From 056c4f9628104ad0d31bd376aaf5bb9f2e0bd5d0 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 19 Feb 2026 18:15:18 +0000
Subject: [PATCH 1/4] Initial plan


From 8056e8fbf0397c50ae074ce365f16ecb69855d24 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 19 Feb 2026 18:18:11 +0000
Subject: [PATCH 2/4] Remove unreachable /test/testParser.html mapping and
 legacy JSP files

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
---
 .../main/webapp/WEB-INF/pages/testParser.jsp  |   2 -
 .../webapp/WEB-INF/pages/testParserResult.jsp | 222 ------------------
 .../main/webapp/WEB-INF/treebase-servlet.xml  |   2 -
 3 files changed, 226 deletions(-)
 delete mode 100644 treebase-web/src/main/webapp/WEB-INF/pages/testParser.jsp
 delete mode 100644 treebase-web/src/main/webapp/WEB-INF/pages/testParserResult.jsp
diff --git a/treebase-web/src/main/webapp/WEB-INF/pages/testParser.jsp b/treebase-web/src/main/webapp/WEB-INF/pages/testParser.jsp
deleted file mode 100644
index 83e8cd41e..000000000
--- a/treebase-web/src/main/webapp/WEB-INF/pages/testParser.jsp
+++ /dev/null
@@ -1,2 +0,0 @@
-<c:url var="treeParser" value="/user/treeParser.html" />
-<c:redirect url="${treeParser}" />
\ No newline at end of file
diff --git a/treebase-web/src/main/webapp/WEB-INF/pages/testParserResult.jsp b/treebase-web/src/main/webapp/WEB-INF/pages/testParserResult.jsp
deleted file mode 100644
index e6fb12c86..000000000
--- a/treebase-web/src/main/webapp/WEB-INF/pages/testParserResult.jsp
+++ /dev/null
@@ -1,222 +0,0 @@
-<%@ include file="/common/taglibs.jsp"%>
-<head>
-<title>Nexus Parser Test Result</title>
-<content tag="heading">Tree View</content>
-
-<script type="text/javascript" src="../scripts/xp_progress.js"></script>
-
-<script type="text/javascript">
-
-function show_or_hide(layer_ref, state) { 
-  if (document.all) { //IS IE 4 or 5 (or 6 beta) 
-    eval( "document.all." + layer_ref + ".style.display = state"); 
-  } 
-  else if (document.layers) { //IS NETSCAPE 4 or below 
-    document.layers[layer_ref].display = state; 
-  } 
-  else if (document.getElementById && !document.all) { 
-    hza = document.getElementById(layer_ref); 
-    hza.style.display = state; 
-  } 
-} 
-
-
-</script>
-<style type="text/css">
-
- h2 span   {margin-left: 2em;  background: #FFE4B5;}
- h3 span   {margin-left: 6em;  background: #B0E0E6;}
- h4 span1  {margin-left: 10em; background: #ffcccc;}
- h4 span2  {margin-left: 13em; background: #F0E68C;}
- h4 span3  {margin-left: 16em; background: #ccffff;}
- h4 span4  {margin-left: 19em; background: #ccff99;}
- h4 span5  {margin-left: 22em; background: #FFEBCD;}
- h4 span6  {margin-left: 25em; background: #E0FFFF;}
- h4 span7  {margin-left: 28em; background: #ffff99;}
- h4 span8  {margin-left: 31em; background: #E6E6FA;}
- h4 span9  {margin-left: 34em; background: #FFEFD5;}
- h4 span10 {margin-left: 37em; background: #ccffff;}
- h4 span11 {margin-left: 40em; background: #FAFAD2;}
- h4 span12 {margin-left: 43em; background: #F0FFF0;}
- h4 span13 {margin-left: 46em; background: #FFFFF0;}
- h4 span14 {margin-left: 49em; }
- h4 span15 {margin-left: 52em; }
- h4 span16 {margin-left: 55em; }
- h4 span17 {margin-left: 58em; }
- h4 span18 {margin-left: 61em; }
-  
- h2.main { background: #F0F8FF; width: 96%; text-align: center;
-    font-family: "Times Roman";  padding: 4Px; }
- p.caption {color: black; background: #EEE; width: 200Px;
-   text-align: center; font-size: 12Px; padding: 3Px;}
-   
- a:link, a:visited, a:after {
-	background: transparent;
-	font-size: 11pt;
-	text-decoration: underline;
- }
- 
- </style>
-</head>
-
-<body id="submissions">
-
-
-<form method="post" >
-
-<p>The result of the Nexus Parsing: </p>
-
-<fieldset>
-<legend>Study Details</legend>
-
-<table border="0" cellpadding="5" cellspacing="5">
-
-	<tr>
-		<th>Study ID:</th>
-		<td><c:out value="${study.id}"/></td>
-       	<td>
-       		<strong>Study Name: </strong>
-        
-            <spring:bind path="study.name">
-            	<c:out value="${status.value}"/>
-            </spring:bind>
-        </td>
-	</tr>	
-	<tr>
-    </tr>
-    </table>
-    
-    <c:url var="xmlURL" value="/test/viewXML.html" />
-    <c:url var="matrixURL" value="/test/matrixList.html" />
-	
-	<a href="<c:out value="${xmlURL}"/>" target = "_blank">View Phylotree(s) in XML format</a> <br/>
-    <a href="<c:out value="${matrixURL}"/>" target = "_blank">View Matrices</a> <br/><br/>
-   			 			
-   			<h2 class = "main"> There 
-   				<c:if test="${treesSize > 1}" > are </c:if>
-   				<c:if test="${treesSize == 1}" > is </c:if>
-   				<c:out value="${treesSize}"/> tree<c:if test="${treesSize > 1}">s</c:if>
-   				 displayed below.  </h2> <br/>
-   				 
-        		<c:forEach var="tree" items="${trees}">
-
-        			<h2 class = "main">Title--<c:out value="${tree.title}"/>  </h2> <br/>	
-        			<h2 class = "main">Root-<c:out value="${tree.rootNode.id}"/> </h2>	<br/>
-        				
-        				<c:forEach var="childnode_1" items="${tree.rootNode.childNodes}">
-        				  
-        				  <h2><span>L1-----------------------------------------------------------------------<c:out value="${childnode_1.id}"/><c:if test="${childnode_1.branchLength ne 0.0}">:<c:out value="${childnode_1.branchLength}"/></c:if><c:if test="${childnode_1.taxonLabelAsString ne null}">-<c:out value="${childnode_1.taxonLabelAsString}"/> </c:if> </span> </h2> 
-        				    
-        				    <c:forEach var="childnode_2" items="${childnode_1.childNodes}">
-        				    	
-        				    	<h3><span>L2-------------------------------------------------------------------------------------<c:out value="${childnode_2.id}"/><c:if test="${childnode_2.branchLength ne 0.0}">:<c:out value="${childnode_2.branchLength}"/></c:if><c:if test="${childnode_2.taxonLabelAsString ne null}">-<c:out value="${childnode_2.taxonLabelAsString}"/> </c:if> </span></h3>
-        				    	<c:forEach var="childnode_3" items="${childnode_2.childNodes}">
-        				    	
-        				    		<h4><span1>L3----------------------------------------------------------------------------------------------<c:out value="${childnode_3.id}"/><c:if test="${childnode_3.branchLength ne 0.0}">:<c:out value="${childnode_3.branchLength}"/></c:if><c:if test="${childnode_3.taxonLabelAsString ne null}">-<c:out value="${childnode_3.taxonLabelAsString}"/>	</c:if></span2> </h4>		    		
-        							<c:forEach var="childnode_4" items="${childnode_3.childNodes}">
-        				    	
-        				    			<h4><span2>L4-----------------------------------------------------------------------------------------<c:out value="${childnode_4.id}"/><c:if test="${childnode_4.branchLength ne 0.0}">:<c:out value="${childnode_4.branchLength}"/></c:if><c:if test="${childnode_4.taxonLabelAsString ne null}">-<c:out value="${childnode_4.taxonLabelAsString}"/></c:if></span2> </h4>
-        				    			<c:forEach var="childnode_5" items="${childnode_4.childNodes}">
-        				    	
-        				    				<h4><span3>L5-----------------------------------------------------------------------------------<c:out value="${childnode_5.id}"/><c:if test="${childnode_5.branchLength ne 0.0}">:<c:out value="${childnode_5.branchLength}"/></c:if><c:if test="${childnode_5.taxonLabelAsString ne null}">-<c:out value="${childnode_5.taxonLabelAsString}"/></c:if></span3> </h4>
-        				    				<c:forEach var="childnode_6" items="${childnode_5.childNodes}">
-        				    	
-        				    					<h4><span4>L6------------------------------------------------------------------------------<c:out value="${childnode_6.id}"/><c:if test="${childnode_6.branchLength ne 0.0}">:<c:out value="${childnode_6.branchLength}"/></c:if><c:if test="${childnode_6.taxonLabelAsString ne null}">-<c:out value="${childnode_6.taxonLabelAsString}"/></c:if></span4> </h4>
-        				    					<c:forEach var="childnode_7" items="${childnode_6.childNodes}">
-        				    	
-        				    						<h4><span5>L7------------------------------------------------------------------------<c:out value="${childnode_7.id}"/><c:if test="${childnode_7.branchLength ne 0.0}">:<c:out value="${childnode_7.branchLength}"/></c:if><c:if test="${childnode_7.taxonLabelAsString ne null}">-<c:out value="${childnode_7.taxonLabelAsString}"/></c:if></span5> </h4>
-        				    						<c:forEach var="childnode_8" items="${childnode_7.childNodes}">
-        				    	
-        				    							<h4><span6>L8------------------------------------------------------------------<c:out value="${childnode_8.id}"/><c:if test="${childnode_8.branchLength ne 0.0}">:<c:out value="${childnode_8.branchLength}"/></c:if><c:if test="${childnode_8.taxonLabelAsString ne null}">-<c:out value="${childnode_8.taxonLabelAsString}"/> </c:if> </span6> </h4>
-        				    							<c:forEach var="childnode_9" items="${childnode_8.childNodes}">
-        				    	
-        				    								<h4><span7>L9-------------------------------------------------------------<c:out value="${childnode_9.id}"/><c:if test="${childnode_9.branchLength ne 0.0}">:<c:out value="${childnode_9.branchLength}"/></c:if><c:if test="${childnode_9.taxonLabelAsString ne null}">-<c:out value="${childnode_9.taxonLabelAsString}"/> </c:if> </span7> </h4>
-        				    								<c:forEach var="childnode_10" items="${childnode_9.childNodes}">
-        				    	
-        				    									<h4><span8>L10------------------------------------------------------<c:out value="${childnode_10.id}"/><c:if test="${childnode_10.branchLength != 0.0}">:<c:out value="${childnode_10.branchLength}"/></c:if><c:if test="${childnode_10.taxonLabelAsString ne null}">-<c:out value="${childnode_10.taxonLabelAsString}"/> </c:if> </span8> </h4>
-        				    									<c:forEach var="childnode_11" items="${childnode_10.childNodes}">
-        				    	
-        				    										<h4><span9>L11-------------------------------------------------<c:out value="${childnode_11.id}"/><c:if test="${childnode_11.branchLength != 0.0}">:<c:out value="${childnode_11.branchLength}"/></c:if><c:if test="${childnode_11.taxonLabelAsString ne null}">-<c:out value="${childnode_11.taxonLabelAsString}"/> </c:if> </span9> </h4>
-        				    										<c:forEach var="childnode_12" items="${childnode_11.childNodes}">
-        				    	
-        				    											<h4><span10>L12-------------------------------------------<c:out value="${childnode_12.id}"/><c:if test="${childnode_12.branchLength != 0.0}">:<c:out value="${childnode_12.branchLength}"/></c:if><c:if test="${childnode_12.taxonLabelAsString ne null}">-<c:out value="${childnode_12.taxonLabelAsString}"/></c:if></span10> </h4>
-        				    											<c:forEach var="childnode_13" items="${childnode_12.childNodes}">
-        				    	
-        				    												<h4><span11>L13---------------------------------------<c:out value="${childnode_13.id}"/><c:if test="${childnode_13.branchLength != 0.0}">:<c:out value="${childnode_13.branchLength}"/></c:if><c:if test="${childnode_13.taxonLabelAsString ne null}">-<c:out value="${childnode_13.taxonLabelAsString}"/> </c:if> </span11> </h4>
-        				    												<c:forEach var="childnode_14" items="${childnode_13.childNodes}">
-        				    	
-        				    													<h4><span12>L14----------------------------------<c:out value="${childnode_14.id}"/><c:if test="${childnode_14.branchLength != 0.0}">:<c:out value="${childnode_14.branchLength}"/></c:if><c:if test="${childnode_14.taxonLabelAsString ne null}"> -<c:out value="${childnode_14.taxonLabelAsString}"/> </c:if> </span12> </h4>
-        				    													<c:forEach var="childnode_15" items="${childnode_14.childNodes}">
-        				    	
-        				    														<h4><span13>L15----------------------------<c:out value="${childnode_15.id}"/><c:if test="${childnode_15.branchLength != 0.0}">:<c:out value="${childnode_15.branchLength}"/></c:if><c:if test="${childnode_15.taxonLabelAsString ne null}">-<c:out value="${childnode_15.taxonLabelAsString}"/> </c:if> </span13> </h4>
-        				    														<c:forEach var="childnode_16" items="${childnode_15.childNodes}">
-        				    	
-        				    															<h4><span14>L16-----------------------<c:out value="${childnode_16.id}"/><c:if test="${childnode_16.branchLength != 0.0}">:<c:out value="${childnode_16.branchLength}"/></c:if><c:if test="${childnode_16.taxonLabelAsString ne null}">-<c:out value="${childnode_16.taxonLabelAsString}"/> </c:if> </span14> </h4>
-        				    															<c:forEach var="childnode_17" items="${childnode_16.childNodes}">
-        				    	
-        				    																<h4><span15>L17------------------<c:out value="${childnode_17.id}"/><c:if test="${childnode_17.branchLength != 0.0}">:<c:out value="${childnode_17.branchLength}"/></c:if><c:if test="${childnode_17.taxonLabelAsString ne null}">-<c:out value="${childnode_17.taxonLabelAsString}"/> </c:if> </span15> </h4>
-        				    																<c:forEach var="childnode_18" items="${childnode_17.childNodes}">
-        				    	
-        				    																	<h4><span16>L18------------<c:out value="${childnode_18.id}"/><c:if test="${childnode_18.branchLength != 0.0}">:<c:out value="${childnode_18.branchLength}"/></c:if><c:if test="${childnode_18.taxonLabelAsString ne null}">-<c:out value="${childnode_18.taxonLabelAsString}"/> </c:if> </span16> </h4>
-        				    																	<c:forEach var="childnode_19" items="${childnode_18.childNodes}">
-        				    	
-        				    																		<h4><span17>L19------<c:out value="${childnode_19.id}"/><c:if test="${childnode_19.branchLength != 0.0}">:<c:out value="${childnode_19.branchLength}"/></c:if><c:if test="${childnode_19.taxonLabelAsString ne null}">-<c:out value="${childnode_19.taxonLabelAsString}"/> </c:if> </span17> </h4>
-        				    																		<c:forEach var="childnode_20" items="${childnode_19.childNodes}">
-        				    	
-        				    																			<h4><span18>L20---<c:out value="${childnode_20.id}"/><c:if test="${childnode_20.branchLength != 0.0}">:<c:out value="${childnode_20.branchLength}"/></c:if><c:if test="${childnode_20.taxonLabelAsString ne null}">-<c:out value="${childnode_20.taxonLabelAsString}"/> </c:if> </span18> </h4>
-        																							</c:forEach>
-        																						</c:forEach>
-        																					</c:forEach>
-        																				</c:forEach>
-        																			</c:forEach>
-        																		</c:forEach>
-        																	</c:forEach>
-        																</c:forEach>
-        															</c:forEach>
-        														</c:forEach>
-        													</c:forEach>
-        												</c:forEach>
-        											</c:forEach>
-        										</c:forEach>
-        									</c:forEach>
-        								</c:forEach>
-        							</c:forEach>
-        						
-        						</c:forEach>
-        					</c:forEach>
-        				</c:forEach>
-        				
-        		</c:forEach>
-        	
- 
-    <table>
-    <!--  tr>
-    	<th>&nbsp;</th>
-    	<td>
-
-    		<input type="submit" name="Delete" value="<fmt:message key="button.clean"/>" onclick="show_or_hide('kids', 'block');" />
-    	</td>
-    </tr -->
-    <!-- tr>
-    		<th>&nbsp;</th>
-    		<td>
-    		Pressing this button <br/>
-    		will erase the tree(s)<br/>
-    		related to this <br/>
-    		particular study.
-    		</td>
-    	
-    </tr -->	
-</table>
-
-<!--  <div id="kids" style="display: none;">
-		<h3>Cleaning ...</h3>
-        <script type="text/javascript">
-          var bar1= createBar(500,15,'white',1,'black','#7DCBDA',85,7,3,"");
-        </script>
-</div> -->
-
-</fieldset>
-</form>
-</body>
-
diff --git a/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml b/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
index 48d7cf12b..879907602 100644
--- a/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
+++ b/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
@@ -1010,8 +1010,6 @@
 				
