUtils;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -25,7 +23,6 @@ import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
 import edu.cornell.mannlib.vitro.webapp.beans.Datatype;
 import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
-import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
@@ -33,6 +30,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
+import edu.cornell.mannlib.vitro.webapp.web.URLEncoder;
 
 public class ShowDataPropertyHierarchyController extends FreemarkerHttpServlet {
 
@@ -106,7 +104,7 @@ public class ShowDataPropertyHierarchyController extends FreemarkerHttpServlet {
                 Iterator<DataProperty> rootIt = roots.iterator();
                 if (!rootIt.hasNext()) {
                     DataProperty dp = new DataProperty();
-                    dp.setURI(ontologyUri+"fake");
+                    dp.setURI(ontologyUri + "fake");
                     String notFoundMessage = "<strong>No data properties found.</strong>"; 
                     dp.setName(notFoundMessage);
                     dp.setName(notFoundMessage);
@@ -142,19 +140,19 @@ public class ShowDataPropertyHierarchyController extends FreemarkerHttpServlet {
         int length = details.length();
         String leaves = "";
         leaves += details;
-        List childURIstrs = dpDao.getSubPropertyURIs(parent.getURI());
-        if ((childURIstrs.size()>0) && position<MAXDEPTH) {
-            List childProps = new ArrayList();
-            Iterator childURIstrIt = childURIstrs.iterator();
+        List<String> childURIstrs = dpDao.getSubPropertyURIs(parent.getURI());
+        if ( (childURIstrs.size() > 0) && (position < MAXDEPTH) ) {
+            List<DataProperty> childProps = new ArrayList<DataProperty>();
+            Iterator<String> childURIstrIt = childURIstrs.iterator();
             while (childURIstrIt.hasNext()) {
-                String URIstr = (String) childURIstrIt.next();
-                DataProperty child = (DataProperty) dpDao.getDataPropertyByURI(URIstr);
+                String URIstr = childURIstrIt.next();
+                DataProperty child = dpDao.getDataPropertyByURI(URIstr);
                 childProps.add(child);
             }
             Collections.sort(childProps);
-            Iterator childPropIt = childProps.iterator();
+            Iterator<DataProperty> childPropIt = childProps.iterator();
             while (childPropIt.hasNext()) {
-                DataProperty child = (DataProperty) childPropIt.next();
+                DataProperty child = childPropIt.next();
                 leaves += addChildren(child, position+1, ontologyUri, counter);
                 if (!childPropIt.hasNext()) {
                     if ( ontologyUri == null ) {
@@ -206,34 +204,40 @@ public class ShowDataPropertyHierarchyController extends FreemarkerHttpServlet {
                 tempString += "}, { \"name\": ";
             }
 
-            String nameStr = dp.getPublicName()==null ? dp.getName()==null ? dp.getURI()==null ? "(no name)" : dp.getURI() : dp.getName() : dp.getPublicName();
-            nameStr = nameStr.replace("\"","\\\"");
-            nameStr = nameStr.replace("\'","\\\'");
-            try {
-                tempString += "\"<a href='datapropEdit?uri="+URLEncoder.encode(dp.getURI(),"UTF-8")+"'>" + nameStr + "</a>\", ";                 
-            } catch (Exception e) {
-                tempString += "\"" + nameStr + "\", "; 
-                log.error("Unsupported: URLEncoder.encode() with UTF-8");
-            }
+            String nameStr = dp.getPublicName() == null 
+                    ? dp.getName() == null 
+                            ? dp.getURI() == null 
+                                    ? "(no name)" : dp.getURI() : dp.getName() : dp.getPublicName();
+  
+            tempString += JSONUtils.quote(
+                    "<a href='datapropEdit?uri=" + URLEncoder.encode(
+                            dp.getURI()) + "'>" + nameStr + "</a>") + ", ";                 
 
-            tempString += "\"data\": { \"internalName\": \"" + dp.getLocalNameWithPrefix() + "\", ";
+            tempString += "\"data\": { \"internalName\": " + JSONUtils.quote(
+                    dp.getLocalNameWithPrefix()) + ", ";
 
