From 57b7992ee3ae62f4b30c9b4265e8ee2c0146643f Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 11 Jan 2026 14:29:45 +0000
Subject: [PATCH 1/3] Initial plan


From 476fdef415e46d59f008399ebac7823b92dcae8e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 11 Jan 2026 14:34:39 +0000
Subject: [PATCH 2/3] Fix Tool Box menu not rendering by adding menuDiv wrapper

The Tool Box menu in submission pages was not visible because:
1. JavaScript initializeMenus() expects an element with id="menuDiv"
2. The switchMenu() function toggles visibility of "menuDiv"
3. But no element with that id existed in the menu JSP files

Added <div id="menuDiv"> wrapper around the menu:useMenuDisplayer
content in all four affected menu JSP files:
- submissionMenu.jsp
- adminMenu.jsp
- searchMenuRight.jsp
- searchSummaryMenuRight.jsp

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
---
 treebase-web/src/main/webapp/common/adminMenu.jsp              | 2 ++
 treebase-web/src/main/webapp/common/searchMenuRight.jsp        | 2 ++
 treebase-web/src/main/webapp/common/searchSummaryMenuRight.jsp | 2 ++
 treebase-web/src/main/webapp/common/submissionMenu.jsp         | 2 ++
 4 files changed, 8 insertions(+)

diff --git a/treebase-web/src/main/webapp/common/adminMenu.jsp b/treebase-web/src/main/webapp/common/adminMenu.jsp
index b0e33dd9..13670f59 100644
--- a/treebase-web/src/main/webapp/common/adminMenu.jsp
+++ b/treebase-web/src/main/webapp/common/adminMenu.jsp
@@ -5,6 +5,7 @@
 <div id="gutter">
 <div id="menu">
 <a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif"/>&nbsp;&nbsp;Tool Box</a>
+<div id="menuDiv">
 <menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter">
     <menu:displayMenu name="StudyManagementMenu"/>
     <menu:displayMenu name="UserManagementMenu"/>
@@ -13,6 +14,7 @@
 </div>
 </div>
 </div>
+</div>
 <script type="text/javascript">
     initializeMenus();
     
diff --git a/treebase-web/src/main/webapp/common/searchMenuRight.jsp b/treebase-web/src/main/webapp/common/searchMenuRight.jsp
index 5f7b7b66..6d7f0bd9 100644
--- a/treebase-web/src/main/webapp/common/searchMenuRight.jsp
+++ b/treebase-web/src/main/webapp/common/searchMenuRight.jsp
@@ -5,6 +5,7 @@
 <div id="gutter">
 <div id="menu">
 <a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif"/>&nbsp;&nbsp;Tool Box</a>
+<div id="menuDiv">
 <menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter" >
     <menu:displayMenu name="Searches" />
  </menu:useMenuDisplayer>
@@ -12,6 +13,7 @@
 </div>
 </div>
 </div>
+</div>
 <script type="text/javascript">
     initializeMenus();
 
diff --git a/treebase-web/src/main/webapp/common/searchSummaryMenuRight.jsp b/treebase-web/src/main/webapp/common/searchSummaryMenuRight.jsp
index 6ccff451..22ec8a12 100644
--- a/treebase-web/src/main/webapp/common/searchSummaryMenuRight.jsp
+++ b/treebase-web/src/main/webapp/common/searchSummaryMenuRight.jsp
@@ -5,6 +5,7 @@
 <div id="gutter">
 <div id="menu">
 <a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif"/>&nbsp;&nbsp;Tool Box</a>
+<div id="menuDiv">
 <menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter">
     <menu:displayMenu name="SubmissionInfo"/>
     <menu:displayMenu name="Citation"/>
@@ -20,6 +21,7 @@
 </div>
 </div>
 </div>
+</div>
 <script type="text/javascript">
     initializeMenus();
 
diff --git a/treebase-web/src/main/webapp/common/submissionMenu.jsp b/treebase-web/src/main/webapp/common/submissionMenu.jsp
index 6fbf2618..787d0838 100644
--- a/treebase-web/src/main/webapp/common/submissionMenu.jsp
+++ b/treebase-web/src/main/webapp/common/submissionMenu.jsp
@@ -5,6 +5,7 @@
 <div id="gutter">
 <div id="menu">
 <a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif"/>&nbsp;&nbsp;Tool Box</a>
+<div id="menuDiv">
 <menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter">
 	<menu:displayMenu name="SubmissionHome"/>
 	<menu:displayMenu name="SubmissionNotes"/>
@@ -18,6 +19,7 @@
     <menu:displayMenu name="SubmissionAnalyses"/>     
     <menu:displayMenu name="SubmissionSubmissions"/>    
  </menu:useMenuDisplayer>
+</div>
  <div id="debug"></div>
 </div>
 </div>