 				<!-- appletInteraction removed - Java applets are no longer supported in browsers -->
 				
-				<prop key="/test/testParser.html">treeParserController</prop>
-				
 				<prop key="/admin/userManagement.html">userManagementController</prop>
 				<prop key="/admin/selectStudies.html">selectStudiesController</prop>
 				<prop key="/admin/changeStudyStatus.html">changeStudyStatusController</prop>

From 52d7a50253f1809ef07ead900753da63d6274f28 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 19 Feb 2026 18:32:10 +0000
Subject: [PATCH 3/4] Fix CI rebase conflict handling in gh-pages deployment
 step

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
---
 .github/workflows/ci.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index becc26c26..02c5c09c1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -191,7 +191,9 @@ jobs:
           # Pull with rebase to handle concurrent updates
           git pull --rebase origin gh-pages || {
             echo "Rebase failed, attempting force push"
+            git rebase --abort
             git push --force
+            exit 0
           }
           git push
         fi

From 530a317f8fe985d52c14ea8ceb4161c2dd51c3f3 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 19 Feb 2026 18:43:20 +0000
Subject: [PATCH 4/4] Minimize treebase-servlet.xml diff: only remove
 testParser prop

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
---
 .../main/webapp/WEB-INF/treebase-servlet.xml  | 774 +++++++++---------
 1 file changed, 387 insertions(+), 387 deletions(-)

diff --git a/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml b/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
index 73bbdac7f..c8205bdd4 100644
--- a/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
+++ b/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-
+
 <beans xmlns="http://www.springframework.org/schema/beans"
 	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
     xmlns:dwr="http://www.directwebremoting.org/schema/spring-dwr"
@@ -7,7 +7,7 @@
     http://www.springframework.org/schema/beans/spring-beans.xsd 
     http://www.directwebremoting.org/schema/spring-dwr  
     http://www.directwebremoting.org/schema/spring-dwr-3.0.xsd">
-
+
 	
 	<!-- ========================================================== -->
 	<!-- velocity configure							                -->
@@ -16,9 +16,9 @@
    <bean id="velocityConfigurer" class="org.springframework.web.servlet.view.velocity.VelocityConfigurer">   
     <property name="resourceLoaderPath" value="/WEB-INF/vmFiles/" />
    </bean>
-	
-	<!-- ========================================================== -->
-	<!-- LIST OF CONTROLLERS FOR WEB-TIER							-->
+	
+	<!-- ========================================================== -->
+	<!-- LIST OF CONTROLLERS FOR WEB-TIER							-->
 	<!-- ========================================================== -->
 	