             VClass tmp = null;
             try {
-            	tempString += "\"domainVClass\": \"" + (((tmp = vcDao.getVClassByURI(dp.getDomainClassURI())) != null && (tmp.getLocalNameWithPrefix() == null)) ? "" : vcDao.getVClassByURI(dp.getDomainClassURI()).getLocalNameWithPrefix()) + "\", " ;
+            	tempString += "\"domainVClass\": " + JSONUtils.quote(
+            	        ((tmp = vcDao.getVClassByURI(dp.getDomainClassURI())) != null
+            	        && (tmp.getLocalNameWithPrefix() == null)) 
+            	                ? "" 
+            	                : vcDao.getVClassByURI(
+            	                        dp.getDomainClassURI())
+            	                        .getLocalNameWithPrefix()) + ", " ;
             } catch (NullPointerException e) {
             	tempString += "\"domainVClass\": \"\",";
             }
             try {
             	Datatype rangeDatatype = dDao.getDatatypeByURI(dp.getRangeDatatypeURI());
                 String rangeDatatypeStr = (rangeDatatype==null)?dp.getRangeDatatypeURI():rangeDatatype.getName();
-            	tempString += "\"rangeVClass\": \"" + ((rangeDatatypeStr != null) ? rangeDatatypeStr : "") + "\", " ; 
+            	tempString += "\"rangeVClass\": " + JSONUtils.quote((rangeDatatypeStr != null) ? rangeDatatypeStr : "") + ", " ; 
             } catch (NullPointerException e) {
             	tempString += "\"rangeVClass\": \"\",";
             }
             if (dp.getGroupURI() != null) {
                 PropertyGroup pGroup = pgDao.getGroupByURI(dp.getGroupURI());
-                tempString += "\"group\": \"" + ((pGroup == null) ? "unknown group" : pGroup.getName()) + "\" " ; 
+                tempString += "\"group\": " + JSONUtils.quote((pGroup == null) ? "unknown group" : pGroup.getName()); 
             } else {
                 tempString += "\"group\": \"unspecified\"";
             }
@@ -244,10 +248,4 @@ public class ShowDataPropertyHierarchyController extends FreemarkerHttpServlet {
         return tempString;
     }
 
-    private class DataPropertyAlphaComparator implements Comparator {
-        public int compare(Object o1, Object o2) {
-        	return Collator.getInstance().compare( ((DataProperty)o1).getName(), ((DataProperty)o2).getName());
-        }
-    }
-	
 }
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowObjectPropertyHierarchyController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowObjectPropertyHierarchyController.java
index 5e2c02f5b..b7547cf74 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowObjectPropertyHierarchyController.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowObjectPropertyHierarchyController.java
@@ -2,22 +2,18 @@
 
 package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
 
-import java.io.UnsupportedEncodingException;
-import java.net.URLEncoder;
 import java.text.Collator;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashMap;
-import java.util.Map;
 import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Map;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import net.sf.json.util.JSONUtils;
 
-import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -26,13 +22,13 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
 import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
-import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
+import edu.cornell.mannlib.vitro.webapp.web.URLEncoder;
 
 public class ShowObjectPropertyHierarchyController extends FreemarkerHttpServlet {
 
