Cleaned up some miscellaneous cruft

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

@@ -43,7 +43,7 @@ public class ApplicationBeanRetryController extends BaseEditController {
         try {
             super.doGet(request,response);
         } catch (Exception e) {
-            log.error("PortalRetryController encountered exception calling super.doGet()");
+            log.error(e,e);
         }
 
         //create an EditProcessObject for this and put it in the session
@@ -88,7 +88,7 @@ public class ApplicationBeanRetryController extends BaseEditController {
    
         RequestDispatcher rd = request.getRequestDispatcher(Controllers.BASIC_JSP);
         request.setAttribute("bodyJsp","/templates/edit/formBasic.jsp");
-        request.setAttribute("formJsp","/templates/edit/specific/portal_retry.jsp");
+        request.setAttribute("formJsp","/templates/edit/specific/applicationBean_retry.jsp");
         request.setAttribute("scripts","/templates/edit/formBasic.js");
         request.setAttribute("title","Site Information Editing Form");
         request.setAttribute("_action",action);

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/WebappDaoFactory.java

@@ -118,8 +118,6 @@ public interface WebappDaoFactory {
     public LinksDao getLinksDao();
     public LinktypeDao getLinktypeDao();
 
-    public FlagDao getFlagDao();
-
     // TODO This goes away when the UserAccounts stuff is fully implemented - jblake.
     public UserDao getUserDao();
     

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/filtering/WebappDaoFactoryFiltering.java

@@ -179,10 +179,6 @@ public class WebappDaoFactoryFiltering implements WebappDaoFactory {
         return innerWebappDaoFactory.getUserURI();
     }
 
-    public FlagDao getFlagDao() {
-        return innerWebappDaoFactory.getFlagDao();
-    }
-
     public KeywordIndividualRelationDao getKeys2EntsDao() {
         return innerWebappDaoFactory.getKeys2EntsDao();
     }

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

@@ -1,13 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao.jena;
-
-import com.hp.hpl.jena.rdf.model.Statement;
-
-public interface ExternalTripleStoreInterface {
-
-	public abstract void addToExternalStore(Statement stmt) throws TripleStoreUnavailableException;
-	
-	public abstract void removeFromExternalStore(Statement stmt) throws TripleStoreUnavailableException; 
-
-}

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

@@ -1,36 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao.jena;
-
-import java.util.HashSet;
-import java.util.List;
-
-import com.hp.hpl.jena.ontology.OntModel;
-
-import edu.cornell.mannlib.vitro.webapp.dao.FlagDao;
-import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
-
-public class FlagDaoJena extends JenaBaseDao implements FlagDao {
-
-    public FlagDaoJena(WebappDaoFactoryJena wadf) {
-        super(wadf);
-    }
-
-    public String convertNumericFlagToInsertString(int numeric, String column,
-            String table) {
-        // TODO Auto-generated method stub
-        return null;
-    }
-
-    public String convertNumericFlagToInsertString(int numeric,
-            String flagColumns) {
-        // TODO Auto-generated method stub
-        return null;
-    }
-
-    public String getFlagNames(String table, String field) {
-        // TODO Auto-generated method stub
-        return null;
-    }
-
-}

