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From: <yo...@us...> - 2009-12-18 19:03:45
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Revision: 399
http://treebase.svn.sourceforge.net/treebase/?rev=399&view=rev
Author: youjun
Date: 2009-12-18 19:03:26 +0000 (Fri, 18 Dec 2009)
Log Message:
-----------
1. make "ready" submission editable by Admin and Assis Editor
2. add link from submissionSummary back to changeStudyStatus
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/addPersonForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/analysisForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/citationForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/matrixList.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/treeBlocks.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/treeBlockList.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/addPersonForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/addPersonForm.jsp 2009-12-16 17:57:12 UTC (rev 398)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/addPersonForm.jsp 2009-12-18 19:03:26 UTC (rev 399)
@@ -81,7 +81,11 @@
<tr>
- <c:if test="${publicationState eq 'NotReady'}">
+ <%if(request.isUserInRole("Admin") || request.isUserInRole("Associate Editor")){%>
+ <% request.setAttribute("isEditable","yes");%>
+ <% } %>
+
+ <c:if test="${publicationState eq 'NotReady'||isEditable eq 'yes'}">
<td></td>
<td colspan="5">
<input type="submit" name="Submit" value="<fmt:message key="button.submit"/>" />
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/analysisForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/analysisForm.jsp 2009-12-16 17:57:12 UTC (rev 398)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/analysisForm.jsp 2009-12-18 19:03:26 UTC (rev 399)
@@ -50,7 +50,11 @@
<tr>
<th></th>
<td>
- <c:if test="${publicationState eq 'NotReady'}">
+ <%if(request.isUserInRole("Admin") || request.isUserInRole("Associate Editor")){%>
+ <% request.setAttribute("isEditable","yes");%>
+ <% } %>
+
+ <c:if test="${publicationState eq 'NotReady'||isEditable eq 'yes'}">
<c:choose>
<c:when test="${analysis.id == null}">
<input type="submit" name="Submit" value="<fmt:message key="button.submit"/>" />
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/citationForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/citationForm.jsp 2009-12-16 17:57:12 UTC (rev 398)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/citationForm.jsp 2009-12-18 19:03:26 UTC (rev 399)
@@ -75,7 +75,12 @@
</c:when>
</c:choose>
<tr>
- <c:if test="${publicationState eq 'NotReady'}">
+
+ <%if(request.isUserInRole("Admin") || request.isUserInRole("Associate Editor")){%>
+ <% request.setAttribute("isEditable","yes");%>
+ <% } %>
+
+ <c:if test="${publicationState eq 'NotReady'||isEditable eq 'yes'}">
<th></th>
<td colspan="5" align="center">
<c:choose>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/matrixList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/matrixList.jsp 2009-12-16 17:57:12 UTC (rev 398)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/matrixList.jsp 2009-12-18 19:03:26 UTC (rev 399)
@@ -131,7 +131,11 @@
</c:if>
<display:footer>
- <c:if test="${publicationState eq 'NotReady'}">
+ <%if(request.isUserInRole("Admin") || request.isUserInRole("Associate Editor")){%>
+ <% request.setAttribute("isEditable","yes");%>
+ <% } %>
+
+ <c:if test="${publicationState eq 'NotReady'||isEditable eq 'yes'}">
<tr>
<td colspan="8" align="center">
<input type="submit" class="button" name="Update" value="<fmt:message key="button.update"/>" />
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/treeBlocks.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/treeBlocks.jsp 2009-12-16 17:57:12 UTC (rev 398)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/treeBlocks.jsp 2009-12-18 19:03:26 UTC (rev 399)
@@ -70,7 +70,11 @@
<a href="javascript:popupWithSizes('${url}',900,800,'1')">View trees</a>
</display:column>
- <c:if test="${publicationState eq 'NotReady'}">
+ <%if(request.isUserInRole("Admin") || request.isUserInRole("Associate Editor")){%>
+ <% request.setAttribute("isEditable","yes");%>
+ <% } %>
+
+ <c:if test="${publicationState eq 'NotReady'||isEditable eq 'yes'}">
<display:column titleKey="link.delete"
sortable="false"
url="/user/deleteATreeBlock.html" paramId="treeblockid" paramProperty="id"
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp 2009-12-16 17:57:12 UTC (rev 398)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp 2009-12-18 19:03:26 UTC (rev 399)
@@ -71,7 +71,11 @@
<c:if test="${publicationState eq 'Ready' || publicationState eq 'Published'}">
<Strong>For now, this study is read only.</Strong>
</c:if>
- <c:if test="${publicationState eq 'NotReady'}">
+ <%if(request.isUserInRole("Admin") || request.isUserInRole("Associate Editor")){%>
+ <% request.setAttribute("isEditable","yes");%>
+ <% } %>
+
+ <c:if test="${publicationState eq 'NotReady'||isEditable eq 'yes'}">
<c:choose>
<c:when test="${study.id == null }">
<input type="submit" name="Submit" value="<fmt:message key="button.submit"/>"/>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2009-12-16 17:57:12 UTC (rev 398)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2009-12-18 19:03:26 UTC (rev 399)
@@ -9,7 +9,7 @@
<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}"/><br/>
+Submission: <c:out value="${submissionNumber}"/>, <c:out value="${studyStatus}"/>, <a href="/treebase-web/admin/changeStudyStatus.html"> Update Status</a><br/>
Submission initiated: <c:out value="${initiatedDate}"/><br/>
<c:if test="${not empty citationsummary.study}">
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/treeBlockList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/treeBlockList.jsp 2009-12-16 17:57:12 UTC (rev 398)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/treeBlockList.jsp 2009-12-18 19:03:26 UTC (rev 399)
