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Migrate tree viewing from Java applet to inline phylotree.js #408

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Merged
rvosa merged 25 commits into from
Jan 27, 2026
Merged

Migrate tree viewing from Java applet to inline phylotree.js #408

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b55e6ac
Initial plan
Copilot Jan 16, 2026
867cd90
Remove legacy applet code and migrate to phylotree.js inline viewer
Copilot Jan 16, 2026
78d0923
Fix XSS vulnerabilities in tree viewer components
Copilot Jan 16, 2026
37c8564
Fix phylotree.js integration with local libraries
Copilot Jan 16, 2026
1951df2
Add shim for phylotree.js UMD bundle
rvosa Jan 18, 2026
00c79ed
Implement library wrapper for lodash and underscore
rvosa Jan 18, 2026
e200d41
Add cladogram support to phylotree.js tree viewer
Copilot Jan 18, 2026
4520ddd
Fix cladogram branch length conversion regex causing NaN errors
Copilot Jan 18, 2026
a22d930
Use phylotree.js tree traversal for cladogram handling
Copilot Jan 18, 2026
33f253b
Fix: Use string type for node.data.attribute in makeUltrametric
Copilot Jan 18, 2026
88960d3
Fix: Set root node attribute to "0" for phylotree.js compatibility
Copilot Jan 18, 2026
474585f
Fix: Manually append SVG to container after render()
Copilot Jan 18, 2026
33f0335
Simplify cladogram handling - use phylotree.js built-in support
Copilot Jan 18, 2026
0f03c35
Load phylotree.js stack BEFORE Prototype.js to fix Array pollution
Copilot Jan 23, 2026
2a8c892
Comment out unused menu toggle and script in adminMenu.jsp
rvosa Jan 27, 2026
aa4f992
Comment out unused Prototype.js scripts in adminTemplate.jsp
rvosa Jan 27, 2026
12651c8
Comment out unused Prototype.js and script.aculo.us scripts in defaul…
rvosa Jan 27, 2026
6606aa1
Comment out unused Prototype.js and script.aculo.us scripts in defaul…
rvosa Jan 27, 2026
3ba6ffd
Comment out center-aligned paragraph in footer.jsp for cleaner markup
rvosa Jan 27, 2026
99d22b0
Comment out unused Prototype.js script in mainTemplate.jsp for cleane…
rvosa Jan 27, 2026
b93d9e4
Comment out unused script and menu link in searchMenuRight.jsp for cl…
rvosa Jan 27, 2026
e2b6904
Comment out unused script and menu link in searchSummaryMenuRight.jsp…
rvosa Jan 27, 2026
9b139ea
Comment out unused Mendeley link and image in sidebarLeft.jsp for cle…
rvosa Jan 27, 2026
7b4f8a7
Comment out unused menu and script elements in submissionMenu.jsp for…
rvosa Jan 27, 2026
b1124ec
Refactor treeViewer.jsp for cleaner markup and improved structure
rvosa Jan 27, 2026
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113 changes: 0 additions & 113 deletions ...se-web/src/main/java/org/cipres/treebase/web/controllers/AppletInteractionController.java
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This file was deleted.

69 changes: 0 additions & 69 deletions ...-web/src/main/java/org/cipres/treebase/web/controllers/DirectToPhyloWidgetController.java
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4 changes: 2 additions & 2 deletions treebase-web/src/main/webapp/WEB-INF/pages/analysisSection-Piece.jsp
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@@ -1,6 +1,6 @@
<%@ include file="/common/taglibs.jsp"%>
<c:url var="matrixRowURL" value="/user/matrixRowList.html"/>
<c:url var="phylowidgetURL" value="/user/directToPhyloWidget.html" />
<c:url var="phylowidgetURL" value="/user/directMapToPhyloWidget.html" />

<li>
<b>Software Used:</b><c:out value="${analysisStepCommand.softwareInfo.name}"/>
Expand All @@ -24,7 +24,7 @@
</c:if>

<c:if test="${analyzedData.dataType eq 'tree'}">
<a href="${phylowidgetURL}?treeid=${analyzedData.dataId}" target = "_blank"><c:out value="${analyzedData.displayName}"/></a>
<a href="${phylowidgetURL}?treeid=${analyzedData.dataId}"><c:out value="${analyzedData.displayName}"/></a>
</c:if>

<c:if test="${search != 'y' && pageContext['request'].remoteUser != null && publicationState eq 'NotReady'}">
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2 changes: 1 addition & 1 deletion treebase-web/src/main/webapp/WEB-INF/pages/search/study/treeBlocks.jsp
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Expand Up @@ -67,7 +67,7 @@
<a href="<c:out value="${phylowidgetMapURL}"/><c:out value="?treeblockid="/><c:out value="${userList.id}" />" >View trees</a>
--%>
<c:set var="url" value="${phylowidgetMapURL}?treeblockid=${userList.id}" />
<a href="javascript:popupWithSizes('${url}',900,800,'1')">View trees</a>
<a href="${url}">View trees</a>
</display:column>