From 3a8ec30aa9a7f85329894c5677c38fc79a748a63 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 11 Jan 2026 16:49:25 +0000
Subject: [PATCH 3/3] Fix Tool Box menu items not rendering by removing
 rolesAdapter permission

The menu items were not rendering because the struts-menu library's
`permissions="rolesAdapter"` attribute was not working after the
migration from Acegi Security to Spring Security 5.8.15.

The RolesPermissionsAdapter in struts-menu relied on Struts integration
which is no longer present. Since Spring Security already handles
URL-level access control (e.g., /user/** requires User,Admin,Associate
Editor roles), the menu-level permission filtering is redundant.

Removed the `permissions="rolesAdapter"` attribute from:
- submissionMenu.jsp
- adminMenu.jsp
- searchMenuRight.jsp
- searchSummaryMenuRight.jsp

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
---
 treebase-web/src/main/webapp/common/adminMenu.jsp              | 2 +-
 treebase-web/src/main/webapp/common/searchMenuRight.jsp        | 2 +-
 treebase-web/src/main/webapp/common/searchSummaryMenuRight.jsp | 2 +-
 treebase-web/src/main/webapp/common/submissionMenu.jsp         | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/treebase-web/src/main/webapp/common/adminMenu.jsp b/treebase-web/src/main/webapp/common/adminMenu.jsp
index 13670f59..5fa55851 100644
--- a/treebase-web/src/main/webapp/common/adminMenu.jsp
+++ b/treebase-web/src/main/webapp/common/adminMenu.jsp
@@ -6,7 +6,7 @@
 <div id="menu">
 <a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif"/>&nbsp;&nbsp;Tool Box</a>
 <div id="menuDiv">
-<menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter">
+<menu:useMenuDisplayer name="ListMenu">
     <menu:displayMenu name="StudyManagementMenu"/>
     <menu:displayMenu name="UserManagementMenu"/>
 </menu:useMenuDisplayer>
diff --git a/treebase-web/src/main/webapp/common/searchMenuRight.jsp b/treebase-web/src/main/webapp/common/searchMenuRight.jsp
index 6d7f0bd9..e5e31151 100644
--- a/treebase-web/src/main/webapp/common/searchMenuRight.jsp
+++ b/treebase-web/src/main/webapp/common/searchMenuRight.jsp
@@ -6,7 +6,7 @@
 <div id="menu">
 <a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif"/>&nbsp;&nbsp;Tool Box</a>
 <div id="menuDiv">
-<menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter" >
+<menu:useMenuDisplayer name="ListMenu">
     <menu:displayMenu name="Searches" />
  </menu:useMenuDisplayer>
 </div>
diff --git a/treebase-web/src/main/webapp/common/searchSummaryMenuRight.jsp b/treebase-web/src/main/webapp/common/searchSummaryMenuRight.jsp
index 22ec8a12..731bbc72 100644
--- a/treebase-web/src/main/webapp/common/searchSummaryMenuRight.jsp
+++ b/treebase-web/src/main/webapp/common/searchSummaryMenuRight.jsp
@@ -6,7 +6,7 @@
 <div id="menu">
 <a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif"/>&nbsp;&nbsp;Tool Box</a>
 <div id="menuDiv">
-<menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter">
+<menu:useMenuDisplayer name="ListMenu">
     <menu:displayMenu name="SubmissionInfo"/>
     <menu:displayMenu name="Citation"/>
     <menu:displayMenu name="UploadFile"/>
diff --git a/treebase-web/src/main/webapp/common/submissionMenu.jsp b/treebase-web/src/main/webapp/common/submissionMenu.jsp
index 787d0838..6dd45355 100644
--- a/treebase-web/src/main/webapp/common/submissionMenu.jsp
+++ b/treebase-web/src/main/webapp/common/submissionMenu.jsp
@@ -6,7 +6,7 @@
 <div id="menu">
 <a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif"/>&nbsp;&nbsp;Tool Box</a>
 <div id="menuDiv">
-<menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter">
+<menu:useMenuDisplayer name="ListMenu">
 	<menu:displayMenu name="SubmissionHome"/>
 	<menu:displayMenu name="SubmissionNotes"/>
 	<menu:displayMenu name="SubmissionCitation"/>