@@ -132,7 +132,11 @@
</c:if>
<display:footer>
- <c:if test="${publicationState eq 'NotReady'}">
+ <%if(request.isUserInRole("Admin") || request.isUserInRole("Associate Editor")){%>
+ <% request.setAttribute("isEditable","yes");%>
+ <% } %>
+
+ <c:if test="${publicationState eq 'NotReady'||isEditable eq 'yes'}">
<tr>
<td colspan="7" align="center">
<input type="submit" class="button" name="Update" value="<fmt:message key="button.update"/>" />
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|
|
From: <yo...@us...> - 2010-03-20 16:08:34
|
Revision: 632
http://treebase.svn.sourceforge.net/treebase/?rev=632&view=rev
Author: youjun
Date: 2010-03-20 16:08:26 +0000 (Sat, 20 Mar 2010)
Log Message:
-----------
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp 2010-03-20 15:51:38 UTC (rev 631)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp 2010-03-20 16:08:26 UTC (rev 632)
@@ -7,14 +7,14 @@
<p>For questions about data submission and data content, please
contact: </p>
-<p><img src="images/help_mail.jpg"> </p>
+<p> <img src="images/help_mail.jpg"> </p>
<h2>Bugs</h2>
<p>To report software bugs, browser conflicts, and ergonomic
inefficiencies, please contact:</p>
-<p><img src="images/bugs_mail.jpg"> </p>
+<p> <img src="images/bugs_mail.jpg"> </p>
<p>Alternatively, you can enter a bug report directly into our
sourceforge online bug tracker. For that, please follow these steps:</p>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2010-03-20 15:51:38 UTC (rev 631)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2010-03-20 16:08:26 UTC (rev 632)
@@ -296,10 +296,6 @@
</tr>
</table>
-<p class=MsoNormal> </p>
-
-<p class=MsoNormal> </p>
-
<p class=MsoNormal><b>Other Journals with a Significant Presence in TreeBASE</b>:
<a
href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%2American+Journal+of+Botany%22"
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp 2010-03-20 15:51:38 UTC (rev 631)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp 2010-03-20 16:08:26 UTC (rev 632)
@@ -1,5 +1,5 @@
-<h1>Reference</h1>
+<h1>References</h1>
<p>
<strong>Blake, J. A., C. J. Bult, M. J. Donoghue, J. Humphries, and C. Fields.</strong>
1994. Interoperability of biological databases: a meeting report.
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|
From: <sfr...@us...> - 2011-05-11 13:35:36
|
Revision: 832
http://treebase.svn.sourceforge.net/treebase/?rev=832&view=rev
Author: sfrgpiel
Date: 2011-05-11 13:35:26 +0000 (Wed, 11 May 2011)
Log Message:
-----------
Slight fixes to the text
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/uploadFile.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp 2011-05-10 19:34:26 UTC (rev 831)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp 2011-05-11 13:35:26 UTC (rev 832)
@@ -7,13 +7,13 @@
<content tag="heading">Create New Submission</content>
<p>Please provide a brief title for your study. Usually this is the same title as the title of your pubication.</p>
<p>The notes for your study are not for the public, but are there for your own benefit and for communicating with TreeBASE staff once your submission status is ready to be made public. </p>
- <p>If your submission is part of a sponsored research data management plan, please indicate this in the Notes so that TreeBASE staff know to provide added attention and to assist in making your submission fully compliant with the expectations of the of the sponsor. For more information, see the <a href="/treebase-web/dataMan.html" target="_blank">NSF Data Management Plan instructions</a>. </p>
+ <p>If your submission is part of a sponsored research data management plan, please indicate this in the Notes so that TreeBASE staff know to provide added attention and to assist in making your submission fully compliant with the expectations of the sponsor. For more information, see the <a href="/treebase-web/dataMan.html" target="_blank">NSF Data Management Plan instructions</a>. </p>
</c:when>
<c:otherwise>
<content tag="heading">Update Submission</content>
<p>Please update the following submission information as needed.</p>
<p>The notes for your study are not for the public, but are there for your own benefit and for communicating with TreeBASE staff once your submission status is ready to be made public. </p>
- <p>If your submission is part of a sponsored research data management plan, please indicate this in the Notes so that TreeBASE staff know to provide added attention and to assist in making your submission fully compliant with the expectations of the of the sponsor. For more information, see the <a href="/treebase-web/dataMan.html" target="_blank">NSF Data Management Plan instructions</a>. </p>
+ <p>If your submission is part of a sponsored research data management plan, please indicate this in the Notes so that TreeBASE staff know to provide added attention and to assist in making your submission fully compliant with the expectations of the sponsor. For more information, see the <a href="/treebase-web/dataMan.html" target="_blank">NSF Data Management Plan instructions</a>. </p>
</c:otherwise>
</c:choose>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/uploadFile.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/uploadFile.jsp 2011-05-10 19:34:26 UTC (rev 831)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/uploadFile.jsp 2011-05-11 13:35:26 UTC (rev 832)
@@ -25,10 +25,10 @@
<body id="submissions"/>
<p>Use the following form to upload your Nexus files for <b>submission ${studyMap['id']} - ${studyMap['name']}</b><br>
-Please limit the number of trees you upload for parsing to ~30, otherwise large numbers of trees resulting from the
+Please note that only the first ~30 trees will be parsed, otherwise large numbers of trees resulting from the
same analysis will overwhelm the user experience in TreeBASE's search interface with what are largely redundant trees.