@@ -146,19 +142,19 @@ public class ShowObjectPropertyHierarchyController extends FreemarkerHttpServlet
         int length = details.length();
         String leaves = "";
         leaves += details;
-        List childURIstrs = opDao.getSubPropertyURIs(parent.getURI());
-        if ((childURIstrs.size()>0) && position<MAXDEPTH) {
-            List childProps = new ArrayList();
-            Iterator childURIstrIt = childURIstrs.iterator();
+        List<String> childURIstrs = opDao.getSubPropertyURIs(parent.getURI());
+        if ( (childURIstrs.size() > 0) && (position < MAXDEPTH) ) {
+            List<ObjectProperty> childProps = new ArrayList<ObjectProperty>();
+            Iterator<String> childURIstrIt = childURIstrs.iterator();
             while (childURIstrIt.hasNext()) {
-                String URIstr = (String) childURIstrIt.next();
-                ObjectProperty child = (ObjectProperty) opDao.getObjectPropertyByURI(URIstr);
+                String URIstr = childURIstrIt.next();
+                ObjectProperty child = opDao.getObjectPropertyByURI(URIstr);
                 childProps.add(child);
             }
             Collections.sort(childProps);
-            Iterator childPropIt = childProps.iterator();
+            Iterator<ObjectProperty> childPropIt = childProps.iterator();
             while (childPropIt.hasNext()) {
-                ObjectProperty child = (ObjectProperty) childPropIt.next();
+                ObjectProperty child = childPropIt.next();
                 leaves += addChildren(child, position+1, ontologyUri, counter);
                 if (!childPropIt.hasNext()) {
                     if ( ontologyUri == null ) {
@@ -208,34 +204,45 @@ public class ShowObjectPropertyHierarchyController extends FreemarkerHttpServlet
                 tempString += "}, { \"name\": ";
             }
             
-            String nameStr = getDisplayLabel(op)==null ? "(no name)" : getDisplayLabel(op);
-            nameStr = nameStr.replace("\"","\\\"");
-            nameStr = nameStr.replace("\'","\\\'");
+            String nameStr = getDisplayLabel(op) == null ? "(no name)" : getDisplayLabel(op);
 
-            try {
-            	tempString +=  "\"<a href='propertyEdit?uri="+URLEncoder.encode(op.getURI(),"UTF-8") + "'>" + nameStr +"</a>\", ";
-            } catch (UnsupportedEncodingException uee) {
-                tempString +=  "\"" + nameStr + "\"";
-            	log.error("Unsupported: URLEncoder.encode() with UTF-8");
-            }
-            
-            tempString += "\"data\": { \"internalName\": \"" + op.getLocalNameWithPrefix() + "\", ";
+        	tempString += JSONUtils.quote(
+        	        "<a href='propertyEdit?uri=" + URLEncoder.encode(
+        	                op.getURI()) + "'>" + nameStr + "</a>") + ", ";
+             
+            tempString += "\"data\": { \"internalName\": " + JSONUtils.quote(
+                    op.getLocalNameWithPrefix()) + ", ";
 
             VClass tmp = null;
             
             try {
-            	tempString += "\"domainVClass\": \"" + (((tmp = vcDao.getVClassByURI(op.getDomainVClassURI())) != null && (tmp.getLocalNameWithPrefix() == null)) ? "" : vcDao.getVClassByURI(op.getDomainVClassURI()).getLocalNameWithPrefix()) + "\", " ;
+            	tempString += "\"domainVClass\": " + JSONUtils.quote(
+            	        ((tmp = vcDao.getVClassByURI(
+            	                op.getDomainVClassURI())) != null 
+            	                && (tmp.getLocalNameWithPrefix() == null)) 
+            	                        ? "" 
+            	                        : vcDao.getVClassByURI(
+            	                                op.getDomainVClassURI())
+            	                                .getLocalNameWithPrefix()) + ", " ;
             } catch (NullPointerException e) {
             	tempString += "\"domainVClass\": \"\",";
             }
             try {
-            	tempString += "\"rangeVClass\": \"" + (((tmp = vcDao.getVClassByURI(op.getRangeVClassURI())) != null && (tmp.getLocalNameWithPrefix() == null)) ? "" : vcDao.getVClassByURI(op.getRangeVClassURI()).getLocalNameWithPrefix()) + "\", " ;
+            	tempString += "\"rangeVClass\": " + JSONUtils.quote(
+            	        ((tmp = vcDao.getVClassByURI(
+            	                op.getRangeVClassURI())) != null 
+            	                && (tmp.getLocalNameWithPrefix() == null)) 
+            	                        ? "" 
+            	                        : vcDao.getVClassByURI(
+            	                                op.getRangeVClassURI())
+            	                                .getLocalNameWithPrefix()) + ", " ;
             } catch (NullPointerException e) {
             	tempString += "\"rangeVClass\": \"\",";
             }
             if (op.getGroupURI() != null) {
                 PropertyGroup pGroup = pgDao.getGroupByURI(op.getGroupURI());
-                tempString += "\"group\": \"" + ((pGroup == null) ? "unknown group" : pGroup.getName()) + "\" " ;
+                tempString += "\"group\": " + JSONUtils.quote(
+                        (pGroup == null) ? "unknown group" : pGroup.getName());
             } else {
                 tempString += "\"group\": \"unspecified\"";
             }
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/VitroVocabulary.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/VitroVocabulary.java
index d06f6ccab..0a6e6fc13 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/VitroVocabulary.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/VitroVocabulary.java
@@ -46,9 +46,10 @@ public class VitroVocabulary {
     
