Skip to content

Update submission summary: GitHub issues link, relative accession URLs, fix toolbar image #376

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
rvosa merged 3 commits into from
Jan 11, 2026
Merged

Update submission summary: GitHub issues link, relative accession URLs, fix toolbar image #376

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
85cb211
Initial plan
Copilot Jan 11, 2026
217d8e2
Update submission summary: GitHub issues link, relative accession URL…
Copilot Jan 11, 2026
4066ac0
Update submissionSummaryView.jsp to remove unnecessary HTML non-break…
rvosa Jan 11, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
82 changes: 41 additions & 41 deletions treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,47 +1,47 @@
<%@ include file="/common/taglibs.jsp"%>
<title><fmt:message key="study.toready.state"/></title>
<content tag="heading"><fmt:message key="study.toready.state"/></content>
<body id="submissions"/>
<form method="post">
<%--
<c:if test="${AnalysesStatus eq false}">
<%@ include file="/common/taglibs.jsp"%>

<title><fmt:message key="study.toready.state"/></title>
<content tag="heading"><fmt:message key="study.toready.state"/></content>
<body id="submissions"/>


<form method="post">
<%--
<c:if test="${AnalysesStatus eq false}">
<p style="color:red;font-weight:bold">
We notice that some of your taxon labels have failed to be validated against an external taxonomy.
Unless it is impossible to validate these labels, TreeBASE may refuse or delay the acceptance of your data.
</p>
</c:if>
</p>
</c:if>
--%>
<p class="readyStateError" style="color:red; font-weight:bold; display:none;">
Sorry! Errors in your submission prevent you from changing the status to 'Ready State' at this time.
</p>
<p class="readyStateError" style="display:none;">
The items in the Tool Box on the right that are highlighted in yellow indicate that the item either has not been visited or there is an error. Hovering your mouse over the item will indicate the nature of the problem. Your submission cannot be changed to "Ready" state until all highlighted items are addressed. Please return to your submission to complete it. If you think this request is in error, please contact <a href='mailto:help@treebase.org?subject=TreeBASE Submission S<c:out value="${submissionNumber}"/>'>help</a>.
<br /><br />
The most common problems include:
<br /><br />
(1) The submitter has not entered a citation that at a minimum must include the authors, year, title, and journal name.<br />
(2) The submitter has "orphaned" matrices or trees: i.e., there are matrices that are not listed as inputs to at least one analysis; or trees that are not listed as outputs from at least one analysis. If your paper does not include a tree, please submit a generic neighbor joining tree to satisfy this requirement.<br />
(3) The output tree of an analysis has taxon labels that do not match with the input matrix (i.e. there are taxon labels in the tree that are missing from the matrix or matrices that produced the tree). Preparing your submission using <a href='http://mesquiteproject.org/'>Mesquite</a>, in which both matrices and trees are part of the same Mesquite project and share a common taxon block, will avoid the problem of mismatched taxon labels.<br />
(4) The submitter has not attempted to validate the taxon labels by clicking the "Validate Taxon Labels" button in the Taxa section.
</p>
<p style="font-weight:bold">
Are you sure that you want to change the status of this study to 'Ready State'?
</p>
<p>
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, <b>except</b> 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.
</p>
<p>
<p class="readyStateError" style="color:red; font-weight:bold; display:none;">
Sorry! Errors in your submission prevent you from changing the status to 'Ready State' at this time.
</p>

<p class="readyStateError" style="display:none;">
The items in the Tool Box on the right that are highlighted in yellow indicate that the item either has not been visited or there is an error. Hovering your mouse over the item will indicate the nature of the problem. Your submission cannot be changed to "Ready" state until all highlighted items are addressed. Please return to your submission to complete it. If you think this request is in error, please contact <a href='https://github.com/TreeBASE/treebase/issues/new?title=TreeBASE Submission S<c:out value="${submissionNumber}"/>'>help</a>.
<br /><br />
The most common problems include:
<br /><br />
(1) The submitter has not entered a citation that at a minimum must include the authors, year, title, and journal name.<br />
(2) The submitter has "orphaned" matrices or trees: i.e., there are matrices that are not listed as inputs to at least one analysis; or trees that are not listed as outputs from at least one analysis. If your paper does not include a tree, please submit a generic neighbor joining tree to satisfy this requirement.<br />
(3) The output tree of an analysis has taxon labels that do not match with the input matrix (i.e. there are taxon labels in the tree that are missing from the matrix or matrices that produced the tree). Preparing your submission using <a href='http://mesquiteproject.org/'>Mesquite</a>, in which both matrices and trees are part of the same Mesquite project and share a common taxon block, will avoid the problem of mismatched taxon labels.<br />
(4) The submitter has not attempted to validate the taxon labels by clicking the "Validate Taxon Labels" button in the Taxa section.
</p>