-If you have a large number of trees, please either select a few preferred trees and upload those for parsing, or upload
-a consensus tree. For information on making large numbers of trees available to users, please see the help
+If you have a large number of trees, please put your preferred trees, or a consensus tree, within the first ~30
+trees in the tree block. For more information, please see the help
<a href="#" class="openHelp" onclick="openHelp('uploadFile')"><img class="iconButton" src="<fmt:message key="icons.help"/>" /></a>.</p>
<!--form method="post" enctype="multipart/form-data" onsubmit="setTimeout('queryStatus()', 200);"-->
<!-- Line above is needed to show the actal amount of data uploaded using Ajax -->
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From: <sfr...@us...> - 2011-09-01 17:15:11
|
Revision: 950
http://treebase.svn.sourceforge.net/treebase/?rev=950&view=rev
Author: sfrgpiel
Date: 2011-09-01 17:15:05 +0000 (Thu, 01 Sep 2011)
Log Message:
-----------
Adding some hard-coded instructions to address FAQs.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/nexusFiles.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionList.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/nexusFiles.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/nexusFiles.jsp 2011-08-29 19:34:58 UTC (rev 949)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/nexusFiles.jsp 2011-09-01 17:15:05 UTC (rev 950)
@@ -5,7 +5,12 @@
<body id="submissions"/>
<c:url var="nexusdownloadURL" value="/user/downloadANexusFile.html" />
<c:url var="nexusrctdownloadURL" value="/user/downloadANexusRCTFile.html" />
-<p>The table below shows a list of all the nexus files for the current study.</p>
+<p>The table below shows a list of all the NEXUS files uploaded to the submission.
+These files cannot be deleted unless the entire submission is deleted, however
+they are not visible to the public unless trees or matrices brought in by them
+are published. Consequently, if all trees and matrices are deleted, the original
+file is only visible to the submitter and to the editors of TreeBASE. Retaining
+these files is useful for TreeBASE staff as a record of prior submission activity.</p>
<form method="post">
<fieldset>
<legend>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp 2011-08-29 19:34:58 UTC (rev 949)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp 2011-09-01 17:15:05 UTC (rev 950)
@@ -5,7 +5,7 @@
<c:choose>
<c:when test="${empty study.submission.id}">
<content tag="heading">Create New Submission</content>
- <p>Please provide a brief title for your study. Usually this is the same title as the title of your pubication.</p>
+ <p>Please provide a brief title for your study. Usually this is the same title as the title of your publication.</p>
<p>The notes for your study are not for the public, but are there for your own benefit and for communicating with TreeBASE staff once your submission status is ready to be made public. </p>
<p>If your submission is part of a sponsored research data management plan, please indicate this in the Notes so that TreeBASE staff know to provide added attention and to assist in making your submission fully compliant with the expectations of the sponsor. For more information, see the <a href="/treebase-web/dataMan.html" target="_blank">NSF Data Management Plan instructions</a>. </p>
</c:when>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionList.jsp 2011-08-29 19:34:58 UTC (rev 949)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionList.jsp 2011-09-01 17:15:05 UTC (rev 950)
@@ -12,7 +12,7 @@
<legend>Submissions
<a href="#" class="openHelp" onclick="openHelp('submissionList')"><img class="iconButton" src="<fmt:message key="icons.help"/>" /></a>
</legend>
-The table below shows a list of your Treebase submissions.
+The table below shows a list of your Treebase submissions. Submissions can only be deleted after all trees and matrices are deleted first.
<display:table
name="${submissionList}"
requestURI=""
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