 	<bean id="processUserController" class="org.cipres.treebase.web.controllers.ProcessUserController">
@@ -27,7 +27,7 @@
 	</bean>
 	<bean id="anyObjectAsRDFController" class="org.cipres.treebase.web.controllers.AnyObjectAsRDFController">
 		<property name="studyService"><ref bean="studyService"></ref></property>	
-	</bean>
+	</bean>
 	<bean id="searchResultsAsRDFController" class="org.cipres.treebase.web.controllers.SearchResultsAsRDFController"/>	
 	
 	<bean id="readyStateStudiesController" class="org.cipres.treebase.web.controllers.ReadyStateStudiesController">
@@ -55,17 +55,17 @@
 	
 	<bean id="phyloWSClassificationController" class="org.cipres.treebase.web.controllers.PhyloWSClassificationController">		 
 	</bean>	
-	
-	<bean id="filenameController" class="org.cipres.treebase.web.controllers.ShortPathUrlFilenameViewController"/>
+	
+	<bean id="filenameController" class="org.cipres.treebase.web.controllers.ShortPathUrlFilenameViewController"/>
 	<!--bean id="filenameController" class="org.springframework.web.servlet.mvc.UrlFilenameViewController"/ -->
-	
-	<!-- for parsing file uploads. Implementation for Commons FileUpload -->
+	
+	<!-- for parsing file uploads. Implementation for Commons FileUpload -->
 	<!--bean id="multipartResolver" class="org.springframework.web.multipart.commons.CommonsMultipartResolver"-->
-	<bean id="multipartResolver" class="org.cipres.treebase.web.controllers.AjaxMultipartResolver">
-		<!--property name="uploadTempDir"><value></value></property-->
-		<property name="maxUploadSize"><value>250000000</value></property>		
+	<bean id="multipartResolver" class="org.cipres.treebase.web.controllers.AjaxMultipartResolver">
+		<!--property name="uploadTempDir"><value></value></property-->
+		<property name="maxUploadSize"><value>250000000</value></property>		
 	</bean>
-		
+		
 	<!--  bean to register a new user -->
 	<bean id="registerUserController" class="org.cipres.treebase.web.controllers.RegisterUserController">
 		<property name="commandName"><value>user</value></property>
@@ -136,29 +136,29 @@
 		<property name="formView"><value>readyState</value></property>
 		<property name="submissionService"><ref bean="submissionService"></ref></property>
 		<property name="studyService"><ref bean="studyService"></ref></property>
-	</bean>
-	
-	<!-- Download A Study -->	
-	<bean id="downloadAStudyController" class="org.cipres.treebase.web.controllers.DownloadAStudyController">
-		<property name="studyService"><ref bean="studyService"></ref></property>
-		<property name="nexmlService"><ref bean="nexmlService"></ref></property>
+	</bean>
+	
+	<!-- Download A Study -->	
+	<bean id="downloadAStudyController" class="org.cipres.treebase.web.controllers.DownloadAStudyController">
+		<property name="studyService"><ref bean="studyService"></ref></property>
+		<property name="nexmlService"><ref bean="nexmlService"></ref></property>
 		<property name="rdfaService"><ref bean="rdfaService"></ref></property>
-		<property name="submissionService"><ref bean="submissionService"></ref></property>
+		<property name="submissionService"><ref bean="submissionService"></ref></property>
 	</bean>	
 	
 	<!-- Download A Tree -->	
 	<bean id="downloadATreeController" class="org.cipres.treebase.web.controllers.DownloadATreeController">
 		<property name="studyService"><ref bean="studyService"></ref></property>
-		<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
-		<property name="nexmlService"><ref bean="nexmlService"></ref></property>
+		<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
+		<property name="nexmlService"><ref bean="nexmlService"></ref></property>
 		<property name="rdfaService"><ref bean="rdfaService"></ref></property>	
 		<property name="submissionService"><ref bean="submissionService"></ref></property>	
 	</bean>
 	
 	<bean id="downloadATreeBlockController" class="org.cipres.treebase.web.controllers.DownloadATreeBlockController">
 		<property name="studyService"><ref bean="studyService"></ref></property>
-		<property name="phyloTreeHome"><ref bean="phyloTreeHome"></ref></property>
-		<property name="nexmlService"><ref bean="nexmlService"></ref></property>
+		<property name="phyloTreeHome"><ref bean="phyloTreeHome"></ref></property>
+		<property name="nexmlService"><ref bean="nexmlService"></ref></property>
 		<property name="rdfaService"><ref bean="rdfaService"></ref></property>	
 		<property name="submissionHome"><ref bean="submissionHome"></ref></property>	
 		<property name="submissionService"><ref bean="submissionService"></ref></property>		
@@ -167,8 +167,8 @@
 	<!-- Download A Matrix -->	
 	<bean id="downloadAMatrixController" class="org.cipres.treebase.web.controllers.DownloadAMatrixController">
 		<property name="matrixService"><ref bean="matrixService"></ref></property>
-		<property name="studyService"><ref bean="studyService"></ref></property>
-		<property name="nexmlService"><ref bean="nexmlService"></ref></property>
+		<property name="studyService"><ref bean="studyService"></ref></property>
+		<property name="nexmlService"><ref bean="nexmlService"></ref></property>
 		<property name="rdfaService"><ref bean="rdfaService"></ref></property>	
 		<property name="submissionService"><ref bean="submissionService"></ref></property>			
 	</bean>
@@ -177,27 +177,27 @@
 	<bean id="downloadANexusFileController" class="org.cipres.treebase.web.controllers.DownloadANexusFileController">
 		<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
 		<property name="studyService"><ref bean="studyService"></ref></property>
-		<property name="matrixService"><ref bean="matrixService"></ref></property>
-		<property name="nexmlService"><ref bean="nexmlService"></ref></property>
+		<property name="matrixService"><ref bean="matrixService"></ref></property>
+		<property name="nexmlService"><ref bean="nexmlService"></ref></property>
 		<property name="rdfaService"><ref bean="rdfaService"></ref></property>	
 		<property name="submissionService"><ref bean="submissionService"></ref></property>			
-	</bean>
-	
-	<!-- Download An AnalysisStep's input and output as a NexusFile -->	
-	<bean id="downloadAnAnalysisStepController" class="org.cipres.treebase.web.controllers.DownloadAnAnalysisStepController">
-		<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
-		<property name="matrixService"><ref bean="matrixService"></ref></property>
-		<property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
-		<property name="nexmlService"><ref bean="nexmlService"></ref></property>
+	</bean>
+	
+	<!-- Download An AnalysisStep's input and output as a NexusFile -->	
+	<bean id="downloadAnAnalysisStepController" class="org.cipres.treebase.web.controllers.DownloadAnAnalysisStepController">
+		<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
+		<property name="matrixService"><ref bean="matrixService"></ref></property>
+		<property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
+		<property name="nexmlService"><ref bean="nexmlService"></ref></property>
 		<property name="rdfaService"><ref bean="rdfaService"></ref></property>	
 		<property name="studyService"><ref bean="studyService"></ref></property>		
-		<property name="submissionService"><ref bean="submissionService"></ref></property>	
+		<property name="submissionService"><ref bean="submissionService"></ref></property>	
 	</bean>	
 	
 	<!-- Download A NexusFile -->	
 	<bean id="downloadANexusRCTFileController" class="org.cipres.treebase.web.controllers.DownloadANexusRCTFileController">		
-		<property name="studyService"><ref bean="studyService"></ref></property>	
-		<property name="nexmlService"><ref bean="nexmlService"></ref></property>
+		<property name="studyService"><ref bean="studyService"></ref></property>	
+		<property name="nexmlService"><ref bean="nexmlService"></ref></property>
 		<property name="rdfaService"><ref bean="rdfaService"></ref></property>
 		<property name="submissionService"><ref bean="submissionService"></ref></property>				
 	</bean>
@@ -228,17 +228,17 @@
 		<property name="commandClass"><value>java.util.ArrayList</value></property>
 		<property name="successView"><value>redirect:/user/editSetTaxonLabel.html</value></property>
 		<property name="formView"><value>taxonLabels</value></property>
-	</bean>
-	<bean id="listTaxaSearchController"  class="org.cipres.treebase.web.controllers.ListTaxaSearchController">
-			<property name="formView"><value>search/taxonList</value></property>
-		    <property name="commandName"><value>taxonLabelStatus</value></property>
+	</bean>
+	<bean id="listTaxaSearchController"  class="org.cipres.treebase.web.controllers.ListTaxaSearchController">
+			<property name="formView"><value>search/taxonList</value></property>
+		    <property name="commandName"><value>taxonLabelStatus</value></property>
 	</bean>
 	
