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

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) ${year}, Cornell University
+Copyright (c) 2017, Cornell University
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without 

api/findbugs.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+mvn -Dfindbugs.maxHeap=4096 -Dfindbugs.timeout=6000000 compile findbugs:findbugs findbugs:gui
+

api/pom.xml

@@ -7,13 +7,13 @@
 
     <groupId>org.vivoweb</groupId>
     <artifactId>vitro-api</artifactId>
-    <version>1.10.0-SNAPSHOT</version>
+    <version>2.0.0-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <parent>
         <groupId>org.vivoweb</groupId>
         <artifactId>vitro-project</artifactId>
-        <version>1.10.0-SNAPSHOT</version>
+        <version>2.0.0-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -32,6 +32,23 @@
                     </execution>
                 </executions>
             </plugin>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>findbugs-maven-plugin</artifactId>
+                <version>3.0.5</version>
+                <configuration>
+                    <effort>Max</effort>
+                    <threshold>Low</threshold>
+                    <failOnError>true</failOnError>
+                    <plugins>
+                        <plugin>
+                            <groupId>com.h3xstream.findsecbugs</groupId>
+                            <artifactId>findsecbugs-plugin</artifactId>
+                            <version>LATEST</version> <!-- Auto-update to the latest stable -->
+                        </plugin>
+                    </plugins>
+                </configuration>
+            </plugin>
         </plugins>
     </build>
 
@@ -39,13 +56,13 @@
         <dependency>
             <groupId>org.vivoweb</groupId>
             <artifactId>vitro-dependencies</artifactId>
-            <version>1.10.0-SNAPSHOT</version>
+            <version>2.0.0-SNAPSHOT</version>
             <type>pom</type>
         </dependency>
         <dependency>
             <groupId>javax.servlet</groupId>
-            <artifactId>servlet-api</artifactId>
+            <artifactId>javax.servlet-api</artifactId>
-            <version>2.5</version>
+            <version>3.1.0</version>
             <scope>provided</scope>
         </dependency>
         <dependency>
@@ -64,7 +81,7 @@
         <dependency>
             <groupId>org.easymock</groupId>
             <artifactId>easymock</artifactId>
-            <version>3.2</version>
+            <version>3.5</version>
             <scope>test</scope>
         </dependency>
         <dependency>

api/src/main/java/edu/cornell/mannlib/semservices/util/XMLUtils.java

@@ -134,10 +134,7 @@ public class XMLUtils {
        Transformer transformer = null;
       try {
          transformer = TransformerFactory.newInstance().newTransformer();
-      } catch (TransformerConfigurationException e) {
+      } catch (TransformerConfigurationException | TransformerFactoryConfigurationError e) {
-         // TODO Auto-generated catch block
-         e.printStackTrace();
-      } catch (TransformerFactoryConfigurationError e) {
          // TODO Auto-generated catch block
          e.printStackTrace();
       }
@@ -164,10 +161,7 @@ public class XMLUtils {
        Transformer transformer = null;
       try {
          transformer = TransformerFactory.newInstance().newTransformer();
-      } catch (TransformerConfigurationException e) {
+      } catch (TransformerConfigurationException | TransformerFactoryConfigurationError e) {
-         // TODO Auto-generated catch block
-         e.printStackTrace();
-      } catch (TransformerFactoryConfigurationError e) {
          // TODO Auto-generated catch block
          e.printStackTrace();
       }

api/src/main/java/edu/cornell/mannlib/vedit/beans/DynamicField.java

@@ -3,7 +3,6 @@
 package edu.cornell.mannlib.vedit.beans;
 
 import java.util.List;
-import java.util.ArrayList;
 import java.util.HashMap;
 
 public class DynamicField {

api/src/main/java/edu/cornell/mannlib/vedit/controller/BaseEditController.java

@@ -32,7 +32,6 @@ import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
-import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess.ReasoningOption;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 
 public class BaseEditController extends VitroHttpServlet {
@@ -137,10 +136,8 @@ public class BaseEditController extends VitroHttpServlet {
             String value = "";
             if (key.equals(MULTIPLEXED_PARAMETER_NAME)) {
                 String multiplexedStr = request.getParameterValues(key)[0];
-                Map paramMap = FormUtils.beanParamMapFromString(multiplexedStr);
+                Map<String, String> paramMap = FormUtils.beanParamMapFromString(multiplexedStr);
-                Iterator paramIt = paramMap.keySet().iterator();
+                for (String param : paramMap.keySet()) {
-                while (paramIt.hasNext()) {
-                    String param = (String) paramIt.next();
                     String demultiplexedValue = (String) paramMap.get(param);
                     FormUtils.beanSet(bean, param, demultiplexedValue);
                 }
@@ -179,19 +176,16 @@ public class BaseEditController extends VitroHttpServlet {
 
        List<String> bodyVal = new ArrayList<String>();
        List<Option> options = new ArrayList<Option>();
-       Iterator<Option> itr = optionList.iterator();
+        for (Option option : optionList) {
-        while(itr.hasNext()){
+            hashMap.put(option.getBody(), option);
-            Option option = itr.next();
+            bodyVal.add(option.getBody());
-            hashMap.put(option.getBody(),option);
-           bodyVal.add(option.getBody());
         }
         
                 
-       Collections.sort(bodyVal, new ListComparator(vreq.getCollator()));
+       bodyVal.sort(new ListComparator(vreq.getCollator()));
-       ListIterator<String> itrStr = bodyVal.listIterator();
+        for (String aBodyVal : bodyVal) {
-       while(itrStr.hasNext()){
+            options.add(hashMap.get(aBodyVal));
-           options.add(hashMap.get(itrStr.next()));
+        }
-       }
        return options;
    }
     

api/src/main/java/edu/cornell/mannlib/vedit/controller/EditFrontController.java

@@ -3,6 +3,8 @@
 package edu.cornell.mannlib.vedit.controller;
 
 import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
+
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
@@ -21,6 +23,7 @@ import java.io.IOException;
  * @author bjl23
  *
  */
+@WebServlet(name = "EditFrontController", urlPatterns = {"/editForm"} )
 public class EditFrontController extends VitroHttpServlet {
     private static final Log log = LogFactory.getLog(EditFrontController.class.getName());
     private static final String CONTROLLER_PKG = "edu.cornell.mannlib.vitro.webapp.controller.edit";

api/src/main/java/edu/cornell/mannlib/vedit/controller/OperationController.java

@@ -11,6 +11,7 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -27,6 +28,7 @@ import edu.cornell.mannlib.vedit.util.OperationUtils;
 import edu.cornell.mannlib.vedit.validator.ValidationObject;
 import edu.cornell.mannlib.vedit.validator.Validator;
 
+@WebServlet(name = "OperationController", urlPatterns = {"/doEdit"} )
 public class OperationController extends BaseEditController {
 	
     private static final Log log = LogFactory.getLog(OperationController.class.getName());
@@ -127,27 +129,31 @@ public class OperationController extends BaseEditController {
             notifyChangeListeners(epo, action);
 
             /* send the user somewhere */
-            if (action.equals("insert")){
+            switch (action) {
-                // Object[] args = new Object[1];
+                case "insert":
-                // args[0] = result;
+                    // Object[] args = new Object[1];
-                // epo.setNewBean(epo.getGetMethod().invoke(facade,args));
+                    // args[0] = result;
-                PageForwarder pipf = epo.getPostInsertPageForwarder();
+                    // epo.setNewBean(epo.getGetMethod().invoke(facade,args));
-                if (pipf != null){
+                    PageForwarder pipf = epo.getPostInsertPageForwarder();
-                    pipf.doForward(request,response,epo);
+                    if (pipf != null) {
-                    return;
+                        pipf.doForward(request, response, epo);
-                }
+                        return;
-            } else if (action.equals("update")){
+                    }
-                PageForwarder pupf = epo.getPostUpdatePageForwarder();
+                    break;
-                if (pupf != null) {
+                case "update":
-                    pupf.doForward(request,response,epo);
+                    PageForwarder pupf = epo.getPostUpdatePageForwarder();
-                    return;
+                    if (pupf != null) {
-                }
+                        pupf.doForward(request, response, epo);
-            } else if (action.equals("delete")){
+                        return;
-                PageForwarder pdpf = epo.getPostDeletePageForwarder();
+                    }
-                if (pdpf != null) {
+                    break;
-                    pdpf.doForward(request,response,epo);
+                case "delete":
-                    return;
+                    PageForwarder pdpf = epo.getPostDeletePageForwarder();
-                }
+                    if (pdpf != null) {
+                        pdpf.doForward(request, response, epo);
+                        return;
+                    }
+                    break;
             }
 
             //if no page forwarder was set, just go back to referring page:
@@ -168,7 +174,6 @@ public class OperationController extends BaseEditController {
        
             try {
             	retry(request, response, epo);
-            	return;
             } catch (IOException ioe) {
             	log.error(this.getClass().getName() + " IOError on redirect: ", ioe);
             }
@@ -196,17 +201,12 @@ public class OperationController extends BaseEditController {
         } else {
         	response.sendRedirect(getDefaultLandingPage(request));
         }
-        return;
     }
     
     private void runPreprocessors(EditProcessObject epo, Object newObj) {
     	if (epo.getPreProcessorList() != null && epo.getPreProcessorList().size()>0) {
-            Iterator preIt = epo.getPreProcessorList().iterator();
+            for (EditPreProcessor epp : epo.getPreProcessorList()) {
-            while (preIt.hasNext()) {
+                epp.process(newObj, epo);
-                try {
-                	EditPreProcessor epp = (EditPreProcessor) preIt.next();
-                	epp.process(newObj, epo);
-                } catch (ClassCastException e) {}
             }
         }
     }
@@ -254,14 +254,14 @@ public class OperationController extends BaseEditController {
                     List validatorList = (List) epo.getValidatorMap().get(currParam);
                     if (validatorList != null) {
                         Iterator valIt = validatorList.iterator();
-                        String errMsg = "";
+                        StringBuilder errMsg = new StringBuilder();
                         while (valIt.hasNext()){
                             Validator val = (Validator)valIt.next();
                             ValidationObject vo = val.validate(currValue);
                             if (!vo.getValid()){
                                 valid = false;
                                 fieldValid = false;
-                                errMsg += vo.getMessage() + " ";
+                                errMsg.append(vo.getMessage()).append(" ");
                                 epo.getBadValueMap().put(currParam,currValue);
                             } else {
                                 try {
@@ -271,7 +271,7 @@ public class OperationController extends BaseEditController {
                             }
                         }
                         if (errMsg.length()>0) {
-                            epo.getErrMsgMap().put(currParam,errMsg);
+                            epo.getErrMsgMap().put(currParam, errMsg.toString());
                             log.info("doPost() putting error message "+errMsg+" for "+currParam);
                         }
                     }
@@ -325,15 +325,18 @@ public class OperationController extends BaseEditController {
     private void notifyChangeListeners(EditProcessObject epo, String action) {
     	List<ChangeListener> changeListeners = epo.getChangeListenerList();
         if (changeListeners != null){
-            Iterator<ChangeListener> changeIt = changeListeners.iterator();
+            for (ChangeListener cl : changeListeners) {
-            while (changeIt.hasNext()) {
+                switch (action) {
-                ChangeListener cl = changeIt.next();
+                    case "insert":
-                if (action.equals("insert"))
+                        cl.doInserted(epo.getNewBean(), epo);
-                    cl.doInserted(epo.getNewBean(),epo);
+                        break;
-                else if (action.equals("update"))
+                    case "update":
-                    cl.doUpdated(epo.getOriginalBean(),epo.getNewBean(),epo);
+                        cl.doUpdated(epo.getOriginalBean(), epo.getNewBean(), epo);
-                else if (action.equals("delete"))
+                        break;
-                    cl.doDeleted(epo.getOriginalBean(),epo);
+                    case "delete":
+                        cl.doDeleted(epo.getOriginalBean(), epo);
+                        break;
+                }
             }
         }
     }
@@ -497,8 +500,6 @@ public class OperationController extends BaseEditController {
                 } catch (InvocationTargetException f) {
                     log.error(f.getTargetException().getMessage());
                 }
-            } catch (NoSuchMethodException e) {
-                //log.error("doPost() could not find setId() method for "+partialClassName);
             } catch (Exception f) {
                 //log.error("doPost() could not set id of new bean.");
             }

api/src/main/java/edu/cornell/mannlib/vedit/forwarder/impl/UrlForwarder.java

@@ -4,11 +4,8 @@ package edu.cornell.mannlib.vedit.forwarder.impl;
 
 import java.io.IOException;
 
-import java.net.URLEncoder;
-
 import edu.cornell.mannlib.vedit.forwarder.PageForwarder;
 import edu.cornell.mannlib.vedit.beans.EditProcessObject;
-import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;

api/src/main/java/edu/cornell/mannlib/vedit/tags/DynamicFieldsTag.java

@@ -8,7 +8,6 @@ import java.util.List;
 import java.util.Iterator;
 
 import java.io.File;
-import java.io.BufferedOutputStream;
 import java.io.InputStream;
 import java.io.FileInputStream;
 import java.io.BufferedInputStream;
@@ -16,18 +15,14 @@ import java.io.InputStreamReader;
 import java.io.BufferedReader;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
 
 import javax.servlet.jsp.JspException;
-import javax.servlet.jsp.tagext.TagSupport;
 import javax.servlet.jsp.JspWriter;
-import javax.servlet.ServletException;
+
 import edu.cornell.mannlib.vedit.beans.FormObject;
 import edu.cornell.mannlib.vedit.beans.DynamicField;
 import edu.cornell.mannlib.vedit.beans.DynamicFieldRow;
 import org.apache.commons.codec.binary.Base64;
-import org.apache.commons.lang3.StringEscapeUtils;
 import edu.cornell.mannlib.vedit.tags.EditTag;
 
 public class DynamicFieldsTag extends EditTag {
@@ -63,7 +58,7 @@ public class DynamicFieldsTag extends EditTag {
             int templateStart = -1;
             int postStart = -1;
 