<p style="font-weight:bold">
Are you sure that you want to change the status of this study to 'Ready State'?
</p>

<p>
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, <b>except</b> 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.
</p>

<p>
<input type="submit" name="Submit" value="Submit" id="submitReadyState"/>
<input type="submit" name="_cancel" value = "Cancel"/>
</p>
<input type="submit" name="_cancel" value = "Cancel"/>
</p>
</form>
148 changes: 73 additions & 75 deletions treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,85 +1,83 @@
<%@page import="org.cipres.treebase.TreebaseUtil"%>
<% String purlBase = TreebaseUtil.getPurlBase(); %>
<%@ include file="/common/taglibs.jsp"%>
<head>
<title>Summary Information</title>
<content tag="heading">Summary for current study</content>
<body id="submissions"/>
<fieldset>
<%@page import="org.cipres.treebase.TreebaseUtil"%>
<% String purlBase = TreebaseUtil.getPurlBase(); %>
<%@ include file="/common/taglibs.jsp"%>

<head>
<title>Summary Information</title>
<content tag="heading">Summary for current study</content>

<body id="submissions"/>

<fieldset>
<legend>Summary
<a href="#" class="openHelp" onclick="openHelp('submissionSummaryView')"><img class="iconButton" alt="help" src="<fmt:message key="icons.help"/>" /></a>
</legend>
Submission: <c:out value="${submissionNumber}"/>, <c:out value="${studyStatus}"/>
<%if(request.isUserInRole("Admin") || request.isUserInRole("Associate Editor")){%>
, <a href="/treebase-web/admin/changeStudyStatus.html"> Update Status</a>
<%}%>
<br/>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Submission initiated:&nbsp;&nbsp;<c:out value="${initiatedDate}"/><br/>

<br/>
<a href='mailto:${submission.submitter.emailAddressString}?subject=TreeBASE Submission S${submission.id}'>
<img class="iconButton" alt="mail" src="<fmt:message key="icons.email"/>" />
Contact Submitter
</a>
<br/>
<a href='mailto:help@treebase.org?subject=TreeBASE Submission S${submission.id}'>
<img class="iconButton" alt="mail" src="<fmt:message key="icons.email"/>" />
Contact TreeBASE Help
</a>
<br/>
<br/>
<a href="<c:out value="${submission.study.phyloWSPath.purl}"/>">
<img class="iconButton" alt="link" src="<fmt:message key="icons.weblink"/>" />
Study Accession URL:<br/>
<c:out value="${submission.study.phyloWSPath.purl}"/>
</a>
<div><strong>You can cite this URL in your manuscript. It will become the permanent and resolvable resource locator after your submission has been approved and the data are made public.</strong></div>
<br/>
<a href="<c:out value="${submission.study.phyloWSPath.purl}"/>?x-access-code=<c:out value="${submission.study.namespacedGUID.hashedIDString}"/>&format=html">
<img class="iconButton" alt="link" src="<fmt:message key="icons.weblink"/>" />
Reviewer access URL:<br/>
<c:out value="${submission.study.phyloWSPath.purl}"/>?x-access-code=<c:out value="${submission.study.namespacedGUID.hashedIDString}"/>&format=html
</a>
<div><strong>You can copy and send this URL to you journal editor to provide reviewers with limited, read-only access to your data, even if your submission has not yet been approved and the data are not yet public.</strong></div>
<br/>
<c:if test="${not empty citationsummary.study}">
<c:if test="${not empty citationsummary.study.name}">
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Study name:&nbsp;&nbsp;<c:out value="${citationsummary.study.name}"/>
</c:if>
</c:if>