 	<!-- Edit Taxon Label -->	
 	<bean id="editTaxonLabelController" class="org.cipres.treebase.web.controllers.EditTaxonLabelController">
 		<property name="commandName"><value>txnlabel</value></property>
 		<property name="commandClass"><value>org.cipres.treebase.domain.taxon.TaxonLabel</value></property>
-		<property name="taxonLabelService"><ref bean="taxonLabelService"></ref></property>
+		<property name="taxonLabelService"><ref bean="taxonLabelService"></ref></property>
 		<property name="taxonHome"><ref bean="taxonHome"></ref></property>
 		<property name="studyService"><ref bean="studyService"></ref></property>
 		<property name="successView"><value>redirect:/user/taxaList.html</value></property>
@@ -269,92 +269,92 @@
 		<property name="commandClass"><value>org.cipres.treebase.domain.study.Citation</value></property>
 		<property name="formView"><value>submissionSummaryView</value></property>
 		<property name="submissionService"><ref bean="submissionService"></ref></property>
-	</bean>
-	
+	</bean>
+	
 	<bean id="searchSummaryController" class="org.cipres.treebase.web.controllers.SearchSummaryController">
-		<property name="sessionForm"><value>true</value></property>
-		<property name="commandName"><value>study</value></property>
-		<property name="commandClass"><value>org.cipres.treebase.domain.study.Study</value></property>
-		<property name="defaultPage"><value>search/summary</value></property>
-		<property name="studyService"><ref bean="studyService"></ref></property>
-		<property name="matrixService"><ref bean="matrixService"></ref></property>
-		<property name="matrixRowService"><ref bean="matrixRowService"></ref></property>
-		<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
-		<property name="analysisService"><ref bean="analysisService"></ref></property>
-		<property name="taxonLabelService"><ref bean="taxonLabelService"></ref></property>
+		<property name="sessionForm"><value>true</value></property>
+		<property name="commandName"><value>study</value></property>
+		<property name="commandClass"><value>org.cipres.treebase.domain.study.Study</value></property>
+		<property name="defaultPage"><value>search/summary</value></property>
+		<property name="studyService"><ref bean="studyService"></ref></property>
+		<property name="matrixService"><ref bean="matrixService"></ref></property>
+		<property name="matrixRowService"><ref bean="matrixRowService"></ref></property>
+		<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
+		<property name="analysisService"><ref bean="analysisService"></ref></property>
+		<property name="taxonLabelService"><ref bean="taxonLabelService"></ref></property>
 	</bean>
 	
 	<bean id="downloadRowSegmentDataController" class="org.cipres.treebase.web.controllers.DownloadRowSegmentDataController">
 		<property name="rowSegmentService"><ref bean="rowSegmentService"></ref></property>	
-	</bean>
-	
-	<!--  MultiActionController to display sumbissions by different criteria -->
-	<bean id="listSubmissionController" class="org.cipres.treebase.web.controllers.ListSubmissionController">
-		<property name="methodNameResolver"><ref bean="methodNameResolver"/></property>
+	</bean>
+	
+	<!--  MultiActionController to display sumbissions by different criteria -->
+	<bean id="listSubmissionController" class="org.cipres.treebase.web.controllers.ListSubmissionController">
+		<property name="methodNameResolver"><ref bean="methodNameResolver"/></property>
 		<property name="userService"><ref bean="userService"></ref></property>
-		<property name="submissionService"><ref bean="submissionService"></ref></property>
+		<property name="submissionService"><ref bean="submissionService"></ref></property>
 	</bean>
-	
-	<bean id="methodNameResolver" class="org.springframework.web.servlet.mvc.multiaction.ParameterMethodNameResolver">
-		<property name="paramName"><value>method</value></property>
-		<property name="defaultMethodName"><value>submissionsByUser</value></property>
+	
+	<bean id="methodNameResolver" class="org.springframework.web.servlet.mvc.multiaction.ParameterMethodNameResolver">
+		<property name="paramName"><value>method</value></property>
+		<property name="defaultMethodName"><value>submissionsByUser</value></property>
 	</bean>
-	
-	<bean id="citationFormController" class="org.cipres.treebase.web.controllers.CitationFormController">
-		<property name="commandName"><value>citation</value></property>
-		<property name="commandClass"><value>org.cipres.treebase.domain.study.Citation</value></property>
+	
+	<bean id="citationFormController" class="org.cipres.treebase.web.controllers.CitationFormController">
+		<property name="commandName"><value>citation</value></property>
+		<property name="commandClass"><value>org.cipres.treebase.domain.study.Citation</value></property>
 		<!-- property name="commandClass"><value>org.cipres.treebase.web.model.CitationCommand</value></property-->
-		<property name="formView"><value>citationForm</value></property>
+		<property name="formView"><value>citationForm</value></property>
 		<!--property name="successView"><value>redirect:/user/submissionMain.html</value></property-->
-		<property name="successView"><value>redirect:/user/summary.html</value></property>
+		<property name="successView"><value>redirect:/user/summary.html</value></property>
 		<!--property name="cancelView"><value>redirect:/user/submissionMain.html</value></property-->
 		<property name="cancelView"><value>redirect:/user/summary.html</value></property>
-		<property name="userService"><ref bean="userService"></ref></property>
-		<property name="submissionService"><ref bean="submissionService"></ref></property>
-		<property name="studyService"><ref bean="studyService"></ref></property>
-		<property name="citationService"><ref bean="citationService"></ref></property>
-	</bean>
-	
-	<bean id="studyFormController" class="org.cipres.treebase.web.controllers.StudyFormController">
-		<property name="commandName"><value>study</value></property>
-		<property name="commandClass"><value>org.cipres.treebase.domain.study.Study</value></property>
-		<property name="formView"><value>studyForm</value></property>
+		<property name="userService"><ref bean="userService"></ref></property>
+		<property name="submissionService"><ref bean="submissionService"></ref></property>
+		<property name="studyService"><ref bean="studyService"></ref></property>
+		<property name="citationService"><ref bean="citationService"></ref></property>
+	</bean>
+	
+	<bean id="studyFormController" class="org.cipres.treebase.web.controllers.StudyFormController">
+		<property name="commandName"><value>study</value></property>
+		<property name="commandClass"><value>org.cipres.treebase.domain.study.Study</value></property>
+		<property name="formView"><value>studyForm</value></property>
 		<!--property name="successView"><value>redirect:/user/submissionMain.html</value></property-->
-		<property name="successView"><value>redirect:/user/summary.html</value></property>
+		<property name="successView"><value>redirect:/user/summary.html</value></property>
 		<property name="cancelView"><value>redirect:/user/submissionList.html</value></property>
-		<property name="studyService"><ref bean="studyService"></ref></property>
-		<property name="submissionService"><ref bean="submissionService"></ref></property>
-		<property name="userService"><ref bean="userService"></ref></property>
-	</bean>
-	
-	<bean id="displaySubmissionMenuController" class="org.cipres.treebase.web.controllers.DisplaySubmissionMenuController">
-		<property name="studyService"><ref bean="studyService"></ref></property>
-	</bean>
-	
-	<bean id="submissionToJsonController" class="org.cipres.treebase.web.controllers.SubmissionToJsonController">
-		<property name="studyService"><ref bean="studyService"></ref></property>
-	</bean>
-	
-	<!-- bean id="displaySubmissionController" class="org.cipres.treebase.web.controllers.DisplaySubmissionController">
-		<property name="studyService"><ref bean="studyService"></ref></property>
-		<property name="submissionService"><ref bean="submissionService"></ref></property>
-	</bean-->
-	
-	<bean id="listSearchStudyController" class="org.cipres.treebase.web.controllers.ListSearchStudyController">
-		<property name="studyService"><ref bean="studyService"></ref></property>
-	</bean> 
-	
-	<!-- authorFormController IS REDUNDAND FOR NOW -->
-	<bean id="authorFormController" class="org.cipres.treebase.web.controllers.AuthorFormController">
-		<property name="commandName"><value>person</value></property>
-		<property name="commandClass"><value>org.cipres.treebase.domain.admin.Person</value></property>
-		<property name="formView"><value>peopleForm</value></property>
+		<property name="studyService"><ref bean="studyService"></ref></property>
+		<property name="submissionService"><ref bean="submissionService"></ref></property>
+		<property name="userService"><ref bean="userService"></ref></property>
+	</bean>
+	
+	<bean id="displaySubmissionMenuController" class="org.cipres.treebase.web.controllers.DisplaySubmissionMenuController">
+		<property name="studyService"><ref bean="studyService"></ref></property>
+	</bean>
+	
+	<bean id="submissionToJsonController" class="org.cipres.treebase.web.controllers.SubmissionToJsonController">
+		<property name="studyService"><ref bean="studyService"></ref></property>
+	</bean>
+	
+	<!-- bean id="displaySubmissionController" class="org.cipres.treebase.web.controllers.DisplaySubmissionController">
+		<property name="studyService"><ref bean="studyService"></ref></property>
+		<property name="submissionService"><ref bean="submissionService"></ref></property>
+	</bean-->
+	
+	<bean id="listSearchStudyController" class="org.cipres.treebase.web.controllers.ListSearchStudyController">
+		<property name="studyService"><ref bean="studyService"></ref></property>
+	</bean> 
+	
+	<!-- authorFormController IS REDUNDAND FOR NOW -->
+	<bean id="authorFormController" class="org.cipres.treebase.web.controllers.AuthorFormController">
+		<property name="commandName"><value>person</value></property>
+		<property name="commandClass"><value>org.cipres.treebase.domain.admin.Person</value></property>
+		<property name="formView"><value>peopleForm</value></property>
 		<!--property name="successView"><value>redirect:/user/submissionMain.html</value></property-->
 		<property name="successView"><value>redirect:/user/summary.html</value></property>
-		<!--property name="cancelView"><value>redirect:/user/submissionMain.html</value></property-->
+		<!--property name="cancelView"><value>redirect:/user/submissionMain.html</value></property-->
 		<property name="cancelView"><value>redirect:/user/summary.html</value></property>
-		<property name="studyService"><ref bean="studyService"></ref></property>
-		<property name="citationService"><ref bean="citationService"></ref></property>
+		<property name="studyService"><ref bean="studyService"></ref></property>
+		<property name="citationService"><ref bean="citationService"></ref></property>
 		<property name="personService"><ref bean="personService"></ref></property>
 		<property name="validators">
         	<list>
@@ -366,7 +366,7 @@
 		</property>
 		<property name="synchronizeOnSession">
     		<value>true</value>
-		</property>			
+		</property>			
 	</bean>
 	