     public static final String DESCRIPTION_ANNOT = vitroURI + "descriptionAnnot";
     public static final String PUBLIC_DESCRIPTION_ANNOT = vitroURI + "publicDescriptionAnnot";
-    public static final String SHORTDEF = vitroURI+"shortDef";
-    public static final String EXAMPLE_ANNOT = vitroURI+"exampleAnnot";
+    public static final String SHORTDEF = "http://purl.obolibrary.org/obo/IAO_0000115";
+    public static final String EXAMPLE_ANNOT = "http://purl.obolibrary.org/obo/IAO_0000112";
 
+    
     public static final String EXTERNALID = vitroURI+"externalId";
     public static final String DATAPROPERTY_ISEXTERNALID = vitroURI+"isExternalId";
         

From dd2c9b8a7b05b539e16618f940f9bcbbcd6066c5 Mon Sep 17 00:00:00 2001
From: Brian Caruso <bdc34@cornell.edu>
Date: Mon, 30 Sep 2013 16:30:41 -0400
Subject: [PATCH 08/10] Moving files to deal with vivo overrides. Adding
 permissions to pageList. VIVO-63

---
 webapp/rdf/display/firsttime/menu.n3          | 37 +--------------
 webapp/rdf/display/firsttime/pageList.n3      | 46 +++++++++++++++++++
 .../display/firsttime}/permissions.n3         |  0
 .../display/firsttime}/sparqlTestMenu.n3      |  0
 4 files changed, 47 insertions(+), 36 deletions(-)
 create mode 100644 webapp/rdf/display/firsttime/pageList.n3
 rename webapp/{web/WEB-INF/ontologies/app => rdf/display/firsttime}/permissions.n3 (100%)
 rename webapp/{web/WEB-INF/ontologies/app => rdf/display/firsttime}/sparqlTestMenu.n3 (100%)

diff --git a/webapp/rdf/display/firsttime/menu.n3 b/webapp/rdf/display/firsttime/menu.n3
index f59cf99b7..cb1239252 100644
--- a/webapp/rdf/display/firsttime/menu.n3
+++ b/webapp/rdf/display/firsttime/menu.n3
@@ -4,6 +4,7 @@
 @prefix display: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#> .
 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix action: <java:edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission#> .
 