-            InputStream fis = new FileInputStream (pageContext.getServletContext().getRealPath(new String())+PATH_SEP+MARKUP_FILE_PATH+usePage);
+            InputStream fis = new FileInputStream (pageContext.getServletContext().getRealPath("")+PATH_SEP+MARKUP_FILE_PATH+usePage);
             InputStream bis = new BufferedInputStream(fis);
             BufferedReader in = new BufferedReader(new InputStreamReader(bis));
             List<String> lines = new ArrayList<String>();
@@ -83,9 +78,9 @@ public class DynamicFieldsTag extends EditTag {
             }
             in.close();
 
-            StringBuffer preMarkupB = new StringBuffer();
+            StringBuilder preMarkupB = new StringBuilder();
-            StringBuffer postMarkupB = new StringBuffer();
+            StringBuilder postMarkupB = new StringBuilder();
-            StringBuffer templateMarkupB = new StringBuffer();
+            StringBuilder templateMarkupB = new StringBuilder();
 
             if (templateStart>preStart  && preStart>0) {
                 for (int i=preStart+1; i<templateStart; i++) {
@@ -119,16 +114,16 @@ public class DynamicFieldsTag extends EditTag {
             postMarkup = postMarkupB.toString();
 
         } catch (FileNotFoundException e) {
-            System.out.println("DynamicFieldsTag could not find markup file at "+pageContext.getServletContext().getRealPath(new String())+"\\"+MARKUP_FILE_PATH+usePage);
+            System.out.println("DynamicFieldsTag could not find markup file at "+pageContext.getServletContext().getRealPath("")+"\\"+MARKUP_FILE_PATH+usePage);
         } catch (IOException ioe) {
-            System.out.println("DynamicFieldsTag encountered IOException reading "+pageContext.getServletContext().getRealPath(new String())+"\\"+MARKUP_FILE_PATH+usePage);
+            System.out.println("DynamicFieldsTag encountered IOException reading "+pageContext.getServletContext().getRealPath("")+"\\"+MARKUP_FILE_PATH+usePage);
         }
 
     }
 
     public String strReplace(String input, String pattern, String replacement) {
         String[] piece = input.split(pattern);
-        StringBuffer output = new StringBuffer();
+        StringBuilder output = new StringBuilder();
         for (int i=0; i<piece.length; i++) {
             output.append(piece[i]);
             if (i<piece.length-1)
@@ -149,7 +144,7 @@ public class DynamicFieldsTag extends EditTag {
                 int i = 9899;
                 while (dynIt.hasNext()) {
                     DynamicField dynf = dynIt.next();
-                    StringBuffer genTaName = new StringBuffer().append("_").append(dynf.getTable()).append("_");
+                    StringBuilder genTaName = new StringBuilder().append("_").append(dynf.getTable()).append("_");
                     genTaName.append("-1").append("_");
                     Iterator pparamIt = dynf.getRowTemplate().getParameterMap().keySet().iterator();
                     while(pparamIt.hasNext()) {
@@ -160,34 +155,33 @@ public class DynamicFieldsTag extends EditTag {
                     }
 
 
-                    String preWithVars = new String(preMarkup);
+                    String preWithVars = preMarkup;
                     preWithVars = strReplace(preWithVars,type+"NN",Integer.toString(i));
                     preWithVars = strReplace(preWithVars,"\\$genTaName",genTaName.toString());
                     preWithVars = strReplace(preWithVars,"\\$fieldName",dynf.getName());
 
                     out.print(preWithVars);
 
-                    Iterator<DynamicFieldRow> rowIt = dynf.getRowList().iterator();
+                    for (DynamicFieldRow dynamicFieldRow : dynf.getRowList()) {
-                     while (rowIt.hasNext()) {
                         ++i;
-                        DynamicFieldRow row = rowIt.next();
+                        DynamicFieldRow row = dynamicFieldRow;
-                        if (row.getValue()==null)
+                        if (row.getValue() == null)
                             row.setValue("");
-                        if (row.getValue().length()>0) {
+                        if (row.getValue().length() > 0) {
-                            StringBuffer taName = new StringBuffer().append("_").append(dynf.getTable()).append("_");
+                            StringBuilder taName = new StringBuilder().append("_").append(dynf.getTable()).append("_");
                             taName.append(row.getId()).append("_");
                             Iterator paramIt = row.getParameterMap().keySet().iterator();
-                            while(paramIt.hasNext()) {
+                            while (paramIt.hasNext()) {
                                 String key = (String) paramIt.next();
                                 String value = (String) row.getParameterMap().get(key);
                                 byte[] valueInBase64 = Base64.encodeBase64(value.getBytes());
                                 taName.append(key).append(":").append(new String(valueInBase64)).append(";");
                             }
-                            if (row.getValue().length()>0) {
+                            if (row.getValue().length() > 0) {
-                                String templateWithVars = new String(templateMarkup);
+                                String templateWithVars = templateMarkup;
-                                templateWithVars = strReplace(templateWithVars,type+"NN",Integer.toString(i));
+                                templateWithVars = strReplace(templateWithVars, type + "NN", Integer.toString(i));
-                                templateWithVars = strReplace(templateWithVars,"\\$taName",taName.toString());
+                                templateWithVars = strReplace(templateWithVars, "\\$taName", taName.toString());
-                                templateWithVars = strReplace(templateWithVars,"\\$\\$",row.getValue());
+                                templateWithVars = strReplace(templateWithVars, "\\$\\$", row.getValue());
                                 out.print(templateWithVars);
                             }
                         }
@@ -199,14 +193,14 @@ public class DynamicFieldsTag extends EditTag {
                 // output the row template for the javascript to clone
 
                 out.println("<!-- row template inserted by DynamicFieldsTag  -->");
-                String hiddenTemplatePreMarkup = new String(preMarkup);
+                String hiddenTemplatePreMarkup = preMarkup;
                 // bit of a hack to hide the template from the user:
                 hiddenTemplatePreMarkup = strReplace(hiddenTemplatePreMarkup,"display\\:none\\;","");
                 hiddenTemplatePreMarkup = strReplace(hiddenTemplatePreMarkup,"display\\:block\\;","");
                 hiddenTemplatePreMarkup = strReplace(hiddenTemplatePreMarkup,"display\\:inline\\;","");
                 hiddenTemplatePreMarkup = strReplace(hiddenTemplatePreMarkup,"style\\=\\\"","style=\"display:none;");
                 out.print(hiddenTemplatePreMarkup);
-                String hiddenTemplateTemplateMarkup = new String(templateMarkup);
+                String hiddenTemplateTemplateMarkup = templateMarkup;
                 hiddenTemplateTemplateMarkup = strReplace(hiddenTemplateTemplateMarkup, "\\$\\$", "");
                 out.print(hiddenTemplateTemplateMarkup);
                 out.print(postMarkup);

api/src/main/java/edu/cornell/mannlib/vedit/tags/EditTag.java

@@ -5,13 +5,10 @@ package edu.cornell.mannlib.vedit.tags;
 import java.util.HashMap;
 
 import javax.servlet.jsp.JspException;
-import javax.servlet.jsp.PageContext;
 import javax.servlet.jsp.tagext.TagSupport;
-import javax.servlet.jsp.JspWriter;
 
 import edu.cornell.mannlib.vedit.beans.EditProcessObject;
 import edu.cornell.mannlib.vedit.beans.FormObject;
-import org.apache.commons.lang3.StringEscapeUtils;
 
 public class EditTag extends TagSupport {
     private String name = null;

api/src/main/java/edu/cornell/mannlib/vedit/tags/ErrorTag.java

@@ -3,9 +3,8 @@
 package edu.cornell.mannlib.vedit.tags;
 
 import javax.servlet.jsp.JspException;
-import javax.servlet.jsp.tagext.TagSupport;
 import javax.servlet.jsp.JspWriter;
-import edu.cornell.mannlib.vedit.beans.FormObject;
+
 import edu.cornell.mannlib.vedit.tags.EditTag;
 import org.apache.commons.lang3.StringEscapeUtils;
 

api/src/main/java/edu/cornell/mannlib/vedit/tags/OptionTag.java

@@ -2,8 +2,8 @@
 
 package edu.cornell.mannlib.vedit.tags;
 
-import org.apache.commons.collections.map.ListOrderedMap;
+import org.apache.commons.collections4.map.ListOrderedMap;
-import org.apache.commons.collections.OrderedMapIterator;
+import org.apache.commons.collections4.OrderedMapIterator;
 import java.util.List;
 import java.util.Iterator;
 import java.io.IOException;
@@ -51,7 +51,7 @@ public class OptionTag extends EditTag {
             } catch (ClassCastException e){
                 // maybe it's a ListOrderedMap of optgroups
                 optGroups = (ListOrderedMap) getFormObject().getOptionLists().get(name);
-                OrderedMapIterator ogKey = optGroups.orderedMapIterator();
+                OrderedMapIterator ogKey = optGroups.mapIterator();
                 while (ogKey.hasNext()) {
                     String optGroupName = (String) ogKey.next();
                     out.println("<optgroup label=\""+StringEscapeUtils.ESCAPE_HTML4.translate(optGroupName)+"\">");

api/src/main/java/edu/cornell/mannlib/vedit/tags/ValueTag.java

@@ -5,7 +5,6 @@ package edu.cornell.mannlib.vedit.tags;
 import java.util.HashMap;
 
 import javax.servlet.jsp.JspException;
-import javax.servlet.jsp.tagext.TagSupport;
 import javax.servlet.jsp.JspWriter;
 import edu.cornell.mannlib.vedit.beans.FormObject;
 import org.apache.commons.lang3.StringEscapeUtils;

api/src/main/java/edu/cornell/mannlib/vedit/util/FormUtils.java

@@ -73,43 +73,38 @@ public class FormUtils {
 
         Method[] meths = beanClass.getMethods();
 
-        for (int i=0; i<meths.length; i++) {
+        for (Method currMeth : meths) {
 
-            if (meths[i].getName().indexOf("set") == 0) {
+            if (currMeth.getName().indexOf("set") == 0) {
 
                 // we have a setter method
-                Method currMeth = meths[i];
                 Class[] currMethParamTypes = currMeth.getParameterTypes();
                 Class currMethType = currMethParamTypes[0];
-                
+
                 if (SUPPORTED_TYPE_LIST.contains(currMethType)) {
-                	//we only want people directly to type in ints, strings, and dates
+                    //we only want people directly to type in ints, strings, and dates
-                	//of course, most of the ints are probably foreign keys anyway...
+                    //of course, most of the ints are probably foreign keys anyway...
 
                     String elementName = currMeth.getName().substring(
-                    		3,currMeth.getName().length());
+                            3, currMeth.getName().length());
 
                     //see if there's something in the bean using
                     //the related getter method
-
-                    Class[] paramClass = new Class[1];
-                    paramClass[0] = currMethType;
                     try {
                         Method getter = beanClass.getMethod(
-                        		"get" + elementName, (Class[]) null);
+                                "get" + elementName, (Class[]) null);
                         Object existingData = null;
                         try {
                             existingData = getter.invoke(bean, (Object[]) null);
                         } catch (Exception e) {
-                            log.error ("Exception invoking getter method");
+                            log.error("Exception invoking getter method");
                         }
                         String value = "";
-                        if (existingData != null){
+                        if (existingData != null) {
-                            if (existingData instanceof String){
+                            if (existingData instanceof String) {
                                 value += existingData;
-                            }
+                            } else if (!(existingData instanceof Integer
-                            else if (!(existingData instanceof Integer 
+                                    && (Integer) existingData < 0)) {
-                            		&& (Integer)existingData < 0)) {
                                 value += existingData.toString();
                             }
                         }
@@ -226,7 +221,7 @@ public class FormUtils {
             Option sOpt = new Option();
             sOpt.setValue(selectedValue);
             if (selectedBody == null || selectedBody.length() == 0)
-                sOpt.setBody(selectedValue.toString());
+                sOpt.setBody(selectedValue);
             else
                 sOpt.setBody(selectedBody);
             sOpt.setSelected(true);
@@ -272,11 +267,7 @@ public class FormUtils {
         	}
 		}
 		
