VIVO-212 Rename WADF access methods on VitroRequest

Use the term Unfiltered instead of Full, for consistency with other places in Vitro.

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/MailUsersServlet.java

@@ -208,8 +208,7 @@ public class MailUsersServlet extends VitroHttpServlet {
     }
     
 	private List<String> getEmailsForAllUserAccounts(VitroRequest vreq) {
-		UserAccountsDao uaDao = vreq.getFullWebappDaoFactory()
+		UserAccountsDao uaDao = vreq.getWebappDaoFactory().getUserAccountsDao();
-				.getUserAccountsDao();
 		
 		List<String> emails = new ArrayList<String>();
 		for (UserAccount user : uaDao.getAllUserAccounts()) {

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/SparqlQueryServlet.java

@@ -273,7 +273,7 @@ public class SparqlQueryServlet extends BaseEditController {
     private void doHelp(HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException {
             VitroRequest vreq = new VitroRequest(req);
             
-            OntologyDao daoObj = vreq.getFullWebappDaoFactory().getOntologyDao();
+            OntologyDao daoObj = vreq.getUnfilteredWebappDaoFactory().getOntologyDao();
             List<Ontology> ontologiesObj = daoObj.getAllOntologies();
             ArrayList<String> prefixList = new ArrayList<String>();
             

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/VitroRequest.java

@@ -72,19 +72,21 @@ public class VitroRequest extends HttpServletRequestWrapper {
         setAttribute("unfilteredRDFService", rdfService);
     }
     
-    /** gets WebappDaoFactory with appropriate filtering for the request */
+    /** Gets WebappDaoFactory with appropriate filtering for the request */
     public WebappDaoFactory getWebappDaoFactory(){
-    	return ModelAccess.on(this).getWebappDaoFactory();
+    	return ModelAccess.on(this).getWebappDaoFactory(FactoryID.UNION);
     }
     
-    /** Gets a WebappDaoFactory with request-specific dataset but no filtering. 
+    /** gets assertions+inference WebappDaoFactory with no policy filtering */
-     * Use this for any servlets that need to bypass filtering.
-     * @return
-     */
     public WebappDaoFactory getUnfilteredWebappDaoFactory() {
     	return ModelAccess.on(this).getWebappDaoFactory(FactoryID.UNFILTERED_UNION);
     }
     
+    /** gets assertions-only WebappDaoFactory with no policy filtering */
+    public WebappDaoFactory getUnfilteredAssertionsWebappDaoFactory() {
+    	return ModelAccess.on(this).getWebappDaoFactory(FactoryID.UNFILTERED_BASE);
+    }
+    
     public Dataset getDataset() {
     	return (Dataset) getAttribute("dataset");
     }
@@ -93,16 +95,6 @@ public class VitroRequest extends HttpServletRequestWrapper {
     	setAttribute("dataset", dataset);
     }
     
-    /** gets assertions + inferences WebappDaoFactory with no filtering **/
-    public WebappDaoFactory getFullWebappDaoFactory() {
-    	return getUnfilteredWebappDaoFactory();
-    }
-    
-    /** gets assertions-only WebappDaoFactory with no filtering */
-    public WebappDaoFactory getAssertionsWebappDaoFactory() {
-    	return ModelAccess.on(this).getWebappDaoFactory(FactoryID.UNFILTERED_BASE);
-    }
-        
     //Method that retrieves write model, returns special model in case of write model
     public OntModel getWriteModel() {
     	//if special write model doesn't exist use get ont model 

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

@@ -52,7 +52,7 @@ public class ApplicationBeanRetryController extends BaseEditController {
 
         String action = "update";
 
-        ApplicationDao aDao = request.getFullWebappDaoFactory().getApplicationDao();
+        ApplicationDao aDao = request.getUnfilteredWebappDaoFactory().getApplicationDao();
         ApplicationBean applicationForEditing = aDao.getApplicationBean();
         epo.setDataAccessObject(aDao);
  

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/Classes2ClassesOperationController.java

@@ -57,7 +57,7 @@ public class Classes2ClassesOperationController extends BaseEditController {
             return;
         }
 
-        VClassDao vcDao = request.getAssertionsWebappDaoFactory().getVClassDao();
+        VClassDao vcDao = request.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
         
         String modeStr = request.getParameter("opMode");
         modeStr = (modeStr == null) ? "" : modeStr;

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/Classes2ClassesRetryController.java

@@ -43,7 +43,7 @@ public class Classes2ClassesRetryController extends BaseEditController {
             action = epo.getAction();
         }
 
-        VClassDao vcDao = request.getFullWebappDaoFactory().getVClassDao();
+        VClassDao vcDao = request.getUnfilteredWebappDaoFactory().getVClassDao();
         epo.setDataAccessObject(vcDao);
         Classes2Classes objectForEditing = new Classes2Classes();
 

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

@@ -51,7 +51,7 @@ public class ClassgroupRetryController extends BaseEditController {
             action = epo.getAction();
         }
 
-        VClassGroupDao cgDao = request.getFullWebappDaoFactory().getVClassGroupDao();
+        VClassGroupDao cgDao = request.getUnfilteredWebappDaoFactory().getVClassGroupDao();
 
         epo.setDataAccessObject(cgDao);
 

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

@@ -47,10 +47,10 @@ public class DataPropertyStatementRetryController extends BaseEditController {
         VitroRequest vreq = new VitroRequest(request);
         
         DataPropertyStatementDao dataPropertyStatementDao = 
-        		vreq.getFullWebappDaoFactory().getDataPropertyStatementDao();
+        		vreq.getUnfilteredWebappDaoFactory().getDataPropertyStatementDao();
         epo.setDataAccessObject(dataPropertyStatementDao);
-        DataPropertyDao dpDao = vreq.getFullWebappDaoFactory().getDataPropertyDao();
+        DataPropertyDao dpDao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyDao();
-        IndividualDao eDao = vreq.getFullWebappDaoFactory().getIndividualDao();
+        IndividualDao eDao = vreq.getUnfilteredWebappDaoFactory().getIndividualDao();
         epo.setBeanClass(DataPropertyStatement.class);
 
         DataPropertyStatement objectForEditing = null;

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

@@ -44,9 +44,9 @@ public class DatapropEditController extends BaseEditController {
 
         String datapropURI = request.getParameter("uri");
 
-        DataPropertyDao dpDao = vreq.getFullWebappDaoFactory().getDataPropertyDao();
+        DataPropertyDao dpDao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyDao();
         DataProperty dp = dpDao.getDataPropertyByURI(datapropURI);
-        PropertyGroupDao pgDao = vreq.getFullWebappDaoFactory().getPropertyGroupDao();
+        PropertyGroupDao pgDao = vreq.getUnfilteredWebappDaoFactory().getPropertyGroupDao();
 
         ArrayList results = new ArrayList();
         results.add("data property");         // column 1
@@ -85,7 +85,7 @@ public class DatapropEditController extends BaseEditController {
         
         String ontologyName = null;
         if (dp.getNamespace() != null) {
-            Ontology ont = vreq.getFullWebappDaoFactory().getOntologyDao().getOntologyByURI(dp.getNamespace());
+            Ontology ont = vreq.getUnfilteredWebappDaoFactory().getOntologyDao().getOntologyByURI(dp.getNamespace());
             if ( (ont != null) && (ont.getName() != null) ) {
                 ontologyName = ont.getName();
             }
@@ -138,9 +138,7 @@ public class DatapropEditController extends BaseEditController {
         foo.setOptionLists(OptionMap);
         epo.setFormObject(foo);
 
-        DataPropertyDao assertionsDpDao = (vreq.getAssertionsWebappDaoFactory() != null) 
+        DataPropertyDao assertionsDpDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getDataPropertyDao();
-            ? vreq.getAssertionsWebappDaoFactory().getDataPropertyDao()
-            : vreq.getFullWebappDaoFactory().getDataPropertyDao();
         
         List superURIs = assertionsDpDao.getSuperPropertyURIs(dp.getURI(),false);
         List superProperties = new ArrayList();

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

@@ -54,11 +54,11 @@ public class DatapropRetryController extends BaseEditController {
         
         VitroRequest vreq = new VitroRequest(request);
 
-        DatatypeDao dDao = vreq.getFullWebappDaoFactory().getDatatypeDao();
+        DatatypeDao dDao = vreq.getUnfilteredWebappDaoFactory().getDatatypeDao();
-        DataPropertyDao dpDao = vreq.getFullWebappDaoFactory().getDataPropertyDao();
+        DataPropertyDao dpDao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyDao();
         epo.setDataAccessObject(dpDao);
-        OntologyDao ontDao = vreq.getFullWebappDaoFactory().getOntologyDao();
+        OntologyDao ontDao = vreq.getUnfilteredWebappDaoFactory().getOntologyDao();
-        VClassDao vclassDao = vreq.getFullWebappDaoFactory().getVClassDao();
+        VClassDao vclassDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
 
         DataProperty objectForEditing = null;
         String action = null;
@@ -135,10 +135,10 @@ public class DatapropRetryController extends BaseEditController {
         
         HashMap optionMap = new HashMap();
         List namespaceList = FormUtils.makeOptionListFromBeans(ontDao.getAllOntologies(),"URI","Name", ((objectForEditing.getNamespace()==null) ? "" : objectForEditing.getNamespace()), null, (objectForEditing.getNamespace()!=null));
-	    namespaceList.add(0, new Option(vreq.getFullWebappDaoFactory().getDefaultNamespace(),"default"));
+	    namespaceList.add(0, new Option(vreq.getUnfilteredWebappDaoFactory().getDefaultNamespace(),"default"));
         optionMap.put("Namespace", namespaceList);
         
-        List<Option> domainOptionList = FormUtils.makeVClassOptionList(vreq.getFullWebappDaoFactory(), objectForEditing.getDomainClassURI());
+        List<Option> domainOptionList = FormUtils.makeVClassOptionList(vreq.getUnfilteredWebappDaoFactory(), objectForEditing.getDomainClassURI());
         if (objectForEditing.getDomainClassURI() != null) {
         	VClass domain = vreq.getWebappDaoFactory().getVClassDao()
         	        .getVClassByURI(objectForEditing.getDomainClassURI());
@@ -157,7 +157,7 @@ public class DatapropRetryController extends BaseEditController {
         datatypeOptionList.add(0,new Option(null,"untyped (use if language tags desired)"));
         optionMap.put("RangeDatatypeURI", datatypeOptionList);
         