 ### This file defines the default menu for vitro. ###
 
@@ -35,39 +36,3 @@ display:Home
     
 <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#homeDataGetter>
       a <java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.BrowseDataGetter> .  
-      
-########## Page Management ##########
-display:pageListPage
-    a display:Page ;              
-    display:title "Pages" ;
-    display:urlMapping "/pageList" ;
-    display:requiresBodyTemplate "pageList.ftl" ;   
-    display:hasDataGetter display:pageListData;
-    display:cannotDeletePage "true" .
-
-display:pageListData
-    a <java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SparqlQueryDataGetter>;
-    display:queryModel <vitro:contextDisplayModel> ;                        
-    display:saveToVar "pages" ;
-     
-    display:query """
-    PREFIX display: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#> 
-    PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-    SELECT ?listedPageUri ?listedPageTitle ?listedPageUrlMapping ?listedPageTemplate ?listedPageMenuItem ?listedPageCannotDeletePage
-    WHERE { 
-        ?listedPageUri a display:Page .
-        OPTIONAL{ ?listedPageUri display:urlMapping ?listedPageUrlMapping. }
-        OPTIONAL{ ?listedPageUri display:title  ?listedPageTitle. }  
-        OPTIONAL {?listedPageUri display:requiresBodyTemplate ?listedPageTemplate .}
-        OPTIONAL {?listedPageMenuItem display:toPage ?listedPageUri .}
-        OPTIONAL {?listedPageUri display:cannotDeletePage ?listedPageCannotDeletePage .}
-     }  ORDER BY ?listedPageTitle """ .      
-###Page Management and Data Getters
-#Data getter type labels
-<java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.ClassGroupPageData>  rdfs:label "Class Group Page" .
-<java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.BrowseDataGetter> rdfs:label "Browse Page" . 
-<java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.IndividualsForClassesDataGetter> rdfs:label "Class Group Page - Selected Classes" .
-<java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SparqlQueryDataGetter> rdfs:label "Sparql Query Results" .
-        
- 
-                
\ No newline at end of file
diff --git a/webapp/rdf/display/firsttime/pageList.n3 b/webapp/rdf/display/firsttime/pageList.n3
new file mode 100644
index 000000000..50c6176cf
--- /dev/null
+++ b/webapp/rdf/display/firsttime/pageList.n3
@@ -0,0 +1,46 @@
+# $This file is distributed under the terms of the license in /doc/license.txt$ 
+
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix display: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix action: <java:edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission#> .
+
+### This file defines the page list menu for vitro. ###
+
+display:pageListPage
+    a display:Page ;              
+    display:title "Pages" ;
+    display:urlMapping "/pageList" ;
+    display:requiresBodyTemplate "pageList.ftl" ;   
+    display:hasDataGetter display:pageListData;
+    display:requiredAction <java:edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission#ManageMenus> ;1
+    display:cannotDeletePage "true" .
+
+display:pageListData
+    a <java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SparqlQueryDataGetter>;
+    display:queryModel <vitro:contextDisplayModel> ;                        
+    display:saveToVar "pages" ;
+     
+    display:query """
+    PREFIX display: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#> 
+    PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+    SELECT ?listedPageUri ?listedPageTitle ?listedPageUrlMapping ?listedPageTemplate ?listedPageMenuItem ?listedPageCannotDeletePage
+    WHERE { 
+        ?listedPageUri a display:Page .
+        OPTIONAL{ ?listedPageUri display:urlMapping ?listedPageUrlMapping. }
+        OPTIONAL{ ?listedPageUri display:title  ?listedPageTitle. }  
+        OPTIONAL {?listedPageUri display:requiresBodyTemplate ?listedPageTemplate .}
+        OPTIONAL {?listedPageMenuItem display:toPage ?listedPageUri .}
+        OPTIONAL {?listedPageUri display:cannotDeletePage ?listedPageCannotDeletePage .}
+     }  ORDER BY ?listedPageTitle """ .      
+###Page Management and Data Getters
+
+#Data getter type labels
+<java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.ClassGroupPageData>  rdfs:label "Class Group Page" .
+<java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.BrowseDataGetter> rdfs:label "Browse Page" . 
+<java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.IndividualsForClassesDataGetter> rdfs:label "Class Group Page - Selected Classes" .
+<java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SparqlQueryDataGetter> rdfs:label "Sparql Query Results" .
+        
+ 
+                
\ No newline at end of file
diff --git a/webapp/web/WEB-INF/ontologies/app/permissions.n3 b/webapp/rdf/display/firsttime/permissions.n3
similarity index 100%
rename from webapp/web/WEB-INF/ontologies/app/permissions.n3
rename to webapp/rdf/display/firsttime/permissions.n3
diff --git a/webapp/web/WEB-INF/ontologies/app/sparqlTestMenu.n3 b/webapp/rdf/display/firsttime/sparqlTestMenu.n3
similarity index 100%
rename from webapp/web/WEB-INF/ontologies/app/sparqlTestMenu.n3
rename to webapp/rdf/display/firsttime/sparqlTestMenu.n3

From e375dc33f609848a222988f3d178a8665b4163ca Mon Sep 17 00:00:00 2001
From: Brian Caruso <bdc34@cornell.edu>
Date: Mon, 30 Sep 2013 16:39:47 -0400
Subject: [PATCH 09/10] Fixing type in previous commit. VIVO-63

