Merge branch 'develop' of https://github.com/vivo-project/Vitro into develop

utilities/testrunner/src/edu/cornell/mannlib/vitro/utilities/testrunner/test-user-model.owl

@@ -16,7 +16,7 @@
     <auth:status rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVE</auth:status>
     <auth:loginCount rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</auth:loginCount>  
     <auth:passwordLinkExpires rdf:datatype="http://www.w3.org/2001/XMLSchema#long">0</auth:passwordLinkExpires>  
-    <auth:hasPermissionSet rdf:resource="http://permissionSet-50"/>
+    <auth:hasPermissionSet rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/authorization#ADMIN"/>
 </auth:UserAccount>
 
 <auth:UserAccount rdf:about="http://vivo.mydomain.edu/individual/JohnCurator">
@@ -28,7 +28,7 @@
     <auth:status rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVE</auth:status>
     <auth:loginCount rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</auth:loginCount>  
     <auth:passwordLinkExpires rdf:datatype="http://www.w3.org/2001/XMLSchema#long">0</auth:passwordLinkExpires>  
-    <auth:hasPermissionSet rdf:resource="http://permissionSet-5"/>
+    <auth:hasPermissionSet rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/authorization#CURATOR"/>
 </auth:UserAccount>
 
 <auth:UserAccount rdf:about="http://vivo.mydomain.edu/individual/SallyEditor">
@@ -40,7 +40,7 @@
     <auth:status rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVE</auth:status>
     <auth:loginCount rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</auth:loginCount>  
     <auth:passwordLinkExpires rdf:datatype="http://www.w3.org/2001/XMLSchema#long">0</auth:passwordLinkExpires>  
-    <auth:hasPermissionSet rdf:resource="http://permissionSet-4"/>
+    <auth:hasPermissionSet rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/authorization#EDITOR"/>
 </auth:UserAccount>
 
 <auth:UserAccount rdf:about="http://vivo.mydomain.edu/individual/JoeUser">
@@ -52,7 +52,7 @@
     <auth:status rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVE</auth:status>
     <auth:loginCount rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</auth:loginCount>  
     <auth:passwordLinkExpires rdf:datatype="http://www.w3.org/2001/XMLSchema#long">0</auth:passwordLinkExpires>  
-    <auth:hasPermissionSet rdf:resource="http://permissionSet-1"/>
+    <auth:hasPermissionSet rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/authorization#SELF_EDITOR"/>
 </auth:UserAccount>
 
 </rdf:RDF>

webapp/rdf/auth/everytime/permission_config.n3

@@ -12,6 +12,7 @@ auth:ADMIN
     
     # ADMIN-only permissions
     auth:hasPermission simplePermission:AccessSpecialDataModels ;
+   	auth:hasPermission simplePermission:EnableDeveloperPanel ;    
     auth:hasPermission simplePermission:LoginDuringMaintenance ;
     auth:hasPermission simplePermission:ManageMenus ;
     auth:hasPermission simplePermission:ManageProxies ;
@@ -23,8 +24,12 @@ auth:ADMIN
     auth:hasPermission simplePermission:UseAdvancedDataToolsPages ;
     auth:hasPermission simplePermission:UseMiscellaneousAdminPages ;
     auth:hasPermission simplePermission:UseSparqlQueryPage ;
-   	auth:hasPermission simplePermission:PageViewableAdmin ;    
+   	auth:hasPermission simplePermission:PageViewableAdmin ;  
-   	auth:hasPermission simplePermission:EnableDeveloperPanel ;    
+   	
+		# Uncomment the following permission line to enable the SPARQL update API. 
+		# Before enabling, be sure that the URL api/sparqlUpdate is secured by SSH, 
+		# so passwords will not be sent in clear text.   	  
+#  	auth:hasPermission simplePermission:UseSparqlUpdateApi ;    
     
     # permissions for CURATOR and above.
     auth:hasPermission simplePermission:EditOntology ;

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/permissions/SimplePermission.java

@@ -38,6 +38,8 @@ public class SimplePermission extends Permission {
 		NAMESPACE + "EditOwnAccount");
 	public static final SimplePermission EDIT_SITE_INFORMATION = new SimplePermission(
 		NAMESPACE + "EditSiteInformation");
+	public static final SimplePermission ENABLE_DEVELOPER_PANEL = new SimplePermission(
+		NAMESPACE + "EnableDeveloperPanel");
 	public static final SimplePermission LOGIN_DURING_MAINTENANCE = new SimplePermission(
 		NAMESPACE + "LoginDuringMaintenance");
 	public static final SimplePermission MANAGE_MENUS = new SimplePermission(
@@ -76,9 +78,8 @@ public class SimplePermission extends Permission {
 		NAMESPACE + "UseAdvancedDataToolsPages");
 	public static final SimplePermission USE_SPARQL_QUERY_PAGE = new SimplePermission(
 		NAMESPACE + "UseSparqlQueryPage");
-	public static final SimplePermission ENABLE_DEVELOPER_PANEL = new SimplePermission(
+	public static final SimplePermission USE_SPARQL_UPDATE_API = new SimplePermission(
-			NAMESPACE + "EnableDeveloperPanel");
+		NAMESPACE + "UseSparqlUpdateApi");
-	
 
 	// ----------------------------------------------------------------------
 	// These instances are "catch all" permissions to cover poorly defined

