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

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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
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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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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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