 	<bean id="authorSearchFormController" class="org.cipres.treebase.web.controllers.AuthorFormController">
@@ -423,19 +423,19 @@
             	<ref bean="beanValidator"/>      <!--Commons Server-side validation -->
         	</list>
         </property>
-	</bean>
-	
-	<bean id="uploadFileController" class="org.cipres.treebase.web.controllers.UploadFileController">
-		<property name="commandClass"><value>org.cipres.treebase.web.model.MultiFileBean</value></property>
-		<property name="formView"><value>uploadFile</value></property>
+	</bean>
+	
+	<bean id="uploadFileController" class="org.cipres.treebase.web.controllers.UploadFileController">
+		<property name="commandClass"><value>org.cipres.treebase.web.model.MultiFileBean</value></property>
+		<property name="formView"><value>uploadFile</value></property>
 		<property name="successView"><value>redirect:/user/uploadFileSummary.html</value></property>
 		<property name="cancelView"><value>redirect:/user/summary.html</value></property>
-		<property name="userService"><ref bean="userService"></ref></property>
-		<property name="submissionService"><ref bean="submissionService"></ref></property>
-		<property name="studyService"><ref bean="studyService"></ref></property>
-		<property name="nexusService"><ref bean="nexusService"></ref></property>
-	</bean>
-	
+		<property name="userService"><ref bean="userService"></ref></property>
+		<property name="submissionService"><ref bean="submissionService"></ref></property>
+		<property name="studyService"><ref bean="studyService"></ref></property>
+		<property name="nexusService"><ref bean="nexusService"></ref></property>
+	</bean>
+	
 	<bean id="uploadFileSummaryController" class="org.cipres.treebase.web.controllers.UploadFileSummaryController">
 		<!--property name="commandClass">NOT NEEDED, as we have no form and spring binding<value>dummy</value></property-->
 		<!--property name="commandName">NOT NEEDED, as we have no form and spring binding<value>dummy</value></property-->
@@ -446,128 +446,128 @@
 	</bean>   
 	   
 
-	<bean id="listAnalysisController" class="org.cipres.treebase.web.controllers.ListAnalysisController">
-		<property name="studyService"><ref bean="studyService"></ref></property>
-	</bean>
-	
-	<bean id="displayAnalysisController" class="org.cipres.treebase.web.controllers.DisplayAnalysisController">
-		<property name="studyService"><ref bean="studyService"></ref></property>
-	</bean>
-	
-	<bean id="analysisFormController" class="org.cipres.treebase.web.controllers.AnalysisFormController">
-		<property name="commandName"><value>analysis</value></property>
-		<property name="commandClass"><value>org.cipres.treebase.domain.study.Analysis</value></property>
-		<property name="formView"><value>analysisForm</value></property>
-		<property name="successView"><value>redirect:/user/analysisDisplay.html</value></property>
+	<bean id="listAnalysisController" class="org.cipres.treebase.web.controllers.ListAnalysisController">
+		<property name="studyService"><ref bean="studyService"></ref></property>
+	</bean>
+	
+	<bean id="displayAnalysisController" class="org.cipres.treebase.web.controllers.DisplayAnalysisController">
+		<property name="studyService"><ref bean="studyService"></ref></property>
+	</bean>
+	
+	<bean id="analysisFormController" class="org.cipres.treebase.web.controllers.AnalysisFormController">
+		<property name="commandName"><value>analysis</value></property>
+		<property name="commandClass"><value>org.cipres.treebase.domain.study.Analysis</value></property>
+		<property name="formView"><value>analysisForm</value></property>
+		<property name="successView"><value>redirect:/user/analysisDisplay.html</value></property>
 		<property name="cancelView"><value>redirect:/user/analysisDisplay.html</value></property>
-		<property name="sessionForm"><value>true</value></property>
-		<property name="studyService"><ref bean="studyService"></ref></property>
+		<property name="sessionForm"><value>true</value></property>
+		<property name="studyService"><ref bean="studyService"></ref></property>
 		<property name="submissionService"><ref bean="submissionService"></ref></property>
-		<property name="analysisService"><ref bean="analysisService"></ref></property>
-	</bean>
-	
-	<bean id="listAnalysisStepController" class="org.cipres.treebase.web.controllers.ListAnalysisStepController">
-		<property name="studyService"><ref bean="studyService"></ref></property>
-		<property name="analysisService"><ref bean="analysisService"></ref></property>
-	</bean>
-	
-	<bean id="analysisStepFormController" class="org.cipres.treebase.web.controllers.AnalysisStepFormController">
-		<property name="commandName"><value>step</value></property>
-		<property name="commandClass"><value>org.cipres.treebase.web.model.AnalysisStepCommand</value></property>
-		<property name="formView"><value>analysisStepForm</value></property>
-		<property name="sessionForm"><value>true</value></property>
-		<!-- property name="successView"><value>redirect:/user/analysisStepList.html</value></property -->
-		<property name="successView"><value>redirect:/user/analysisDisplay.html</value></property>
+		<property name="analysisService"><ref bean="analysisService"></ref></property>
+	</bean>
+	
+	<bean id="listAnalysisStepController" class="org.cipres.treebase.web.controllers.ListAnalysisStepController">
+		<property name="studyService"><ref bean="studyService"></ref></property>
+		<property name="analysisService"><ref bean="analysisService"></ref></property>
+	</bean>
+	
+	<bean id="analysisStepFormController" class="org.cipres.treebase.web.controllers.AnalysisStepFormController">
+		<property name="commandName"><value>step</value></property>
+		<property name="commandClass"><value>org.cipres.treebase.web.model.AnalysisStepCommand</value></property>
+		<property name="formView"><value>analysisStepForm</value></property>
+		<property name="sessionForm"><value>true</value></property>
+		<!-- property name="successView"><value>redirect:/user/analysisStepList.html</value></property -->
+		<property name="successView"><value>redirect:/user/analysisDisplay.html</value></property>
 		<property name="cancelView"><value>redirect:/user/analysisDisplay.html</value></property>
-		<property name="studyService"><ref bean="studyService"></ref></property>
-		<property name="analysisService"><ref bean="analysisService"></ref></property>
+		<property name="studyService"><ref bean="studyService"></ref></property>
+		<property name="analysisService"><ref bean="analysisService"></ref></property>
 		<property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
 		<property name="analysisStepHome"><ref bean="analysisStepHome"></ref></property>
-		<property name="submissionService"><ref bean="submissionService"></ref></property>
-	</bean>
-	    
-	<bean id="searchFormController" class="org.cipres.treebase.web.controllers.SearchFormController">
-		<property name="commandName"><value>search</value></property>
-		<property name="commandClass"><value>org.cipres.treebase.web.model.SearchCommand</value></property>
-		<property name="formView"><value>searchForm</value></property>
-		<property name="successView"><value>redirect:/searchResult.html</value></property>
-	</bean>    
-	<bean id="updateStudyQueryController" class="org.cipres.treebase.web.controllers.UpdateStudyQueryController">
-		<property name="commandName"><value>search</value></property>
-		<property name="commandClass"><value>org.cipres.treebase.web.model.SearchCommand</value></property>
-		<property name="formView"><value>study-query</value></property>
-		<property name="successView"><value>redirect:/searchResult.html</value></property>
-	</bean>    
-	<bean id="searchStudyController" class="org.cipres.treebase.web.controllers.SearchStudyController">
-		<property name="studyService"><ref bean="studyService"></ref></property>
-		<property name="userService"><ref bean="userService"></ref></property>
-	</bean> 
-	<bean id="listAnalyzedDataController" class="org.cipres.treebase.web.controllers.ListAnalyzedDataController">
-		<property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
+		<property name="submissionService"><ref bean="submissionService"></ref></property>
+	</bean>
+	    
+	<bean id="searchFormController" class="org.cipres.treebase.web.controllers.SearchFormController">
+		<property name="commandName"><value>search</value></property>
+		<property name="commandClass"><value>org.cipres.treebase.web.model.SearchCommand</value></property>
+		<property name="formView"><value>searchForm</value></property>
+		<property name="successView"><value>redirect:/searchResult.html</value></property>
+	</bean>    
+	<bean id="updateStudyQueryController" class="org.cipres.treebase.web.controllers.UpdateStudyQueryController">
+		<property name="commandName"><value>search</value></property>
+		<property name="commandClass"><value>org.cipres.treebase.web.model.SearchCommand</value></property>
+		<property name="formView"><value>study-query</value></property>
+		<property name="successView"><value>redirect:/searchResult.html</value></property>
+	</bean>    
+	<bean id="searchStudyController" class="org.cipres.treebase.web.controllers.SearchStudyController">
+		<property name="studyService"><ref bean="studyService"></ref></property>
+		<property name="userService"><ref bean="userService"></ref></property>
+	</bean> 
+	<bean id="listAnalyzedDataController" class="org.cipres.treebase.web.controllers.ListAnalyzedDataController">
+		<property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
+	</bean> 
+	
+	 <bean id="analyzedDataFormController" class="org.cipres.treebase.web.controllers.AnalyzedDataFormController">
+		<property name="commandName"><value>data</value></property>
+		<property name="commandClass"><value>org.cipres.treebase.web.model.AnalyzedDataCommand</value></property>
+		<property name="analysisService"><ref bean="analysisService"></ref></property>
+		<property name="studyService"><ref bean="studyService"></ref></property>
+		<property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
+		<property name="matrixService"><ref bean="matrixService"></ref></property>
+		<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
+		<property name="analyzedDataService"><ref bean="analyzedDataService"></ref></property>
+		<property name="pages">
+			<list>
+				<value>analyzedDataForm</value>
+				<value>analyzedDataForm-matrixSelection</value>
+				<value>analyzedDataForm-treeSelection</value>
+				<value>analyzedDataForm-treeBlockSelection</value>
+			</list>
+		</property>
 	</bean> 
-	
-	 <bean id="analyzedDataFormController" class="org.cipres.treebase.web.controllers.AnalyzedDataFormController">
-		<property name="commandName"><value>data</value></property>
-		<property name="commandClass"><value>org.cipres.treebase.web.model.AnalyzedDataCommand</value></property>
-		<property name="analysisService"><ref bean="analysisService"></ref></property>
-		<property name="studyService"><ref bean="studyService"></ref></property>
-		<property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
-		<property name="matrixService"><ref bean="matrixService"></ref></property>
-		<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
-		<property name="analyzedDataService"><ref bean="analyzedDataService"></ref></property>
-		<property name="pages">
-			<list>
-				<value>analyzedDataForm</value>
-				<value>analyzedDataForm-matrixSelection</value>
-				<value>analyzedDataForm-treeSelection</value>
-				<value>analyzedDataForm-treeBlockSelection</value>
-			</list>
-		</property>
-	</bean> 
-	 
-	 <bean id="updateAnalyzedDataListController" class="org.cipres.treebase.web.controllers.UpdateAnalyzedDataListController">
-	 	<property name="analyzedDataService"><ref bean="analyzedDataService"></ref></property>
-	 	<property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
-	</bean>  
-	
-	 <bean id="addAnalyzedDataController" class="org.cipres.treebase.web.controllers.AddAnalyzedDataController">
-	 	<property name="analyzedDataService"><ref bean="analyzedDataService"></ref></property>
-	 	<property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
-	 	<property name="analysisService"><ref bean="analysisService"></ref></property>
-	 	<property name="studyService"><ref bean="studyService"></ref></property>
-	 	<property name="matrixService"><ref bean="matrixService"></ref></property>
-	 	<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
-	 	<property name="submissionService"><ref bean="submissionService"></ref></property>	 	
-	</bean>	
-	
+	 
+	 <bean id="updateAnalyzedDataListController" class="org.cipres.treebase.web.controllers.UpdateAnalyzedDataListController">
+	 	<property name="analyzedDataService"><ref bean="analyzedDataService"></ref></property>
+	 	<property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
+	</bean>  
+	
+	 <bean id="addAnalyzedDataController" class="org.cipres.treebase.web.controllers.AddAnalyzedDataController">
+	 	<property name="analyzedDataService"><ref bean="analyzedDataService"></ref></property>
+	 	<property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
+	 	<property name="analysisService"><ref bean="analysisService"></ref></property>
+	 	<property name="studyService"><ref bean="studyService"></ref></property>
+	 	<property name="matrixService"><ref bean="matrixService"></ref></property>
+	 	<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
+	 	<property name="submissionService"><ref bean="submissionService"></ref></property>	 	
+	</bean>	
+	
 	<bean id="listMatrixController" class="org.cipres.treebase.web.controllers.ListMatrixController">
 		<property name="commandName"><value>amatrixcollection</value></property>
-		<property name="commandClass"><value>org.cipres.treebase.web.model.AGenericList</value></property>
+		<property name="commandClass"><value>org.cipres.treebase.web.model.AGenericList</value></property>
 	 	<property name="studyService"><ref bean="studyService"></ref></property>
 	 	<property name="matrixService"><ref bean="matrixService"></ref></property>
 	 	<property name="matrixHome"><ref bean="matrixHome"></ref></property>
 	 	<property name="formView"><value>matrixList</value></property>
 	 	<property name="successView"><value>redirect:/user/matrixList.html</value></property>
-		<property name="cancelView"><value>redirect:/user/matrixList.html</value></property>	
+		<property name="cancelView"><value>redirect:/user/matrixList.html</value></property>	
 	</bean> 
-	
-	<bean id="listMatrixRowController" class="org.cipres.treebase.web.controllers.ListMatrixRowController">
-	 	<property name="matrixService"><ref bean="matrixService"></ref></property>
-	</bean>
-	       
-	<bean id="listMatrixRowSegmentController" class="org.cipres.treebase.web.controllers.ListMatrixRowSegmentController">
-		<property name="rowSegmentService"><ref bean="rowSegmentService"></ref></property>
-		<property name="matrixRowService"><ref bean="matrixRowService"></ref></property>
-	</bean>
-	
-	<bean id="matrixRowSegmentFormController" class="org.cipres.treebase.web.controllers.SingleRowSegmentController">
-		<property name="commandName"><value>arowsegment</value></property>
-		<property name="commandClass"><value>org.cipres.treebase.domain.matrix.RowSegment</value></property>
-		<property name="formView"><value>matrixRowSegmentForm</value></property>
-		<property name="successView"><value>redirect:/user/matrixRowSegmentList.html</value></property>
+	
+	<bean id="listMatrixRowController" class="org.cipres.treebase.web.controllers.ListMatrixRowController">
+	 	<property name="matrixService"><ref bean="matrixService"></ref></property>
+	</bean>
+	       
+	<bean id="listMatrixRowSegmentController" class="org.cipres.treebase.web.controllers.ListMatrixRowSegmentController">
+		<property name="rowSegmentService"><ref bean="rowSegmentService"></ref></property>
+		<property name="matrixRowService"><ref bean="matrixRowService"></ref></property>
+	</bean>
+	
+	<bean id="matrixRowSegmentFormController" class="org.cipres.treebase.web.controllers.SingleRowSegmentController">
+		<property name="commandName"><value>arowsegment</value></property>
+		<property name="commandClass"><value>org.cipres.treebase.domain.matrix.RowSegment</value></property>
+		<property name="formView"><value>matrixRowSegmentForm</value></property>
+		<property name="successView"><value>redirect:/user/matrixRowSegmentList.html</value></property>
 		<property name="cancelView"><value>redirect:/user/matrixRowSegmentList.html</value></property>
-		<property name="rowSegmentService"><ref bean="rowSegmentService"></ref></property>
-		<property name="matrixRowService"><ref bean="matrixRowService"></ref></property>
+		<property name="rowSegmentService"><ref bean="rowSegmentService"></ref></property>
+		<property name="matrixRowService"><ref bean="matrixRowService"></ref></property>
 	</bean>
 	