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/PolicyHelper.java

@@ -83,11 +83,11 @@ public class PolicyHelper {
         }
         
         try{    
-            Authenticator basicAuth = new BasicAuthenticator(req);            
+            Authenticator auth = Authenticator.getInstance(req);            
-            UserAccount user = basicAuth.getAccountForInternalAuth( email );
+            UserAccount user = auth.getAccountForInternalAuth( email );
             log.debug("userAccount is " + user==null?"null":user.getUri() );
                 
-            if( ! basicAuth.isCurrentPassword( user, password ) ){
+            if( ! auth.isCurrentPassword( user, password ) ){
                 log.debug(String.format("UNAUTHORIZED, password not accepted for %s, account URI: %s",
                                         user.getEmailAddress(), user.getUri()));
                 return false;

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/api/SparqlUpdateApiController.java

@@ -0,0 +1,201 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.controller.api;
+
+import static javax.servlet.http.HttpServletResponse.SC_BAD_REQUEST;
+import static javax.servlet.http.HttpServletResponse.SC_FORBIDDEN;
+import static javax.servlet.http.HttpServletResponse.SC_INTERNAL_SERVER_ERROR;
+import static javax.servlet.http.HttpServletResponse.SC_OK;
+
+import java.io.IOException;
+import java.io.PrintWriter;
+
+import javax.servlet.ServletContext;
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServlet;
+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;
+
+import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.update.GraphStore;
+import com.hp.hpl.jena.update.GraphStoreFactory;
+import com.hp.hpl.jena.update.UpdateAction;
+import com.hp.hpl.jena.update.UpdateFactory;
+import com.hp.hpl.jena.update.UpdateRequest;
+
+import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
+import edu.cornell.mannlib.vitro.webapp.auth.policy.PolicyHelper;
+import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
+import edu.cornell.mannlib.vitro.webapp.beans.UserAccount;
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.controller.authenticate.Authenticator;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
+import edu.cornell.mannlib.vitro.webapp.search.indexing.IndexBuilder;
+
+/**
+ * This extends HttpServlet instead of VitroHttpServlet because we want to have
+ * full control over the response:
+ * <ul>
+ * <li>No redirecting to the login page if not authorized</li>
+ * <li>No redirecting to the home page on insufficient authorization</li>
+ * <li>No support for GET or HEAD requests, only POST.</li>
+ * </ul>
+ * 
+ * So these responses will be produced:
+ * 
+ * <pre>
+ * 200 Success
+ * 400 Failed to parse SPARQL update
+ * 400 SPARQL update must specify a GRAPH URI.
+ * 403 username/password combination is not valid
+ * 403 Account is not authorized
+ * 405 Method not allowed
+ * 500 Unknown error
+ * </pre>
+ */
+public class SparqlUpdateApiController extends HttpServlet {
+	private static final Log log = LogFactory
+			.getLog(SparqlUpdateApiController.class);
+
+	private static final Actions REQUIRED_ACTIONS = SimplePermission.USE_SPARQL_UPDATE_API.ACTIONS;
+
+	@Override
+	protected void doPost(HttpServletRequest req, HttpServletResponse resp)
+			throws ServletException, IOException {
+		try {
+			checkAuthorization(req);
+			UpdateRequest parsed = parseUpdateString(req);
+			executeUpdate(req, parsed);
+			do200response(resp);
+		} catch (AuthException e) {
+			do403response(resp, e);
+		} catch (ParseException e) {
+			do400response(resp, e);
+		} catch (Exception e) {
+			do500response(resp, e);
+		}
+	}
+
+	private void checkAuthorization(HttpServletRequest req)
+			throws AuthException {
+		String email = req.getParameter("email");
+		String password = req.getParameter("password");
+
+		Authenticator auth = Authenticator.getInstance(req);
+		UserAccount account = auth.getAccountForInternalAuth(email);
+		if (!auth.isCurrentPassword(account, password)) {
+			log.debug("Invalid: '" + email + "'/'" + password + "'");
+			throw new AuthException("email/password combination is not valid");
+		}
+
+		if (!PolicyHelper.isAuthorizedForActions(req, email, password,
+				REQUIRED_ACTIONS)) {
+			log.debug("Not authorized: '" + email + "'");
+			throw new AuthException("Account is not authorized");
+		}
+
+		log.debug("Authorized for '" + email + "'");
+	}
+
+	private UpdateRequest parseUpdateString(HttpServletRequest req)
+			throws ParseException {
+		String update = req.getParameter("update");
+		if (StringUtils.isBlank(update)) {
+			log.debug("No update parameter.");
+			throw new ParseException("No 'update' parameter.");
+		}
+
+		if (!StringUtils.containsIgnoreCase(update, "GRAPH")) {
+			if (log.isDebugEnabled()) {
+				log.debug("No GRAPH uri in '" + update + "'");
+			}
+			throw new ParseException("SPARQL update must specify a GRAPH URI.");
+		}
+
+		try {
+			return UpdateFactory.create(update);
+		} catch (Exception e) {
+			log.debug("Problem parsing", e);
+			throw new ParseException("Failed to parse SPARQL update", e);
+		}
+	}
+
+	private void executeUpdate(HttpServletRequest req, UpdateRequest parsed) {
+		ServletContext ctx = req.getSession().getServletContext();
+		VitroRequest vreq = new VitroRequest(req);
+
+		IndexBuilder.getBuilder(ctx).pause();
+		try {
+			Dataset ds = new RDFServiceDataset(vreq.getUnfilteredRDFService());
+			GraphStore graphStore = GraphStoreFactory.create(ds);
+			UpdateAction.execute(parsed, graphStore);
+		} finally {
+			IndexBuilder.getBuilder(ctx).unpause();
+		}
+	}
+
+	private void do200response(HttpServletResponse resp) throws IOException {
+		doResponse(resp, SC_OK, "SPARQL update accepted.");
+	}
+
+	private void do403response(HttpServletResponse resp, AuthException e)
+			throws IOException {
+		doResponse(resp, SC_FORBIDDEN, e.getMessage());
+	}
+
+	private void do400response(HttpServletResponse resp, ParseException e)
+			throws IOException {
+		if (e.getCause() == null) {
+			doResponse(resp, SC_BAD_REQUEST, e.getMessage());
+		} else {
+			doResponse(resp, SC_BAD_REQUEST, e.getMessage(), e.getCause());
+		}
+	}
+
+	private void do500response(HttpServletResponse resp, Exception e)
+			throws IOException {
+		doResponse(resp, SC_INTERNAL_SERVER_ERROR, "Unknown error", e);
+	}
+
+	private void doResponse(HttpServletResponse resp, int statusCode,
+			String message) throws IOException {
+		resp.setStatus(statusCode);
+		PrintWriter writer = resp.getWriter();
+		writer.println("<H1>" + statusCode + " " + message + "</H1>");
+	}
+
+	private void doResponse(HttpServletResponse resp, int statusCode,
+			String message, Throwable e) throws IOException {
+		resp.setStatus(statusCode);
+		PrintWriter writer = resp.getWriter();
+		writer.println("<H1>" + statusCode + " " + message + "</H1>");
+		writer.println("<pre>");
+		e.printStackTrace(writer);
+		writer.println("</pre>");
+	}
+
+	// ----------------------------------------------------------------------
+	// Helper classes
+	// ----------------------------------------------------------------------
+
+	private static class AuthException extends Exception {
+		private AuthException(String message) {
+			super(message);
+		}
+	}
+
+	private static class ParseException extends Exception {
+		private ParseException(String message) {
+			super(message);
+		}
+
+		private ParseException(String message, Throwable cause) {
+			super(message, cause);
+		}
+	}
+
+}