-		Collections.sort(options, new Comparator<Option>() {
+		options.sort((o1, o2) -> o1.getBody().compareTo(o2.getBody()));
-			@Override
-			public int compare(Option o1, Option o2) {
-				return o1.getBody().compareTo(o2.getBody());
-			}});
 		
 		return options;
 	}
@@ -372,12 +363,12 @@ public class FormUtils {
      * key:value;key2:value2;key3:value, and puts the keys and values in a Map
      * @param params Parameters
      */
-    public static Map beanParamMapFromString(String params) {
+    public static Map<String, String> beanParamMapFromString(String params) {
         String[] param = params.split(";");
-        Map beanParamMap = new HashMap();
+        Map<String, String> beanParamMap = new HashMap<String, String>();
-        for (int i=0; i<param.length; i++) {
+        for (String aParam : param) {
-            String[] p = param[i].split(":");
+            String[] p = aParam.split(":");
-            beanParamMap.put(p[0],new String(Base64.decodeBase64(p[1].getBytes())));
+            beanParamMap.put(p[0], new String(Base64.decodeBase64(p[1].getBytes())));
         }
         return beanParamMap;
     }

api/src/main/java/edu/cornell/mannlib/vedit/util/OperationUtils.java

@@ -46,19 +46,21 @@ public class OperationUtils {
 
 			}
 		}
-		Object[] arglist = new Object[1];
+		if (setterMethod != null) {
-		if (isInt)
+			Object[] arglist = new Object[1];
-			arglist[0] = Integer.decode(value);
+			if (isInt)
-		else if (isBoolean)
+				arglist[0] = Integer.decode(value);
-			arglist[0] = (value.equalsIgnoreCase("TRUE"));
+			else if (isBoolean)
-		else
+				arglist[0] = (value.equalsIgnoreCase("TRUE"));
-			arglist[0] = value;
+			else
-		try {
+				arglist[0] = value;
-			setterMethod.invoke(newObj, arglist);
+			try {
-		} catch (Exception e) {
+				setterMethod.invoke(newObj, arglist);
-			log.error("Couldn't invoke method");
+			} catch (Exception e) {
-			log.error(e.getMessage());
+				log.error("Couldn't invoke method");
-			log.error(field + " " + arglist[0]);
+				log.error(e.getMessage());
+				log.error(field + " " + arglist[0]);
+			}
 		}
 	}
 

api/src/main/java/edu/cornell/mannlib/vedit/util/Stemmer.java

@@ -71,7 +71,7 @@ class Stemmer
    public void add(char ch)
    {  if (i == b.length)
       {  char[] new_b = new char[i+INC];
-         for (int c = 0; c < i; c++) new_b[c] = b[c];
+          System.arraycopy(b, 0, new_b, 0, i);
          b = new_b;
       }
       b[i++] = ch;
@@ -86,7 +86,7 @@ class Stemmer
    public void add(char[] w, int wLen)
    {  if (i+wLen >= b.length)
       {  char[] new_b = new char[i+wLen+INC];
-         for (int c = 0; c < i; c++) new_b[c] = b[c];
+          System.arraycopy(b, 0, new_b, 0, i);
          b = new_b;
       }
       for (int c = 0; c < wLen; c++) b[i++] = w[c];
@@ -116,7 +116,7 @@ class Stemmer
    private final boolean cons(int i)
    {  switch (b[i])
       {  case 'a': case 'e': case 'i': case 'o': case 'u': return false;
-         case 'y': return (i==0) ? true : !cons(i-1);
+         case 'y': return (i == 0) || !cons(i - 1);
          default: return true;
       }
    }
@@ -368,7 +368,7 @@ class Stemmer
 
     public static String StemString( String inputStr, int maxLength )
     {
-        String outputStr="";
+        StringBuilder outputStr= new StringBuilder();
 
         int previousCh=0;
         char[] w = new char[maxLength];
@@ -396,19 +396,19 @@ class Stemmer
                             {
                             String u;
                             u = s.toString();
-                            outputStr += u;
+                            outputStr.append(u);
                             if ( ch == '-' ) { // replace - with space
-                                outputStr += " ";
+                                outputStr.append(" ");
                             } else if ( ch == '.' ) {
                                 if ( Character.isDigit( (char) previousCh )) {
-                                    outputStr += ".";
+                                    outputStr.append(".");
                                 } else {
-                                    outputStr += " ";
+                                    outputStr.append(" ");
                                     //previousCh = 32; // set to whitespace; extra spaces should be filtered out on next pass
                                 }
                             } else {
                                 Character Ch = new Character((char) ch);
-                                outputStr += Ch.toString();
+                                outputStr.append(Ch.toString());
                             }
                             stemmerInputBufferIndex=0; // to avoid repeats after )
                             }
@@ -422,7 +422,7 @@ class Stemmer
                 if ( !Character.isWhitespace((char) previousCh ) ) {
                     if ( previousCh != '.' ) {
                         Character Ch = new Character((char) ch);
-                        outputStr += Ch.toString();
+                        outputStr.append(Ch.toString());
                     }
                 }
             } else if ( ch == '(' ) { // open paren; copy all characters until close paren
@@ -449,21 +449,21 @@ class Stemmer
                 stemmerInputBufferIndex=0;
             } else if ( ch == ')' ) { // when is last character of input string
                 Character Ch = new Character((char) ch);
-                outputStr += Ch.toString();
+                outputStr.append(Ch.toString());
                 log.trace( Ch.toString() );
                 log.trace("found close paren at position: " + inputArrayIndex + " of input term " + inputStr );
             } else if ( ch == '-' ) { // replace - with space
-                outputStr += " ";
+                outputStr.append(" ");
             } else if ( ch == '.' ) {
                 if ( Character.isDigit( (char) previousCh )) {
-                    outputStr += ".";
+                    outputStr.append(".");
                 } else {
-                    outputStr += " ";
+                    outputStr.append(" ");
                     //previousCh = 32; // set to whitespace; extra spaces should be filtered out on next pass
                 }
             } else {
                 Character Ch = new Character((char) ch);
-                outputStr += Ch.toString();
+                outputStr.append(Ch.toString());
             }
             previousCh = ch;
             if (ch < 0) break;
@@ -477,10 +477,10 @@ class Stemmer
 
             String u;
             u = s.toString();
-            outputStr += u;
+            outputStr.append(u);
         }
 
-        return outputStr == null ? ( outputStr.equals("") ? null : outputStr.trim() ) : outputStr.trim();
+        return outputStr.length() == 0 ? null : outputStr.toString().trim();
     }
 
 /*
@@ -549,8 +549,8 @@ class Stemmer
    {
       char[] w = new char[501];
       Stemmer s = new Stemmer();
-      for (int i = 0; i < args.length; i++) {
+       for (String arg : args) {
-    	  System.out.println( StemString( args[i], 100 ));
+           System.out.println(StemString(arg, 100));
-     }
+       }
    }
 }

api/src/main/java/edu/cornell/mannlib/vedit/validator/impl/EnumValuesValidator.java

@@ -3,6 +3,8 @@
 package edu.cornell.mannlib.vedit.validator.impl;
 
 import edu.cornell.mannlib.vedit.validator.*;
+
+import java.util.Collections;
 import java.util.HashSet;
 import java.util.Iterator;
 
@@ -17,17 +19,17 @@ public class EnumValuesValidator implements Validator {
         } else {
             vo.setValid(false);
             if (legalValues.size()<7){
-                String msgString = "Please enter one of ";
+                StringBuilder msgString = new StringBuilder("Please enter one of ");
                 Iterator valuesIt = legalValues.iterator();
                 while (valuesIt.hasNext()) {
                     String legalValue = (String) valuesIt.next();
-                    msgString += "'"+legalValue+"'";
+                    msgString.append("'").append(legalValue).append("'");
                     if (valuesIt.hasNext())
-                        msgString += ", ";
+                        msgString.append(", ");
                     else
-                        msgString += ".";
+                        msgString.append(".");
                 }
-                vo.setMessage(msgString);
+                vo.setMessage(msgString.toString());
             }
             else {
                 vo.setMessage("Please enter a legal value.");
@@ -38,7 +40,6 @@ public class EnumValuesValidator implements Validator {
     }
 
     public EnumValuesValidator (String[] legalValues){
-        for (int i=0; i<legalValues.length; i++)
+        Collections.addAll(this.legalValues, legalValues);
-            this.legalValues.add(legalValues[i]);
     }
 }

api/src/main/java/edu/cornell/mannlib/vedit/validator/impl/UrlValidator.java

@@ -24,10 +24,10 @@ public class UrlValidator implements Validator {
         IRIFactory factory = IRIFactory.jenaImplementation();
         IRI iri = factory.create((String) obj);
         if (iri.hasViolation(false) ) {
-            String errorStr = "";
+            StringBuilder errorStr = new StringBuilder();
             Iterator<Violation> violIt = iri.violations(false);
             while(violIt.hasNext()) {
-                errorStr += violIt.next().getShortMessage() + "  ";
+                errorStr.append(violIt.next().getShortMessage()).append("  ");
             }
             vo.setValid(false);
             vo.setMessage("Please enter a valid URL.  " + errorStr);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/application/ApplicationImpl.java

@@ -171,14 +171,17 @@ public class ApplicationImpl implements Application {
 			ss.info(this, "Started the ContentTripleSource: "
 					+ contentTripleSource);
 
-			ConfigurationTripleSource configurationTripleSource = app
+			// Ensure that we haven't failed setting up the content triple store before continuing
-					.getConfigurationTripleSource();
+			if (!ss.isStartupAborted()) {
-			configurationTripleSource.startup(app, css);
+				ConfigurationTripleSource configurationTripleSource = app
-			ss.info(this, "Started the ConfigurationTripleSource: "
+						.getConfigurationTripleSource();
-					+ configurationTripleSource);
+				configurationTripleSource.startup(app, css);
+				ss.info(this, "Started the ConfigurationTripleSource: "
+						+ configurationTripleSource);
 
-			configureJena();
+				configureJena();
-			prepareCombinedTripleSource(app, ctx);
+				prepareCombinedTripleSource(app, ctx);
+			}
 		}
 
 		private void configureJena() {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/application/VitroHomeDirectory.java

@@ -159,8 +159,8 @@ public class VitroHomeDirectory {
 						VHD_BUILD_PROPERTY);
 				throw new IllegalStateException(message);
 			} else if (foundLocations.size() > 1) {
-				String message = String.format("Found multiple values for the "
+				String message = "Found multiple values for the "
-						+ "Vitro home directory: " + foundLocations);
+						+ "Vitro home directory: " + foundLocations;
 				log.warn(message);
 			}
 		}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/auth/policy/bean/PropertyRestrictionBeanImpl.java

@@ -145,11 +145,8 @@ public class PropertyRestrictionBeanImpl extends PropertyRestrictionBean {
 		if (resourceUri == null || userRole == null) {
 			return false;
 		}
-		if (prohibitedNamespaces.contains(namespace(resourceUri))
+		return !prohibitedNamespaces.contains(namespace(resourceUri))
-				&& !permittedExceptions.contains(resourceUri)) {
+				|| permittedExceptions.contains(resourceUri);
-			return false;
-		}
-		return true;
 	}
 
 	@Override
@@ -241,9 +238,7 @@ public class PropertyRestrictionBeanImpl extends PropertyRestrictionBean {
 
 		StringBuilder buffer = new StringBuilder();
 		for (FullPropertyKey key : keys) {
-			buffer.append(key + " " + thresholdMap.get(key).getLevel(DISPLAY)
+			buffer.append(key).append(" ").append(thresholdMap.get(key).getLevel(DISPLAY)).append(" ").append(thresholdMap.get(key).getLevel(MODIFY)).append(" ").append(thresholdMap.get(key).getLevel(PUBLISH)).append("\n");
-					+ " " + thresholdMap.get(key).getLevel(MODIFY) + " "
-					+ thresholdMap.get(key).getLevel(PUBLISH) + "\n");
 		}
 		return buffer.toString();
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/publish/PublishObjectPropertyStatement.java

@@ -6,7 +6,6 @@ import static edu.cornell.mannlib.vitro.webapp.auth.requestedAction.RequestedAct
 
 import org.apache.jena.ontology.OntModel;
 
-import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.RequestedAction;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AbstractObjectPropertyStatementAction;
 import edu.cornell.mannlib.vitro.webapp.beans.Property;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/ApplicationBean.java

@@ -7,8 +7,6 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
-import javax.servlet.ServletContext;
-
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/Classes2Classes.java

@@ -22,18 +22,18 @@ public class Classes2Classes {
     public void setSuperclassURI(String in){ superclassURI=in;}
 
     public String getSuperclassNamespace(){ return superclassNamespace; }
-    public void setSuperclassNamespace(){ this.superclassNamespace=superclassNamespace;}
+    public void setSuperclassNamespace(String superclassNamespace){ this.superclassNamespace=superclassNamespace;}
 
     public String getSuperclassLocalName(){ return superclassLocalName; }
-    public void setSuperclassLocalName(){ this.superclassLocalName=superclassLocalName;}
+    public void setSuperclassLocalName(String superclassLocalName){ this.superclassLocalName=superclassLocalName;}
 
     public String getSubclassURI(){ return subclassURI;}
     public void setSubclassURI(String in){ subclassURI=in;}
 
     public String getSubclassNamespace(){ return subclassNamespace; }
-    public void setSubclassNamespace(){ this.subclassNamespace=subclassNamespace;}
+    public void setSubclassNamespace(String subclassNamespace){ this.subclassNamespace=subclassNamespace;}
 
     public String getSubclassLocalName(){ return subclassLocalName; }
-    public void setSubclassLocalName(){ this.subclassLocalName=subclassLocalName;}
+    public void setSubclassLocalName(String subclassLocalName){ this.subclassLocalName=subclassLocalName;}
 
 }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/DataPropertyComparator.java

@@ -51,7 +51,7 @@ public class DataPropertyComparator implements Comparator<Individual> {
             if (XSD.xint.toString().equals(datatype)) {
                 int i1 = Integer.valueOf(dps1.getData());
                 int i2 = Integer.valueOf(dps2.getData());
-                result = ((Integer) i1).compareTo(i2);
+                result = Integer.compare(i1, i2);
             }
             else if (XSD.xstring.toString().equals(datatype)) {
                 result = dps1.getData().compareTo(dps2.getData());            

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/DataPropertyStatement.java

@@ -2,10 +2,6 @@
 
 package edu.cornell.mannlib.vitro.webapp.beans;
 
-import java.util.Date;
-
-import org.apache.jena.rdf.model.Property;
-
 /**
  * a class representing a particular instance of a data property
  *

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/DataPropertyStatementImpl.java

@@ -2,8 +2,6 @@
 
 package edu.cornell.mannlib.vitro.webapp.beans;
 
-import java.util.Date;
-
 /**
  * a class representing an particular instance of a data property
  *

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/Individual.java

@@ -2,13 +2,12 @@
 
 package edu.cornell.mannlib.vitro.webapp.beans;
 