 	<bean id="deleteAMatrixController" class="org.cipres.treebase.web.controllers.DeleteAMatrixController">
@@ -592,10 +592,10 @@
 		<property name="successView"><value>redirect:/user/viewAllRowSegmentData.html</value></property>
 		<property name="cancelView"><value>redirect:/user/viewAllRowSegmentData.html</value></property>						
 	</bean>
-	     
+	     
 	<bean id="listTreeController" class="org.cipres.treebase.web.controllers.ListTreeController">
 		<property name="commandName"><value>atreecollection</value></property>
-		<property name="commandClass"><value>org.cipres.treebase.web.model.AGenericList</value></property>
+		<property name="commandClass"><value>org.cipres.treebase.web.model.AGenericList</value></property>
 		<property name="studyService"><ref bean="studyService"></ref></property>
 		<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
 		<property name="submissionService"><ref bean="submissionService"></ref></property>	
@@ -609,7 +609,7 @@
 		</property>
 		<property name="synchronizeOnSession">
     		<value>true</value>
-		</property>		
+		</property>		
 	</bean> 
 	
 	<bean id="deleteATreeController" class="org.cipres.treebase.web.controllers.DeleteATreeController">
@@ -660,12 +660,12 @@
 	<bean id="readOnlyListTreeController" class="org.cipres.treebase.web.controllers.ReadOnlyListTreeController">
 		<property name="studyService"><ref bean="studyService"></ref></property>
 		<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>		
-	</bean> 
-	
-	<bean id="mailSender" class="org.springframework.mail.javamail.JavaMailSenderImpl">
-		<property name="host" value="smtp.ucsd.edu"></property>
+	</bean> 
+	
+	<bean id="mailSender" class="org.springframework.mail.javamail.JavaMailSenderImpl">
+		<property name="host" value="smtp.ucsd.edu"></property>
 	</bean>
-	
+	
 	<bean id="treeParserController" class="org.cipres.treebase.web.controllers.TreeParserController">
 		<property name="commandClass"><value>org.cipres.treebase.web.model.MultiFileBean</value></property>
 		<property name="formView"><value>treeParser</value></property>
@@ -735,8 +735,8 @@
 		<property name="formView"><value>selectStudies</value></property>
 		
 		<!--property name="submissionService"><ref bean="submissionService"></ref></property-->
-	</bean>
-	
+	</bean>
+	
 	<bean id="adminSelectUsersController" class="org.cipres.treebase.web.controllers.AdminSelectUsersController">
 		<property name="successView"><value>redirect:/admin/userList.html</value></property>
 		<property name="cancelView"><value>redirect:/admin/administrationPage.html</value></property>
@@ -761,53 +761,53 @@
 		<property name="formView"><value>changeStudyStatus</value></property>
 		<property name="userService"><ref bean="userService"></ref></property>
 		<property name="submissionService"><ref bean="submissionService"></ref></property>
-	</bean>
-	
-	<bean id="searchController" abstract="true" >
-        <property name="commandName"><value>search</value></property>
-        <property name="commandClass"><value>org.cipres.treebase.web.model.SearchCommand</value></property>
-        <property name="taxonLabelService"><ref bean="taxonLabelService"></ref></property>
+	</bean>
+	
+	<bean id="searchController" abstract="true" >
+        <property name="commandName"><value>search</value></property>
+        <property name="commandClass"><value>org.cipres.treebase.web.model.SearchCommand</value></property>
+        <property name="taxonLabelService"><ref bean="taxonLabelService"></ref></property>
         <property name="searchService"><ref bean="searchService"></ref></property>
-        <property name="taxonLabelHome"><ref bean="taxonLabelHome"></ref></property>
-  	</bean>
+        <property name="taxonLabelHome"><ref bean="taxonLabelHome"></ref></property>
+  	</bean>
  
