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rvosarvosa
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Merge pull request #408 from TreeBASE/copilot/update-tree-viewing-solution
Migrate tree viewing from Java applet to inline phylotree.js
2 parents aa2f710 + b1124ec commit e949d89

26 files changed

+34961
-577
lines changed

‎treebase-web/src/main/java/org/cipres/treebase/web/controllers/AppletInteractionController.java‎

Lines changed: 0 additions & 113 deletions
This file was deleted.

‎treebase-web/src/main/java/org/cipres/treebase/web/controllers/DirectToPhyloWidgetController.java‎

Lines changed: 0 additions & 69 deletions
This file was deleted.

‎treebase-web/src/main/webapp/WEB-INF/pages/analysisSection-Piece.jsp‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
<%@ include file="/common/taglibs.jsp"%>
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<c:url var="matrixRowURL" value="/user/matrixRowList.html"/>
3-
<c:url var="phylowidgetURL" value="/user/directToPhyloWidget.html" />
3+
<c:url var="phylowidgetURL" value="/user/directMapToPhyloWidget.html" />
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55
<li>
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<b>Software Used:</b><c:out value="${analysisStepCommand.softwareInfo.name}"/>
@@ -24,7 +24,7 @@
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</c:if>
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<c:if test="${analyzedData.dataType eq 'tree'}">
27-
<a href="${phylowidgetURL}?treeid=${analyzedData.dataId}" target = "_blank"><c:out value="${analyzedData.displayName}"/></a>
27+
<a href="${phylowidgetURL}?treeid=${analyzedData.dataId}"><c:out value="${analyzedData.displayName}"/></a>
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</c:if>
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<c:if test="${search != 'y' && pageContext['request'].remoteUser != null && publicationState eq 'NotReady'}">

‎treebase-web/src/main/webapp/WEB-INF/pages/search/study/treeBlocks.jsp‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -67,7 +67,7 @@
6767
<a href="<c:out value="${phylowidgetMapURL}"/><c:out value="?treeblockid="/><c:out value="${userList.id}" />" >View trees</a>
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--%>
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<c:set var="url" value="${phylowidgetMapURL}?treeblockid=${userList.id}" />
70-
<a href="javascript:popupWithSizes('${url}',900,800,'1')">View trees</a>
70+
<a href="${url}">View trees</a>
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</display:column>
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<%if(request.isUserInRole("Admin") || request.isUserInRole("Associate Editor")){%>

‎treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp‎

Lines changed: 15 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -12,13 +12,7 @@
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<%
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pageContext.setAttribute("accesscode",request.getSession().getAttribute("x-access-code"));
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%>
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<script type="text/javascript">
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function openTreeViewer(tree_id)
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{
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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>;
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window.open(realURL,'treeviewer','width=1000,height=800,scrollbars=yes,resizable=yes')
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}
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</script>
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<display:table name="trees"
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requestURI=""
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class="list"
@@ -28,7 +22,13 @@
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export="false">
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<display:column sortable="false" title="ID">
31-
<a href="javascript:void(0)" onClick="openTreeViewer(${tree.id})">Tr${tree.id}</a>
25+
<c:url var="treeViewerURL" value="/search/study/tree.html">
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<c:param name="treeid" value="${tree.id}"/>
27+
<c:if test="${!empty accesscode}">
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<c:param name="x-access-code" value="${accesscode}"/>
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</c:if>
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</c:url>
31+
<a href="${treeViewerURL}">Tr${tree.id}</a>
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</display:column>
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<display:column
@@ -143,7 +143,13 @@
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sortable="false"
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class="iconColumn"
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headerClass="iconColumn">
146-
<a href="javascript:void(0)" onClick="openTreeViewer(${tree.id})">
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<c:url var="treeViewerURL" value="/search/study/tree.html">
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<c:param name="treeid" value="${tree.id}"/>
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<c:if test="${!empty accesscode}">
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<c:param name="x-access-code" value="${accesscode}"/>
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</c:if>
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</c:url>
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<a href="${treeViewerURL}">
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<img
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class="iconButton"
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src="<fmt:message key="icons.tree.view"/>"

‎treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp‎

Lines changed: 10 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -4,15 +4,6 @@
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<%--content tag="heading"><fmt:message key="search.results.title.trees"/></content>
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<body id="trees"/ --%>
66

7-
<script type="text/javascript">
8-
function openTreeViewer(tree_id)
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{
10-
var realURL = "/treebase-web/search/study/tree.html?treeid="+tree_id;
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window.open(realURL,'treeviewer','width=1000,height=800,scrollbars=yes,resizable=yes')
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}
13-
14-
</script>
15-
167
<display:table name="${resultSet.results}"
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requestURI=""
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class="list"
@@ -23,7 +14,10 @@
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<display:column title="" sortable="true" class="checkBoxColumn">
2516
<input type="checkbox" id="s-${tree.id }" name="selection" value="${tree.id }" />
26-
<a href="javascript:void(0)" onClick="openTreeViewer(${tree.id})">Tr${tree.id}</a>
17+
<c:url var="treeViewerURL" value="/search/study/tree.html">
18+
<c:param name="treeid" value="${tree.id}"/>
19+
</c:url>
20+
<a href="${treeViewerURL}">Tr${tree.id}</a>
2721
</display:column>
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2923

@@ -85,7 +79,10 @@
8579
sortable="false"
8680
class="iconColumn"
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headerClass="iconColumn">
88-
<a href="javascript:void(0)" onClick="openTreeViewer(${tree.id})">
82+
<c:url var="treeViewerURL" value="/search/study/tree.html">
83+
<c:param name="treeid" value="${tree.id}"/>
84+
</c:url>
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<a href="${treeViewerURL}">
8986
<img
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class="iconButton"
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src="<fmt:message key="icons.tree.view"/>"
@@ -117,7 +114,7 @@
117114
</display:footer>
118115
<display:setProperty name="basic.empty.showtable" value="true"/>
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120-
</display:table>
121-
117+
</display:table>
118+
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‎treebase-web/src/main/webapp/WEB-INF/pages/treeBlockList.jsp‎

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -87,18 +87,18 @@ Tree blocks
8787
alt="<fmt:message key="tree.list"/>"/>
8888
</display:column>
8989

90-
<display:column
91-
sortable="false"
92-
class="iconColumn"
93-
headerClass="iconColumn">
94-
<c:set var="url" value="${phylowidgetMapURL}?treeblockid=${userList.id}" />
95-
<a href="javascript:popupWithSizes('${url}',900,800,'1')">
96-
<img
97-
class="iconButton"
98-
src="<fmt:message key="icons.tree.edit"/>"
99-
title="<fmt:message key="tree.edit"/>"
100-
alt="<fmt:message key="tree.edit"/>"/>
101-
</a>
90+
<display:column
91+
sortable="false"
92+
class="iconColumn"
93+
headerClass="iconColumn">
94+
<c:set var="url" value="${phylowidgetMapURL}?treeblockid=${userList.id}" />
95+
<a href="${url}">
96+
<img
97+
class="iconButton"
98+
src="<fmt:message key="icons.tree.edit"/>"
99+
title="<fmt:message key="tree.view"/>"
100+
alt="<fmt:message key="tree.view"/>"/>
101+
</a>
102102
</display:column>
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104104
<display:column

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