+import com.fasterxml.jackson.databind.JsonNode;
+
 import java.sql.Timestamp;
 import java.util.List;
 import java.util.Map;
 
-import org.json.JSONException;
-import org.json.JSONObject;
-
 /**
  * User: bdc34
  * Date: Oct 18, 2007
@@ -97,7 +96,7 @@ public interface Individual extends ResourceBean, Comparable<Individual> {
 
     void sortForDisplay();
 
-    JSONObject toJSON() throws JSONException;
+    JsonNode toJSON();
     
     Float getSearchBoost();
     void setSearchBoost( Float boost );

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/IndividualImpl.java

@@ -11,9 +11,9 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
-import org.json.JSONException;
+import com.fasterxml.jackson.databind.JsonNode;
-import org.json.JSONObject;
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
-
+import com.fasterxml.jackson.databind.node.ObjectNode;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.filestorage.model.ImageInfo;
 
@@ -301,27 +301,21 @@ public class IndividualImpl extends BaseResourceBean implements Individual, Comp
     protected void sortEnts2EntsForDisplay(){
         if( getObjectPropertyList() == null ) return;
 
-        Iterator it = getObjectPropertyList().iterator();
+        for (ObjectProperty prop : getObjectPropertyList()) {
-        while(it.hasNext()){
+            prop.sortObjectPropertyStatementsForDisplay(prop, prop.getObjectPropertyStatements());
-            ObjectProperty prop = (ObjectProperty)it.next();
-            prop.sortObjectPropertyStatementsForDisplay(prop,prop.getObjectPropertyStatements());
         }
     }
 
     protected void sortPropertiesForDisplay( ){
         //here we sort the Property objects
-        Collections.sort(getObjectPropertyList(), new ObjectProperty.DisplayComparator());
+        getObjectPropertyList().sort(new ObjectProperty.DisplayComparator());
     }
 
-    public static final String [] INCLUDED_IN_JSON = {
+    public JsonNode toJSON() {
-         "URI",
+        ObjectNode jsonObj = JsonNodeFactory.instance.objectNode();
-         "name",
+        jsonObj.put("URI", this.URI);
-         "vClassId"
+        jsonObj.put("name", this.name);
-    };
+        jsonObj.put("vClassId", this.vClassURI);
-
-
-    public JSONObject toJSON() throws JSONException {
-        JSONObject jsonObj = new JSONObject(this, INCLUDED_IN_JSON);
         return jsonObj;
     }
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/ObjectProperty.java

@@ -463,7 +463,7 @@ public class ObjectProperty extends Property implements Comparable<ObjectPropert
                 }
             };
             try {
-                Collections.sort(objPropStmtsList, fieldComp);
+                objPropStmtsList.sort(fieldComp);
             } catch (Exception e) {
                 log.error("Exception sorting object property statements for object property "+prop.getURI());
             }
@@ -562,7 +562,7 @@ public class ObjectProperty extends Property implements Comparable<ObjectPropert
                 }
             };
             try {
-                Collections.sort(objPropStmtsList, dpComp);
+                objPropStmtsList.sort(dpComp);
             } catch (Exception e) {
                 log.error("Exception sorting object property statements " +
                           "for object property " + prop.getURI(), e);
@@ -576,16 +576,16 @@ public class ObjectProperty extends Property implements Comparable<ObjectPropert
      * @return Readable text identifying this property's attributes
      */
     public String toString(){
-        String list = "null";
+        StringBuilder list = new StringBuilder("null");
         if( getObjectPropertyStatements() != null ){
             Iterator it = getObjectPropertyStatements().iterator();
-            if( !it.hasNext() ) list = " none";
+            if( !it.hasNext() ) list = new StringBuilder(" none");
             while(it.hasNext()){
                 Object obj = it.next();
                 if( obj != null && obj instanceof ObjectPropertyStatement){
-                    list += "\n\t\t" + ((ObjectPropertyStatement)obj).toString();
+                    list.append("\n\t\t").append(((ObjectPropertyStatement) obj).toString());
                 }else{
-                    list += "\n\t\t" + obj.toString();
+                    list.append("\n\t\t").append(obj.toString());
                 }
             }
         }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/ObjectPropertyStatement.java

@@ -1,7 +1,6 @@
 /* $This file is distributed under the terms of the license in LICENSE$ */
 
 package edu.cornell.mannlib.vitro.webapp.beans;
-import java.util.Date;
 
 public interface ObjectPropertyStatement {
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/ObjectPropertyStatementImpl.java

@@ -3,7 +3,6 @@
 package edu.cornell.mannlib.vitro.webapp.beans;
 
 import java.util.Comparator;
-import java.util.Date;
 
 /**
  * a class representing a particular instance of an object property

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/PermissionSet.java

@@ -45,8 +45,7 @@ public class PermissionSet {
 	}
 
 	public void setForNewUsers(Boolean forNewUsers) {
-		this.forNewUsers = (forNewUsers == null) ? false
+		this.forNewUsers = (forNewUsers != null) && forNewUsers.booleanValue();
-				: forNewUsers.booleanValue();
 	}
 
 	public boolean isForPublic() {
@@ -54,8 +53,7 @@ public class PermissionSet {
 	}
 
 	public void setForPublic(Boolean forPublic) {
-		this.forPublic = (forPublic == null) ? false
+		this.forPublic = (forPublic != null) && forPublic.booleanValue();
-				: forPublic.booleanValue();
 	}
 
 	public Set<String> getPermissionUris() {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/PropertyInstance.java

@@ -2,8 +2,6 @@
 
 package edu.cornell.mannlib.vitro.webapp.beans;
 
-import java.util.Date;
-
 /**
    Represents a Vitro object property instance.  It includes values
    from the entities, object property statements, properties, and ent2relationships tables

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/PropertyInstanceIface.java

@@ -2,8 +2,6 @@
 
 package edu.cornell.mannlib.vitro.webapp.beans;
 
-import java.util.Date;
-
 public interface PropertyInstanceIface {
 //needed for PropertyInstance
 //object property statements

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/VClassList.java

@@ -35,7 +35,7 @@ public class VClassList extends VClass {
     }
 
     public void sort(){
-        Collections.sort(getEntities(), getCompare() );
+        getEntities().sort(getCompare());
     }
 
     public int getSize(){

api/src/main/java/edu/cornell/mannlib/vitro/webapp/config/ConfigurationPropertiesSmokeTests.java

@@ -2,7 +2,6 @@
 
 package edu.cornell.mannlib.vitro.webapp.config;
 
-import java.io.File;
 import java.net.URI;
 import java.net.URISyntaxException;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/Controllers.java

@@ -73,8 +73,8 @@ public class Controllers {
         if (Controllers.letters == null) {
             char c[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZ".toCharArray();
             Controllers.letters = new ArrayList<String>(c.length);
-            for (int i = 0; i < c.length; i++) {
+            for (char aC : c) {
-                letters.add("" + c[i]);
+                letters.add("" + aC);
             }
         }
         return Controllers.letters;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/DashboardPropertyListController.java

@@ -11,6 +11,7 @@ import java.util.List;
 
 import javax.servlet.ServletException;
 import javax.servlet.ServletOutputStream;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -36,6 +37,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
  * @author bdc34
  *
  */
+@WebServlet(name = "DashboardPropertyListController", urlPatterns = {"/dashboardPropList"} )
 public class DashboardPropertyListController extends VitroHttpServlet {
 
     /**
@@ -155,7 +157,7 @@ public class DashboardPropertyListController extends VitroHttpServlet {
             
             if (mergedPropertyList!=null) {
                 try {
-                    Collections.sort(mergedPropertyList,new PropertyRanker(vreq));
+                    mergedPropertyList.sort(new PropertyRanker(vreq));
                 } catch (Exception ex) {
                     log.error("Exception sorting merged property list: " + ex.getMessage());
                 }
@@ -274,7 +276,7 @@ public class DashboardPropertyListController extends VitroHttpServlet {
              }
              if (pg.getPropertyList().size()>1) {
                  try {
-                     Collections.sort(pg.getPropertyList(),new Property.DisplayComparatorIgnoringPropertyGroup());
+                     pg.getPropertyList().sort(new Property.DisplayComparatorIgnoringPropertyGroup());
                  } catch (Exception ex) {
                      log.error("Exception sorting property group "+pg.getName()+" property list: "+ex.getMessage());
                  }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/IndividualListRdfController.java

@@ -12,6 +12,7 @@ import java.io.IOException;
 import java.util.Collection;
 
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -37,6 +38,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.http.AcceptHeaderParsingException;
 import edu.cornell.mannlib.vitro.webapp.utils.http.NotAcceptableException;
 
+@WebServlet(name = "IndividualListRdf", urlPatterns = {"/listrdf/*"} )
 public class IndividualListRdfController extends VitroApiServlet {
 	private static final Log log = LogFactory
 			.getLog(IndividualListRdfController.class);

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

@@ -17,6 +17,7 @@ import javax.mail.internet.AddressException;
 import javax.mail.internet.InternetAddress;
 import javax.mail.internet.MimeMessage;
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -27,6 +28,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.UserAccount;
 import edu.cornell.mannlib.vitro.webapp.dao.UserAccountsDao;
 import edu.cornell.mannlib.vitro.webapp.email.FreemarkerEmailFactory;
 
+@WebServlet(name = "mailusers", urlPatterns = {"/mailusers"}, loadOnStartup = 5)
 public class MailUsersServlet extends VitroHttpServlet {
 	private static final Log log = LogFactory.getLog(MailUsersServlet.class);
 	
@@ -102,30 +104,30 @@ public class MailUsersServlet extends VitroHttpServlet {
        comments=comments.trim();
         //Removed spam filtering code
 
-        StringBuffer msgBuf = new StringBuffer(); // contains the intro copy for the body of the email message
+        StringBuilder msgBuf = new StringBuilder(); // contains the intro copy for the body of the email message
         String lineSeparator = System.getProperty("line.separator"); // \r\n on windows, \n on unix
         // from MyLibrary
         msgBuf.setLength(0);
         //msgBuf.append("Content-Type: text/html; charset='us-ascii'" + lineSeparator);
-        msgBuf.append("<html>" + lineSeparator );
+        msgBuf.append("<html>").append(lineSeparator);
-        msgBuf.append("<head>" + lineSeparator );
+        msgBuf.append("<head>").append(lineSeparator);
-        msgBuf.append("<style>a {text-decoration: none}</style>" + lineSeparator );
+        msgBuf.append("<style>a {text-decoration: none}</style>").append(lineSeparator);
-        msgBuf.append("<title>" + deliveryfrom + "</title>" + lineSeparator );
+        msgBuf.append("<title>").append(deliveryfrom).append("</title>").append(lineSeparator);
-        msgBuf.append("</head>" + lineSeparator );
+        msgBuf.append("</head>").append(lineSeparator);
-        msgBuf.append("<body>" + lineSeparator );
+        msgBuf.append("<body>").append(lineSeparator);
-        msgBuf.append("<h4>" + deliveryfrom + "</h4>" + lineSeparator );
+        msgBuf.append("<h4>").append(deliveryfrom).append("</h4>").append(lineSeparator);
-        msgBuf.append("<h4>From: "+webusername +" (" + webuseremail + ")"+" at IP address "+request.getRemoteAddr()+"</h4>"+lineSeparator);
+        msgBuf.append("<h4>From: ").append(webusername).append(" (").append(webuseremail).append(")").append(" at IP address ").append(request.getRemoteAddr()).append("</h4>").append(lineSeparator);
 
         //Don't need any 'likely viewing page' portion to be emailed out to the others
 
-        msgBuf.append(lineSeparator + "</i></p><h3>Comments:</h3>" + lineSeparator );
+        msgBuf.append(lineSeparator).append("</i></p><h3>Comments:</h3>").append(lineSeparator);
         if (comments==null || comments.equals("")) {
             msgBuf.append("<p>BLANK MESSAGE</p>");
         } else {
-            msgBuf.append("<p>"+comments+"</p>");
+            msgBuf.append("<p>").append(comments).append("</p>");
         }
-        msgBuf.append("</body>" + lineSeparator );
+        msgBuf.append("</body>").append(lineSeparator);
-        msgBuf.append("</html>" + lineSeparator );
+        msgBuf.append("</html>").append(lineSeparator);
 
         String msgText = msgBuf.toString();
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/MultipartRequestWrapper.java

@@ -4,6 +4,7 @@ package edu.cornell.mannlib.vitro.webapp.controller;
 
 import java.io.File;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.UnsupportedEncodingException;
 import java.net.URLDecoder;
 import java.util.ArrayList;
@@ -190,6 +191,15 @@ public class MultipartRequestWrapper extends HttpServletRequestWrapper {
 		try {
 			return upload.parseRequest(req);
 		} catch (FileSizeLimitExceededException | SizeLimitExceededException e) {
+			// Fully consume input stream, so that error message is displayed
+			try {
+				InputStream in = req.getInputStream();
+				byte[] buffer = new byte[4096];
+				while (in.read(buffer) != -1) ;
+			} catch (IOException ioe) {
+				// Ignore any errors at this point
+			}
+
 			if (strategy.stashFileSizeException()) {
 				req.setAttribute(ATTRIBUTE_FILE_SIZE_EXCEPTION, e);
 				return Collections.emptyList();
@@ -233,7 +243,7 @@ public class MultipartRequestWrapper extends HttpServletRequestWrapper {
 	 * Look in the map of parsed parameters. Make a protective copy.
 	 */
 	@Override
-	public Enumeration<?> getParameterNames() {
+	public Enumeration<String> getParameterNames() {
 		return Collections.enumeration(new HashSet<>(parameters.keySet()));
 	}
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/OntologyController.java

@@ -8,6 +8,7 @@ import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -30,6 +31,7 @@ import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaOutputUtils;
 import edu.cornell.mannlib.vitro.webapp.web.ContentType;
 