-        List groupOptList = FormUtils.makeOptionListFromBeans(vreq.getFullWebappDaoFactory().getPropertyGroupDao().getPublicGroups(true),"URI","Name", ((objectForEditing.getGroupURI()==null) ? "" : objectForEditing.getGroupURI()), null, (objectForEditing.getGroupURI()!=null));
+        List groupOptList = FormUtils.makeOptionListFromBeans(vreq.getUnfilteredWebappDaoFactory().getPropertyGroupDao().getPublicGroups(true),"URI","Name", ((objectForEditing.getGroupURI()==null) ? "" : objectForEditing.getGroupURI()), null, (objectForEditing.getGroupURI()!=null));
         groupOptList.add(0,new Option("","none"));
         optionMap.put("GroupURI", groupOptList);
 

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

@@ -37,7 +37,7 @@ public class DatatypeRetryController extends BaseEditController {
         //create an EditProcessObject for this and put it in the session
         EditProcessObject epo = super.createEpo(request);
 
-        DatatypeDao dDao = request.getFullWebappDaoFactory().getDatatypeDao();
+        DatatypeDao dDao = request.getUnfilteredWebappDaoFactory().getDatatypeDao();
         epo.setDataAccessObject(dDao);
         Datatype objectForEditing = null;
         String action = "";

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

@@ -49,7 +49,7 @@ public class EntityEditController extends BaseEditController {
         ApplicationBean application = vreq.getAppBean();
         
         //Individual ent = vreq.getWebappDaoFactory().getIndividualDao().getIndividualByURI(entURI);
-        Individual ent = vreq.getAssertionsWebappDaoFactory().getIndividualDao().getIndividualByURI(entURI);
+        Individual ent = vreq.getUnfilteredAssertionsWebappDaoFactory().getIndividualDao().getIndividualByURI(entURI);
         if (ent == null) {
         	try {
         		RequestDispatcher rd = request.getRequestDispatcher(Controllers.BASIC_JSP);
@@ -64,7 +64,7 @@ public class EntityEditController extends BaseEditController {
             }
         }
         
-        Individual inferredEnt = vreq.getFullWebappDaoFactory().getIndividualDao().getIndividualByURI(entURI);
+        Individual inferredEnt = vreq.getUnfilteredWebappDaoFactory().getIndividualDao().getIndividualByURI(entURI);
         if (inferredEnt == null) {
         	inferredEnt = new IndividualImpl(entURI);
         }
@@ -150,13 +150,13 @@ public class EntityEditController extends BaseEditController {
                 
         try{
             OptionMap.put("VClassURI", FormUtils.makeOptionListFromBeans(
-                    vreq.getFullWebappDaoFactory().getVClassDao().getAllVclasses(),
+                    vreq.getUnfilteredWebappDaoFactory().getVClassDao().getAllVclasses(),
                             "URI", "PickListName", ent.getVClassURI(), null, false));        
         } catch (Exception e) {
             log.error(e, e);
         }
         
-        PropertyInstanceDao piDao = vreq.getFullWebappDaoFactory().getPropertyInstanceDao();
+        PropertyInstanceDao piDao = vreq.getUnfilteredWebappDaoFactory().getPropertyInstanceDao();
         // existing property statements
         try {
             List epiOptionList = new LinkedList();

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

@@ -182,7 +182,7 @@ public class EntityRetryController extends BaseEditController {
         	vclasses = new ArrayList<VClass>();
         	if (individualForEditing.getVClassURI() != null) {
         		try {
-	        		VClass cls = vreq.getFullWebappDaoFactory().getVClassDao().getVClassByURI(individualForEditing.getVClassURI());
+	        		VClass cls = vreq.getUnfilteredWebappDaoFactory().getVClassDao().getVClassByURI(individualForEditing.getVClassURI());
 	        		if (cls != null) {
 	        			vclasses.add(cls);
 	        		}

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

@@ -46,12 +46,12 @@ public class ExternalIdRetryController extends BaseEditController {
 
         String action = "insert";
 
-        DataPropertyDao dpDao = vreq.getFullWebappDaoFactory().getDataPropertyDao();
+        DataPropertyDao dpDao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyDao();
-        DataPropertyStatementDao edDao = vreq.getFullWebappDaoFactory().getDataPropertyStatementDao();
+        DataPropertyStatementDao edDao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyStatementDao();
         epo.setDataAccessObject(edDao);
         epo.setBeanClass(DataPropertyStatement.class);
 
-        IndividualDao eDao = vreq.getFullWebappDaoFactory().getIndividualDao();
+        IndividualDao eDao = vreq.getUnfilteredWebappDaoFactory().getIndividualDao();
 
         DataPropertyStatement eidForEditing = null;
         if (!epo.getUseRecycledBean()){

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

@@ -57,7 +57,7 @@ public class IndividualTypeOperationController extends BaseEditController {
             return;
         }
 
-        IndividualDao dao = request.getAssertionsWebappDaoFactory().getIndividualDao();
+        IndividualDao dao = request.getUnfilteredAssertionsWebappDaoFactory().getIndividualDao();
         
         if (request.getParameter("_cancel") == null) {
 	        try {

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

@@ -51,8 +51,7 @@ public class IndividualTypeRetryController extends BaseEditController {
 		
         VitroRequest vreq = new VitroRequest(request);
         
-        WebappDaoFactory t;
+        WebappDaoFactory wadf = vreq.getUnfilteredAssertionsWebappDaoFactory();
-        WebappDaoFactory wadf = ((t = vreq.getAssertionsWebappDaoFactory()) != null) ? t : vreq.getFullWebappDaoFactory();
         IndividualDao iDao = wadf.getIndividualDao();
         VClassDao vcDao = wadf.getVClassDao();
         

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

@@ -71,11 +71,11 @@ public class ObjectPropertyStatementRetryController extends BaseEditController {
                 
         String action = "insert";
 
-        PropertyInstanceDao piDao = vreq.getFullWebappDaoFactory().getPropertyInstanceDao();
+        PropertyInstanceDao piDao = vreq.getUnfilteredWebappDaoFactory().getPropertyInstanceDao();
         epo.setDataAccessObject(piDao);
-        ObjectPropertyDao pDao = vreq.getFullWebappDaoFactory().getObjectPropertyDao();
+        ObjectPropertyDao pDao = vreq.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
-        IndividualDao eDao = vreq.getFullWebappDaoFactory().getIndividualDao();
+        IndividualDao eDao = vreq.getUnfilteredWebappDaoFactory().getIndividualDao();
-        VClassDao vcDao = vreq.getFullWebappDaoFactory().getVClassDao();
+        VClassDao vcDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
 
         PropertyInstance objectForEditing = null;
         if (!epo.getUseRecycledBean()){

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

@@ -39,7 +39,7 @@ public class OntologyEditController extends BaseEditController {
         EditProcessObject epo = super.createEpo(request);
         request.setAttribute("epoKey", epo.getKey());
 
-        OntologyDao oDao = request.getFullWebappDaoFactory().getOntologyDao();
+        OntologyDao oDao = request.getUnfilteredWebappDaoFactory().getOntologyDao();
         Ontology o = null;
         if (request.getParameter("uri")==null){
             log.error("doPost() expects non-null uri parameter");

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

@@ -49,7 +49,7 @@ public class OntologyRetryController extends BaseEditController {
 
         String action = "insert";
 
-        OntologyDao oDao = request.getFullWebappDaoFactory().getOntologyDao();
+        OntologyDao oDao = request.getUnfilteredWebappDaoFactory().getOntologyDao();
         epo.setDataAccessObject(oDao);
 
         Ontology ontologyForEditing = null;

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

@@ -46,7 +46,7 @@ public class PrimitiveDelete extends VitroAjaxController {
             return;
         }
 
-        WebappDaoFactory wdf = vreq.getFullWebappDaoFactory();
+        WebappDaoFactory wdf = vreq.getUnfilteredWebappDaoFactory();
         IndividualDao idao = wdf.getIndividualDao();
         int result = idao.deleteIndividual(uriToDelete);
         if (result == 1) {

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/Properties2PropertiesOperationController.java

@@ -122,7 +122,7 @@ public class Properties2PropertiesOperationController extends
     }
     
     private void doEdit(String modeStr, boolean operation, VitroRequest request) {
-    	PropertyDao opDao = request.getFullWebappDaoFactory().getObjectPropertyDao();
+    	PropertyDao opDao = request.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
    	 
         if (operation == REMOVE) {
             String[] subpropertyURIstrs = request.getParameterValues("SubpropertyURI");

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/Properties2PropertiesRetryController.java

@@ -51,8 +51,8 @@ public class Properties2PropertiesRetryController extends BaseEditController {
             action = epo.getAction();
         }
 
-        ObjectPropertyDao opDao = request.getFullWebappDaoFactory().getObjectPropertyDao();
+        ObjectPropertyDao opDao = request.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
-        DataPropertyDao dpDao = request.getFullWebappDaoFactory().getDataPropertyDao();
+        DataPropertyDao dpDao = request.getUnfilteredWebappDaoFactory().getDataPropertyDao();
         epo.setDataAccessObject(opDao);
         
         List propList = ("data".equals(request.getParameter("propertyType"))) 

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

@@ -46,10 +46,10 @@ public class PropertyEditController extends BaseEditController {
 
         VitroRequest vreq = new VitroRequest(request);
         
-        ObjectPropertyDao propDao = vreq.getFullWebappDaoFactory().getObjectPropertyDao();
+        ObjectPropertyDao propDao = vreq.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
-        VClassDao vcDao = vreq.getFullWebappDaoFactory().getVClassDao();
+        VClassDao vcDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
-        PropertyGroupDao pgDao = vreq.getFullWebappDaoFactory().getPropertyGroupDao();
+        PropertyGroupDao pgDao = vreq.getUnfilteredWebappDaoFactory().getPropertyGroupDao();
-        DataPropertyDao dpDao = vreq.getFullWebappDaoFactory().getDataPropertyDao();
+        DataPropertyDao dpDao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyDao();
         ObjectProperty p = (ObjectProperty)propDao.getObjectPropertyByURI(request.getParameter("uri"));
         request.setAttribute("property",p);
 
@@ -107,7 +107,7 @@ public class PropertyEditController extends BaseEditController {
         