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

@@ -1,120 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.controller.edit;
-
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.LinkedList;
-import java.util.List;
-
-import javax.servlet.RequestDispatcher;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import edu.cornell.mannlib.vedit.beans.EditProcessObject;
-import edu.cornell.mannlib.vedit.beans.FormObject;
-import edu.cornell.mannlib.vedit.beans.Option;
-import edu.cornell.mannlib.vedit.controller.BaseEditController;
-import edu.cornell.mannlib.vedit.util.FormUtils;
-import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
-import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
-import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatementImpl;
-import edu.cornell.mannlib.vitro.webapp.beans.Individual;
-import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
-import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
-import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
-import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
-
-public class ExternalIdRetryController extends BaseEditController {
-	
-	private static final Log log = LogFactory.getLog(ExternalIdRetryController.class.getName());
-
-    public void doPost (HttpServletRequest request, HttpServletResponse response) {
-		if (!isAuthorizedToDisplayPage(request, response,
-				SimplePermission.DO_BACK_END_EDITING.ACTIONS)) {
-        	return;
-        }
-
-        VitroRequest vreq = new VitroRequest(request);
-
-        //create an EditProcessObject for this and put it in the session
-        EditProcessObject epo = super.createEpo(request);
-
-        String action = "insert";
-
-        DataPropertyDao dpDao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyDao();
-        DataPropertyStatementDao edDao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyStatementDao();
-        epo.setDataAccessObject(edDao);
-        epo.setBeanClass(DataPropertyStatement.class);
-
-        IndividualDao eDao = vreq.getUnfilteredWebappDaoFactory().getIndividualDao();
-
-        DataPropertyStatement eidForEditing = null;
-        if (!epo.getUseRecycledBean()){
-            eidForEditing = new DataPropertyStatementImpl();
-            populateBeanFromParams(eidForEditing,vreq);
-            if (vreq.getParameter(MULTIPLEXED_PARAMETER_NAME) != null) {
-                action = "update";
-            }
-            epo.setOriginalBean(eidForEditing);
-        } else {
-            eidForEditing = (DataPropertyStatement) epo.getNewBean();
-        }
-
-        //make a simple mask for the class's id
-        Object[] simpleMaskPair = new Object[2];
-        simpleMaskPair[0]="Id";
-        //simpleMaskPair[1]=Integer.valueOf(eidForEditing.getId());
-        epo.getSimpleMask().add(simpleMaskPair);
-
-        //set up any listeners
-
-        FormObject foo = new FormObject();
-        HashMap OptionMap = new HashMap();
-        List entityList = new LinkedList();
-        if (eidForEditing.getIndividualURI() != null) {
-            Individual individual = eDao.getIndividualByURI(eidForEditing.getIndividualURI());
-            entityList.add(new Option(individual.getURI(),individual.getName(),true));
-        } else {
-            entityList.add(new Option ("-1", "Error: the entity must be specified", true));
-        }
-        OptionMap.put("IndividualURI",entityList);
-        // TOOD change following DAO call to getAllExternalIdDataProperties once implemented
-        List allExternalIdDataProperties = dpDao.getAllExternalIdDataProperties();
-        Collections.sort(allExternalIdDataProperties);
-        OptionMap.put("DatapropURI", FormUtils.makeOptionListFromBeans(allExternalIdDataProperties, "URI", "PublicName", eidForEditing.getDatapropURI(),""));
-        foo.setOptionLists(OptionMap);
-        foo.setErrorMap(epo.getErrMsgMap());
-
-        epo.setFormObject(foo);
-
-        FormUtils.populateFormFromBean(eidForEditing,action,foo,epo.getBadValueMap());
-
-        RequestDispatcher rd = request.getRequestDispatcher(Controllers.BASIC_JSP);
-        request.setAttribute("bodyJsp","/templates/edit/formBasic.jsp");
-        request.setAttribute("formJsp","/templates/edit/specific/externalIds_retry.jsp");
-        request.setAttribute("scripts","/templates/edit/formBasic.js");
-        request.setAttribute("title","External Id Editing Form");
-        request.setAttribute("_action",action);
-        request.setAttribute("unqualifiedClassName","External Id");
-        setRequestAttributes(request,epo);
-
-        try {
-            rd.forward(request, response);
-        } catch (Exception e) {
-            log.error("ExternalIdRetryController could not forward to view.");
-            log.error(e.getMessage());
-            log.error(e.getStackTrace());
-        }
-
-    }
-
-    public void doGet (HttpServletRequest request, HttpServletResponse response) {
-        doPost(request, response);
-    }
-
-}