+@WebServlet(name = "ontology", urlPatterns = {"/ontology/*"})
 public class OntologyController extends VitroHttpServlet{
     private static final Log log = LogFactory.getLog(OntologyController.class.getName());
     
@@ -56,8 +58,7 @@ public class OntologyController extends VitroHttpServlet{
    
        if( rdfFormat != null ){
         	doRdf(req, res, rdfFormat );
-        	return;
+       }
-        }         
 	}
 	
 	private static Pattern RDF_REQUEST = Pattern.compile("^/ontology/([^/]*)/([^/]*).rdf$");
@@ -157,8 +158,7 @@ public class OntologyController extends VitroHttpServlet{
         if( ! found ){
             //respond to HTTP outside of critical section
             doNotFound(req,res);
-            return;
+        } else {
-        } else {	
         	JenaOutputUtils.setNameSpacePrefixes(newModel,vreq.getWebappDaoFactory());
             res.setContentType(rdfFormat.getMediaType());
             String format = ""; 
@@ -169,8 +169,7 @@ public class OntologyController extends VitroHttpServlet{
             else if ( TTL_MIMETYPE.equals(rdfFormat.getMediaType()))
                 format ="TTL";
 		
-            newModel.write( res.getOutputStream(), format );		
+            newModel.write( res.getOutputStream(), format );
-            return;
         }
 	}
 	

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/SparqlQueryBuilderServlet.java

@@ -7,6 +7,7 @@ import java.util.HashMap;
 
 import javax.servlet.ServletException;
 import javax.servlet.ServletOutputStream;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -25,6 +26,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
  *  This servlet works as a RequestDispatcher to direct to the sparl query builder page.
  *  @author yuysun
  */
+@WebServlet(name = "SparlQueryBuilder", urlPatterns = {"/admin/sparqlquerybuilder"})
 public class SparqlQueryBuilderServlet extends BaseEditController {
 
     private static final Log log = LogFactory.getLog(SparqlQueryBuilderServlet.class.getName());
@@ -85,7 +87,6 @@ public class SparqlQueryBuilderServlet extends BaseEditController {
         }
 
         doHelp(request,response);
-        return;
     }
     
     private void doNoModelInContext(HttpServletRequest request, HttpServletResponse res){

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/VitroHttpServlet.java

@@ -205,7 +205,7 @@ public class VitroHttpServlet extends HttpServlet implements MultipartRequestWra
 	
 	protected void sortForPickList(List<? extends ResourceBean> beans, 
 	        VitroRequest vreq) {
-	    Collections.sort(beans, new PickListSorter(vreq));
+	    beans.sort(new PickListSorter(vreq));
 	}
 	
 	protected class PickListSorter implements Comparator<ResourceBean> {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/UserAccountsPage.java

@@ -60,12 +60,12 @@ public abstract class UserAccountsPage extends AbstractPageHandler {
 			}
 		}
 
-		Collections.sort(list, new Comparator<PermissionSet>() {
+		list.sort(new Comparator<PermissionSet>() {
-			@Override
+            @Override
-			public int compare(PermissionSet ps1, PermissionSet ps2) {
+            public int compare(PermissionSet ps1, PermissionSet ps2) {
-				return ps1.getUri().compareTo(ps2.getUri());
+                return ps1.getUri().compareTo(ps2.getUri());
-			}
+            }
-		});
+        });
 		return list;
 	}
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/admin/UserAccountsAdminController.java

@@ -15,10 +15,13 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerHttpServ
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.RedirectResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 
+import javax.servlet.annotation.WebServlet;
+
 /**
  * Parcel out the different actions required of the Administrators portion of
  * the UserAccounts GUI.
  */
+@WebServlet(name = "AccountsAdmin", urlPatterns = {"/accountsAdmin/*"} )
 public class UserAccountsAdminController extends FreemarkerHttpServlet {
 	private static final Log log = LogFactory
 			.getLog(UserAccountsAdminController.class);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/admin/UserAccountsEditPage.java

@@ -127,8 +127,7 @@ public class UserAccountsEditPage extends UserAccountsPage {
 						+ "but is not authorized to do so. Logged in as: "
 						+ LoginStatusBean.getCurrentUser(vreq));
 				bogusMessage = getBogusStandardMessage(vreq);
-				return;
+            }
-			}
 		}
 	}
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/admin/ajax/ExternalAuthChecker.java

@@ -8,10 +8,10 @@ import java.util.List;
 import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletResponse;
 
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import com.fasterxml.jackson.databind.node.ObjectNode;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.json.JSONException;
-import org.json.JSONObject;
 
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.SelfEditingConfiguration;
@@ -56,7 +56,7 @@ class ExternalAuthChecker extends AbstractAjaxResponder {
 	}
 
 	@Override
-	public String prepareResponse() throws IOException, JSONException {
+	public String prepareResponse() throws IOException {
 		if (someoneElseIsUsingThisExternalAuthId()) {
 			return respondExternalAuthIdAlreadyUsed();
 		}
@@ -93,8 +93,8 @@ class ExternalAuthChecker extends AbstractAjaxResponder {
 		return true;
 	}
 
-	private String respondExternalAuthIdAlreadyUsed() throws JSONException {
+	private String respondExternalAuthIdAlreadyUsed() {
-		JSONObject jsonObject = new JSONObject();
+		ObjectNode jsonObject = JsonNodeFactory.instance.objectNode();
 		jsonObject.put(RESPONSE_ID_IN_USE, true);
 		return jsonObject.toString();
 	}
@@ -110,12 +110,12 @@ class ExternalAuthChecker extends AbstractAjaxResponder {
 		this.matchingProfile = inds.get(0);
 	}
 
-	private String respondWithMatchingProfile() throws JSONException {
+	private String respondWithMatchingProfile() {
 		String uri = matchingProfile.getURI();
 		String url = UrlBuilder.getIndividualProfileUrl(uri, vreq);
 		String label = matchingProfile.getRdfsLabel();
 
-		JSONObject jsonObject = new JSONObject();
+		ObjectNode jsonObject = JsonNodeFactory.instance.objectNode();
 		jsonObject.put(RESPONSE_MATCHES_PROFILE, true);
 		jsonObject.put(RESPONSE_PROFILE_URI, uri);
 		jsonObject.put(RESPONSE_PROFILE_URL, url);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/admin/ajax/ProfileAutoCompleter.java

@@ -20,7 +20,6 @@ import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.json.JSONException;
 
 import org.apache.jena.ontology.OntModel;
 import org.apache.jena.query.Query;
@@ -107,7 +106,7 @@ class ProfileAutoCompleter extends AbstractAjaxResponder implements
 	}
 
 	@Override
-	public String prepareResponse() throws IOException, JSONException {
+	public String prepareResponse() throws IOException {
 		if (term.isEmpty()) {
 			return EMPTY_RESPONSE;
 		}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/admin/ajax/UserAccountsAjaxController.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.controller.accounts.admin.ajax;
 import java.io.IOException;
 
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.logging.Log;
@@ -18,6 +19,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.ajax.VitroAjaxController;
 /**
  * Handle the AJAX functions that are specific to the UserAccounts pages.
  */
+@WebServlet(name = "AccountsAjax", urlPatterns = {"/accountsAjax/*"} )
 public class UserAccountsAjaxController extends VitroAjaxController {
 	private static final Log log = LogFactory
 			.getLog(UserAccountsAjaxController.class);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/manageproxies/ManageProxiesController.java

@@ -15,9 +15,12 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerHttpServ
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.RedirectResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 
+import javax.servlet.annotation.WebServlet;
+
 /**
  * Parcel out the different actions required of the ManageProxies GUI.
  */
+@WebServlet(name = "ManageProxies", urlPatterns = {"/manageProxies/*"} )
 public class ManageProxiesController extends FreemarkerHttpServlet {
 	private static final Log log = LogFactory
 			.getLog(ManageProxiesController.class);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/manageproxies/ajax/BasicProfilesGetter.java

@@ -19,7 +19,6 @@ import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.json.JSONException;
 
 import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
 import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
@@ -80,7 +79,7 @@ public class BasicProfilesGetter extends AbstractAjaxResponder {
 	}
 
 	@Override
-	public String prepareResponse() throws IOException, JSONException {
+	public String prepareResponse() throws IOException {
 		log.debug("search term is '" + term + "'");
 		if (this.term.isEmpty() || this.profileTypes.isEmpty()) {
 			return EMPTY_RESPONSE;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/manageproxies/ajax/BasicProxiesGetter.java

@@ -11,10 +11,9 @@ import java.util.Map;
 import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletResponse;
 
+import com.fasterxml.jackson.databind.node.ArrayNode;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.json.JSONArray;
-import org.json.JSONException;
 
 import org.apache.jena.ontology.OntModel;
 import org.apache.jena.query.QuerySolution;
@@ -68,7 +67,7 @@ public class BasicProxiesGetter extends AbstractAjaxResponder {
 	}
 
 	@Override
-	public String prepareResponse() throws IOException, JSONException {
+	public String prepareResponse() throws IOException {
 		log.debug("search term is '" + term + "'");
 		if (term.isEmpty()) {
 			return EMPTY_RESPONSE;
@@ -76,7 +75,7 @@ public class BasicProxiesGetter extends AbstractAjaxResponder {
 			String cleanTerm = SparqlQueryUtils.escapeForRegex(term);
 			String queryStr = QUERY_BASIC_PROXIES.replace("%term%", cleanTerm);
 
-			JSONArray jsonArray = SparqlQueryRunner
+			ArrayNode jsonArray = SparqlQueryRunner
 					.createSelectQueryContext(userAccountsModel, queryStr)
 					.execute()
 					.parse(new BasicProxyInfoParser(placeholderImageUrl));

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/manageproxies/ajax/ManageProxiesAjaxController.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.controller.accounts.manageproxies.ajax;
 import java.io.IOException;
 
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.logging.Log;
@@ -18,6 +19,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.ajax.VitroAjaxController;
 /**
  * Handle the AJAX functions that are specific to the ManageProxies pages.
  */
+@WebServlet(name = "ProxiesAjax", urlPatterns = {"/proxiesAjax/*"} )
 public class ManageProxiesAjaxController extends VitroAjaxController {
 	private static final Log log = LogFactory
 			.getLog(ManageProxiesAjaxController.class);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/manageproxies/ajax/MoreProfileInfo.java

@@ -9,10 +9,11 @@ import java.util.Map;
 import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletResponse;
 
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import com.fasterxml.jackson.databind.node.ObjectNode;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.json.JSONArray;
-import org.json.JSONException;
 
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@@ -42,7 +43,7 @@ public class MoreProfileInfo extends AbstractAjaxResponder {
 	}
 
 	@Override
-	public String prepareResponse() throws IOException, JSONException {
+	public String prepareResponse() throws IOException {
 		log.debug("profile URI is '" + profileUri + "'");
 		if (profileUri.isEmpty()) {
 			return EMPTY_RESPONSE;
@@ -58,8 +59,12 @@ public class MoreProfileInfo extends AbstractAjaxResponder {
 		map.put("imageUrl", getFullImageUrl(profileInd));
 		map.put("classLabel", getMostSpecificTypeLabel(profileInd.getURI()));
 
-		JSONArray jsonArray = new JSONArray();
+		ArrayNode jsonArray = JsonNodeFactory.instance.arrayNode();
-		jsonArray.put(map);
+		ObjectNode jsonObj = JsonNodeFactory.instance.objectNode();
+		for (Map.Entry<String, String> entry : map.entrySet()) {
+			jsonObj.put(entry.getKey(), entry.getValue());
+		}
+		jsonArray.add(jsonObj);
 		String response = jsonArray.toString();
 
 		log.debug("response is '" + response + "'");

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/manageproxies/ajax/MoreProxyInfo.java

@@ -10,10 +10,11 @@ import java.util.Map;
 import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletResponse;
 
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import com.fasterxml.jackson.databind.node.ObjectNode;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.json.JSONArray;
-import org.json.JSONException;
 
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.SelfEditingConfiguration;
@@ -47,7 +48,7 @@ public class MoreProxyInfo extends AbstractAjaxResponder {
 	}
 
 	@Override
-	public String prepareResponse() throws IOException, JSONException {
+	public String prepareResponse() throws IOException {
 		log.debug("proxy URI is '" + proxyUri + "'");
 		if (proxyUri.isEmpty()) {
 			return EMPTY_RESPONSE;
@@ -74,8 +75,12 @@ public class MoreProxyInfo extends AbstractAjaxResponder {
 		}
 		map.put("classLabel", getMostSpecificTypeLabel(profileInd.getURI()));
 
-		JSONArray jsonArray = new JSONArray();
+		ArrayNode jsonArray = JsonNodeFactory.instance.arrayNode();
-		jsonArray.put(map);
+		ObjectNode jsonObj = JsonNodeFactory.instance.objectNode();
+		for (Map.Entry<String, String> entry : map.entrySet()) {
+			jsonObj.put(entry.getKey(), entry.getValue());
+		}
+		jsonArray.add(jsonObj);
 		String response = jsonArray.toString();
 
 		log.debug("response is '" + response + "'");

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/user/UserAccountsFirstTimeExternalPage.java

@@ -126,8 +126,7 @@ public class UserAccountsFirstTimeExternalPage extends UserAccountsPage {
 		}
 		if (!Authenticator.getInstance(vreq).isUserPermittedToLogin(null)) {
 			bogusMessage = i18n.text("logins_disabled_for_maintenance");
-			return;
+        }
-		}
 	}
 
 	public boolean isBogus() {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/user/UserAccountsPasswordBasePage.java