         String ontologyName = null;
         if (p.getNamespace() != null) {
-            Ontology ont = vreq.getFullWebappDaoFactory().getOntologyDao().getOntologyByURI(p.getNamespace());
+            Ontology ont = vreq.getUnfilteredWebappDaoFactory().getOntologyDao().getOntologyByURI(p.getNamespace());
             if ( (ont != null) && (ont.getName() != null) ) {
                 ontologyName = ont.getName();
             }
@@ -209,12 +209,7 @@ public class PropertyEditController extends BaseEditController {
 
         // superproperties and subproperties
         
-        ObjectPropertyDao opDao;
+        ObjectPropertyDao opDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getObjectPropertyDao();
-        if (vreq.getAssertionsWebappDaoFactory() != null) {
-        	opDao = vreq.getAssertionsWebappDaoFactory().getObjectPropertyDao();
-        } else {
-        	opDao = vreq.getFullWebappDaoFactory().getObjectPropertyDao();
-        }
         List superURIs = opDao.getSuperPropertyURIs(p.getURI(),false);
         List superProperties = new ArrayList();
         Iterator superURIit = superURIs.iterator();

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

@@ -50,7 +50,7 @@ public class PropertyGroupRetryController extends BaseEditController {
             action = epo.getAction();
         }
 
-        PropertyGroupDao pgDao = request.getFullWebappDaoFactory().getPropertyGroupDao();
+        PropertyGroupDao pgDao = request.getUnfilteredWebappDaoFactory().getPropertyGroupDao();
 
         epo.setDataAccessObject(pgDao);
 

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

@@ -69,10 +69,10 @@ public class PropertyRetryController extends BaseEditController {
             action = epo.getAction();
         }
 
-        ObjectPropertyDao propDao = request.getFullWebappDaoFactory().getObjectPropertyDao();
+        ObjectPropertyDao propDao = request.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
         epo.setDataAccessObject(propDao);
-        OntologyDao ontDao = request.getFullWebappDaoFactory().getOntologyDao();
+        OntologyDao ontDao = request.getUnfilteredWebappDaoFactory().getOntologyDao();
-        VClassDao vclassDao = request.getFullWebappDaoFactory().getVClassDao();
+        VClassDao vclassDao = request.getUnfilteredWebappDaoFactory().getVClassDao();
 
         ObjectProperty propertyForEditing = null;
         if (!epo.getUseRecycledBean()){
@@ -150,7 +150,7 @@ public class PropertyRetryController extends BaseEditController {
         optionMap.put("HiddenFromDisplayBelowRoleLevelUsingRoleUri",RoleLevelOptionsSetup.getDisplayOptionsList(propertyForEditing));    
         optionMap.put("ProhibitedFromUpdateBelowRoleLevelUsingRoleUri",RoleLevelOptionsSetup.getUpdateOptionsList(propertyForEditing));
 
-        List groupOptList = FormUtils.makeOptionListFromBeans(request.getFullWebappDaoFactory().getPropertyGroupDao().getPublicGroups(true),"URI","Name", ((propertyForEditing.getGroupURI()==null) ? "" : propertyForEditing.getGroupURI()), null, (propertyForEditing.getGroupURI()!=null));
+        List groupOptList = FormUtils.makeOptionListFromBeans(request.getUnfilteredWebappDaoFactory().getPropertyGroupDao().getPublicGroups(true),"URI","Name", ((propertyForEditing.getGroupURI()==null) ? "" : propertyForEditing.getGroupURI()), null, (propertyForEditing.getGroupURI()!=null));
         HashMap<String,Option> hashMap = new HashMap<String,Option>();
         groupOptList = getSortedList(hashMap,groupOptList);
         groupOptList.add(0,new Option("","none"));
@@ -221,7 +221,7 @@ public class PropertyRetryController extends BaseEditController {
                                 : propertyForEditing.getNamespace()), 
                         null, (propertyForEditing.getNamespace() != null));
         namespaceIdList.add(0, new Option(
-                request.getFullWebappDaoFactory().getDefaultNamespace(), "default"));
+                request.getUnfilteredWebappDaoFactory().getDefaultNamespace(), "default"));
         optionMap.put("Namespace", namespaceIdList);
         
         List<Option> namespaceIdInverseList = FormUtils.makeOptionListFromBeans(
@@ -231,7 +231,7 @@ public class PropertyRetryController extends BaseEditController {
                                 : propertyForEditing.getNamespaceInverse()), 
                         null, (propertyForEditing.getNamespaceInverse() != null));
         namespaceIdInverseList.add(0, new Option(
-                request.getFullWebappDaoFactory().getDefaultNamespace(),"default"));
+                request.getUnfilteredWebappDaoFactory().getDefaultNamespace(),"default"));
         optionMap.put("NamespaceInverse", namespaceIdInverseList);
         
         List<ObjectProperty> objPropList = propDao.getAllObjectProperties();
@@ -258,7 +258,7 @@ public class PropertyRetryController extends BaseEditController {
         */
         
         List<Option> domainOptionList = FormUtils.makeVClassOptionList(
-                request.getFullWebappDaoFactory(), 
+                request.getUnfilteredWebappDaoFactory(), 
                         propertyForEditing.getDomainVClassURI());
         if (propertyForEditing.getDomainVClass() != null 
                 && propertyForEditing.getDomainVClass().isAnonymous()) {
@@ -271,7 +271,7 @@ public class PropertyRetryController extends BaseEditController {
         optionMap.put("DomainVClassURI", domainOptionList);
         
         List<Option> rangeOptionList = FormUtils.makeVClassOptionList(
-                request.getFullWebappDaoFactory(), 
+                request.getUnfilteredWebappDaoFactory(), 
                         propertyForEditing.getRangeVClassURI());
         if (propertyForEditing.getRangeVClass() != null 
                 && propertyForEditing.getRangeVClass().isAnonymous()) {

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

@@ -188,7 +188,7 @@ public class RefactorOperationController extends BaseEditController {
 		// validateURI
 		String errorMsg = null;
 		try {
-			request.getFullWebappDaoFactory().checkURI(newURIStr);
+			request.getUnfilteredWebappDaoFactory().checkURI(newURIStr);
 		} catch (InvalidPropertyURIException ipue) {
 			// TODO We don't know if we're editing a property's URI or not here!
 		}
@@ -255,7 +255,7 @@ public class RefactorOperationController extends BaseEditController {
 				        userURI, oldURIStr, newURIStr, !NOTIFY);
     	
 		// there are no statements to delete, but we want indexes updated appropriately
-		request.getFullWebappDaoFactory().getIndividualDao().deleteIndividual(oldURIStr);
+		request.getUnfilteredWebappDaoFactory().getIndividualDao().deleteIndividual(oldURIStr);
 		
 		String redirectStr = null;
 		

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

@@ -54,18 +54,18 @@ public class RefactorRetryController extends BaseEditController {
 		epo.setFormObject(foo);
 		HashMap<String,List<Option>> optMap = new HashMap<String,List<Option>>();
 		foo.setOptionLists(optMap);
-		List<Option> subjectClassOpts = FormUtils.makeOptionListFromBeans(request.getFullWebappDaoFactory().getVClassDao().getAllVclasses(),"URI","Name", null, null);
+		List<Option> subjectClassOpts = FormUtils.makeOptionListFromBeans(request.getUnfilteredWebappDaoFactory().getVClassDao().getAllVclasses(),"URI","Name", null, null);
 		subjectClassOpts.add(0,new Option("","? wildcard",true));
 		optMap.put("SubjectClassURI", subjectClassOpts);
 		optMap.put("ObjectClassURI", subjectClassOpts);
 		
 		List newPropertyOpts;
 		if (epo.getAttribute("propertyType").equals("ObjectProperty"))  {
-			List<ObjectProperty> opList = request.getFullWebappDaoFactory().getObjectPropertyDao().getAllObjectProperties();
+			List<ObjectProperty> opList = request.getUnfilteredWebappDaoFactory().getObjectPropertyDao().getAllObjectProperties();
 			Collections.sort(opList);
 			newPropertyOpts = FormUtils.makeOptionListFromBeans(opList,"URI","LocalNameWithPrefix", null, null);
 		} else {
-			List<DataProperty> dpList = request.getFullWebappDaoFactory().getDataPropertyDao().getAllDataProperties();
+			List<DataProperty> dpList = request.getUnfilteredWebappDaoFactory().getDataPropertyDao().getAllDataProperties();
 			Collections.sort(dpList);
 			newPropertyOpts = FormUtils.makeOptionListFromBeans(dpList,"URI","Name", null, null);
 		}
@@ -90,7 +90,7 @@ public class RefactorRetryController extends BaseEditController {
 		epo.setFormObject(foo);
 		HashMap<String,List<Option>> optMap = new HashMap<String,List<Option>>();
 		foo.setOptionLists(optMap);
-		List<Option> newClassURIopts = FormUtils.makeOptionListFromBeans(request.getFullWebappDaoFactory().getVClassDao().getAllVclasses(),"URI","LocalNameWithPrefix", null, null);
+		List<Option> newClassURIopts = FormUtils.makeOptionListFromBeans(request.getUnfilteredWebappDaoFactory().getVClassDao().getAllVclasses(),"URI","LocalNameWithPrefix", null, null);
 		newClassURIopts.add(new Option ("","move to trash"));
 		optMap.put("NewVClassURI", newClassURIopts);
 		request.setAttribute("editAction","refactorOp");

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

@@ -90,7 +90,7 @@ public class RestrictionOperationController extends BaseEditController {
         ontModel.enterCriticalSection(Lock.WRITE);
         try {
             
-            ontModel.getBaseModel().notifyEvent(new EditEvent(request.getFullWebappDaoFactory().getUserURI(),true));
+            ontModel.getBaseModel().notifyEvent(new EditEvent(request.getUnfilteredWebappDaoFactory().getUserURI(),true));
             
             if ("delete".equals(request.getParameter("_action"))) {
                 processDelete(request, ontModel);   
@@ -99,7 +99,7 @@ public class RestrictionOperationController extends BaseEditController {
             }
             
         } finally {
-            ontModel.getBaseModel().notifyEvent(new EditEvent(request.getFullWebappDaoFactory().getUserURI(),false));
+            ontModel.getBaseModel().notifyEvent(new EditEvent(request.getUnfilteredWebappDaoFactory().getUserURI(),false));
             ontModel.leaveCriticalSection();
         }
     