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

@@ -143,24 +143,25 @@ public class VclassEditController extends BaseEditController {
 
         // if supported, we want to show only the asserted superclasses and subclasses.
         VClassDao vcDao = ModelAccess.on(getServletContext()).getBaseWebappDaoFactory().getVClassDao();
+        VClassDao displayVcDao = ModelAccess.on(getServletContext()).getWebappDaoFactory().getVClassDao();
         
         List<VClass> superVClasses = getVClassesForURIList(
-                vcDao.getSuperClassURIs(vcl.getURI(),false), vcDao);
+                vcDao.getSuperClassURIs(vcl.getURI(),false), displayVcDao);
         sortForPickList(superVClasses, request);
         request.setAttribute("superclasses",superVClasses);
 
         List<VClass> subVClasses = getVClassesForURIList(
-                vcDao.getSubClassURIs(vcl.getURI()), vcDao);
+                vcDao.getSubClassURIs(vcl.getURI()), displayVcDao);
         sortForPickList(subVClasses, request);
         request.setAttribute("subclasses",subVClasses);
             
         List<VClass> djVClasses = getVClassesForURIList(
-                vcDao.getDisjointWithClassURIs(vcl.getURI()), vcDao);
+                vcDao.getDisjointWithClassURIs(vcl.getURI()), displayVcDao);
         sortForPickList(djVClasses, request);
         request.setAttribute("disjointClasses",djVClasses);
 
         List<VClass> eqVClasses = getVClassesForURIList(
-                vcDao.getEquivalentClassURIs(vcl.getURI()), vcDao);
+                vcDao.getEquivalentClassURIs(vcl.getURI()), displayVcDao);
         sortForPickList(eqVClasses, request);
         request.setAttribute("equivalentClasses",eqVClasses);
    

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

@@ -58,15 +58,16 @@ public class PageController extends FreemarkerHttpServlet{
 
             if( pageActs == null && dgActs == null){
                 return Actions.AUTHORIZED;
-            }else if( pageActs == null && dgActs != null ){
+            }else if( pageActs == null ){
                 return dgActs;
+            }else if( dgActs == null ){
+            	return pageActs;
             }else{
-                return pageActs;
+                return pageActs.and(dgActs);
             }                
             
         } catch (Exception e) {
-            // TODO Auto-generated catch block
+            log.warn(e);
-            log.debug(e);
             return Actions.UNAUTHORIZED;
         }                
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/PageDaoJena.java

@@ -537,13 +537,14 @@ public class PageDaoJena extends JenaBaseDao implements PageDao {
         List<String> actions = new ArrayList<String>();
         
         Model dModel = getOntModelSelector().getDisplayModel();
+        dModel.enterCriticalSection(false);
         try{
             QueryExecution qe = 
                 QueryExecutionFactory.create( requiredActionsQuery, dModel, initialBindings);
             actions = executeQueryToList( qe );
             qe.close();
         }finally{
-            dModel.enterCriticalSection(false);
+            dModel.leaveCriticalSection();
         }
         return actions;            
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/DefaultObjectPropertyFormGenerator.java

@@ -112,7 +112,7 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
     	Individual subject = EditConfigurationUtils.getSubjectIndividual(vreq);
    		String predicateUri = EditConfigurationUtils.getPredicateUri(vreq);
    		String rangeUri = EditConfigurationUtils.getRangeUri(vreq);
-   		if (rangeUri != null) {
+   		if (rangeUri != null && !rangeUri.isEmpty()) {
    		    VClass rangeVClass = ctxDaoFact.getVClassDao().getVClassByURI(rangeUri);
    		    if (!rangeVClass.isUnion()) {
    		        types.add(rangeVClass);    
@@ -125,18 +125,23 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
    		}
    		WebappDaoFactory wDaoFact = vreq.getWebappDaoFactory();
 		//Get all vclasses applicable to subject
-		List<VClass> vClasses = subject.getVClasses();
+   		if(subject != null) {
-		HashMap<String, VClass> typesHash = new HashMap<String, VClass>();
+			List<VClass> vClasses = subject.getVClasses();
-		for(VClass vclass: vClasses) {
+			HashMap<String, VClass> typesHash = new HashMap<String, VClass>();
-			 List<VClass> rangeVclasses = wDaoFact.getVClassDao().getVClassesForProperty(vclass.getURI(),predicateUri);
+			for(VClass vclass: vClasses) {
-			 if(rangeVclasses !=  null) {
+				 List<VClass> rangeVclasses = wDaoFact.getVClassDao().getVClassesForProperty(vclass.getURI(),predicateUri);
-				 for(VClass range: rangeVclasses) {
+				 if(rangeVclasses !=  null) {
-					 //a hash will keep a unique list of types and so prevent duplicates
+					 for(VClass range: rangeVclasses) {
-					 typesHash.put(range.getURI(), range);
+						 //a hash will keep a unique list of types and so prevent duplicates
+						 typesHash.put(range.getURI(), range);
+					 }
 				 }
-			 }
+			}
-		}
+			types.addAll(typesHash.values());
-		types.addAll(typesHash.values());
+   		} else {
+   			log.error("Subject individual was null for");
+   		}
+		
         return types;
 	}	
 	

webapp/src/edu/cornell/mannlib/vitro/webapp/freemarker/config/FreemarkerConfigurationImpl.java