<br/>


<c:if test="${empty citationsummary.title}">
Citation information not yet entered. Click the <strong>Citation</strong> menu item on the right.<br/><br/>
</c:if>
<c:if test="${not empty citationsummary.title}">

<strong><u>Citation</u></strong>
<p>&nbsp; <c:out value="${citationsummary.citationType}"/>,&nbsp;<c:out value="${citationsummary.citationStatusDescription}"/> </p>
<p>&nbsp;&nbsp;&nbsp;${citationsummary.authorsCitationStyle}</p>
<br/>

</c:if>

<c:if test="${not empty citationsummary.abstract}">
<strong><u>Abstract</u></strong>
<p>&nbsp; <c:out value="${citationsummary.abstract}"/></p>
<br/>
</c:if>
</legend>
Submission: <c:out value="${submissionNumber}"/>, <c:out value="${studyStatus}"/>
<%if(request.isUserInRole("Admin") || request.isUserInRole("Associate Editor")){%>
, <a href="/treebase-web/admin/changeStudyStatus.html"> Update Status</a>
<%}%>
<br/>
Submission initiated: <c:out value="${initiatedDate}"/><br/>

<br/>
<a href='mailto:${submission.submitter.emailAddressString}?subject=TreeBASE Submission S${submission.id}'>
<img class="iconButton" alt="mail" src="<fmt:message key="icons.email"/>" />
Contact Submitter
</a>
<br/>
<a href='https://github.com/TreeBASE/treebase/issues/new?title=TreeBASE Submission S${submission.id}'>
<img class="iconButton" alt="Help link" src="<fmt:message key="icons.weblink"/>" />
Contact TreeBASE Help
</a>
<br/>
<br/>
<a href="/treebase-web/phylows/study/TB2:S${submission.study.id}">
<img class="iconButton" alt="link" src="<fmt:message key="icons.weblink"/>" />
Study Accession: TB2:S${submission.study.id}
</a>
<div><strong>You can cite this accession in your manuscript. It will become the permanent and resolvable resource locator after your submission has been approved and the data are made public.</strong></div>
<br/>
<a href="/treebase-web/phylows/study/TB2:S${submission.study.id}?x-access-code=<c:out value="${submission.study.namespacedGUID.hashedIDString}"/>&format=html">
<img class="iconButton" alt="link" src="<fmt:message key="icons.weblink"/>" />
Reviewer access: TB2:S${submission.study.id}?x-access-code=<c:out value="${submission.study.namespacedGUID.hashedIDString}"/>
</a>
<div><strong>You can copy and send this accession to your journal editor to provide reviewers with limited, read-only access to your data, even if your submission has not yet been approved and the data are not yet public.</strong></div>
<br/>
<c:if test="${not empty citationsummary.study}">
<c:if test="${not empty citationsummary.study.name}">
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Study name:&nbsp;&nbsp;<c:out value="${citationsummary.study.name}"/>
</c:if>
</c:if>

<br/>


<c:if test="${empty citationsummary.title}">
Citation information not yet entered. Click the <strong>Citation</strong> menu item on the right.<br/><br/>
</c:if>
<c:if test="${not empty citationsummary.title}">

<strong><u>Citation</u></strong>
<p>&nbsp; <c:out value="${citationsummary.citationType}"/>,&nbsp;<c:out value="${citationsummary.citationStatusDescription}"/> </p>
<p>&nbsp;&nbsp;&nbsp;${citationsummary.authorsCitationStyle}</p>
<br/>

</c:if>

<c:if test="${not empty citationsummary.abstract}">
<strong><u>Abstract</u></strong>
<p>&nbsp; <c:out value="${citationsummary.abstract}"/></p>
<br/>
</c:if>
</fieldset>

<!-- imports & variables necessary before running analysis jsps -->
<c:set var="editable" value="${false}" scope="request"/>
<!-- also need studyCommand from controller -->