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

@@ -58,8 +58,8 @@ public class RestrictionRetryController extends BaseEditController {
 			boolean propertyType = ("data".equals(request.getParameter("propertyType"))) ? DATA : OBJECT ;
 			
 			List<? extends Property> pList = (propertyType == OBJECT) 
-				? request.getFullWebappDaoFactory().getObjectPropertyDao().getAllObjectProperties()
+				? request.getUnfilteredWebappDaoFactory().getObjectPropertyDao().getAllObjectProperties()
-			    : request.getFullWebappDaoFactory().getDataPropertyDao().getAllDataProperties();
+			    : request.getUnfilteredWebappDaoFactory().getDataPropertyDao().getAllDataProperties();
 			List<Option> onPropertyList = new LinkedList<Option>(); 
 			Collections.sort(pList, new PropSorter());
 			for (Property p: pList) {
@@ -116,7 +116,7 @@ public class RestrictionRetryController extends BaseEditController {
 	
 	private List<Option> getValueClassOptionList(VitroRequest request) {
 		List<Option> valueClassOptionList = new LinkedList<Option>();
-		VClassDao vcDao = request.getFullWebappDaoFactory().getVClassDao();
+		VClassDao vcDao = request.getUnfilteredWebappDaoFactory().getVClassDao();
 		for (VClass vc: vcDao.getAllVclasses()) {
 			valueClassOptionList.add(new Option(vc.getURI(), vc.getLocalNameWithPrefix()));
 		}
@@ -125,7 +125,7 @@ public class RestrictionRetryController extends BaseEditController {
 	
 	private List<Option> getValueDatatypeOptionList(VitroRequest request) {
 		List<Option> valueDatatypeOptionList = new LinkedList<Option>();
-		DatatypeDao dtDao = request.getFullWebappDaoFactory().getDatatypeDao();
+		DatatypeDao dtDao = request.getUnfilteredWebappDaoFactory().getDatatypeDao();
 		for (Datatype dt: dtDao.getAllDatatypes()) {
 			valueDatatypeOptionList.add(new Option(dt.getUri(), dt.getName()));
 		}

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

@@ -44,11 +44,11 @@ public class VclassEditController extends BaseEditController {
         EditProcessObject epo = super.createEpo(request, FORCE_NEW);
         request.setAttribute("epoKey", epo.getKey());
 
-        VClassDao vcwDao = request.getFullWebappDaoFactory().getVClassDao();
+        VClassDao vcwDao = request.getUnfilteredWebappDaoFactory().getVClassDao();
         VClass vcl = (VClass)vcwDao.getVClassByURI(request.getParameter("uri"));
         
         if (vcl == null) {
-        	vcl = request.getFullWebappDaoFactory()
+        	vcl = request.getUnfilteredWebappDaoFactory()
         	        .getVClassDao().getTopConcept();
         }
 
@@ -72,13 +72,13 @@ public class VclassEditController extends BaseEditController {
         
         String ontologyName = null;
         if (vcl.getNamespace() != null) {
-            Ontology ont = request.getFullWebappDaoFactory().getOntologyDao().getOntologyByURI(vcl.getNamespace());
+            Ontology ont = request.getUnfilteredWebappDaoFactory().getOntologyDao().getOntologyByURI(vcl.getNamespace());
             if ( (ont != null) && (ont.getName() != null) ) {
                 ontologyName = ont.getName();
             }
         }
 
-        WebappDaoFactory wadf = request.getFullWebappDaoFactory();
+        WebappDaoFactory wadf = request.getUnfilteredWebappDaoFactory();
         String groupURI = vcl.getGroupURI();
         String groupName = "none";
         if(groupURI != null) { 
@@ -95,7 +95,7 @@ public class VclassEditController extends BaseEditController {
         
         boolean foundComment = false;
         StringBuffer commSb = null;
-        for (Iterator<String> commIt = request.getFullWebappDaoFactory().getCommentsForResource(vcl.getURI()).iterator(); commIt.hasNext();) { 
+        for (Iterator<String> commIt = request.getUnfilteredWebappDaoFactory().getCommentsForResource(vcl.getURI()).iterator(); commIt.hasNext();) { 
             if (commSb==null) {
                 commSb = new StringBuffer();
                 foundComment=true;
@@ -141,12 +141,7 @@ public class VclassEditController extends BaseEditController {
         request.setAttribute("formSelect",formSelect);
 
         // if supported, we want to show only the asserted superclasses and subclasses.  Don't want to see anonymous classes, restrictions, etc.
-        VClassDao vcDao;
+        VClassDao vcDao = request.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
-        if (request.getAssertionsWebappDaoFactory() != null) {
-        	vcDao = request.getAssertionsWebappDaoFactory().getVClassDao();
-        } else {
-        	vcDao = request.getFullWebappDaoFactory().getVClassDao();
-        }
         List superURIs = vcDao.getSuperClassURIs(vcl.getURI(),false);
         List superVClasses = new ArrayList();
         Iterator superURIit = superURIs.iterator();

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

@@ -64,10 +64,10 @@ public class VclassRetryController extends BaseEditController {
             action = epo.getAction();
         }
 
-        VClassDao vcwDao = request.getAssertionsWebappDaoFactory().getVClassDao();
+        VClassDao vcwDao = request.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
         epo.setDataAccessObject(vcwDao);
-        VClassGroupDao cgDao = request.getFullWebappDaoFactory().getVClassGroupDao();
+        VClassGroupDao cgDao = request.getUnfilteredWebappDaoFactory().getVClassGroupDao();
-        OntologyDao oDao = request.getFullWebappDaoFactory().getOntologyDao();
+        OntologyDao oDao = request.getUnfilteredWebappDaoFactory().getOntologyDao();
 
         VClass vclassForEditing = null;
         if (!epo.getUseRecycledBean()){
@@ -110,7 +110,7 @@ public class VclassRetryController extends BaseEditController {
         //set up any listeners
         List changeListenerList = new LinkedList();
         if (request.getParameter("superclassUri") != null) {
-            changeListenerList.add(new SubclassListener(request.getParameter("superclassUri"), request.getFullWebappDaoFactory()));
+            changeListenerList.add(new SubclassListener(request.getParameter("superclassUri"), request.getUnfilteredWebappDaoFactory()));
         }
         epo.setChangeListenerList(changeListenerList);
 
@@ -130,7 +130,7 @@ public class VclassRetryController extends BaseEditController {
 
         HashMap<String, List<Option>> optionMap = new HashMap<String,List<Option>>();
         try {
-            VClassGroupDao vcgDao = request.getFullWebappDaoFactory().getVClassGroupDao();
+            VClassGroupDao vcgDao = request.getUnfilteredWebappDaoFactory().getVClassGroupDao();
             List classGroupOptionList = FormUtils.makeOptionListFromBeans(vcgDao.getPublicGroupsWithVClasses(),"URI","PublicName",vclassForEditing.getGroupURI(),null,(vclassForEditing.getGroupURI()!=null && !(vclassForEditing.getGroupURI().equals(""))));
             classGroupOptionList.add(0,new Option("", "none", ("update".equals(action) && (vclassForEditing.getGroupURI()==null || vclassForEditing.getGroupURI().equals("")))));
             optionMap.put("GroupURI", classGroupOptionList);
@@ -142,7 +142,7 @@ public class VclassRetryController extends BaseEditController {
             List namespaceIdList = (action.equals("insert"))
                     ? FormUtils.makeOptionListFromBeans(oDao.getAllOntologies(),"URI","Name", ((vclassForEditing.getNamespace()==null) ? "" : vclassForEditing.getNamespace()), null, false)
                     : FormUtils.makeOptionListFromBeans(oDao.getAllOntologies(),"URI","Name", ((vclassForEditing.getNamespace()==null) ? "" : vclassForEditing.getNamespace()), null, true);
-	        namespaceIdList.add(0, new Option(request.getFullWebappDaoFactory().getDefaultNamespace(),"default"));
+	        namespaceIdList.add(0, new Option(request.getUnfilteredWebappDaoFactory().getDefaultNamespace(),"default"));
             optionMap.put("Namespace", namespaceIdList);
         } catch (Exception e) {
             log.error(this.getClass().getName() + "unable to create Namespace option list");

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/AllClassGroupsListingController.java

@@ -33,7 +33,7 @@ public class AllClassGroupsListingController extends BaseEditController {
     	
         VitroRequest vreq = new VitroRequest(request);
 
-        VClassGroupDao dao = vreq.getFullWebappDaoFactory().getVClassGroupDao();
+        VClassGroupDao dao = vreq.getUnfilteredWebappDaoFactory().getVClassGroupDao();
 
         List<VClassGroup> groups = dao.getPublicGroupsWithVClasses(); 
         // uses an unfiltered dao so will see all classes

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/ClassHierarchyListingController.java

@@ -56,7 +56,7 @@ public class ClassHierarchyListingController extends BaseEditController {
         if (!inferred) {
         	vcDao = ModelAccess.on(vrequest).getBaseWebappDaoFactory().getVClassDao();
         } else {
-        	vcDao = vrequest.getFullWebappDaoFactory().getVClassDao();
+        	vcDao = vrequest.getUnfilteredWebappDaoFactory().getVClassDao();
         }
 
         ArrayList<String> results = new ArrayList<String>();
@@ -86,7 +86,7 @@ public class ClassHierarchyListingController extends BaseEditController {
         
         if (roots.isEmpty()) {
         	roots = new LinkedList<VClass>();
-        	roots.add(vrequest.getFullWebappDaoFactory().getVClassDao()
+        	roots.add(vrequest.getUnfilteredWebappDaoFactory().getVClassDao()
         			.getTopConcept());
         }
         
@@ -96,13 +96,13 @@ public class ClassHierarchyListingController extends BaseEditController {
         if (!rootIt.hasNext()) {
             VClass vcw = new VClass();
             vcw.setName("<strong>No classes found.</strong>");
-            results.addAll(addVClassDataToResultsList(vrequest.getFullWebappDaoFactory(), vcw,0,ontologyUri));
+            results.addAll(addVClassDataToResultsList(vrequest.getUnfilteredWebappDaoFactory(), vcw,0,ontologyUri));
         } else {
             while (rootIt.hasNext()) {
                 VClass root = (VClass) rootIt.next();
 	            if (root != null) {
 	                ArrayList childResults = new ArrayList();
-	                addChildren(vrequest.getFullWebappDaoFactory(), root, childResults, 0, ontologyUri);
+	                addChildren(vrequest.getUnfilteredWebappDaoFactory(), root, childResults, 0, ontologyUri);
 	                results.addAll(childResults);
                 }
             }