@@ -121,8 +121,7 @@ public abstract class UserAccountsPasswordBasePage extends UserAccountsPage {
 						+ "' when already logged in as '" + currentUserEmail
 						+ "'");
 				bogusMessage = alreadyLoggedInMessage(currentUserEmail);
-				return;
+            }
-			}
 		}
 	}
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/user/UserAccountsUserController.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.controller.accounts.user;
 import static edu.cornell.mannlib.vedit.beans.LoginStatusBean.AuthenticationSource.EXTERNAL;
 import static edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest.AUTHORIZED;
 
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 
 import org.apache.commons.logging.Log;
@@ -26,6 +27,7 @@ import edu.cornell.mannlib.vitro.webapp.i18n.I18n;
 /**
  * Parcel out the different actions required of the UserAccounts GUI.
  */
+@WebServlet(name = "AccountsUser", urlPatterns = {"/accounts/*"} )
 public class UserAccountsUserController extends FreemarkerHttpServlet {
 	private static final Log log = LogFactory
 			.getLog(UserAccountsUserController.class);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/admin/RestrictLoginsController.java

@@ -18,10 +18,13 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.Res
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
 import edu.cornell.mannlib.vitro.webapp.i18n.I18n;
 
+import javax.servlet.annotation.WebServlet;
+
 /**
  * Offer the user the ability to apply a RestrictedAuthenticator or revert to a
  * BasicAuthenticator.
  */
+@WebServlet(name = "RestrictLogins", urlPatterns = {"/admin/restrictLogins"} )
 public class RestrictLoginsController extends FreemarkerHttpServlet {
 	public static final String PARAMETER_RESTRICT = "restrict";
 	public static final String PARAMETER_OPEN = "open";

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/admin/ShowAuthController.java

@@ -13,6 +13,7 @@ import java.util.Map;
 import java.util.TreeMap;
 
 import javax.servlet.ServletContext;
+import javax.servlet.annotation.WebServlet;
 
 import edu.cornell.mannlib.vedit.beans.LoginStatusBean;
 import edu.cornell.mannlib.vitro.webapp.auth.identifier.ActiveIdentifierBundleFactories;
@@ -36,6 +37,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.Tem
  * Show a summary of who is logged in and how they are to be treated by the
  * authorization system.
  */
+@WebServlet(name = "ShowAuth", urlPatterns = {"/admin/showAuth"} )
 public class ShowAuthController extends FreemarkerHttpServlet {
 
 	@Override

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/admin/ShowBackgroundThreadsController.java

@@ -17,10 +17,13 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.Res
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
 import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
 
+import javax.servlet.annotation.WebServlet;
+
 /**
  * Show the list of living background threads (instances of
  * VitroBackgroundThread), and their status.
  */
+@WebServlet(name = "ShowBackgroundThreads", urlPatterns = {"/admin/showThreads"} )
 public class ShowBackgroundThreadsController extends FreemarkerHttpServlet {
 
 	private static final String TEMPLATE_NAME = "admin-showThreads.ftl";

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/admin/ShowConfiguration.java

@@ -16,9 +16,12 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerHttpServ
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
 
+import javax.servlet.annotation.WebServlet;
+
 /**
  * Show the current ConfigurationProperties and the Java system properties.
  */
+@WebServlet(name = "ShowConfiguration", urlPatterns = {"/admin/showConfiguration"} )
 public class ShowConfiguration extends FreemarkerHttpServlet {
 	@Override
 	protected AuthorizationRequest requiredActions(VitroRequest vreq) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/admin/ShowSourcesController.java

@@ -34,6 +34,8 @@ import edu.cornell.mannlib.vitro.webapp.modelaccess.RequestModelAccess;
 import edu.cornell.mannlib.vitro.webapp.utils.logging.ComplexStringFormatter;
 import edu.cornell.mannlib.vitro.webapp.utils.logging.ToString;
 
+import javax.servlet.annotation.WebServlet;
+
 /**
  * Show the details of where our RDF data is coming from. What are the
  * structures that supply the triples?
@@ -103,6 +105,7 @@ import edu.cornell.mannlib.vitro.webapp.utils.logging.ToString;
  * At the same time, write these to the log as INFO messages, without the fancy formatting.
  * </pre>
  */
+@WebServlet(name = "ShowRDFSources", urlPatterns = {"/admin/showSources"} )
 public class ShowSourcesController extends FreemarkerHttpServlet {
 	private static final Log log = LogFactory
 			.getLog(ShowSourcesController.class);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/admin/SparqlQueryController.java

@@ -13,6 +13,7 @@ import java.util.List;
 import java.util.Map;
 
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -43,6 +44,7 @@ import edu.cornell.mannlib.vitro.webapp.utils.sparql.SparqlQueryUtils;
 /**
  * Present the SPARQL Query form, and execute the queries.
  */
+@WebServlet(name = "SparqlQuery", urlPatterns = {"/admin/sparqlquery"})
 public class SparqlQueryController extends FreemarkerHttpServlet {
 	private static final Log log = LogFactory
 			.getLog(SparqlQueryController.class);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/admin/StartupStatusController.java

@@ -14,9 +14,12 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.Tem
 import edu.cornell.mannlib.vitro.webapp.i18n.I18n;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
 
+import javax.servlet.annotation.WebServlet;
+
 /**
  * Display the startup status page.
  */
+@WebServlet(name = "StartupStatus", urlPatterns = {"/startupStatus"} )
 public class StartupStatusController extends FreemarkerHttpServlet {
 
 	@Override

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/admin/WaitForBackgroundThreadsController.java

@@ -14,6 +14,7 @@ import java.util.Enumeration;
 import java.util.List;
 
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -41,6 +42,7 @@ import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread.Work
  * 
  * Otherwise, the result will be 200 (OK), with a brief message.
  */
+@WebServlet(name = "WaitForBackgroundThreads", urlPatterns = {"/admin/wait"} )
 public class WaitForBackgroundThreadsController extends VitroHttpServlet {
 	private static final Log log = LogFactory
 			.getLog(WaitForBackgroundThreadsController.class);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/ajax/AbstractAjaxResponder.java

@@ -13,10 +13,11 @@ import java.util.Map;
 import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletResponse;
 
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import com.fasterxml.jackson.databind.node.ObjectNode;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.json.JSONArray;
-import org.json.JSONException;
 
 import org.apache.jena.query.QuerySolution;
 import org.apache.jena.query.ResultSet;
@@ -59,8 +60,7 @@ public abstract class AbstractAjaxResponder {
 		}
 	}
 
-	protected abstract String prepareResponse() throws IOException,
+	protected abstract String prepareResponse() throws IOException;
-			JSONException;
 
 	protected String getStringParameter(String key, String defaultValue) {
 		String value = vreq.getParameter(key);
@@ -81,9 +81,13 @@ public abstract class AbstractAjaxResponder {
 	 * objects with fields.
 	 */
 	protected String assembleJsonResponse(List<Map<String, String>> maps) {
-		JSONArray jsonArray = new JSONArray();
+		ArrayNode jsonArray = JsonNodeFactory.instance.arrayNode();
 		for (Map<String, String> map : maps) {
-			jsonArray.put(map);
+			ObjectNode jsonObj = JsonNodeFactory.instance.objectNode();
+			for (Map.Entry<String, String> entry : map.entrySet()) {
+				jsonObj.put(entry.getKey(), entry.getValue());
+			}
+			jsonArray.add(jsonObj);
 		}
 		return jsonArray.toString();
 	}
@@ -93,19 +97,23 @@ public abstract class AbstractAjaxResponder {
 	 * implement "parseSolutionRow()"
 	 */
 	protected abstract static class JsonArrayParser extends
-			ResultSetParser<JSONArray> {
+			ResultSetParser<ArrayNode> {
 		@Override
-		protected JSONArray defaultValue() {
+		protected ArrayNode defaultValue() {
-			return new JSONArray();
+			return JsonNodeFactory.instance.arrayNode();
 		}
 
 		@Override
-		protected JSONArray parseResults(String queryStr, ResultSet results) {
+		protected ArrayNode parseResults(String queryStr, ResultSet results) {
-			JSONArray jsonArray = new JSONArray();
+			ArrayNode jsonArray = JsonNodeFactory.instance.arrayNode();
 			while (results.hasNext()) {
 				Map<String, String> map = parseSolutionRow(results.next());
 				if (map != null) {
-					jsonArray.put(map);
+					ObjectNode jsonObj = JsonNodeFactory.instance.objectNode();
+					for (Map.Entry<String, String> entry : map.entrySet()) {
+						jsonObj.put(entry.getKey(), entry.getValue());
+					}
+					jsonArray.add(jsonObj);
 				}
 			}
 			return jsonArray;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/ajax/SparqlQueryAjaxController.java

@@ -8,6 +8,7 @@ import static javax.servlet.http.HttpServletResponse.SC_NOT_FOUND;
 import java.io.IOException;
 
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -29,6 +30,7 @@ import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
  * 
  * The result is delivered in JSON format.
  */
+@WebServlet(name = "ajaxSparqlQuery", urlPatterns = {"/ajax/sparqlQuery"} )
 public class SparqlQueryAjaxController extends VitroAjaxController {
 	private static final Log log = LogFactory
 			.getLog(SparqlQueryAjaxController.class);
@@ -59,8 +61,7 @@ public class SparqlQueryAjaxController extends VitroAjaxController {
 			String queryParam = locateQueryParam(vreq);
 			Query query = SparqlUtils.createQuery(queryParam);
 			SparqlUtils.executeQuery(response, query, model);
-			return;
+        } catch (AjaxControllerException e) {
-		} catch (AjaxControllerException e) {
 			log.error(e.getMessage());
 			response.sendError(e.getStatusCode());
 		}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/api/SparqlQueryApiController.java

@@ -10,6 +10,7 @@ import static javax.servlet.http.HttpServletResponse.SC_NOT_ACCEPTABLE;
 import java.io.IOException;
 
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -40,6 +41,7 @@ import edu.cornell.mannlib.vitro.webapp.utils.http.NotAcceptableException;
  * 500 Unknown error
  * </pre>
  */
+@WebServlet(name = "SparqlQueryApi", urlPatterns = {"/api/sparqlQuery"})
 public class SparqlQueryApiController extends VitroApiServlet {
 
 	private static final AuthorizationRequest REQUIRED_ACTIONS = SimplePermission.USE_SPARQL_QUERY_API.ACTION;

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

@@ -9,8 +9,8 @@ import static javax.servlet.http.HttpServletResponse.SC_OK;
 
 import java.io.IOException;
 
-import javax.servlet.ServletContext;
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -48,6 +48,7 @@ import edu.cornell.mannlib.vitro.webapp.modules.searchIndexer.SearchIndexer;
  * 500 Unknown error
  * </pre>
  */
+@WebServlet(name = "SparqlUpdateApi", urlPatterns = {"/api/sparqlUpdate"})
 public class SparqlUpdateApiController extends VitroApiServlet {
 	private static final Log log = LogFactory
 			.getLog(SparqlUpdateApiController.class);
@@ -81,11 +82,11 @@ public class SparqlUpdateApiController extends VitroApiServlet {
 			throw new ParseException("No 'update' parameter.");
 		}
 
-		if (!StringUtils.containsIgnoreCase(update, "GRAPH")) {
+		if (!StringUtils.containsIgnoreCase(update, "GRAPH") && !StringUtils.containsIgnoreCase(update, "WITH")) {
 			if (log.isDebugEnabled()) {
-				log.debug("No GRAPH uri in '" + update + "'");
+				log.debug("No GRAPH or WITH uri in '" + update + "'");
 			}
-			throw new ParseException("SPARQL update must specify a GRAPH URI.");
+			throw new ParseException("SPARQL update must specify a GRAPH ( or WITH) URI.");
 		}
 
 		try {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/api/sparqlquery/SparqlQueryApiRdfProducer.java

@@ -5,7 +5,6 @@ package edu.cornell.mannlib.vitro.webapp.controller.api.sparqlquery;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
-import java.io.OutputStreamWriter;
 import java.util.Collection;
 
 import org.apache.commons.io.IOUtils;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/authenticate/AdminLoginController.java

@@ -23,6 +23,8 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.Red
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
 
+import javax.servlet.annotation.WebServlet;
+
 /**
  * Provide a "hidden" login page for systems where the Login Widget has been
  * modified to only show the link to an External Authentication system.
@@ -30,6 +32,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.Tem
  * This page is only hidden because there is no link to it. Anyone who knows the
  * URL can come here, but they need to pass Internal Authentication to proceed.
  */
+@WebServlet(name = "adminLogin", urlPatterns = {"/admin/login"})
 public class AdminLoginController extends FreemarkerHttpServlet {
 	private static final Log log = LogFactory
 			.getLog(AdminLoginController.class);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/authenticate/Authenticator.java

@@ -197,11 +197,7 @@ public abstract class Authenticator {
 
 			// InternetAddress permits a localname without hostname.
 			// Guard against that.
-			if (emailAddress.indexOf('@') == -1) {
+			return emailAddress.indexOf('@') != -1;
-				return false;
-			}
-
-			return true;
 		} catch (AddressException e) {
 			return false;
 		}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/authenticate/LoginExternalAuthReturn.java

@@ -8,6 +8,7 @@ import java.io.IOException;
 import java.util.Enumeration;
 