  	<!-- bean id="mainSearchController" parent="searchController" class="org.cipres.treebase.web.controllers.MainSearchController">
         <property name="formView"><value>search/mainSearch</value></property>
         <property name="successView"><value>search/mainSearch</value></property>        
     </bean-->
- 
-	<bean id="studySearchController" parent="searchController" class="org.cipres.treebase.web.controllers.StudySearchController">
-        <property name="formView"><value>search/studySearch</value></property>
+ 
+	<bean id="studySearchController" parent="searchController" class="org.cipres.treebase.web.controllers.StudySearchController">
+        <property name="formView"><value>search/studySearch</value></property>
         <property name="successView"><value>search/studySearch</value></property>
-        <property name="identify"><ref bean="top.identify"></ref></property>        
-    </bean>
-    
-    <bean id="treeSearchController" parent="searchController" class="org.cipres.treebase.web.controllers.TreeSearchController">
-        <property name="formView"><value>search/treeSearch</value></property>
-        <property name="successView"><value>search/treeSearch</value></property>
-    </bean>
-    
-    <bean id="treeTopSearchController" parent="searchController" class="org.cipres.treebase.web.controllers.TreeTopSearchController">
-        <property name="formView"><value>search/treeTopSearch</value></property>
-        <property name="successView"><value>search/treeTopSearch</value></property>
-    </bean>
-    
-       <bean id="matrixSearchController" parent="searchController" class="org.cipres.treebase.web.controllers.MatrixSearchController">
-        <property name="formView"><value>search/matrixSearch</value></property>
-        <property name="successView"><value>search/matrixSearch</value></property>
-    </bean>
-    
-    <bean id="taxonSearchController" parent="searchController" class="org.cipres.treebase.web.controllers.TaxonSearchController">
-        <property name="formView"><value>search/taxonSearch</value></property>
-        <property name="successView"><value>search/taxonSearch</value></property>   
-        <property name="taxonHome"><ref bean="taxonHome"></ref></property>
-        <property name="taxonLabelHome"><ref bean="taxonLabelHome"></ref></property>	
+        <property name="identify"><ref bean="top.identify"></ref></property>        
+    </bean>
+    
+    <bean id="treeSearchController" parent="searchController" class="org.cipres.treebase.web.controllers.TreeSearchController">
+        <property name="formView"><value>search/treeSearch</value></property>
+        <property name="successView"><value>search/treeSearch</value></property>
+    </bean>
+    
+    <bean id="treeTopSearchController" parent="searchController" class="org.cipres.treebase.web.controllers.TreeTopSearchController">
+        <property name="formView"><value>search/treeTopSearch</value></property>
+        <property name="successView"><value>search/treeTopSearch</value></property>
+    </bean>
+    
+       <bean id="matrixSearchController" parent="searchController" class="org.cipres.treebase.web.controllers.MatrixSearchController">
+        <property name="formView"><value>search/matrixSearch</value></property>
+        <property name="successView"><value>search/matrixSearch</value></property>
+    </bean>
+    
+    <bean id="taxonSearchController" parent="searchController" class="org.cipres.treebase.web.controllers.TaxonSearchController">
+        <property name="formView"><value>search/taxonSearch</value></property>
+        <property name="successView"><value>search/taxonSearch</value></property>   
+        <property name="taxonHome"><ref bean="taxonHome"></ref></property>
+        <property name="taxonLabelHome"><ref bean="taxonLabelHome"></ref></property>	
    	</bean>
    	
    	<bean id="classificationSearchController" parent="searchController" class="org.cipres.treebase.web.controllers.ClassificationSearchController">
         <property name="formView"><value>search/classificationSearch</value></property>
         <property name="successView"><value>search/classificationSearch</value></property>
-   	</bean>
+   	</bean>
       
     <bean id="searchBySubmissionIDController" class="org.cipres.treebase.web.controllers.SearchBySubmissionIDController">
         <property name="formView"><value>searchBySubmissionID</value></property>
@@ -872,16 +872,16 @@
 			</list>
 		</property>
 		<!--property name="submissionService"><ref bean="submissionService"></ref></property-->
-	</bean>
-	
-		<!--  bean to supply help texts -->
-	<bean id="helpController" class="org.cipres.treebase.web.controllers.HelpController">
-		<property name="commandClass"><value>org.cipres.treebase.web.model.HelpControllerAction</value></property>
-		<property name="formView"><value>help</value></property>
-		<property name="successView"><value>help</value></property>
-		<property name="failureView"><value>FAILfailFAIL</value></property>
-		<property name="userService"><ref bean="userService"></ref></property>
-		<property name="helpService"><ref bean="helpService"></ref></property>
+	</bean>
+	
+		<!--  bean to supply help texts -->
+	<bean id="helpController" class="org.cipres.treebase.web.controllers.HelpController">
+		<property name="commandClass"><value>org.cipres.treebase.web.model.HelpControllerAction</value></property>
+		<property name="formView"><value>help</value></property>
+		<property name="successView"><value>help</value></property>
+		<property name="failureView"><value>FAILfailFAIL</value></property>
+		<property name="userService"><ref bean="userService"></ref></property>
+		<property name="helpService"><ref bean="helpService"></ref></property>
 	</bean>
 	
 	
@@ -894,19 +894,19 @@
 		</property>	
 	</bean>
  
-	<!-- ========================================================== -->
-	<!-- LIST OF VALIDATORS FOR CONTROLLER							-->
-	<!-- ========================================================== -->
-	<!-- ========================================================== -->
-	<!-- MESSAGE SOURCE DEFINITION									-->
-	<!-- ========================================================== -->
-	<bean id="messageSource" class="org.springframework.context.support.ResourceBundleMessageSource">
-		<property name="basename"><value>ApplicationResources</value></property>
-	</bean>
-	
-	<!-- ========================================================== -->
-	<!-- Spring View Resolvers for JSPs	and .vm files							-->
-	<!-- ========================================================== -->
+	<!-- ========================================================== -->
+	<!-- LIST OF VALIDATORS FOR CONTROLLER							-->
+	<!-- ========================================================== -->
+	<!-- ========================================================== -->
+	<!-- MESSAGE SOURCE DEFINITION									-->
+	<!-- ========================================================== -->
+	<bean id="messageSource" class="org.springframework.context.support.ResourceBundleMessageSource">
+		<property name="basename"><value>ApplicationResources</value></property>
+	</bean>
+	
+	<!-- ========================================================== -->
+	<!-- Spring View Resolvers for JSPs	and .vm files							-->
+	<!-- ========================================================== -->
    
     <bean id="chainableVelocityViewResolver" class="org.cipres.treebase.web.viewresolver.ChainableVelocityViewResolver">        
           <property name="chainableResolver">                 
@@ -941,10 +941,10 @@
         <property name="prefix" value="/WEB-INF/pages/"/>
         <property name="suffix" value=".jsp"/>
     </bean>
-   
-	<!-- ========================================================== -->
-	<!-- URL MAPPING												-->
-	<!-- ========================================================== -->
+   
+	<!-- ========================================================== -->
+	<!-- URL MAPPING												-->
+	<!-- ========================================================== -->
 	<bean id="urlMapping" class="org.springframework.web.servlet.handler.SimpleUrlHandlerMapping">
 	
 		<property name="alwaysUseFullPath" value="true"/>
@@ -985,8 +985,8 @@
 				<prop key="/user/taxaList.html">listTaxaController</prop>
 				<prop key="/user/editTaxonLabel.html">editTaxonLabelController</prop>
 				<prop key="/user/editSetTaxonLabel.html">editSetTaxonLabelController</prop>
-				<prop key="/user/summary.html">summaryController</prop>
-				<prop key="/user/analyses.html">summaryController</prop>
+				<prop key="/user/summary.html">summaryController</prop>
+				<prop key="/user/analyses.html">summaryController</prop>
 				
 				<prop key="/search/summary.html">summaryController</prop>
 				
@@ -1018,7 +1018,7 @@
 				<prop key="/admin/adminMergingUsers.html">adminMergingUsersController</prop>
 				<prop key="/admin/administrationPage.html">filenameController</prop>
 				<prop key="/admin/messageToAdminAfterAction.html">filenameController</prop>
-				<prop key="/admin/userList.html">filenameController</prop>
+				<prop key="/admin/userList.html">filenameController</prop>
 				<prop key="/admin/personList.html">filenameController</prop>
 				<prop key="/admin/adminSelectPersons.html">adminSelectPersonsController</prop>
 				<prop key="/admin/adminMergingPersons.html">adminMergingPersonsController</prop>
@@ -1035,82 +1035,82 @@
 				<prop key="/searchStudy.html">searchStudyController</prop>
 				<prop key="/study-query.html">updateStudyQueryController</prop>
 				
-				<!-- SEARCH SECTION -->
-				<prop key="/search/">studySearchController</prop>
-				<prop key="/search/studySearch.html">studySearchController</prop>
-				<prop key="/search/treeSearch.html">treeSearchController</prop>
-				<prop key="/search/treeTopSearch.html">treeTopSearchController</prop>
-				<prop key="/search/matrixSearch.html">matrixSearchController</prop>	
+				<!-- SEARCH SECTION -->
+				<prop key="/search/">studySearchController</prop>
+				<prop key="/search/studySearch.html">studySearchController</prop>
+				<prop key="/search/treeSearch.html">treeSearchController</prop>
+				<prop key="/search/treeTopSearch.html">treeTopSearchController</prop>
+				<prop key="/search/matrixSearch.html">matrixSearchController</prop>	
 				<prop key="/search/taxonSearch.html">taxonSearchController</prop>
 				<prop key="/search/classificationSearch.html">classificationSearchController</prop>
 				<!-- prop key="/search/mainSearch.html">mainSearchController</prop-->
 				