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/DataPropertyHierarchyListingController.java

@@ -54,10 +54,10 @@ public class DataPropertyHierarchyListingController extends BaseEditController {
         VitroRequest vrequest = new VitroRequest(request);
         try {
 
-        dpDao = vrequest.getAssertionsWebappDaoFactory().getDataPropertyDao();
+        dpDao = vrequest.getUnfilteredAssertionsWebappDaoFactory().getDataPropertyDao();
-        vcDao = vrequest.getAssertionsWebappDaoFactory().getVClassDao();
+        vcDao = vrequest.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
-        pgDao = vrequest.getAssertionsWebappDaoFactory().getPropertyGroupDao();
+        pgDao = vrequest.getUnfilteredAssertionsWebappDaoFactory().getPropertyGroupDao();
-        dDao = vrequest.getAssertionsWebappDaoFactory().getDatatypeDao();
+        dDao = vrequest.getUnfilteredAssertionsWebappDaoFactory().getDatatypeDao();
 
         ArrayList<String> results = new ArrayList<String>();
         results.add("XX");            // column 1

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/DataPropertyStatementListingController.java

@@ -71,9 +71,9 @@ public class DataPropertyStatementListingController extends BaseEditController {
         results.add("property");
         results.add("object");
         
-        DataPropertyStatementDao dpsDao = vrequest.getFullWebappDaoFactory().getDataPropertyStatementDao();
+        DataPropertyStatementDao dpsDao = vrequest.getUnfilteredWebappDaoFactory().getDataPropertyStatementDao();
-        DataPropertyDao dpDao = vrequest.getFullWebappDaoFactory().getDataPropertyDao();
+        DataPropertyDao dpDao = vrequest.getUnfilteredWebappDaoFactory().getDataPropertyDao();
-        IndividualDao iDao = vrequest.getFullWebappDaoFactory().getIndividualDao();
+        IndividualDao iDao = vrequest.getUnfilteredWebappDaoFactory().getIndividualDao();
         
         String propURIStr = request.getParameter("propertyURI");
         

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/DatatypePropertiesListingController.java

@@ -43,10 +43,10 @@ public class DatatypePropertiesListingController extends BaseEditController {
 
         String ontologyUri = request.getParameter("ontologyUri");
 
-        DataPropertyDao dao = vrequest.getFullWebappDaoFactory().getDataPropertyDao();
+        DataPropertyDao dao = vrequest.getUnfilteredWebappDaoFactory().getDataPropertyDao();
-        VClassDao vcDao = vrequest.getFullWebappDaoFactory().getVClassDao();
+        VClassDao vcDao = vrequest.getUnfilteredWebappDaoFactory().getVClassDao();
-        DatatypeDao dDao = vrequest.getFullWebappDaoFactory().getDatatypeDao();
+        DatatypeDao dDao = vrequest.getUnfilteredWebappDaoFactory().getDatatypeDao();
-        PropertyGroupDao pgDao = vrequest.getFullWebappDaoFactory().getPropertyGroupDao();
+        PropertyGroupDao pgDao = vrequest.getUnfilteredWebappDaoFactory().getPropertyGroupDao();
 
         List<DataProperty> props = new ArrayList<DataProperty>();
 

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/IndividualsListingController.java

@@ -41,10 +41,10 @@ public class IndividualsListingController extends BaseEditController {
         WebappDaoFactory wadf = null;
         
         if (assertedOnlyStr != null && assertedOnlyStr.equalsIgnoreCase("true")) {
-        	wadf = vrequest.getAssertionsWebappDaoFactory();
+        	wadf = vrequest.getUnfilteredAssertionsWebappDaoFactory();
         }
         if (wadf == null) {
-        	wadf = vrequest.getFullWebappDaoFactory();
+        	wadf = vrequest.getUnfilteredWebappDaoFactory();
         }
         
         IndividualDao dao = wadf.getIndividualDao();

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/ObjectPropertyHierarchyListingController.java

@@ -52,9 +52,9 @@ public class ObjectPropertyHierarchyListingController extends BaseEditController
         VitroRequest vrequest = new VitroRequest(request);
         try {
 
-        opDao = vrequest.getAssertionsWebappDaoFactory().getObjectPropertyDao();
+        opDao = vrequest.getUnfilteredAssertionsWebappDaoFactory().getObjectPropertyDao();
-        vcDao = vrequest.getAssertionsWebappDaoFactory().getVClassDao();
+        vcDao = vrequest.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
-        pgDao = vrequest.getAssertionsWebappDaoFactory().getPropertyGroupDao();
+        pgDao = vrequest.getUnfilteredAssertionsWebappDaoFactory().getPropertyGroupDao();
 
         ArrayList<String> results = new ArrayList<String>();
         results.add("XX");            // column 1

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/ObjectPropertyStatementListingController.java

@@ -91,19 +91,19 @@ public class ObjectPropertyStatementListingController extends
         
         ObjectPropertyStatementDao opsDao = null;
         if (assertedStatementsOnly){ // get only asserted, not inferred, object property statements
-            opsDao = vrequest.getAssertionsWebappDaoFactory().getObjectPropertyStatementDao();
+            opsDao = vrequest.getUnfilteredAssertionsWebappDaoFactory().getObjectPropertyStatementDao();
         } else {
-            opsDao = vrequest.getFullWebappDaoFactory().getObjectPropertyStatementDao();
+            opsDao = vrequest.getUnfilteredWebappDaoFactory().getObjectPropertyStatementDao();
         }
 
         // get all object properties -- no concept of asserted vs. inferred object properties
-        ObjectPropertyDao opDao = vrequest.getFullWebappDaoFactory().getObjectPropertyDao();
+        ObjectPropertyDao opDao = vrequest.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
         
         IndividualDao iDao = null;
         if (showVClasses) {
-            iDao = vrequest.getAssertionsWebappDaoFactory().getIndividualDao();
+            iDao = vrequest.getUnfilteredAssertionsWebappDaoFactory().getIndividualDao();
         } else {
-            iDao = vrequest.getFullWebappDaoFactory().getIndividualDao();
+            iDao = vrequest.getUnfilteredWebappDaoFactory().getIndividualDao();
         }
         
         String propURIStr = request.getParameter("propertyURI");

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/OntologiesListingController.java

@@ -31,7 +31,7 @@ public class OntologiesListingController extends BaseEditController {
 
 	    String noResultsMsgStr = "No ontologies found";
 
-        OntologyDao dao = vrequest.getFullWebappDaoFactory().getOntologyDao();
+        OntologyDao dao = vrequest.getUnfilteredWebappDaoFactory().getOntologyDao();
 
         List<Ontology> onts = dao.getAllOntologies();
 

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/PropertyGroupsListingController.java

@@ -43,7 +43,7 @@ public class PropertyGroupsListingController extends BaseEditController {
     	
         VitroRequest vreq = new VitroRequest(request);
 
-        PropertyGroupDao dao = vreq.getFullWebappDaoFactory().getPropertyGroupDao();
+        PropertyGroupDao dao = vreq.getUnfilteredWebappDaoFactory().getPropertyGroupDao();
 
         List<PropertyGroup> groups = dao.getPublicGroups(WITH_PROPERTIES);
         

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/PropertyWebappsListingController.java

@@ -51,10 +51,10 @@ public class PropertyWebappsListingController extends BaseEditController {
 
         String ontologyUri = request.getParameter("ontologyUri");
 
-        ObjectPropertyDao dao = vrequest.getFullWebappDaoFactory().getObjectPropertyDao();
+        ObjectPropertyDao dao = vrequest.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
-        PropertyInstanceDao piDao = vrequest.getFullWebappDaoFactory().getPropertyInstanceDao();
+        PropertyInstanceDao piDao = vrequest.getUnfilteredWebappDaoFactory().getPropertyInstanceDao();
-        VClassDao vcDao = vrequest.getFullWebappDaoFactory().getVClassDao();
+        VClassDao vcDao = vrequest.getUnfilteredWebappDaoFactory().getVClassDao();
-        PropertyGroupDao pgDao = vrequest.getFullWebappDaoFactory().getPropertyGroupDao();
+        PropertyGroupDao pgDao = vrequest.getUnfilteredWebappDaoFactory().getPropertyGroupDao();
 
         String vclassURI = request.getParameter("vclassUri");
         
@@ -96,7 +96,7 @@ public class PropertyWebappsListingController extends BaseEditController {
             : dao.getAllObjectProperties();
         }
         
-        OntologyDao oDao = vrequest.getFullWebappDaoFactory().getOntologyDao();
+        OntologyDao oDao = vrequest.getUnfilteredWebappDaoFactory().getOntologyDao();
         HashMap<String,String> ontologyHash = new HashMap<String,String>();
 
         Iterator propIt = props.iterator();

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/VClassWebappWithInstancesListingController.java

@@ -40,7 +40,7 @@ public class VClassWebappWithInstancesListingController extends BaseEditControll
 
         if(uriStr != null) {
 
-            VClassDao dao = vrequest.getFullWebappDaoFactory().getVClassDao();
+            VClassDao dao = vrequest.getUnfilteredWebappDaoFactory().getVClassDao();
 
             results.add("XX");
             results.add("name");
@@ -64,7 +64,7 @@ public class VClassWebappWithInstancesListingController extends BaseEditControll
                 results.add(lastModifiedStr);
                 results.add("XX");
 
-                IndividualDao ewDao = vrequest.getFullWebappDaoFactory().getIndividualDao();
+                IndividualDao ewDao = vrequest.getUnfilteredWebappDaoFactory().getIndividualDao();
 
                 List ents = ewDao.getIndividualsByVClassURI(vcw.getURI(), -2, -2);
                 if (ents != null && ents.size()>0) {

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/VClassWebappsListingController.java