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -27,6 +28,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.login.LoginProcessBean.Messag
  * Handle the return from the external authorization login server. If we are
  * successful, record the login. Otherwise, display the failure.
  */
+@WebServlet(name = "loginExternalAuthReturn", urlPatterns = {"/loginExternalAuthReturn"})
 public class LoginExternalAuthReturn extends BaseLoginServlet {
 	private static final Log log = LogFactory
 			.getLog(LoginExternalAuthReturn.class);
@@ -102,14 +104,12 @@ public class LoginExternalAuthReturn extends BaseLoginServlet {
 			getAuthenticator(req).recordLoginAgainstUserAccount(userAccount,
 					AuthenticationSource.EXTERNAL);
 			new LoginRedirector(req, afterLoginUrl).redirectLoggedInUser(resp);
-			return;
+        } catch (LoginNotPermitted e) {
-		} catch (LoginNotPermitted e) {
 			// should have been caught by isUserPermittedToLogin()
 			log.debug("Logins disabled for " + userAccount);
 			complainAndReturnToReferrer(req, resp, ATTRIBUTE_REFERRER,
 					messageLoginDisabled(req));
-			return;
+        }
-		}
 	}
 
 	@Override

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/authenticate/LoginExternalAuthSetup.java

@@ -6,6 +6,7 @@ import java.io.IOException;
 import java.util.Enumeration;
 
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -22,6 +23,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.login.LoginProcessBean;
  * Send a request to the external authorization server that will return us to
  * the LoginExternalAuthReturn servlet for further processing.
  */
+@WebServlet(name = "loginExternalAuthSetup", urlPatterns = {"/loginExternalAuth"})
 public class LoginExternalAuthSetup extends BaseLoginServlet {
 	private static final Log log = LogFactory
 			.getLog(LoginExternalAuthSetup.class);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/authenticate/ProgramLogin.java

@@ -10,6 +10,7 @@ import java.io.IOException;
 import java.io.PrintWriter;
 
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
@@ -24,6 +25,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.authenticate.Authenticator.Lo
  * Provide a means for programmatic login If they provide the right parameters,
  * log them in and send 200. Otherwise, send 403 error.
  */
+@WebServlet(name = "programLogin", urlPatterns = {"/programLogin"})
 public class ProgramLogin extends HttpServlet {
 	private static final Log log = LogFactory.getLog(ProgramLogin.class);
 
@@ -142,8 +144,7 @@ public class ProgramLogin extends HttpServlet {
 				}
 				recordLoginWithPasswordChange();
 				sendSuccess(MESSAGE_SUCCESS_FIRST_TIME);
-				return;
+            }
-			}
 
 		}
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/datatools/dumprestore/DumpNode.java

@@ -5,8 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.controller.datatools.dumprestore;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import javax.json.JsonObject;
+import com.fasterxml.jackson.databind.JsonNode;
-import javax.json.JsonString;
 
 import org.apache.jena.atlas.lib.EscapeStr;
 
@@ -16,7 +15,7 @@ import org.apache.jena.atlas.lib.EscapeStr;
  * able to write to a different format.
  */
 public abstract class DumpNode {
-	public static DumpNode fromJson(JsonObject json) throws BadNodeException {
+	public static DumpNode fromJson(JsonNode json) throws BadNodeException {
 		if (json == null) {
 			return new DumpNullNode();
 		}
@@ -74,9 +73,9 @@ public abstract class DumpNode {
 		return (s == null) ? null : EscapeStr.unescapeStr(s);
 	}
 
-	private static String getString(JsonObject json, String name) {
+	private static String getString(JsonNode json, String name) {
-		JsonString jsString = json.getJsonString(name);
+		JsonNode node = json.get(name);
-		return (jsString == null) ? null : json.getString(name);
+		return node == null ? null : node.asText();
 	}
 
 	public abstract String getValue();

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/datatools/dumprestore/DumpRestoreController.java

@@ -3,11 +3,11 @@
 package edu.cornell.mannlib.vitro.webapp.controller.datatools.dumprestore;
 
 import java.io.IOException;
-import java.io.InputStream;
 import java.util.HashMap;
 import java.util.Map;
 
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -21,7 +21,6 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerHttpServ
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService.ResultFormat;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 
 /**
@@ -35,6 +34,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
  * The first request, the selection and the redirected dump should all be GET
  * requests. A restore should be a POST request.
  */
+@WebServlet(name = "DumpRestoreController", urlPatterns = {"/dumpRestore/*"} )
 public class DumpRestoreController extends FreemarkerHttpServlet {
 
 	private static final RequestedAction REQUIRED_ACTION = SimplePermission.USE_ADVANCED_DATA_TOOLS_PAGES.ACTION;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/datatools/dumprestore/NQuadLineSplitter.java

@@ -95,11 +95,7 @@ class NQuadLineSplitter {
 		while (!atEnd() && isWhiteSpace()) {
 			i++;
 		}
-		if (atEnd()) {
+		if (!atEnd() && line.charAt(i) != '#') {
-			return;
-		} else if (line.charAt(i) == '#') {
-			return;
-		} else {
 			throw new BadNodeException(
 					"Period was not followed by end of line: '" + line + "'");
 		}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/Authenticate.java

@@ -18,6 +18,7 @@ import java.util.Map;
 
 import javax.servlet.ServletContext;
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import javax.servlet.http.HttpSession;
@@ -42,6 +43,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.login.LoginProcessBean.State;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.LoginLogoutEvent;
 
+@WebServlet(name = "authenticate", urlPatterns = {"/authenticate"})
 public class Authenticate extends VitroHttpServlet {
 	private static final Log log = LogFactory.getLog(Authenticate.class
 			.getName());
@@ -349,8 +351,7 @@ public class Authenticate extends VitroHttpServlet {
 				// This should have been caught by isUserPermittedToLogin()
 				bean.setMessage(request, ERROR,
 						"logins_disabled_for_maintenance");
-				return;
+            }
-			}
 		}
 	}
 
@@ -411,8 +412,7 @@ public class Authenticate extends VitroHttpServlet {
 		} catch (LoginNotPermitted e) {
 			// This should have been caught by isUserPermittedToLogin()
 			bean.setMessage(request, ERROR, "logins_disabled_for_maintenance");
-			return;
+        }
-		}
 	}
 
 	/**
@@ -495,8 +495,7 @@ public class Authenticate extends VitroHttpServlet {
 		String loginProcessPage = LoginProcessBean.getBean(vreq)
 				.getLoginPageUrl();
 		response.sendRedirect(loginProcessPage);
-		return;
+    }
-	}
 
 	/**
 	 * Exit: user has completed the login. Redirect appropriately and clear the

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

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.controller.edit;
 import java.io.IOException;
 import java.util.HashMap;
 
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -18,6 +19,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.Classes2Classes;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 
+@WebServlet(name = "Classes2ClassesOperationController", urlPatterns = {"/classes2ClassesOp"} )
 public class Classes2ClassesOperationController extends BaseEditController {
 
     private static final Log log = LogFactory.getLog(Classes2ClassesOperationController.class.getName());
@@ -70,48 +72,60 @@ public class Classes2ClassesOperationController extends BaseEditController {
 	                if ((subclassURIstrs != null) && (subclassURIstrs.length > 1)) {
 	                    String superclassURIstr = request.getParameter("SuperclassURI");
 	                    if (superclassURIstr != null) {
-	                        for (int i=0; i<subclassURIstrs.length; i++) {
+                            for (String subclassURIstr : subclassURIstrs) {
-	                        	if (modeStr.equals("disjointWith")) {
+                                switch (modeStr) {
-	                        		vcDao.removeDisjointWithClass(superclassURIstr, subclassURIstrs[i]);
+                                    case "disjointWith":
-	                        	} else if (modeStr.equals("equivalentClass")) {
+                                        vcDao.removeDisjointWithClass(superclassURIstr, subclassURIstr);
-	                        		vcDao.removeEquivalentClass(superclassURIstr, subclassURIstrs[i]);
+                                        break;
-	                        	} else {
+                                    case "equivalentClass":
-		                            Classes2Classes c2c = new Classes2Classes();
+                                        vcDao.removeEquivalentClass(superclassURIstr, subclassURIstr);
-		                            c2c.setSubclassURI(subclassURIstrs[i]);
+                                        break;
-		                            c2c.setSuperclassURI(superclassURIstr);
+                                    default:
-		                            vcDao.deleteClasses2Classes(c2c);
+                                        Classes2Classes c2c = new Classes2Classes();
-	                        	}
+                                        c2c.setSubclassURI(subclassURIstr);
-	                        }
+                                        c2c.setSuperclassURI(superclassURIstr);
+                                        vcDao.deleteClasses2Classes(c2c);
+                                        break;
+                                }
+                            }
 	                    }
 	                } else {
 	                    String subclassURIstr = subclassURIstrs[0];
 	                    String[] superclassURIstrs = request.getParameterValues("SuperclassURI");
 	                    if (superclassURIstrs != null) {
-	                        for (int i=0; i<superclassURIstrs.length; i++) {
+                            for (String superclassURIstr : superclassURIstrs) {
-	                        	if (modeStr.equals("disjointWith")) {
+                                switch (modeStr) {
-	                        		vcDao.removeDisjointWithClass(superclassURIstrs[i],subclassURIstr);
+                                    case "disjointWith":
-		                        } else if (modeStr.equals("equivalentClass")) {
+                                        vcDao.removeDisjointWithClass(superclassURIstr, subclassURIstr);
-		                        	vcDao.removeEquivalentClass(subclassURIstr,superclassURIstrs[i]);
+                                        break;
-		                        } else {
+                                    case "equivalentClass":
-		                            Classes2Classes c2c = new Classes2Classes();
+                                        vcDao.removeEquivalentClass(subclassURIstr, superclassURIstr);
-		                            c2c.setSuperclassURI(superclassURIstrs[i]);
+                                        break;
-		                            c2c.setSubclassURI(subclassURIstr);
+                                    default:
-		                            vcDao.deleteClasses2Classes(c2c);
+                                        Classes2Classes c2c = new Classes2Classes();
-	                        	}
+                                        c2c.setSuperclassURI(superclassURIstr);
-	                        }
+                                        c2c.setSubclassURI(subclassURIstr);
+                                        vcDao.deleteClasses2Classes(c2c);
+                                        break;
+                                }
+                            }
 	                    }
 	                }
 	            } else if (request.getParameter("operation").equals("add")) {
-	            	if (modeStr.equals("disjointWith")) {
+                    switch (modeStr) {
-	            		vcDao.addDisjointWithClass(request.getParameter("SuperclassURI"), request.getParameter("SubclassURI"));
+                        case "disjointWith":
-	            	} else if (modeStr.equals("equivalentClass")) {
+                            vcDao.addDisjointWithClass(request.getParameter("SuperclassURI"), request.getParameter("SubclassURI"));
-	            		vcDao.addEquivalentClass(request.getParameter("SuperclassURI"), request.getParameter("SubclassURI"));
+                            break;
-	            	} else {
+                        case "equivalentClass":
-		            	Classes2Classes c2c = new Classes2Classes();
+                            vcDao.addEquivalentClass(request.getParameter("SuperclassURI"), request.getParameter("SubclassURI"));
-		                c2c.setSuperclassURI(request.getParameter("SuperclassURI"));
+                            break;
-		                c2c.setSubclassURI(request.getParameter("SubclassURI"));
+                        default:
-		                vcDao.insertNewClasses2Classes(c2c);
+                            Classes2Classes c2c = new Classes2Classes();
-	            	}
+                            c2c.setSuperclassURI(request.getParameter("SuperclassURI"));
+                            c2c.setSubclassURI(request.getParameter("SubclassURI"));
+                            vcDao.insertNewClasses2Classes(c2c);
+                            break;
+                    }
 	            }
 	        } catch (Exception e) {
 	            log.error(e, e);

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

@@ -68,7 +68,7 @@ public class ClassgroupRetryController extends BaseEditController {
                 }
                 if (vclassGroupForEditing == null) {                    
                     //UTF-8 expected due to URIEncoding on Connector in server.xml
-                    String uriToFind = new String(request.getParameter("uri"));
+                    String uriToFind = request.getParameter("uri");
                     vclassGroupForEditing = (VClassGroup)cgDao.getGroupByURI(uriToFind);
                 }
             } else {

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

@@ -8,6 +8,7 @@ import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -29,6 +30,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 
+@WebServlet(name = "DatapropEditController", urlPatterns = {"/datapropEdit"} )
 public class DatapropEditController extends BaseEditController {
 	
 	private static final Log log = LogFactory.getLog(DatapropEditController.class.getName());

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

@@ -4,6 +4,7 @@ package edu.cornell.mannlib.vitro.webapp.controller.edit;
 
 import java.io.IOException;
 
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -22,6 +23,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
 
 
+@WebServlet(name = "DatatypeRetryController", urlPatterns = {"/datatype_retry"} )
 public class DatatypeRetryController extends BaseEditController {
 
 	private static final Log log = LogFactory.getLog(DatatypeRetryController.class.getName());

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/DeletePageController.java

@@ -7,6 +7,7 @@ import java.io.IOException;
 import java.io.StringWriter;
 
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -31,6 +32,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
 /**
  *Process deletions for page, deleting page, data getters and any associated menu items.
  */
+@WebServlet(name = "DeletePageController", urlPatterns = {"/deletePageController"} )
 public class DeletePageController extends VitroHttpServlet {
    
    private final static String REDIRECT_URL = "/pageList";

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

@@ -10,6 +10,7 @@ import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.List;
 
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -33,6 +34,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyInstanceDao;
 
+@WebServlet(name = "EntityEditController", urlPatterns = {"/entityEdit"} )
 public class EntityEditController extends BaseEditController {
 	
 	private static final Log log = LogFactory.getLog(EntityEditController.class.getName());
@@ -93,7 +95,7 @@ public class EntityEditController extends BaseEditController {
         }
         results.add(rName);
         