<%if(request.isUserInRole("Admin") || request.isUserInRole("Associate Editor")){%>
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24 changes: 15 additions & 9 deletions treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp
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Expand Up @@ -12,13 +12,7 @@
<%
pageContext.setAttribute("accesscode",request.getSession().getAttribute("x-access-code"));
%>
<script type="text/javascript">
function openTreeViewer(tree_id)
{
var realURL = "/treebase-web/search/study/tree.html?treeid="+tree_id<c:if test="${!empty accesscode}">+"&x-access-code=<c:out value='${accesscode}' />"</c:if>;
window.open(realURL,'treeviewer','width=1000,height=800,scrollbars=yes,resizable=yes')
}
</script>

<display:table name="trees"
requestURI=""
class="list"
Expand All @@ -28,7 +22,13 @@
export="false">

<display:column sortable="false" title="ID">
<a href="javascript:void(0)" onClick="openTreeViewer(${tree.id})">Tr${tree.id}</a>
<c:url var="treeViewerURL" value="/search/study/tree.html">
<c:param name="treeid" value="${tree.id}"/>
<c:if test="${!empty accesscode}">
<c:param name="x-access-code" value="${accesscode}"/>
</c:if>
</c:url>
<a href="${treeViewerURL}">Tr${tree.id}</a>
</display:column>

<display:column
Expand Down Expand Up @@ -143,7 +143,13 @@
sortable="false"
class="iconColumn"
headerClass="iconColumn">
<a href="javascript:void(0)" onClick="openTreeViewer(${tree.id})">
<c:url var="treeViewerURL" value="/search/study/tree.html">
<c:param name="treeid" value="${tree.id}"/>
<c:if test="${!empty accesscode}">
<c:param name="x-access-code" value="${accesscode}"/>
</c:if>
</c:url>
<a href="${treeViewerURL}">
<img
class="iconButton"
src="<fmt:message key="icons.tree.view"/>"
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23 changes: 10 additions & 13 deletions treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp
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Expand Up @@ -4,15 +4,6 @@
<%--content tag="heading"><fmt:message key="search.results.title.trees"/></content>
<body id="trees"/ --%>

<script type="text/javascript">
function openTreeViewer(tree_id)
{
var realURL = "/treebase-web/search/study/tree.html?treeid="+tree_id;
window.open(realURL,'treeviewer','width=1000,height=800,scrollbars=yes,resizable=yes')
}

</script>

<display:table name="${resultSet.results}"
requestURI=""
class="list"
Expand All @@ -23,7 +14,10 @@

<display:column title="" sortable="true" class="checkBoxColumn">
<input type="checkbox" id="s-${tree.id }" name="selection" value="${tree.id }" />
<a href="javascript:void(0)" onClick="openTreeViewer(${tree.id})">Tr${tree.id}</a>
<c:url var="treeViewerURL" value="/search/study/tree.html">
<c:param name="treeid" value="${tree.id}"/>
</c:url>
<a href="${treeViewerURL}">Tr${tree.id}</a>
</display:column>


Expand Down Expand Up @@ -85,7 +79,10 @@
sortable="false"
class="iconColumn"
headerClass="iconColumn">
<a href="javascript:void(0)" onClick="openTreeViewer(${tree.id})">
<c:url var="treeViewerURL" value="/search/study/tree.html">
<c:param name="treeid" value="${tree.id}"/>
</c:url>
<a href="${treeViewerURL}">
<img
class="iconButton"
src="<fmt:message key="icons.tree.view"/>"
Expand Down Expand Up @@ -117,7 +114,7 @@
</display:footer>
<display:setProperty name="basic.empty.showtable" value="true"/>

</display:table>

</display:table>


24 changes: 12 additions & 12 deletions treebase-web/src/main/webapp/WEB-INF/pages/treeBlockList.jsp
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Expand Up @@ -87,18 +87,18 @@ Tree blocks
alt="<fmt:message key="tree.list"/>"/>
</display:column>

<display:column
sortable="false"
class="iconColumn"
headerClass="iconColumn">
<c:set var="url" value="${phylowidgetMapURL}?treeblockid=${userList.id}" />
<a href="javascript:popupWithSizes('${url}',900,800,'1')">
<img
class="iconButton"
src="<fmt:message key="icons.tree.edit"/>"
title="<fmt:message key="tree.edit"/>"
alt="<fmt:message key="tree.edit"/>"/>
</a>
<display:column
sortable="false"
class="iconColumn"
headerClass="iconColumn">
<c:set var="url" value="${phylowidgetMapURL}?treeblockid=${userList.id}" />
<a href="${url}">
<img
class="iconButton"
src="<fmt:message key="icons.tree.edit"/>"
title="<fmt:message key="tree.view"/>"
alt="<fmt:message key="tree.view"/>"/>
</a>
</display:column>

<display:column
Expand Down
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