@@ -43,10 +43,10 @@ public class VClassWebappsListingController extends BaseEditController {
         List<VClass> classes = null;
         
         if (request.getParameter("showPropertyRestrictions") != null) {
-        	PropertyDao pdao = vrequest.getFullWebappDaoFactory().getObjectPropertyDao();
+        	PropertyDao pdao = vrequest.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
         	classes = pdao.getClassesWithRestrictionOnProperty(request.getParameter("propertyURI"));
         } else {
-        	VClassDao vcdao = vrequest.getFullWebappDaoFactory().getVClassDao();
+        	VClassDao vcdao = vrequest.getUnfilteredWebappDaoFactory().getVClassDao();
         	
         	if (request.getParameter("iffRoot") != null) {
                 classes = vcdao.getRootClasses();
@@ -88,12 +88,12 @@ public class VClassWebappsListingController extends BaseEditController {
 	                String shortDef = (cls.getShortDef()==null) ? "" : cls.getShortDef();
 	                String example = (cls.getExample()==null) ? "" : cls.getExample();
 	                StringBuffer commSb = new StringBuffer();
-	                for (Iterator<String> commIt = vrequest.getFullWebappDaoFactory().getCommentsForResource(cls.getURI()).iterator(); commIt.hasNext();) { 
+	                for (Iterator<String> commIt = vrequest.getUnfilteredWebappDaoFactory().getCommentsForResource(cls.getURI()).iterator(); commIt.hasNext();) { 
 	                	commSb.append(commIt.next()).append(" ");
 	                }
 	                
 	                // get group name
-	                WebappDaoFactory wadf = vrequest.getFullWebappDaoFactory();
+	                WebappDaoFactory wadf = vrequest.getUnfilteredWebappDaoFactory();
 	                VClassGroupDao groupDao= wadf.getVClassGroupDao();
 	                String groupURI = cls.getGroupURI();                
 	                String groupName = "";

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/jena/RestrictionsListingController.java

@@ -54,9 +54,9 @@ public class RestrictionsListingController extends BaseEditController {
         
 		OntModel ontModel = ModelAccess.on(getServletContext()).getJenaOntModel();
 
-        ObjectPropertyDao opDao = vrequest.getFullWebappDaoFactory().getObjectPropertyDao();
+        ObjectPropertyDao opDao = vrequest.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
-        VClassDao vcDao = vrequest.getFullWebappDaoFactory().getVClassDao();
+        VClassDao vcDao = vrequest.getUnfilteredWebappDaoFactory().getVClassDao();
-        IndividualDao iDao = vrequest.getFullWebappDaoFactory().getIndividualDao();
+        IndividualDao iDao = vrequest.getUnfilteredWebappDaoFactory().getIndividualDao();
         
         ArrayList results = new ArrayList();
         request.setAttribute("results",results);

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/utils/LocalNamespaceClassUtils.java

@@ -58,7 +58,7 @@ public class LocalNamespaceClassUtils {
     	//There's an APP for that!
         //defualt namespace pattern is null if the default namespace does not employ /individual
         if(defaultNamespacePattern != null) {
-	    	 OntologyDao dao = vreq.getFullWebappDaoFactory().getOntologyDao();
+	    	 OntologyDao dao = vreq.getUnfilteredWebappDaoFactory().getOntologyDao();
 	         List<Ontology> onts = dao.getAllOntologies();
 	         for(Ontology on: onts) {
 	        	String uri = on.getURI();

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/BaseSiteAdminController.java

@@ -85,7 +85,7 @@ public class BaseSiteAdminController extends FreemarkerHttpServlet {
 
             map.put("formAction", UrlBuilder.getUrl("/editRequestDispatch"));
             
-            WebappDaoFactory wadf = vreq.getFullWebappDaoFactory();
+            WebappDaoFactory wadf = vreq.getUnfilteredWebappDaoFactory();
             
             // Create map for data input entry form options list
             List<VClassGroup> classGroups = wadf.getVClassGroupDao().getPublicGroupsWithVClasses(true,true,false); // order by displayRank, include uninstantiated classes, don't get the counts of individuals

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ImageUploadController.java

@@ -256,7 +256,7 @@ public class ImageUploadController extends FreemarkerHttpServlet {
 	 */
 	private ResponseValues doIntroScreen(VitroRequest vreq, Individual entity) {
 		ImageInfo imageInfo = ImageInfo.instanceFromEntityUri(
-				vreq.getFullWebappDaoFactory(), entity);
+				vreq.getUnfilteredWebappDaoFactory(), entity);
 		if (imageInfo == null) {
 			return showAddImagePage(vreq, entity);
 		} else {
@@ -270,7 +270,7 @@ public class ImageUploadController extends FreemarkerHttpServlet {
 	 */
 	private ResponseValues doUploadImage(VitroRequest vreq, Individual entity) {
 		ImageUploadHelper helper = new ImageUploadHelper(fileStorage,
-				vreq.getFullWebappDaoFactory(), getServletContext());
+				vreq.getUnfilteredWebappDaoFactory(), getServletContext());
 
 		try {
 			// Did they provide a file to upload? If not, show an error.
@@ -298,7 +298,7 @@ public class ImageUploadController extends FreemarkerHttpServlet {
 			Individual entity, String message) {
 
 		ImageInfo imageInfo = ImageInfo.instanceFromEntityUri(
-				vreq.getFullWebappDaoFactory(), entity);
+				vreq.getUnfilteredWebappDaoFactory(), entity);
 		if (imageInfo == null) {
 			return showAddImagePageWithError(vreq, entity, message);
 		} else {
@@ -314,7 +314,7 @@ public class ImageUploadController extends FreemarkerHttpServlet {
 	private ResponseValues doCreateThumbnail(VitroRequest vreq,
 			Individual entity) {
 		ImageUploadHelper helper = new ImageUploadHelper(fileStorage,
-				vreq.getFullWebappDaoFactory(), getServletContext());
+				vreq.getUnfilteredWebappDaoFactory(), getServletContext());
 
 		try {
 			CropRectangle crop = validateCropCoordinates(vreq);
@@ -336,7 +336,7 @@ public class ImageUploadController extends FreemarkerHttpServlet {
 	 */
 	private ResponseValues doDeleteImage(VitroRequest vreq, Individual entity) {
 		ImageUploadHelper helper = new ImageUploadHelper(fileStorage,
-				vreq.getFullWebappDaoFactory(), getServletContext());
+				vreq.getUnfilteredWebappDaoFactory(), getServletContext());
 
 		helper.removeExistingImage(entity);
 
@@ -349,7 +349,7 @@ public class ImageUploadController extends FreemarkerHttpServlet {
 	 */
 	private ResponseValues doDeleteThenEdit(VitroRequest vreq, Individual entity) {
 		ImageUploadHelper helper = new ImageUploadHelper(fileStorage,
-				vreq.getFullWebappDaoFactory(), getServletContext());
+				vreq.getUnfilteredWebappDaoFactory(), getServletContext());
 
 		helper.removeExistingImage(entity);
 
@@ -366,7 +366,7 @@ public class ImageUploadController extends FreemarkerHttpServlet {
 			throw new UserMistakeException(ERROR_CODE_NO_URI);
 		}
 
-		Individual entity = vreq.getFullWebappDaoFactory().getIndividualDao()
+		Individual entity = vreq.getUnfilteredWebappDaoFactory().getIndividualDao()
 				.getIndividualByURI(entityUri);
 		if (entity == null) {
 			throw new UserMistakeException(ERROR_CODE_UNRECOGNIZED_URI,

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListClassGroupsController.java

@@ -48,7 +48,7 @@ public class ListClassGroupsController extends FreemarkerHttpServlet {
             body.put("displayOption", "group");
             body.put("pageTitle", "Class Groups");
 
-            VClassGroupDao dao = vreq.getFullWebappDaoFactory().getVClassGroupDao();
+            VClassGroupDao dao = vreq.getUnfilteredWebappDaoFactory().getVClassGroupDao();
 
             List<VClassGroup> groups = dao.getPublicGroupsWithVClasses(); 
 

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListDatatypePropertiesController.java

@@ -60,10 +60,10 @@ public class ListDatatypePropertiesController extends FreemarkerHttpServlet {
 
             String ontologyUri = vreq.getParameter("ontologyUri");
 
-            DataPropertyDao dao = vreq.getFullWebappDaoFactory().getDataPropertyDao();
+            DataPropertyDao dao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyDao();
-            VClassDao vcDao = vreq.getFullWebappDaoFactory().getVClassDao();
+            VClassDao vcDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
-            DatatypeDao dDao = vreq.getFullWebappDaoFactory().getDatatypeDao();
+            DatatypeDao dDao = vreq.getUnfilteredWebappDaoFactory().getDatatypeDao();
-            PropertyGroupDao pgDao = vreq.getFullWebappDaoFactory().getPropertyGroupDao();
+            PropertyGroupDao pgDao = vreq.getUnfilteredWebappDaoFactory().getPropertyGroupDao();
 
             List<DataProperty> props = new ArrayList<DataProperty>();
             if (vreq.getParameter("propsForClass") != null) {

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListPropertyGroupsController.java

@@ -52,7 +52,7 @@ public class ListPropertyGroupsController extends FreemarkerHttpServlet {
             body.put("displayOption", "group");
             body.put("pageTitle", "Property Groups");
 
-            PropertyGroupDao dao = vreq.getFullWebappDaoFactory().getPropertyGroupDao();
+            PropertyGroupDao dao = vreq.getUnfilteredWebappDaoFactory().getPropertyGroupDao();
 
             List<PropertyGroup> groups = dao.getPublicGroups(WITH_PROPERTIES);
         

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListPropertyWebappsController.java

@@ -60,10 +60,10 @@ public class ListPropertyWebappsController extends FreemarkerHttpServlet {
 
             String ontologyUri = vreq.getParameter("ontologyUri");
 
-            ObjectPropertyDao dao = vreq.getFullWebappDaoFactory().getObjectPropertyDao();
+            ObjectPropertyDao dao = vreq.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
-            PropertyInstanceDao piDao = vreq.getFullWebappDaoFactory().getPropertyInstanceDao();
+            PropertyInstanceDao piDao = vreq.getUnfilteredWebappDaoFactory().getPropertyInstanceDao();
-            VClassDao vcDao = vreq.getFullWebappDaoFactory().getVClassDao();
+            VClassDao vcDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
-            PropertyGroupDao pgDao = vreq.getFullWebappDaoFactory().getPropertyGroupDao();
+            PropertyGroupDao pgDao = vreq.getUnfilteredWebappDaoFactory().getPropertyGroupDao();
 