---
 webapp/rdf/display/firsttime/pageList.n3 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/webapp/rdf/display/firsttime/pageList.n3 b/webapp/rdf/display/firsttime/pageList.n3
index 50c6176cf..4db1c18d0 100644
--- a/webapp/rdf/display/firsttime/pageList.n3
+++ b/webapp/rdf/display/firsttime/pageList.n3
@@ -14,7 +14,7 @@ display:pageListPage
     display:urlMapping "/pageList" ;
     display:requiresBodyTemplate "pageList.ftl" ;   
     display:hasDataGetter display:pageListData;
-    display:requiredAction <java:edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission#ManageMenus> ;1
+    display:requiredAction <java:edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission#ManageMenus> ;
     display:cannotDeletePage "true" .
 
 display:pageListData

From 1db72b3397f58b023c37c7d20872a65d5007bcab Mon Sep 17 00:00:00 2001
From: brianjlowe <bjl23@cornell.edu>
Date: Tue, 1 Oct 2013 10:21:08 -0400
Subject: [PATCH 10/10] various small fixes

---
 .../vitro/webapp/dao/jena/VClassDaoJena.java  | 72 +++++++++++--------
 .../servlet/setup/UpdateKnowledgeBase.java    | 38 +++++-----
 2 files changed, 62 insertions(+), 48 deletions(-)

diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoJena.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoJena.java
index 1d168eb63..67dc61ea4 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoJena.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoJena.java
@@ -2,7 +2,6 @@
 
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
-import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashSet;
@@ -61,7 +60,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
-import edu.cornell.mannlib.vitro.webapp.dao.jena.pellet.PelletListener;
+import edu.cornell.mannlib.vitro.webapp.web.URLEncoder;
 
 public class VClassDaoJena extends JenaBaseDao implements VClassDao {
 
@@ -148,8 +147,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
                         labelStr += getLabelForClass(ccls.getOperand(),withPrefix,forPickList);		    			
                     } else if (cls.isIntersectionClass()) {
                         IntersectionClass icls = cls.as(IntersectionClass.class);
-                        for (Iterator operandIt = icls.listOperands(); operandIt.hasNext();) {
-                            OntClass operand = (OntClass) operandIt.next();
+                        for (Iterator<? extends OntClass> operandIt = 
+                                icls.listOperands(); operandIt.hasNext();) {
+                            OntClass operand = operandIt.next();
                             labelStr += getLabelForClass(operand,withPrefix,forPickList);
                             if (operandIt.hasNext()) {
                                 labelStr += " and ";
@@ -157,8 +157,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
                         }
                     } else if (cls.isUnionClass()) {
                         UnionClass icls = cls.as(UnionClass.class);
-                        for (Iterator operandIt = icls.listOperands(); operandIt.hasNext();) {
-                            OntClass operand = (OntClass) operandIt.next();
+                        for (Iterator<? extends OntClass> operandIt = 
+                                icls.listOperands(); operandIt.hasNext();) {
+                            OntClass operand = operandIt.next();
                             labelStr += getLabelForClass(operand,withPrefix,forPickList);
                             if (operandIt.hasNext()) {
                                 labelStr += " or ";
@@ -170,7 +171,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
                     // BJL23 2009-02-19
                     // I'm putting the link markup in because I need it,
                     // but obviously we need to factor this out into the display layer.
-                    return "<a href=\"vclassEdit?uri="+URLEncoder.encode(getClassURIStr(cls),"UTF-8")+"\">[anonymous class]</a>";
+                    return "<a href=\"vclassEdit?uri=" + 
+                            URLEncoder.encode(getClassURIStr(cls)) + 
+                                    "\">[anonymous class]</a>";
                 }
             } else {
                 if (withPrefix || forPickList) {
@@ -244,8 +247,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
         List<String> uriList = new ArrayList<String>();
         getOntModel().enterCriticalSection(Lock.READ);
         try {
-            for (Iterator i = ontClass.listDisjointWith(); i.hasNext(); ) {
-                OntClass disjointClass = (OntClass) i.next();
+            for (Iterator<? extends OntClass> i = 
+                    ontClass.listDisjointWith(); i.hasNext(); ) {
+                OntClass disjointClass = i.next();
                 uriList.add(getClassURIStr(disjointClass));
             }
         } catch (ProfileException pe) {
@@ -288,10 +292,11 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
         getOntModel().enterCriticalSection(Lock.READ);
         try {
             OntClass ontClass = getOntClass(getOntModel(), classURI);
-            ClosableIterator equivalentOntClassIt = ontClass.listEquivalentClasses();
+            ClosableIterator<OntClass> equivalentOntClassIt = ontClass.listEquivalentClasses();
             try {
-                for (Iterator eqOntClassIt = equivalentOntClassIt; eqOntClassIt.hasNext(); ) {
-                    OntClass eqClass = (OntClass) eqOntClassIt.next();
+                for (Iterator<OntClass> eqOntClassIt = 
+                        equivalentOntClassIt; eqOntClassIt.hasNext(); ) {
+                    OntClass eqClass = eqOntClassIt.next();
                     equivalentClassURIs.add(getClassURIStr(eqClass));
                 }
             } finally {
@@ -482,10 +487,6 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
         return classes;
     }
 