@@ -3,6 +3,7 @@
 package edu.cornell.mannlib.vitro.webapp.freemarker.config;
 
 import java.io.IOException;
+import java.lang.ref.WeakReference;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
@@ -35,28 +36,52 @@ import freemarker.template.utility.DeepUnwrap;
  * Extend the Freemarker Configuration class to include some information that is
  * particular to the current request.
  * 
- * Takes advantage of the fact that each servlet request runs in a separate
+ * A reference to the current request is not always available to the Freemarker
- * thread. Stores the request-based information in a ThreadLocal. Override any
+ * Configuration, so we take advantage of the fact that each request runs in a
- * methods that should return that information instead of (or in addition to)
+ * separate thread, and store a reference to that request in a ThreadLocal
- * the common info.
+ * object.
+ * 
+ * Then, we override any methods that should return that request-based
+ * information instead of (or in addition to) the common info.
  * 
  * Only the getters are overridden, not the setters. So if you call
  * setAllSharedVariables(), for example, it will have no effect on the
  * request-based information.
+ * 
+ * Notice that the reference to the current request is actually stored through a
+ * WeakReference. This is because the ThreadLocal will not be cleared when the
+ * webapp is stopped, so none of the references from that ThreadLocal are
+ * eligible for garbage collection. If any of those references is an instance of
+ * a class that is loaded by the webapp, then the webapp ClassLoader is not
+ * eligible for garbage collection. This would be a huge memory leak.
+ * 
+ * Thanks to the WeakReference, the request is eligible for garbage collection
+ * if nothing else refers to it. In theory, this means that the WeakReference
+ * could return a null, but if the garbage collector has taken the request, then
+ * who is invoking this object?
  */
 public class FreemarkerConfigurationImpl extends Configuration {
 	private static final Log log = LogFactory
 			.getLog(FreemarkerConfigurationImpl.class);
 
-	private final ThreadLocal<RequestBasedInformation> rbiRef = new ThreadLocal<>();
+	private static final String ATTRIBUTE_NAME = RequestBasedInformation.class
+			.getName();
+
+	private final ThreadLocal<WeakReference<HttpServletRequest>> reqRef = new ThreadLocal<>();
 
 	void setRequestInfo(HttpServletRequest req) {
-		rbiRef.set(new RequestBasedInformation(req, this));
+		reqRef.set(new WeakReference<>(req));
+		req.setAttribute(ATTRIBUTE_NAME, new RequestBasedInformation(req, this));
+	}
+
+	private RequestBasedInformation getRequestInfo() {
+		HttpServletRequest req = reqRef.get().get();
+		return (RequestBasedInformation) req.getAttribute(ATTRIBUTE_NAME);
 	}
 
 	@Override
 	public Object getCustomAttribute(String name) {
-		Map<String, Object> attribs = rbiRef.get().getCustomAttributes();
+		Map<String, Object> attribs = getRequestInfo().getCustomAttributes();
 		if (attribs.containsKey(name)) {
 			return attribs.get(name);
 		} else {
@@ -66,13 +91,13 @@ public class FreemarkerConfigurationImpl extends Configuration {
 
 	@Override
 	public String[] getCustomAttributeNames() {
-		Set<String> rbiNames = rbiRef.get().getCustomAttributes().keySet();
+		Set<String> rbiNames = getRequestInfo().getCustomAttributes().keySet();
 		return joinNames(rbiNames, super.getCustomAttributeNames());
 	}
 
 	@Override
 	public TemplateModel getSharedVariable(String name) {
-		Map<String, TemplateModel> vars = rbiRef.get().getSharedVariables();
+		Map<String, TemplateModel> vars = getRequestInfo().getSharedVariables();
 		if (vars.containsKey(name)) {
 			return vars.get(name);
 		} else {
@@ -82,7 +107,7 @@ public class FreemarkerConfigurationImpl extends Configuration {
 
 	@Override
 	public Set<String> getSharedVariableNames() {
-		Set<String> rbiNames = rbiRef.get().getSharedVariables().keySet();
+		Set<String> rbiNames = getRequestInfo().getSharedVariables().keySet();
 
 		@SuppressWarnings("unchecked")
 		Set<String> superNames = super.getSharedVariableNames();
@@ -94,7 +119,7 @@ public class FreemarkerConfigurationImpl extends Configuration {
 
 	@Override
 	public Locale getLocale() {
-		return rbiRef.get().getReq().getLocale();
+		return getRequestInfo().getReq().getLocale();
 	}
 
 	private String[] joinNames(Set<String> nameSet, String[] nameArray) {

webapp/src/edu/cornell/mannlib/vitro/webapp/freemarker/loader/FreemarkerTemplateLoader.java