-				<!-- SEARCH RESULTS SECTION -->
+				<!-- SEARCH RESULTS SECTION -->
 			    <prop key="/search/study/summary.html">searchSummaryController</prop>								
-			    <prop key="/search/study/analyses.html">searchSummaryController</prop>
-			    <prop key="/search/study/matrices.html">searchSummaryController</prop>
-			    <prop key="/search/study/trees.html">searchSummaryController</prop>
-			    <prop key="/search/study/treeBlocks.html">searchSummaryController</prop>
-			    <prop key="/search/study/treeBlock.html">searchMapToPhyloWidgetController</prop>
-			    <prop key="/search/study/tree.html">searchMapToPhyloWidgetController</prop>
-			    <prop key="/search/study/matrix.html">searchSummaryController</prop>
-			    <prop key="/search/study/analysis.html">searchSummaryController</prop>
-			    <prop key="/search/study/taxa.html">searchSummaryController</prop>
+			    <prop key="/search/study/analyses.html">searchSummaryController</prop>
+			    <prop key="/search/study/matrices.html">searchSummaryController</prop>
+			    <prop key="/search/study/trees.html">searchSummaryController</prop>
+			    <prop key="/search/study/treeBlocks.html">searchSummaryController</prop>
+			    <prop key="/search/study/treeBlock.html">searchMapToPhyloWidgetController</prop>
+			    <prop key="/search/study/tree.html">searchMapToPhyloWidgetController</prop>
+			    <prop key="/search/study/matrix.html">searchSummaryController</prop>
+			    <prop key="/search/study/analysis.html">searchSummaryController</prop>
+			    <prop key="/search/study/taxa.html">searchSummaryController</prop>
 			    <prop key="/search/study/rowSegments.html">searchSummaryController</prop>
-			    <prop key="/search/study/rowSegmentsTSV.html">downloadRowSegmentDataController</prop>
+			    <prop key="/search/study/rowSegmentsTSV.html">downloadRowSegmentDataController</prop>
 			    <prop key="/search/study/anyObjectAsRDF.rdf">anyObjectAsRDFController</prop>
-			    
-			    <prop key="/search/searchResultsAsRDF.rdf">searchResultsAsRDFController</prop>
-				<prop key="/search/matrixRowList.html">listMatrixRowController</prop>
-				<prop key="/search/taxonList.html">listTaxaSearchController</prop>
-				<prop key="/search/downloadAStudy.html">downloadAStudyController</prop>				
-				<prop key="/search/downloadATree.html">downloadATreeController</prop>
-				<prop key="/search/downloadATreeBlock.html">downloadATreeBlockController</prop>
-				<prop key="/search/downloadAMatrix.html">downloadAMatrixController</prop>
-				<prop key="/search/downloadAnAnalysisStep.html">downloadAnAnalysisStepController</prop>
-				<prop key="/search/downloadANexusFile.html">downloadANexusFileController</prop>
+			    
+			    <prop key="/search/searchResultsAsRDF.rdf">searchResultsAsRDFController</prop>
+				<prop key="/search/matrixRowList.html">listMatrixRowController</prop>
+				<prop key="/search/taxonList.html">listTaxaSearchController</prop>
+				<prop key="/search/downloadAStudy.html">downloadAStudyController</prop>				
+				<prop key="/search/downloadATree.html">downloadATreeController</prop>
+				<prop key="/search/downloadATreeBlock.html">downloadATreeBlockController</prop>
+				<prop key="/search/downloadAMatrix.html">downloadAMatrixController</prop>
+				<prop key="/search/downloadAnAnalysisStep.html">downloadAnAnalysisStepController</prop>
+				<prop key="/search/downloadANexusFile.html">downloadANexusFileController</prop>
 				<prop key="/search/downloadANexusRCTFile.html">downloadANexusRCTFileController</prop>
 				
-				<prop key="/sitemap.xml">siteMapController</prop>
+				<prop key="/sitemap.xml">siteMapController</prop>
 				
-				<!-- SUBMISSION SECTION -->
-				<prop key="/user/updateProfile.html">userFormController</prop>
-				<prop key="/user/submissionList.html">listSubmissionController</prop>
+				<!-- SUBMISSION SECTION -->
+				<prop key="/user/updateProfile.html">userFormController</prop>
+				<prop key="/user/submissionList.html">listSubmissionController</prop>
 				<prop key="/user/studyForm.html">studyFormController</prop>
-				
+				
 				<!--  prop key="/user/submissionMain.html">displaySubmissionController</prop-->
-				<prop key="/user/submissionMain.html">filenameController</prop>
-				<prop key="/user/displaySubmissionMenu.html">displaySubmissionMenuController</prop>
-				<prop key="/user/citationForm.html">citationFormController</prop>
-				
+				<prop key="/user/submissionMain.html">filenameController</prop>
+				<prop key="/user/displaySubmissionMenu.html">displaySubmissionMenuController</prop>
+				<prop key="/user/citationForm.html">citationFormController</prop>
+				
 				<prop key="/user/authorForm.html">authorFormController</prop>
 				<prop key="/user/authorSearchForm.html">authorSearchFormController</prop>
-				<prop key="/user/addAuthor.html">addAuthorController</prop>
+				<prop key="/user/addAuthor.html">addAuthorController</prop>
 				<prop key="/user/authorList.html">authorFormController</prop>
 				
 				<prop key="/user/editorForm.html">editorFormController</prop>
-				
-				<prop key="/user/analysisList.html">listAnalysisController</prop>
-				<prop key="/user/analysisForm.html">analysisFormController</prop>
-				<prop key="/user/analysisStepList.html">listAnalysisStepController</prop>
-				<prop key="/user/analysisStepForm.html">analysisStepFormController</prop>
-				<!--prop key="/analysisDisplay.html">displayAnalysisController</prop-->
-				<prop key="/user/analysisDisplay.html">displayAnalysisController</prop>
-				
-				<prop key="/user/uploadFile.html">uploadFileController</prop>
+				
+				<prop key="/user/analysisList.html">listAnalysisController</prop>
+				<prop key="/user/analysisForm.html">analysisFormController</prop>
+				<prop key="/user/analysisStepList.html">listAnalysisStepController</prop>
+				<prop key="/user/analysisStepForm.html">analysisStepFormController</prop>
+				<!--prop key="/analysisDisplay.html">displayAnalysisController</prop-->
+				<prop key="/user/analysisDisplay.html">displayAnalysisController</prop>
+				
+				<prop key="/user/uploadFile.html">uploadFileController</prop>
 				<prop key="/user/uploadFileSummary.html">uploadFileSummaryController</prop>
-				<!-- prop key="/user/treeList.html">filenameController</prop -->
-				
-				<prop key="/user/analyzedDataList.html">listAnalyzedDataController</prop>
-				<prop key="/user/analyzedDataForm.html">analyzedDataFormController</prop>
-				<prop key="/user/analyzedDataForm.html">analyzedDataFormController</prop>
-				<prop key="/user/addAnalyzedData.html">addAnalyzedDataController</prop>
-				
-				<prop key="/user/matrixList.html">listMatrixController</prop>
-				<prop key="/user/matrixRowList.html">listMatrixRowController</prop>
-				<prop key="/user/matrixRowSegmentList.html">listMatrixRowSegmentController</prop>
-				<prop key="/user/matrixRowSegmentForm.html">matrixRowSegmentFormController</prop>
-								
+				<!-- prop key="/user/treeList.html">filenameController</prop -->
+				
+				<prop key="/user/analyzedDataList.html">listAnalyzedDataController</prop>
+				<prop key="/user/analyzedDataForm.html">analyzedDataFormController</prop>
+				<prop key="/user/analyzedDataForm.html">analyzedDataFormController</prop>
+				<prop key="/user/addAnalyzedData.html">addAnalyzedDataController</prop>
+				
+				<prop key="/user/matrixList.html">listMatrixController</prop>
+				<prop key="/user/matrixRowList.html">listMatrixRowController</prop>
+				<prop key="/user/matrixRowSegmentList.html">listMatrixRowSegmentController</prop>
+				<prop key="/user/matrixRowSegmentForm.html">matrixRowSegmentFormController</prop>
+								
 				<prop key="/user/treeList.html">listTreeController</prop>
 				<prop key="/user/treeBlockList.html">listTreeBlockController</prop>
 				
@@ -1118,25 +1118,25 @@
 				<prop key="/user/treeParserResult.html">treeParserResultController</prop>
 				
 				<!-- JSON related bean mappings -->
-				<prop key="/json/submissionIsland.html">submissionToJsonController</prop>			       		
-			</props>
-		</property>
-	</bean>
-	<!-- ==================================================================================================== -->
-	<!-- Exception Mappings											                                          -->
-	<!-- This bean resolves specific types of exception to corresponding error views                          -->
-	<!-- The default behavior of DispatcherServlet is to propagate all exceptions to the servlet container    -->
-	<!-- This will happen here with all other types of exception                                              -->
-	<!-- ==================================================================================================== -->
-	<bean id="exceptionResolver" class="org.springframework.web.servlet.handler.SimpleMappingExceptionResolver">
-		<property name="exceptionMappings">
-			<props>
-				<prop key="org.springframework.dao.DataAccessException">/errors/dataAccessFailure</prop>
-				<prop key="org.springframework.transaction.TransactionException">/errors/dataAccessFailure</prop>
+				<prop key="/json/submissionIsland.html">submissionToJsonController</prop>			       		
+			</props>
+		</property>
+	</bean>
+	<!-- ==================================================================================================== -->
+	<!-- Exception Mappings											                                          -->
+	<!-- This bean resolves specific types of exception to corresponding error views                          -->
+	<!-- The default behavior of DispatcherServlet is to propagate all exceptions to the servlet container    -->
+	<!-- This will happen here with all other types of exception                                              -->
+	<!-- ==================================================================================================== -->
+	<bean id="exceptionResolver" class="org.springframework.web.servlet.handler.SimpleMappingExceptionResolver">
+		<property name="exceptionMappings">
+			<props>
+				<prop key="org.springframework.dao.DataAccessException">/errors/dataAccessFailure</prop>
+				<prop key="org.springframework.transaction.TransactionException">/errors/dataAccessFailure</prop>
 				<prop key="org.cipres.treebase.web.exceptions.EmptyStudyException">/errors/studyAccessFailure</prop>
-				<prop key="org.cipres.treebase.web.exceptions.NoStudySpecifiedError">/errors/itemNotFound</prop>
-			</props>
-		</property>
-	</bean>
-	
-</beans>
+				<prop key="org.cipres.treebase.web.exceptions.NoStudySpecifiedError">/errors/itemNotFound</prop>
+			</props>
+		</property>
+	</bean>
+	
+</beans>