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

@@ -1,108 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao.jena;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.servlet.ServletContextEvent;
-import javax.servlet.ServletContextListener;
-
-//import org.openrdf.repository.Repository;
-//import org.openrdf.repository.RepositoryConnection;
-//import org.openrdf.repository.RepositoryResult;
-//import org.openrdf.repository.http.HTTPRepository;
-//import org.openrdf.repository.sail.SailRepository;
-//import org.openrdf.rio.RDFFormat;
-//import org.openrdf.sail.memory.MemoryStore;
-
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.rdf.listeners.StatementListener;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.rdf.model.StmtIterator;
-
-public class JenaToExternalTripleStoreSynchronizer extends StatementListener implements ServletContextListener {
-
-	private ExternalTripleStoreInterface extStore;
-	
-	public JenaToExternalTripleStoreSynchronizer(ExternalTripleStoreInterface extStore, Model additionsQueue, Model retractionsQueue) {
-		this.extStore = extStore;
-	}
-	
-	private Model additionsQueue = ModelFactory.createDefaultModel();
-	private Model retractionsQueue = ModelFactory.createDefaultModel();
-	
-	// TODO: add a statement filter to filter out password props
-	
-	@Override
-	public void addedStatement(Statement stmt) {
-		if (!retractionsQueue.contains(stmt)) {
-			additionsQueue.add(stmt);
-		} else {
-			retractionsQueue.remove(stmt);
-		}
-//		try {
-			StmtIterator sit = retractionsQueue.listStatements();
-			while (sit.hasNext()) {
-				Statement s = sit.nextStatement();
-				
-			}
-//		} catch (TripleStoreUnavailableException e) {
-//			// log something?
-//		} 
-	}
-	
-	@Override
-	public void removedStatement(Statement stmt) {
-		processUpdate(stmt, REMOVE);
-	}
-	
-	public void processUpdate(Statement stmt, boolean mode) {
-//		Repository myRepository = new HTTPRepository(sesameServer, repositoryID);
-//		myRepository.initialize();
-//		RepositoryConnection myConn = myRepository.getConnection();
-//		System.out.println(myConn.size()+" statements in remote Sesame");
-//		
-//		Repository tempRepository = new SailRepository(new MemoryStore());
-//		tempRepository.initialize();
-//		tempRepository.getConnection().add(retractionsFile, null, RDFFormat.N3);
-//		System.out.println(tempRepository.getConnection().size()+" statements to retract");
-//		RepositoryResult<Statement> retractStmts = tempRepository.getConnection().getStatements(null, null, null, false);
-//		System.out.println("Retracting statements from repository...");
-//		//myConn.remove(retractStmts);
-//		while (retractStmts.hasNext()) {
-//			Statement stmt = retractStmts.next();
-//			myConn.remove(stmt.getSubject(), stmt.getPredicate(), null);
-//		}
-	}
-	
-	public static final boolean ADD = true;
-	public static final boolean REMOVE = false;
-	
-	public static final int SESAME_SERVER_URI = 0;
-	public static final int SESAME_REPOSITORY_NAME = 1;
-	
-	public List<String[]> getSesameRepositories() {
-		List<String[]> sesameRepositoryList = new ArrayList<String[]>();
-		String[] testRepository = new String[2];
-		testRepository[SESAME_SERVER_URI] = "http://vivosesame.mannlib.cornell.edu:8080/openrdf-sesame";
-		testRepository[SESAME_REPOSITORY_NAME] = "syncTest";
-		sesameRepositoryList.add(testRepository);
-		return sesameRepositoryList;
-	}
-	
-	public void contextInitialized(ServletContextEvent sce) {
-		
-		OntModel jenaOntModel = (OntModel) sce.getServletContext().getAttribute(JenaBaseDao.JENA_ONT_MODEL_ATTRIBUTE_NAME);
-		jenaOntModel.getBaseModel().register(this);
-	}
-	
-	public void contextDestroyed(ServletContextEvent sce) {
-		
-	}
-	
-	
-	
-}

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

@@ -444,13 +444,6 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
             return entityWebappDao = new IndividualDaoJena(this);
     }
 
-    public FlagDao getFlagDao() {
-        if (flagDao != null)
-            return flagDao;
-        else
-            return flagDao = new FlagDaoJena(this);
-    }
-
     public KeywordIndividualRelationDao getKeys2EntsDao() {
         if (keys2EntsDao != null)
             return keys2EntsDao;

webapp/test/stubs/edu/cornell/mannlib/vitro/webapp/dao/WebappDaoFactoryStub.java

@@ -214,12 +214,6 @@ public class WebappDaoFactoryStub implements WebappDaoFactory {
 				"WebappDaoFactory.getLinktypeDao() not implemented.");
 	}
 
-	@Override
-	public FlagDao getFlagDao() {
-		throw new RuntimeException(
-				"WebappDaoFactory.getFlagDao() not implemented.");
-	}
-
     // TODO This goes away when the UserAccounts stuff is fully implemented -- jb
 	@Override
 	public UserDao getUserDao() {