@@ -285,7 +285,7 @@ public class FreemarkerTemplateLoader implements TemplateLoader {
 		}
 
 		public boolean fileQualifies(Path path) {
-			return Files.isRegularFile(path) && Files.isReadable(path);
+			return Files.isReadable(path) && !Files.isDirectory(path);
 		}
 
 		public SortedSet<PathPieces> getMatches() {

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/ThemeInfoSetup.java

@@ -73,8 +73,8 @@ public class ThemeInfoSetup implements ServletContextListener {
 
 		ApplicationBean.themeInfo = new ThemeInfo(themesBaseDir,
 				defaultThemeName, themeNames);
-		ss.info(this, ", current theme: " + currentThemeName
+		ss.info(this, "current theme: " + currentThemeName
-				+ "default theme: " + defaultThemeName + ", available themes: "
+				+ ", default theme: " + defaultThemeName + ", available themes: "
 				+ themeNames);
 	}
 

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

@@ -1,96 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.utils.dataGetter;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import javax.servlet.ServletContext;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import com.hp.hpl.jena.query.Dataset;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.update.GraphStore;
-import com.hp.hpl.jena.update.GraphStoreFactory;
-import com.hp.hpl.jena.update.UpdateAction;
-
-import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
-import edu.cornell.mannlib.vitro.webapp.auth.policy.PolicyHelper;
-import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
-import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequiresActions;
-import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
-import edu.cornell.mannlib.vitro.webapp.search.indexing.IndexBuilder;
-
-/**
- * Handle a SPARQL Update request. This uses Jena ARQ and the RDFServiceDataset to
- * evaluate a SPARQL Update with the RDFService.
- * 
- * The reason to make this a DataGettere was to allow configuration in RDF of this
- * service.  
- */
-public class SparqlUpdate implements DataGetter, RequiresActions{
-    
-    private static final Log log = LogFactory.getLog(SparqlUpdate.class);
-
-    VitroRequest vreq;
-    ServletContext context;
-    
-    public SparqlUpdate( 
-            VitroRequest vreq, Model displayModel, String dataGetterURI ) {
-    	if( vreq == null ) 
-    		throw new IllegalArgumentException("VitroRequest  may not be null.");                
-        this.vreq = vreq;
-        this.context = vreq.getSession().getServletContext();
-    }        
-
-
-    /**
-     * Gets the update from the request and then executes it on
-     * the RDFService.
-     */
-    @Override
-	public Map<String,Object> getData( Map<String, Object> valueMap ) {
-    	HashMap<String, Object> data = new HashMap<String,Object>();
-
-        String update = vreq.getParameter("update");
-
-        if( update != null && !update.trim().isEmpty()){
-            try{
-                IndexBuilder.getBuilder(context).pause();
-                Dataset ds = new RDFServiceDataset( vreq.getUnfilteredRDFService() );
-                GraphStore graphStore = GraphStoreFactory.create(ds);
-                log.warn("The SPARQL update is '"+vreq.getParameter("update")+"'");
-                UpdateAction.parseExecute( vreq.getParameter("update") , graphStore );
-            }finally{
-                IndexBuilder.getBuilder(context).unpause();
-            }
-
-        }
-
-        data.put("bodyTemplate", "page-sparqlUpdateTest.ftl");        
-        return data;
-    }
-
-
-    /**
-     * Check if this request is authorized by the email/password.
-     * If not do normal authorization. 
-     */
-    @Override
-    public Actions requiredActions(VitroRequest vreq) {
-        String email = vreq.getParameter("email");
-        String password = vreq.getParameter("password");
-                        
-        boolean isAuth = PolicyHelper.isAuthorizedForActions(vreq, 
-                email, password, SimplePermission.MANAGE_SEARCH_INDEX.ACTIONS);
-        
-        if( isAuth )
-            return Actions.AUTHORIZED;
-        else
-            return SimplePermission.MANAGE_SEARCH_INDEX.ACTIONS;
-    }        
-       
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/utils/developer/DeveloperSettings.java

@@ -179,7 +179,7 @@ public class DeveloperSettings {
 	// The factory
 	// ----------------------------------------------------------------------
 
-	private static final String ATTRIBUTE_NAME = DeveloperSettings.class
+	protected static final String ATTRIBUTE_NAME = DeveloperSettings.class
 			.getName();
 
 	public static DeveloperSettings getBean(HttpServletRequest req) {
@@ -203,7 +203,7 @@ public class DeveloperSettings {
 
 	private final Map<Keys, Object> settings = new EnumMap<>(Keys.class);
 
-	private DeveloperSettings(ServletContext ctx) {
+	protected DeveloperSettings(ServletContext ctx) {
 		updateFromFile(ctx);
 	}
 

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/edit/EditConfigurationTemplateModel.java