-    private Iterator<OntClass> smarterListHierarchyRootClasses(OntModel ontModel) {
-        return smarterListHierarchyRootClasses(ontModel, null);
-    }
-
     /** 
      * The basic idea here is that we ignore anonymous superclasses for the purpose 
      * of determining whether something is a root class.
@@ -569,16 +570,21 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
         OntModel ontModel = getOntModel();
         ontModel.enterCriticalSection(Lock.READ);
         try {
-            Iterator<OntClass> ontClassIt = ontModel.listClasses();
+            Iterator<Resource> ontClassIt = ontModel.listResourcesWithProperty(
+                    RDF.type, OWL.Class);
             while (ontClassIt.hasNext()) {
-                OntClass ontClass = ontClassIt.next();
+                Resource ontClass = ontClassIt.next();
                 if (ontologyURI.equals(ontClass.getNameSpace())) {
                     boolean root = true;
-                    StmtIterator superStmtIt = ontModel.listStatements(ontClass, RDFS.subClassOf, (RDFNode) null);
+                    StmtIterator superStmtIt = ontModel.listStatements(
+                            ontClass, RDFS.subClassOf, (RDFNode) null);
                     try {
                         while (superStmtIt.hasNext()) {
                             Statement superStmt = superStmtIt.nextStatement();
-                            if ( superStmt.getObject().isResource() && ontologyURI.equals(((Resource) superStmt.getObject()).getNameSpace()) ) {
+                            if ( superStmt.getObject().isResource() 
+                                    && ontologyURI.equals(
+                                            ((Resource) superStmt.getObject())
+                                            .getNameSpace()) ) {
                                 root = false;
                                 break;
                             }
@@ -586,8 +592,10 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
                     } finally {
                         superStmtIt.close();
                     }
-                    if (root) {
-                        ontologyRootClasses.add(new VClassJena(ontClass,getWebappDaoFactory()));
+                    if (root && ontClass.canAs(OntClass.class)) {
+                        ontologyRootClasses.add(new VClassJena(
+                                (OntClass) ontClass.as(OntClass.class), 
+                                getWebappDaoFactory()));
                     }
                 }
             }
@@ -598,12 +606,12 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
     }
 
     public List <String> getSubClassURIs(String classURI) {
-        List subURIs = new ArrayList();
+        List<String> subURIs = new ArrayList<String>();
         OntClass superClass = getOntClass(getOntModel(),classURI);
         try {
-            Iterator subIt = superClass.listSubClasses(true);
+            Iterator<OntClass> subIt = superClass.listSubClasses(true);
             while (subIt.hasNext()) {
-                OntClass cls = (OntClass) subIt.next();
+                OntClass cls = subIt.next();
                 subURIs.add(getClassURIStr(cls));
             }
         } catch (Exception e) {
@@ -617,10 +625,10 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
     }
 