             String vclassURI = vreq.getParameter("vclassUri");
         
@@ -105,7 +105,7 @@ public class ListPropertyWebappsController extends FreemarkerHttpServlet {
                     : dao.getAllObjectProperties();
             }
         
-            OntologyDao oDao = vreq.getFullWebappDaoFactory().getOntologyDao();
+            OntologyDao oDao = vreq.getUnfilteredWebappDaoFactory().getOntologyDao();
             HashMap<String,String> ontologyHash = new HashMap<String,String>();
 
             Iterator propIt = props.iterator();

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListVClassWebappsController.java

@@ -60,10 +60,10 @@ public class ListVClassWebappsController extends FreemarkerHttpServlet {
             List<VClass> classes = null;
 
             if (vreq.getParameter("showPropertyRestrictions") != null) {
-            	PropertyDao pdao = vreq.getFullWebappDaoFactory().getObjectPropertyDao();
+            	PropertyDao pdao = vreq.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
             	classes = pdao.getClassesWithRestrictionOnProperty(vreq.getParameter("propertyURI"));
             } else {
-            	VClassDao vcdao = vreq.getFullWebappDaoFactory().getVClassDao();
+            	VClassDao vcdao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
 
             	if (vreq.getParameter("iffRoot") != null) {
                     classes = vcdao.getRootClasses();
@@ -99,7 +99,7 @@ public class ListVClassWebappsController extends FreemarkerHttpServlet {
     	                json += "\"data\": { \"shortDef\": \"" + shortDef + "\", ";
 
     	                // get group name
-    	                WebappDaoFactory wadf = vreq.getFullWebappDaoFactory();
+    	                WebappDaoFactory wadf = vreq.getUnfilteredWebappDaoFactory();
     	                VClassGroupDao groupDao= wadf.getVClassGroupDao();
     	                String groupURI = cls.getGroupURI();                
     	                String groupName = "";

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowClassHierarchyController.java

@@ -6,15 +6,11 @@ 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.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -25,7 +21,6 @@ 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;
@@ -74,10 +69,10 @@ public class ShowClassHierarchyController extends FreemarkerHttpServlet {
                 body.put("pageTitle", "Asserted Class Hierarchy");
             }
 
-            if (vreq.getAssertionsWebappDaoFactory() != null && !inferred) {
+            if (!inferred) {
-            	vcDao = vreq.getAssertionsWebappDaoFactory().getVClassDao();
+            	vcDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
             } else {
-            	vcDao = vreq.getFullWebappDaoFactory().getVClassDao();
+            	vcDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
             }
             String json = new String();
 
@@ -97,7 +92,7 @@ public class ShowClassHierarchyController extends FreemarkerHttpServlet {
 
             if (roots.isEmpty()) {
             	roots = new LinkedList<VClass>();
-            	roots.add(vreq.getFullWebappDaoFactory().getVClassDao()
+            	roots.add(vreq.getUnfilteredWebappDaoFactory().getVClassDao()
             			.getTopConcept());
             }
             Collections.sort(roots);
@@ -107,12 +102,12 @@ public class ShowClassHierarchyController extends FreemarkerHttpServlet {
             if (!rootIt.hasNext()) {
                 VClass vcw = new VClass();
                 vcw.setName("<strong>No classes found.</strong>");
-                json += addVClassDataToResultsList(vreq.getFullWebappDaoFactory(), vcw,0,ontologyUri,counter);
+                json += addVClassDataToResultsList(vreq.getUnfilteredWebappDaoFactory(), vcw,0,ontologyUri,counter);
             } else {
                 while (rootIt.hasNext()) {
                     VClass root = (VClass) rootIt.next();
     	            if (root != null) {
-    	                json += addChildren(vreq.getFullWebappDaoFactory(), root, 0, ontologyUri,counter);
+    	                json += addChildren(vreq.getUnfilteredWebappDaoFactory(), root, 0, ontologyUri,counter);
     	                counter += 1;
                     }
                 }

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowDataPropertyHierarchyController.java

@@ -78,10 +78,10 @@ public class ShowDataPropertyHierarchyController extends FreemarkerHttpServlet {
             
             body.put("propertyType", "data");
             
-            dpDao = vreq.getAssertionsWebappDaoFactory().getDataPropertyDao();
+            dpDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getDataPropertyDao();
-            vcDao = vreq.getAssertionsWebappDaoFactory().getVClassDao();
+            vcDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
-            pgDao = vreq.getAssertionsWebappDaoFactory().getPropertyGroupDao();
+            pgDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getPropertyGroupDao();
-            dDao = vreq.getAssertionsWebappDaoFactory().getDatatypeDao();
+            dDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getDatatypeDao();
 
             String json = new String();
 

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowObjectPropertyHierarchyController.java

@@ -78,9 +78,9 @@ public class ShowObjectPropertyHierarchyController extends FreemarkerHttpServlet
             
             body.put("propertyType", "object");
             
-            opDao = vreq.getAssertionsWebappDaoFactory().getObjectPropertyDao();
+            opDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getObjectPropertyDao();
-            vcDao = vreq.getAssertionsWebappDaoFactory().getVClassDao();
+            vcDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
-            pgDao = vreq.getAssertionsWebappDaoFactory().getPropertyGroupDao();
+            pgDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getPropertyGroupDao();
 
             String json = new String();
 

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/grefine/GrefinePropertyListServlet.java

@@ -72,8 +72,8 @@ public class GrefinePropertyListServlet extends VitroHttpServlet {
 				// *******
 				// methodology adopted from DatatypePropertiesListingController and ClassHierarchyListingController
 				// *******
-				VClassDao vcDao = vreq.getFullWebappDaoFactory().getVClassDao();
+				VClassDao vcDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
-				DataPropertyDao dao = vreq.getFullWebappDaoFactory().getDataPropertyDao();
+				DataPropertyDao dao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyDao();
 				String topUri = vreq.getParameter("type");
 				VClass topClass = vcDao.getVClassByURI(topUri);
 				HashSet<String> propURIs = new HashSet<String>();
@@ -137,7 +137,7 @@ public class GrefinePropertyListServlet extends VitroHttpServlet {
 			                VClass root = (VClass) rootIt.next();
 				            if (root != null) {
 				            	List<VClass> lvl2ChildClasses = new ArrayList<VClass>();
-				                addChildren(vcDao, vreq.getFullWebappDaoFactory(), root, lvl2ChildClasses, 0, ontologyUri);
+				                addChildren(vcDao, vreq.getUnfilteredWebappDaoFactory(), root, lvl2ChildClasses, 0, ontologyUri);
 				                lvl2Classes.addAll(lvl2ChildClasses);
 			                }
 			            }

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

@@ -548,7 +548,7 @@ public class JenaIngestController extends BaseEditController {
             jenaOntModel.leaveCriticalSection();
         }
         /*ass92*/
-        OntologyDao daoObj = vreq.getFullWebappDaoFactory().getOntologyDao();
+        OntologyDao daoObj = vreq.getUnfilteredWebappDaoFactory().getOntologyDao();
         List ontologiesObj = daoObj.getAllOntologies();
         ArrayList prefixList = new ArrayList();       
         if(ontologiesObj !=null && ontologiesObj.size()>0){
@@ -637,7 +637,7 @@ public class JenaIngestController extends BaseEditController {
             } else {
                 namespaceList.add("no resources present");
             }
-            String defaultNamespace = vreq.getFullWebappDaoFactory().getDefaultNamespace();
+            String defaultNamespace = vreq.getUnfilteredWebappDaoFactory().getDefaultNamespace();
             vreq.setAttribute("modelName", modelName);
             vreq.setAttribute("defaultNamespace", defaultNamespace);
               vreq.setAttribute("namespaceList", namespaceList);

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

@@ -182,13 +182,13 @@ public class RDFUploadController extends JenaIngestController {
                 boolean AGGRESSIVE = true;
                 tboxChangeModel = xutil.extractTBox(uploadModel, AGGRESSIVE);
                 // aggressively seek all statements that are part of the TBox  
-                tboxstmtCount = operateOnModel(request.getFullWebappDaoFactory(),
+                tboxstmtCount = operateOnModel(request.getUnfilteredWebappDaoFactory(),
                         tboxModel, tboxChangeModel, ontModelSelector,
                                 remove, makeClassgroups, loginBean.getUserURI());
             }
             if (aboxModel != null) {
                 aboxChangeModel = uploadModel.remove(tboxChangeModel);
-                aboxstmtCount = operateOnModel(request.getFullWebappDaoFactory(),
+                aboxstmtCount = operateOnModel(request.getUnfilteredWebappDaoFactory(),
                         aboxModel, aboxChangeModel, ontModelSelector, 
                                 remove, makeClassgroups, loginBean.getUserURI());
             }

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/json/GetEntitiesByVClass.java

@@ -52,7 +52,7 @@ public class GetEntitiesByVClass extends JsonArrayProducer {
 	protected JSONArray process() throws ServletException {
         log.debug("in getEntitiesByVClass()");
         String vclassURI = vreq.getParameter("vclassURI");
-        WebappDaoFactory daos = vreq.getFullWebappDaoFactory();
+        WebappDaoFactory daos = vreq.getUnfilteredWebappDaoFactory();
         
         if( vclassURI == null ){
             throw new ServletException("getEntitiesByVClass(): no value for 'vclassURI' found in the HTTP request");

webapp/src/edu/cornell/mannlib/vitro/webapp/dwr/PropertyDWR.java

@@ -55,7 +55,7 @@ public class PropertyDWR {
         WebContext ctx = WebContextFactory.get();
         HttpServletRequest req = ctx.getHttpServletRequest();
         VitroRequest vreq = new VitroRequest(req);
-        WebappDaoFactory wdf = vreq.getFullWebappDaoFactory();
+        WebappDaoFactory wdf = vreq.getUnfilteredWebappDaoFactory();
         
         Collection c = 
             wdf.getPropertyInstanceDao().getAllPropInstByVClass(classURI);
@@ -66,7 +66,7 @@ public class PropertyDWR {
         WebContext ctx = WebContextFactory.get();
         HttpServletRequest req = ctx.getHttpServletRequest();
         VitroRequest vreq = new VitroRequest(req);
-        WebappDaoFactory wdf = vreq.getFullWebappDaoFactory();
+        WebappDaoFactory wdf = vreq.getUnfilteredWebappDaoFactory();
 