@@ -547,11 +547,14 @@ public class EditConfigurationTemplateModel extends BaseTemplateModel {
     	        rangeVClasses.addAll(rangeClass.getUnionComponents());
     	    }
             for(VClass rangeVClass : rangeVClasses) {	
-                vclasses.add(rangeVClass);
+            	if(rangeVClass.getGroupURI() != null) {
+            		vclasses.add(rangeVClass);
+            	}
         	    List<String> subURIs = wdf.getVClassDao().getAllSubClassURIs(rangeVClass.getURI());
         	    for (String subClassURI : subURIs) {
         	        VClass subClass = wdf.getVClassDao().getVClassByURI(subClassURI);
-        	        if (subClass != null) {
+        	        //if the subclass exists and also belongs to a particular class group
+        	        if (subClass != null && subClass.getGroupURI() != null) {
         	            vclasses.add(subClass);
         	        }
         	    }
@@ -567,7 +570,8 @@ public class EditConfigurationTemplateModel extends BaseTemplateModel {
 	        	//add range vclass to hash
 	        	if(rangeVclasses != null) {
 	        		for(VClass v: rangeVclasses) {
-	        			if(!vclassesURIs.contains(v.getURI())) {
+	        			//Need to make sure any class added will belong to a class group
+	        			if(!vclassesURIs.contains(v.getURI()) && v.getGroupURI() != null) {
 	        				vclassesURIs.add(v.getURI());
 	        				vclasses.add(v);
 	        			}
@@ -577,7 +581,13 @@ public class EditConfigurationTemplateModel extends BaseTemplateModel {
     	}
     	//if each subject vclass resulted in null being returned for range vclasses, then size of vclasses would be zero
     	if(vclasses.size() == 0) {
-    		vclasses = wdf.getVClassDao().getAllVclasses();
+    		List<VClass> allVClasses  = wdf.getVClassDao().getAllVclasses();
+    		//Since these are all vclasses, we should check whether vclasses included are in a class group
+    		for(VClass v:allVClasses) {
+    			if(v.getGroupURI() != null) {
+    				vclasses.add(v);
+    			}
+    		}
     	}
     	
     	

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/GroupedPropertyList.java

@@ -81,7 +81,7 @@ public class GroupedPropertyList extends BaseTemplateModel {
         
         // save applicable ranges before deduping to filter later 
         populatedObjectPropertyList = dedupe(populatedObjectPropertyList);
-        
+                
         Collection<ObjectProperty> additions = ApplicationConfigurationOntologyUtils
                 .getAdditionalFauxSubpropertiesForList(
                         populatedObjectPropertyList, subject, vreq);
@@ -121,13 +121,7 @@ public class GroupedPropertyList extends BaseTemplateModel {
         if (editing) {
             mergeAllPossibleDataProperties(propertyList);
         }
-        
+                
-// Not currently necessary since the language-specific version is now added
-// during the merge
-//        if (editing) {
-//            propertyList = correctLanguageForProperties(propertyList);
-//        }
-        
         sort(propertyList);
 
         // Put the list into groups
@@ -176,35 +170,6 @@ public class GroupedPropertyList extends BaseTemplateModel {
         return filteredAdditions;
     }
     
-    // Use the language-filtering WebappDaoFactory to get the right version of
-    // each property.  When editing, the methods that add to the property list
-    // are blissfully (and intentionally) language-unaware.
-    private List<Property> correctLanguageForProperties(List<Property> properties) {
-        List<Property> languageCorrectedProps = new ArrayList<Property>();
-        for (Property p : properties) {
-            Property correctedProp = null;
-            if (p instanceof ObjectProperty) {
-                ObjectProperty op = (ObjectProperty) p;
-                correctedProp = wdf.getObjectPropertyDao()
-                        .getObjectPropertyByURIs(op.getURI(), 
-                                op.getDomainVClassURI(), op.getRangeVClassURI());
-            } else if (p instanceof DataProperty) {
-                correctedProp = wdf.getDataPropertyDao()
-                        .getDataPropertyByURI(((DataProperty) p).getURI());                
-            } else {
-                log.warn("Ignoring " + p.getURI() + " which is neither an " +
-                		 "ObjectProperty nor a DatatypeProperty.");
-            }
-            if (correctedProp != null) {
-                languageCorrectedProps.add(correctedProp);
-            } else {
-                log.error("Unable to retrieve property " + p.getURI() + 
-                        " using the WebappDaoFactory associated with the request.");                
-            }
-        }
-        return languageCorrectedProps;
-    }
-
     // It's possible that an object property retrieved in the call to getPopulatedObjectPropertyList()
     // is now empty of statements, because if not editing, some statements without a linked individual
     // are not retrieved by the query. (See <linked-individual-required> elements in queries.)
@@ -281,16 +246,17 @@ public class GroupedPropertyList extends BaseTemplateModel {
                         continue;
                     }
                     boolean addToList = true;
-                    int opIndex = 0;
                     for(ObjectProperty op : populatedObjectPropertyList) {
-                        if(redundant(op, piOp)) {
+                        RedundancyReason reason = redundant(op, piOp); 
+                        if(reason != null) {
                             addToList = false;
-                            if (moreRestrictiveRange(piOp, op, wadf)) {
+                            if (reason == RedundancyReason.LABEL_AND_URI_MATCH 
-                                propertyList = replaceOpWithPiOpInList(piOp, op, opIndex, propertyList);
+                                    && moreRestrictiveRange(piOp, op, wadf)) {
+                                op.setRangeVClassURI(piOp.getRangeVClassURI());
+                                op.setRangeVClass(piOp.getRangeVClass());
                             }
                             break;
                         } 
-                        opIndex++;
                     }
                     if(addToList) {
                         propertyList.add(piOp);         
@@ -315,6 +281,10 @@ public class GroupedPropertyList extends BaseTemplateModel {
         return propertyList;
     }
     
+    private enum RedundancyReason {
+         LABEL_AND_URI_MATCH, LABEL_URI_DOMAIN_AND_RANGE_MATCH   
+    }
+    
     private boolean moreRestrictiveRange(ObjectProperty piOp, ObjectProperty op, 
             WebappDaoFactory wadf) {
         if(piOp.getRangeVClassURI() == null) {
@@ -327,25 +297,9 @@ public class GroupedPropertyList extends BaseTemplateModel {
         }
     }
     