     public List <String> getSuperClassURIs(String classURI, boolean direct) {
-        List supURIs = new ArrayList();
+        List<String> supURIs = new ArrayList<String>();
         OntClass subClass = getOntClass(getOntModel(), classURI);
         try {
-            Iterator supIt = subClass.listSuperClasses(direct);
+            Iterator<OntClass> supIt = subClass.listSuperClasses(direct);
             while (supIt.hasNext()) {
                 OntClass cls = (OntClass) supIt.next();
                 supURIs.add(getClassURIStr(cls));
@@ -717,12 +725,16 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
                 OntResource superclass = null;
                 if (vclassURI != null) {
                     // TODO need a getAllSuperPropertyURIs method in ObjectPropertyDao
-                    List<String> superproperties = getWebappDaoFactory().getObjectPropertyDao().getSuperPropertyURIs(propertyURI,false);
+                    List<String> superproperties = getWebappDaoFactory()
+                            .getObjectPropertyDao()
+                            .getSuperPropertyURIs(propertyURI, false);
                     superproperties.add(propertyURI);
-                    HashSet<String> subjSuperclasses = new HashSet<String>(getAllSuperClassURIs(vclassURI));
+                    HashSet<String> subjSuperclasses = new HashSet<String>(
+                            getAllSuperClassURIs(vclassURI));
                     subjSuperclasses.add(vclassURI); 
                     for (String objectPropertyURI : superproperties) {
-                        for (Iterator restStmtIt = getOntModel().listStatements(null,OWL.onProperty,getOntModel().getProperty(objectPropertyURI)); restStmtIt.hasNext();) {
+                        for (Iterator restStmtIt = getOntModel().listStatements(
+                                null,OWL.onProperty,getOntModel().getProperty(objectPropertyURI)); restStmtIt.hasNext();) {
                             Statement restStmt = (Statement) restStmtIt.next();
                             Resource restRes = restStmt.getSubject();	            		
                             for (Iterator axStmtIt = getOntModel().listStatements(null,null,restRes); axStmtIt.hasNext();) {
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 d02bbeceb..d68ca6433 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
@@ -138,24 +138,26 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 			KnowledgeBaseUpdater ontologyUpdater = new KnowledgeBaseUpdater(settings);
 			boolean requiredUpdate = ontologyUpdater.updateRequired(ctx);
 
-			try {
-			    ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
-			    log.info("Data migration required");
-			    migrationChangesMade = ontologyUpdater.update(ctx);
-			    if (tryMigrateDisplay) {
-			        try {
-			            migrateDisplayModel(settings);
-			            log.info("Migrated display model");
-			        } catch (Exception e) {
-			            log.warn("unable to successfully update display model: " + e.getMessage());
-			        }
-			    }
-			    // reload the display model since the TBoxUpdater may have 
-			    // modified it
-			    new ApplicationModelSetup().contextInitialized(sce);				  
-			} catch (Exception ioe) {
-			    ss.fatal(this, "Exception updating knowledge base for ontology changes: ", ioe);
-			}	
+			if(!JenaDataSourceSetupBase.isFirstStartup()) {
+    			try {
+    			    ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
+    			    log.info("Data migration required");
+    			    migrationChangesMade = ontologyUpdater.update(ctx);
+    			    if (tryMigrateDisplay) {
+    			        try {
+    			            migrateDisplayModel(settings);
+    			            log.info("Migrated display model");
+    			        } catch (Exception e) {
+    			            log.warn("unable to successfully update display model: " + e.getMessage());
+    			        }
+    			    }
+    			    // reload the display model since the TBoxUpdater may have 
+    			    // modified it
+    			    new ApplicationModelSetup().contextInitialized(sce);				  
+    			} catch (Exception ioe) {
+    			    ss.fatal(this, "Exception updating knowledge base for ontology changes: ", ioe);
+    			}	
+			}
 
 		    SimpleReasoner simpleReasoner = (SimpleReasoner) sce.getServletContext()
 		            .getAttribute(SimpleReasoner.class.getName());