<!-- now run analysis jsps -->
<jsp:include page="analysisList.jsp"/>
</body>


</body>

62 changes: 31 additions & 31 deletions treebase-web/src/main/webapp/common/adminMenu.jsp
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,31 +1,31 @@
<%@ include file="/common/taglibs.jsp"%>
<div id="sidebar">
<div id="mainMenu">
<div id="gutter">
<div id="menu">
<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif;"/>&nbsp;&nbsp;Tool Box</a>
<menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter">
<menu:displayMenu name="StudyManagementMenu"/>
<menu:displayMenu name="UserManagementMenu"/>
</menu:useMenuDisplayer>
</div>
</div>
</div>
</div>
<script type="text/javascript">
initializeMenus();
function switchMenu() {
var el = document.getElementById('menuDiv');
var tb = document.getElementById('tb');
if ( el.style.display != "none" ) {
el.style.display = 'none';
tb.src="../images/plus.gif";
}
else {
el.style.display = 'block';
tb.src="../images/minus.gif";
}
}
</script>
<%@ include file="/common/taglibs.jsp"%>

<div id="sidebar">
<div id="mainMenu">
<div id="gutter">
<div id="menu">
<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif"/>&nbsp;&nbsp;Tool Box</a>
<menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter">
<menu:displayMenu name="StudyManagementMenu"/>
<menu:displayMenu name="UserManagementMenu"/>
</menu:useMenuDisplayer>
</div>
</div>
</div>
</div>
<script type="text/javascript">
initializeMenus();

function switchMenu() {
var el = document.getElementById('menuDiv');
var tb = document.getElementById('tb');
if ( el.style.display != "none" ) {
el.style.display = 'none';
tb.src="../images/plus.gif";
}
else {
el.style.display = 'block';
tb.src="../images/minus.gif";
}
}
</script>
2 changes: 1 addition & 1 deletion treebase-web/src/main/webapp/common/searchMenuRight.jsp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<div id="mainMenu">
<div id="gutter">
<div id="menu">
<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif;"/>&nbsp;&nbsp;Tool Box</a>
<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif"/>&nbsp;&nbsp;Tool Box</a>
<menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter" >
<menu:displayMenu name="Searches" />
</menu:useMenuDisplayer>
Expand Down
10 changes: 5 additions & 5 deletions treebase-web/src/main/webapp/common/searchSummaryMenuRight.jsp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,16 +4,16 @@
<div id="mainMenu">
<div id="gutter">
<div id="menu">
<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif;"/>&nbsp;&nbsp;Tool Box</a>
<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif"/>&nbsp;&nbsp;Tool Box</a>
<menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter">
<menu:displayMenu name="SubmissionInfo"/>
<menu:displayMenu name="Citation"/>
<menu:displayMenu name="UploadFile"/>
<menu:displayMenu name="Matrices"/>
<menu:displayMenu name="Trees"/>
<menu:displayMenu name="Taxa"/>
<menu:displayMenu name="Analysis"/>
<menu:displayMenu name="Summary"/>
<menu:displayMenu name="Trees"/>
<menu:displayMenu name="Taxa"/>
<menu:displayMenu name="Analysis"/>
<menu:displayMenu name="Summary"/>
<menu:displayMenu name="NexusFiles"/>
</menu:useMenuDisplayer>
</div>
Expand Down
4 changes: 2 additions & 2 deletions treebase-web/src/main/webapp/common/submissionMenu.jsp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,15 +4,15 @@
<div id="mainMenu">
<div id="gutter">
<div id="menu">
<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif;"/>&nbsp;&nbsp;Tool Box</a>
<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif"/>&nbsp;&nbsp;Tool Box</a>
<menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter">
<menu:displayMenu name="SubmissionHome"/>
<menu:displayMenu name="SubmissionNotes"/>
<menu:displayMenu name="SubmissionCitation"/>
<menu:displayMenu name="SubmissionAuthors"/>
<menu:displayMenu name="SubmissionUploadFile"/>
<menu:displayMenu name="SubmissionNexusFiles"/>
<menu:displayMenu name="SubmissionTaxa"/>
<menu:displayMenu name="SubmissionTaxa"/>
<menu:displayMenu name="SubmissionMatrices"/>
<menu:displayMenu name="SubmissionTrees"/>
<menu:displayMenu name="SubmissionAnalyses"/>
Expand Down