From 85cb2119ee17967d0cbe448fb7092b0a1239ce56 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sun, 11 Jan 2026 13:55:26 +0000 Subject: [PATCH 1/3] Initial plan From 217d8e266ffde73c78075233036db57ec424c047 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sun, 11 Jan 2026 14:01:20 +0000 Subject: [PATCH 2/3] Update submission summary: GitHub issues link, relative accession URLs, fix toolbar image Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com> --- .../main/webapp/WEB-INF/pages/readyState.jsp | 82 +++++----- .../WEB-INF/pages/submissionSummaryView.jsp | 148 +++++++++--------- .../src/main/webapp/common/adminMenu.jsp | 62 ++++---- .../main/webapp/common/searchMenuRight.jsp | 2 +- .../webapp/common/searchSummaryMenuRight.jsp | 10 +- .../src/main/webapp/common/submissionMenu.jsp | 4 +- 6 files changed, 153 insertions(+), 155 deletions(-) diff --git a/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp b/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp index bf2ecb0d5..c767cf7fe 100644 --- a/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp +++ b/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp @@ -1,47 +1,47 @@ -<%@ include file="/common/taglibs.jsp"%> - -<fmt:message key="study.toready.state"/> - - - - -
-<%-- - +<%@ include file="/common/taglibs.jsp"%> + +<fmt:message key="study.toready.state"/> + + + + + +<%-- +

We notice that some of your taxon labels have failed to be validated against an external taxonomy. Unless it is impossible to validate these labels, TreeBASE may refuse or delay the acceptance of your data. -

- +

+ --%> - - - - -

- Are you sure that you want to change the status of this study to 'Ready State'? -

- -

- Changing the status of your study to 'Ready State' means that you are ready for the review process. If yes, please press Submit, - otherwise choose the Cancel button. Note that after you press the Submit button you will no longer be able to make any further - changes to your study, except for updating your citation information. We strongly encourage you to return to your - submission to update citation metadata, such as volume, issue, page numbers, or DOI, as needed. -

- -

+

+ + + +

+ Are you sure that you want to change the status of this study to 'Ready State'? +

+ +

+ Changing the status of your study to 'Ready State' means that you are ready for the review process. If yes, please press Submit, + otherwise choose the Cancel button. Note that after you press the Submit button you will no longer be able to make any further + changes to your study, except for updating your citation information. We strongly encourage you to return to your + submission to update citation metadata, such as volume, issue, page numbers, or DOI, as needed. +

+ +

- -

+ +

\ No newline at end of file diff --git a/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp b/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp index 1e603b87d..e19f5a3ad 100644 --- a/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp +++ b/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp @@ -1,85 +1,83 @@ -<%@page import="org.cipres.treebase.TreebaseUtil"%> -<% String purlBase = TreebaseUtil.getPurlBase(); %> -<%@ include file="/common/taglibs.jsp"%> - - -Summary Information -Summary for current study - - - -
+<%@page import="org.cipres.treebase.TreebaseUtil"%> +<% String purlBase = TreebaseUtil.getPurlBase(); %> +<%@ include file="/common/taglibs.jsp"%> + + +Summary Information +Summary for current study + + + +
Summary help" /> - -Submission: , -<%if(request.isUserInRole("Admin") || request.isUserInRole("Associate Editor")){%> -, Update Status -<%}%> -
-     Submission initiated:  
- -
- - mail" /> - Contact Submitter - -
- - mail" /> - Contact TreeBASE Help - -
-
-"> - link" /> - Study Accession URL:
- - -
You can cite this URL in your manuscript. It will become the permanent and resolvable resource locator after your submission has been approved and the data are made public.
-
-?x-access-code=&format=html"> - link" /> - Reviewer access URL:
- ?x-access-code=&format=html - -
You can copy and send this URL to you journal editor to provide reviewers with limited, read-only access to your data, even if your submission has not yet been approved and the data are not yet public.
-
- - -      Study name:   - - - -
- - - - Citation information not yet entered. Click the Citation menu item on the right.

- - - - Citation -

  , 

-

   ${citationsummary.authorsCitationStyle}

-
- - - - - Abstract -

 

-
- + +Submission: , +<%if(request.isUserInRole("Admin") || request.isUserInRole("Associate Editor")){%> +, Update Status +<%}%> +
+     Submission initiated:  
+ +
+ + mail" /> + Contact Submitter + +
+ + Help link" /> + Contact TreeBASE Help + +
+
+ + link" /> + Study Accession: TB2:S${submission.study.id} + +
You can cite this accession in your manuscript. It will become the permanent and resolvable resource locator after your submission has been approved and the data are made public.
+
+&format=html"> + link" /> + Reviewer access: TB2:S${submission.study.id}?x-access-code= + +
You can copy and send this accession to your journal editor to provide reviewers with limited, read-only access to your data, even if your submission has not yet been approved and the data are not yet public.
+
+ + +      Study name:   + + + +
+ + + + Citation information not yet entered. Click the Citation menu item on the right.

+ + + + Citation +

  , 

+

   ${citationsummary.authorsCitationStyle}

+
+ + + + + Abstract +

 

+
+
- + - - - + + + \ No newline at end of file diff --git a/treebase-web/src/main/webapp/common/adminMenu.jsp b/treebase-web/src/main/webapp/common/adminMenu.jsp index f718a8ac2..b0e33dd9b 100644 --- a/treebase-web/src/main/webapp/common/adminMenu.jsp +++ b/treebase-web/src/main/webapp/common/adminMenu.jsp @@ -1,31 +1,31 @@ -<%@ include file="/common/taglibs.jsp"%> - - - +<%@ include file="/common/taglibs.jsp"%> + + + diff --git a/treebase-web/src/main/webapp/common/searchMenuRight.jsp b/treebase-web/src/main/webapp/common/searchMenuRight.jsp index b9a31d12e..5f7b7b668 100644 --- a/treebase-web/src/main/webapp/common/searchMenuRight.jsp +++ b/treebase-web/src/main/webapp/common/searchMenuRight.jsp @@ -4,7 +4,7 @@