-        String classStr = "";
+        StringBuilder classStr = new StringBuilder();
         List<VClass> classList = inferredEnt.getVClasses(false);
         sortForPickList(classList, vreq);
         if (classList != null) {
@@ -107,13 +109,13 @@ public class EntityEditController extends BaseEditController {
 	            } catch (Exception e) {
 	                rClassName = vc.getLocalNameWithPrefix();
 	            }
-	            classStr += rClassName;
+	            classStr.append(rClassName);
 	            if (classIt.hasNext()) {
-	            	classStr += ", ";
+	            	classStr.append(", ");
 	            }
 	        }
         }
-        results.add(classStr);
+        results.add(classStr.toString());
                 
 		results.add(ent.getHiddenFromDisplayBelowRoleLevel() == null ? "unspecified"
 				: ent.getHiddenFromDisplayBelowRoleLevel().getDisplayLabel());
@@ -142,10 +144,8 @@ public class EntityEditController extends BaseEditController {
         try {
             List<Option> externalIdOptionList = new LinkedList<Option>();
             if (ent.getExternalIds() != null) {
-                Iterator<DataPropertyStatement> externalIdIt = ent.getExternalIds().iterator();
+                for (DataPropertyStatement eid : ent.getExternalIds()) {
-                while (externalIdIt.hasNext()) {
+                    String multiplexedString = "DatapropURI:" + new String(Base64.encodeBase64(eid.getDatapropURI().getBytes())) + ";" + "Data:" + new String(Base64.encodeBase64(eid.getData().getBytes()));
-                    DataPropertyStatement eid = externalIdIt.next();
-                    String multiplexedString = new String ("DatapropURI:" + new String(Base64.encodeBase64(eid.getDatapropURI().getBytes())) + ";" + "Data:" + new String(Base64.encodeBase64(eid.getData().getBytes())));
                     externalIdOptionList.add(new Option(multiplexedString, eid.getData()));
                 }
             }
@@ -167,11 +167,9 @@ public class EntityEditController extends BaseEditController {
         try {
             List epiOptionList = new LinkedList();
             Collection<PropertyInstance> epiColl = piDao.getExistingProperties(ent.getURI(),null);
-            Iterator<PropertyInstance> epiIt = epiColl.iterator();
+            for (PropertyInstance pi : epiColl) {
-            while (epiIt.hasNext()) {
+                String multiplexedString = "PropertyURI:" + new String(Base64.encodeBase64(pi.getPropertyURI().getBytes())) + ";" + "ObjectEntURI:" + new String(Base64.encodeBase64(pi.getObjectEntURI().getBytes()));
-                PropertyInstance pi = epiIt.next();
+                epiOptionList.add(new Option(multiplexedString, pi.getDomainPublic() + " " + pi.getObjectName()));
-                String multiplexedString = new String ("PropertyURI:" + new String(Base64.encodeBase64(pi.getPropertyURI().getBytes())) + ";" + "ObjectEntURI:" + new String(Base64.encodeBase64(pi.getObjectEntURI().getBytes())));
-                epiOptionList.add(new Option(multiplexedString, pi.getDomainPublic()+" "+pi.getObjectName()));
             }
             OptionMap.put("ExistingPropertyInstances", epiOptionList);
         } catch (Exception e) {
@@ -209,7 +207,7 @@ public class EntityEditController extends BaseEditController {
 
     public void doPost (HttpServletRequest request, HttpServletResponse response) {
     	log.trace("Please don't POST to the "+this.getClass().getName()+". Use GET instead as there should be no change of state.");
-        doPost(request,response);
+        doGet(request,response);
     }
 
 }

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

@@ -14,11 +14,12 @@ import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import edu.cornell.mannlib.vitro.webapp.utils.JSPPageHandler;
-import org.apache.commons.collections.map.ListOrderedMap;
+import org.apache.commons.collections4.map.ListOrderedMap;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -51,6 +52,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.edit.listener.impl.IndividualDataPropertyStatementProcessor;
 
+@WebServlet(name = "EntityRetryController", urlPatterns = {"/entity_retry"} )
 public class EntityRetryController extends BaseEditController {
 	
 	private static final Log log = LogFactory.getLog(EntityRetryController.class.getName());
@@ -209,30 +211,26 @@ public class EntityRetryController extends BaseEditController {
         Collections.sort(allApplicableDataprops);
         
         if (allApplicableDataprops != null) {
-            Iterator<DataProperty> datapropsIt = allApplicableDataprops.iterator();
 
-            while (datapropsIt.hasNext()){
+            for (DataProperty d : allApplicableDataprops) {
-                DataProperty d = datapropsIt.next();
                 if (!dpMap.containsKey(d.getURI())) {
-                    dpMap.put(d.getURI(),d);
+                    dpMap.put(d.getURI(), d);
                 }
-				
+
             }
 
             if (individualForEditing.getDataPropertyList() != null) {
-                Iterator<DataProperty> existingDps = individualForEditing.getDataPropertyList().iterator();
+                for (DataProperty existingDp : individualForEditing.getDataPropertyList()) {
-                while (existingDps.hasNext()) {
+                    // Since the edit form begins with a "name" field, which gets saved as the rdfs:label,
-                    DataProperty existingDp = existingDps.next();
+                    // do not want to include the label as well.
-					// Since the edit form begins with a "name" field, which gets saved as the rdfs:label,
+                    if (!existingDp.getPublicName().equals("label")) {
-					// do not want to include the label as well. 
+                        dpMap.put(existingDp.getURI(), existingDp);
-					if ( !existingDp.getPublicName().equals("label") ) {
+                    }
-						dpMap.put(existingDp.getURI(),existingDp);
-					}
                 }
             }
 
             List<DynamicField> dynamicFields = new ArrayList();
-            Iterator<String> dpHashIt = dpMap.orderedMapIterator();
+            Iterator<String> dpHashIt = dpMap.mapIterator();
             while (dpHashIt.hasNext()) {
                 String uri = dpHashIt.next();
                 DataProperty dp = (DataProperty) dpMap.get(uri);
@@ -247,9 +245,7 @@ public class EntityRetryController extends BaseEditController {
                 rowTemplate.setParameterMap(parameterMap);
                 dynamo.setRowTemplate(rowTemplate);
                 try {
-                    Iterator<DataPropertyStatement> existingValues = dp.getDataPropertyStatements().iterator();
+                    for (DataPropertyStatement existingValue : dp.getDataPropertyStatements()) {
-                    while (existingValues.hasNext()) {
-                        DataPropertyStatement existingValue = existingValues.next();
                         DynamicFieldRow row = new DynamicFieldRow();
                         //TODO: UGH
                         //row.setId(existingValue.getId());

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/FauxPropertyRetryController.java

@@ -244,8 +244,7 @@ public class FauxPropertyRetryController extends BaseEditController {
 		private List<Option> createClassGroupOptionList() {
 			List<Option> groupOptList = getGroupOptList(beanForEditing
 					.getGroupURI());
-			Collections.sort(groupOptList,
+			groupOptList.sort(new OptionsBodyComparator(req.getCollator()));
-					new OptionsBodyComparator(req.getCollator()));
 			groupOptList.add(0, new Option("", "none"));
 			return groupOptList;
 		}
@@ -322,12 +321,12 @@ public class FauxPropertyRetryController extends BaseEditController {
 					list.add(option);
 				}
 			}
-			Collections.sort(list, new Comparator<Option>() {
+			list.sort(new Comparator<Option>() {
-				@Override
+                @Override
-				public int compare(Option o1, Option o2) {
+                public int compare(Option o1, Option o2) {
-					return o1.getBody().compareTo(o2.getBody());
+                    return o1.getBody().compareTo(o2.getBody());
-				}
+                }
-			});
+            });
 		}
 
 		private static class OptionsBodyComparator implements

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

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.controller.edit;
 import java.io.IOException;
 import java.util.HashMap;
 
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -17,6 +18,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
 
+@WebServlet(name = "IndividualTypeOperationController", urlPatterns = {"/individualTypeOp"} )
 public class IndividualTypeOperationController extends BaseEditController {
 
     private static final Log log = LogFactory.getLog(IndividualTypeOperationController.class.getName());
@@ -65,9 +67,9 @@ public class IndividualTypeOperationController extends BaseEditController {
 	                String[] typeURIstrs = request.getParameterValues("TypeURI");
 	                String individualURIstr = request.getParameter("individualURI");
 	                    if (individualURIstr != null) {
-	                        for (int i=0; i<typeURIstrs.length; i++) {                        	
+                            for (String typeURIstr : typeURIstrs) {
-	                            dao.removeVClass(individualURIstr, typeURIstrs[i]);
+                                dao.removeVClass(individualURIstr, typeURIstr);
-	                        }
+                            }
 	                    }
 	            } else if (request.getParameter("operation").equals("add")) {
 		                dao.addVClass(request.getParameter("individualURI"),request.getParameter("TypeURI"));

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

@@ -60,16 +60,12 @@ public class IndividualTypeRetryController extends BaseEditController {
 	    sortForPickList(allVClasses, vreq);
 			
 		Set<String> prohibitedURIset = new HashSet<String>();
-		for (Iterator<VClass> indClassIt = ind.getVClasses(false).iterator(); indClassIt.hasNext(); ) {
+		for (VClass vc : ind.getVClasses(false)) {
-			VClass vc = indClassIt.next();
+			if (vc.isAnonymous()) {
-			if(vc.isAnonymous()) {
+				continue;
-			    continue;
 			}
 			prohibitedURIset.add(vc.getURI());
-			for (Iterator<String> djURIIt = vcDao.getDisjointWithClassURIs(vc.getURI()).iterator(); djURIIt.hasNext(); ) {
+			prohibitedURIset.addAll(vcDao.getDisjointWithClassURIs(vc.getURI()));
-				String djURI = djURIIt.next();
-	            prohibitedURIset.add(djURI);
-			}
 		}
 		
 		List<VClass> eligibleVClasses = new ArrayList<VClass>();

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/Logout.java

@@ -2,6 +2,7 @@
 
 package edu.cornell.mannlib.vitro.webapp.controller.edit;
 
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
@@ -17,6 +18,7 @@ import edu.cornell.mannlib.vitro.webapp.i18n.I18n;
 /**
  * Provide a means for programmatic logout.
  */
+@WebServlet(name = "logout", urlPatterns = {"/logout"})
 public class Logout extends HttpServlet {
 	private static final Log log = LogFactory.getLog(Logout.class.getName());
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/MenuManagementEdit.java

@@ -8,12 +8,14 @@ import java.io.StringWriter;
 import java.io.Writer;
 
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import com.fasterxml.jackson.databind.node.ObjectNode;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.json.JSONObject;
 
 import org.apache.jena.ontology.OntModel;
 import org.apache.jena.rdf.model.Model;
@@ -31,6 +33,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
  *Process edits from display model editing, so form should submit to this page which should
  *then process the parameters and then make the necessary changes to the model.
  */
+@WebServlet(name = "MenuManagementEdit", urlPatterns = {"/menuManagementEdit"} )
 public class MenuManagementEdit extends VitroHttpServlet {
    private static final String CMD_PARAM = "cmd";   
    private final static String REORDER_PARAM_VALUE = "Reorder";
@@ -137,7 +140,7 @@ public class MenuManagementEdit extends VitroHttpServlet {
     
     private void sendReorderResponse(String errorMessage, HttpServletResponse resp) {
     	try{
-			JSONObject rObj = new JSONObject();
+			ObjectNode rObj = JsonNodeFactory.instance.objectNode();
 			resp.setCharacterEncoding("UTF-8");
 			resp.setContentType("application/json;charset=UTF-8");
       

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/NamespacePrefixOperationController.java

@@ -6,6 +6,7 @@ import java.io.IOException;
 import java.util.HashMap;
 import java.util.HashSet;
 
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -27,6 +28,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 
+@WebServlet(name = "NamespacePrefixOperationController", urlPatterns = {"/namespacePrefixOp"} )
 public class NamespacePrefixOperationController extends BaseEditController {
 
     private static final Log log = LogFactory.getLog(IndividualTypeOperationController.class.getName());

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

@@ -122,9 +122,7 @@ public class ObjectPropertyStatementRetryController extends BaseEditController {
         indList.addAll(possIndSet);
         sortForPickList(indList, vreq);
         List objectEntOptionList = new LinkedList();
-        Iterator<Individual> indIt = indList.iterator();
+        for (Individual objInd : indList) {
-        while (indIt.hasNext()) {
-            Individual objInd = indIt.next();
             Option objIndOpt = new Option(objInd.getURI(), objInd.getName());
             if (objectForEditing.getObjectEntURI() != null && objectForEditing.getObjectEntURI().equals(objInd.getURI())) {
                 objIndOpt.setSelected(true);

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

@@ -6,6 +6,7 @@ import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -25,6 +26,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.OntologyDaoJena;
 
+@WebServlet(name = "OntologyEditController", urlPatterns = {"/ontologyEdit"} )
 public class OntologyEditController extends BaseEditController {
     private static final Log log = LogFactory.getLog(OntologyEditController.class.getName());
 

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

@@ -4,6 +4,7 @@ package edu.cornell.mannlib.vitro.webapp.controller.edit;
 
 import static javax.servlet.http.HttpServletResponse.SC_UNAUTHORIZED;
 
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.lang3.StringUtils;
@@ -18,6 +19,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 
 
+@WebServlet(name = "primitiveDelete", urlPatterns = {"/edit/primitiveDelete"})
 public class PrimitiveDelete extends VitroAjaxController {
 
     private static final long serialVersionUID = 1L;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/PrimitiveRdfEdit.java

@@ -12,6 +12,7 @@ import java.util.HashSet;
 import java.util.Set;
 
 import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.logging.Log;
@@ -30,6 +31,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.N3EditUtils;
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.StandardModelSelector;
 
+@WebServlet(name = "primitiveRdfEdit", urlPatterns = {"/edit/primitiveRdfEdit"})
 public class PrimitiveRdfEdit extends VitroAjaxController {
 
     private static final long serialVersionUID = 1L;