         Collection c = 
             wdf.getPropertyInstanceDao().getAllPossiblePropInstForIndividual(individualURI);
@@ -77,7 +77,7 @@ public class PropertyDWR {
         WebContext ctx = WebContextFactory.get();
         HttpServletRequest req = ctx.getHttpServletRequest();
         VitroRequest vreq = new VitroRequest(req);
-        WebappDaoFactory wdf = vreq.getFullWebappDaoFactory();
+        WebappDaoFactory wdf = vreq.getUnfilteredWebappDaoFactory();
         
        return wdf.getPropertyInstanceDao().getProperty(subjectURI, predicateURI, objectURI);
     }
@@ -86,14 +86,14 @@ public class PropertyDWR {
         WebContext ctx = WebContextFactory.get();
         HttpServletRequest req = ctx.getHttpServletRequest();
         VitroRequest vreq = new VitroRequest(req);
-        return vreq.getFullWebappDaoFactory().getPropertyInstanceDao().insertProp(prop);                
+        return vreq.getUnfilteredWebappDaoFactory().getPropertyInstanceDao().insertProp(prop);                
     }
 
     public int deleteProp(String subjectUri, String predicateUri, String objectUri){
         WebContext ctx = WebContextFactory.get();
         HttpServletRequest req = ctx.getHttpServletRequest();
         VitroRequest vreq = new VitroRequest(req);
-        vreq.getFullWebappDaoFactory().getPropertyInstanceDao().deleteObjectPropertyStatement(subjectUri, predicateUri, objectUri);
+        vreq.getUnfilteredWebappDaoFactory().getPropertyInstanceDao().deleteObjectPropertyStatement(subjectUri, predicateUri, objectUri);
         return 0;
     }
 
@@ -117,7 +117,7 @@ public class PropertyDWR {
        WebContext ctx = WebContextFactory.get();
        HttpServletRequest req = ctx.getHttpServletRequest();
        VitroRequest vreq = new VitroRequest(req);
-       WebappDaoFactory wdf = vreq.getFullWebappDaoFactory();
+       WebappDaoFactory wdf = vreq.getUnfilteredWebappDaoFactory();
        
        return wdf.getPropertyInstanceDao().getExistingProperties(entityURI, null);       
    }

webapp/src/edu/cornell/mannlib/vitro/webapp/sparql/GetAllClasses.java

@@ -54,7 +54,7 @@ public class GetAllClasses extends BaseEditController {
 
 		// EditProcessObject epo = super.createEpo(request);
 
-		List classGroups = vreq.getFullWebappDaoFactory().getVClassGroupDao()
+		List classGroups = vreq.getUnfilteredWebappDaoFactory().getVClassGroupDao()
 				.getPublicGroupsWithVClasses(true, true, false); // order by
 																	// displayRank,
 																	// include

webapp/src/edu/cornell/mannlib/vitro/webapp/sparql/GetAllPrefix.java

@@ -63,7 +63,7 @@ public class GetAllPrefix extends BaseEditController {
 		}
 
 		VitroRequest vreq = new VitroRequest(request);	
-		Map<String, String> prefixMap = getPrefixMap(vreq.getFullWebappDaoFactory());		
+		Map<String, String> prefixMap = getPrefixMap(vreq.getUnfilteredWebappDaoFactory());		
 		
 		response.setContentType("text/xml");
 		response.setCharacterEncoding("UTF-8");

webapp/src/edu/cornell/mannlib/vitro/webapp/sparql/GetClazzAllProperties.java

@@ -66,7 +66,7 @@ public class GetClazzAllProperties extends BaseEditController {
 		 * "http://www.w3.org/2000/01/rdf-schema#label" + "</value>" +
 		 * "<type>0</type>" + "</option>";
 		 */
-		DataPropertyDao ddao = vreq.getFullWebappDaoFactory()
+		DataPropertyDao ddao = vreq.getUnfilteredWebappDaoFactory()
 				.getDataPropertyDao();
 
 		Collection<DataProperty> dataProps = ddao
@@ -95,11 +95,11 @@ public class GetClazzAllProperties extends BaseEditController {
 
 		// Get Object Properties
 
-		ObjectPropertyDao odao = vreq.getFullWebappDaoFactory()
+		ObjectPropertyDao odao = vreq.getUnfilteredWebappDaoFactory()
 				.getObjectPropertyDao();
-		PropertyInstanceDao piDao = vreq.getFullWebappDaoFactory()
+		PropertyInstanceDao piDao = vreq.getUnfilteredWebappDaoFactory()
 				.getPropertyInstanceDao();
-		VClassDao vcDao = vreq.getFullWebappDaoFactory().getVClassDao();
+		VClassDao vcDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
 
 		// incomplete list of classes to check, but better than before
 		List<String> superclassURIs = vcDao.getAllSuperClassURIs(vClassURI);

webapp/src/edu/cornell/mannlib/vitro/webapp/sparql/GetClazzDataProperties.java

@@ -53,7 +53,7 @@ public class GetClazzDataProperties extends BaseEditController {
 				+ "http://www.w3.org/2000/01/rdf-schema#label" + "</value>"
 				+ "</option>";
 
-		DataPropertyDao ddao = vreq.getFullWebappDaoFactory()
+		DataPropertyDao ddao = vreq.getUnfilteredWebappDaoFactory()
 				.getDataPropertyDao();
 
 		Collection<DataProperty> dataProps = ddao

webapp/src/edu/cornell/mannlib/vitro/webapp/sparql/GetClazzObjectProperties.java

@@ -55,11 +55,11 @@ public class GetClazzObjectProperties extends BaseEditController {
 		String respo = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
 		respo += "<options>";
 
-		ObjectPropertyDao odao = vreq.getFullWebappDaoFactory()
+		ObjectPropertyDao odao = vreq.getUnfilteredWebappDaoFactory()
 				.getObjectPropertyDao();
-		PropertyInstanceDao piDao = vreq.getFullWebappDaoFactory()
+		PropertyInstanceDao piDao = vreq.getUnfilteredWebappDaoFactory()
 				.getPropertyInstanceDao();
-		VClassDao vcDao = vreq.getFullWebappDaoFactory().getVClassDao();
+		VClassDao vcDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
 
 		// incomplete list of classes to check, but better than before
 		List<String> superclassURIs = vcDao.getAllSuperClassURIs(vClassURI);

webapp/src/edu/cornell/mannlib/vitro/webapp/sparql/GetObjectClasses.java

@@ -61,12 +61,12 @@ public class GetObjectClasses extends BaseEditController {
 			return;
 		}
 
-		ObjectPropertyDao odao = vreq.getFullWebappDaoFactory()
+		ObjectPropertyDao odao = vreq.getUnfilteredWebappDaoFactory()
 				.getObjectPropertyDao();
 		ObjectProperty oprop = (ObjectProperty) odao
 				.getObjectPropertyByURI(predicate);
 
-		VClassDao vcDao = vreq.getFullWebappDaoFactory().getVClassDao();
+		VClassDao vcDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
 		VClass vClass = (oprop.getRangeVClassURI() != null) ? vcDao
 				.getVClassByURI(oprop.getRangeVClassURI()) : null;
 
@@ -79,7 +79,7 @@ public class GetObjectClasses extends BaseEditController {
 			respo += "<option>" + "<key>" + vClass.getPickListName() + "</key>"
 					+ "<value>" + vClass.getURI() + "</value>" + "</option>";
 		} else {
-			List classGroups = vreq.getFullWebappDaoFactory()
+			List classGroups = vreq.getUnfilteredWebappDaoFactory()
 					.getVClassGroupDao().getPublicGroupsWithVClasses(true,
 							true, false); // order by displayRank, include
 											// uninstantiated classes, don't get

webapp/src/edu/cornell/mannlib/vitro/webapp/utils/dataGetter/DataGetterUtils.java

@@ -343,7 +343,7 @@ public class DataGetterUtils {
             }
               
             //need an unfiltered dao to get firstnames and lastnames
-            WebappDaoFactory fullWdf = vreq.getFullWebappDaoFactory();
+            WebappDaoFactory fullWdf = vreq.getUnfilteredWebappDaoFactory();
                       
             String[] vitroClassIdStr = vreq.getParameterValues("vclassId");                            
             if ( vitroClassIdStr != null && vitroClassIdStr.length > 0){    

webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/JenaIngestUtils.java

@@ -733,7 +733,7 @@ public class JenaIngestUtils {
             String newNamespace, String dNamespace, ModelMaker maker, 
             VitroRequest vreq) {
 
-        WebappDaoFactory wdf = vreq.getFullWebappDaoFactory();
+        WebappDaoFactory wdf = vreq.getUnfilteredWebappDaoFactory();
         Model m = maker.getModel(oldModel);
         Model saveModel = maker.getModel(newModel);
         Model tempModel = ModelFactory.createDefaultModel();
@@ -766,7 +766,7 @@ public class JenaIngestUtils {
                     }while(!urlFound);
                     urlFound = false;
                 }
-                else if(dNamespace.equals(vreq.getFullWebappDaoFactory().getDefaultNamespace())){
+                else if(dNamespace.equals(vreq.getUnfilteredWebappDaoFactory().getDefaultNamespace())){
                     try{
                         do{
                             uri = wdf.getIndividualDao().getUnusedURI(null);
@@ -788,7 +788,7 @@ public class JenaIngestUtils {
         if(!newNamespace.equals("")){
             changeNamespace = newNamespace;
         }
-        else if(dNamespace.equals(vreq.getFullWebappDaoFactory().getDefaultNamespace())){
+        else if(dNamespace.equals(vreq.getUnfilteredWebappDaoFactory().getDefaultNamespace())){
             changeNamespace = dNamespace;
         }
         if(!oldModel.equals(newModel)){

webapp/src/edu/cornell/mannlib/vitro/webapp/utils/pageDataGetter/PageDataGetterUtils.java

@@ -185,7 +185,7 @@ public class PageDataGetterUtils {
             }
               
             //need an unfiltered dao to get firstnames and lastnames
-            WebappDaoFactory fullWdf = vreq.getFullWebappDaoFactory();
+            WebappDaoFactory fullWdf = vreq.getUnfilteredWebappDaoFactory();
                       
             String[] vitroClassIdStr = vreq.getParameterValues("vclassId");                            
             if ( vitroClassIdStr != null && vitroClassIdStr.length > 0){