-    private List<Property> replaceOpWithPiOpInList(ObjectProperty piOp, 
+    private RedundancyReason redundant(ObjectProperty op, ObjectProperty op2) {
-            ObjectProperty op, int opIndex, List<Property> propertyList) {
-                
-        List<Property> returnList = new ArrayList<Property>();
-        int index = 0;
-        for(Property p : propertyList) {
-            if(index == opIndex /* p.equals(op) */) {
-                returnList.add(piOp);
-            } else {
-                returnList.add(p);
-            }
-            index++;
-        }
-        return returnList;
-    }
-    
-    private boolean redundant(ObjectProperty op, ObjectProperty op2) {
         if (op2.getURI() == null) {
-            return false;
+            return null;
         }
         boolean uriMatches = (op.getURI() != null 
                 && op.getURI().equals(op2.getURI()));
@@ -360,7 +314,7 @@ public class GroupedPropertyList extends BaseTemplateModel {
             labelMatches = true;
         }
         if(uriMatches && labelMatches) {
-            return true;
+            return RedundancyReason.LABEL_AND_URI_MATCH;
         }
         if(op.getDomainVClassURI() == null) {
             if(op2.getDomainVClassURI() == null) {
@@ -377,9 +331,9 @@ public class GroupedPropertyList extends BaseTemplateModel {
             rangeMatches = true;
         }
         if (uriMatches && domainMatches && rangeMatches) {
-            return true;
+            return RedundancyReason.LABEL_URI_DOMAIN_AND_RANGE_MATCH;
         }
-        return false;
+        return null;
     }
 
     private void addObjectPropertyToPropertyList(String propertyUri, String domainUri, String rangeUri,

webapp/test/stubs/edu/cornell/mannlib/vitro/webapp/utils/developer/DeveloperSettingsStub.java

@@ -0,0 +1,33 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package stubs.edu.cornell.mannlib.vitro.webapp.utils.developer;
+
+import javax.servlet.ServletContext;
+
+import edu.cornell.mannlib.vitro.webapp.utils.developer.DeveloperSettings;
+
+/**
+ * Do everything that a standard DeveloperSettings would do, except loading from
+ * a properties file.
+ * 
+ * That way, we don't require ConfigurationProperties to find the Vitro home
+ * directory, so we don't throw errors if there is no ConfigurationProperties.
+ */
+public class DeveloperSettingsStub extends DeveloperSettings {
+	/**
+	 * Factory method. Create the stub and set it into the ServletContext.
+	 */
+	public static void set(ServletContext ctx) {
+		ctx.setAttribute(ATTRIBUTE_NAME, new DeveloperSettingsStub(ctx));
+	}
+
+	protected DeveloperSettingsStub(ServletContext ctx) {
+		super(ctx);
+	}
+
+	@Override
+	protected void updateFromFile(ServletContext ctx) {
+		// Don't bother.
+	}
+
+}

webapp/test/stubs/javax/servlet/ServletContextStub.java

@@ -21,6 +21,8 @@ import javax.servlet.ServletException;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import stubs.edu.cornell.mannlib.vitro.webapp.utils.developer.DeveloperSettingsStub;
+
 /**
  * A simple stand-in for the {@link ServletContext}, for use in unit tests.
  */
@@ -36,6 +38,11 @@ public class ServletContextStub implements ServletContext {
 	private final Map<String, String> mockResources = new HashMap<String, String>();
 	private final Map<String, String> realPaths = new HashMap<String, String>();
 
+	public ServletContextStub() {
+		// Assume that unit tests won't want to use Developer mode.
+		DeveloperSettingsStub.set(this);
+	}
+	
 	public void setContextPath(String contextPath) {
 		if (contextPath == null) {
 			throw new NullPointerException("contextPath may not be null.");

webapp/web/WEB-INF/web.xml

@@ -1025,6 +1025,16 @@
     <url-pattern>/admin/sparqlquery</url-pattern>
   </servlet-mapping>
   
+  <servlet>
+    <servlet-name>SparqlUpdateApi</servlet-name>
+    <servlet-class>edu.cornell.mannlib.vitro.webapp.controller.api.SparqlUpdateApiController</servlet-class>
+  </servlet>
+
+  <servlet-mapping>
+    <servlet-name>SparqlUpdateApi</servlet-name>
+    <url-pattern>/api/sparqlUpdate</url-pattern>
+  </servlet-mapping>
+  
   <servlet>
   	<servlet-name>primitiveRdfEdit</servlet-name>
   	<servlet-class>edu.cornell.mannlib.vitro.webapp.controller.edit.PrimitiveRdfEdit</servlet-class>  	

webapp/web/templates/edit/specific/ents_edit.jsp

@@ -99,11 +99,6 @@
             	<input type="hidden" name="controller" value="Entity"/>
         	</form>
         	<form action="editForm" method="get">
-            	<input type="submit" class="form-button" value="Add an External Identifier"/>
-            	<input type="hidden" name="IndividualURI" value="${individual.URI}"/>
-            	<input type="hidden" name="controller" value="ExternalId"/>
-        	</form>
-        	<form action="editForm" method="get">
             	<input type="submit" class="form-button" value="Change URI"/>
             	<input type="hidden" name="oldURI" value="${individual.URI}"/>
             	<input type="hidden" name="mode" value="renameResource"/>

webapp/web/templates/freemarker/body/menupage/page-sparqlUpdateTest.ftl

@@ -1,12 +0,0 @@
-<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
-
-<h3>SPARQL Update Test</h3>
-
-<p>This is an expermental SPARQL update service.</p>
-
-<form action="${urls.base}/sparqlUpdateTest" method="post">
-      <p>
-      <textarea name="update" rows="20" cols="80" ></textarea>
-      <input type="submit" />
-      </p>
-</form>