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From: SourceForge.net <no...@so...> - 2010-03-26 11:06:40
|
Bugs item #2974771, was opened at 2010-03-22 18:59 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974771&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: Hilmar Lapp (hlapp) >Assigned to: Rutger Vos (rvos) Summary: Accessing phyloWS URLs yields exception for HTML view Initial Comment: For example the following works: http://www.treebase.org/treebase-web/phylows/tree/TB2:Tr6917?format=rdf whereas removing the format= parameter (i.e., the HTML view) results in the following YIKES. I suspect that this means that depending on the path from which you access a page, the phyloWSPath (and possibly other page or request parameters) are not properly initialized. javax.servlet.jsp.el.ELException: An error occurred while getting property "phyloWSPath" from an instance of class org.cipres.treebase.domain.study.Study$$EnhancerByCGLIB$$4d099cbc at org.apache.commons.el.Logger.logError(Logger.java:484) at org.apache.commons.el.Logger.logError(Logger.java:588) at org.apache.commons.el.ArraySuffix.evaluate(ArraySuffix.java:318) at org.apache.commons.el.ComplexValue.evaluate(ComplexValue.java:145) at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:263) at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:190) at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:924) at org.apache.jsp.WEB_002dINF.pages.anyObjectAsRDF_jsp._jspx_meth_c_005fout_005f1(anyObjectAsRDF_jsp.java:224) at org.apache.jsp.WEB_002dINF.pages.anyObjectAsRDF_jsp._jspx_meth_c_005fif_005f0(anyObjectAsRDF_jsp.java:199) at org.apache.jsp.WEB_002dINF.pages.anyObjectAsRDF_jsp._jspService(anyObjectAsRDF_jsp.java:100) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:39) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679) at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461) at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399) at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301) at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142) at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:239) at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1142) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:879) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2010-03-26 11:06 Message: Thanks for reporting this bug. We'll look into it as soon as possible. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974771&group_id=248804 |
|
From: <sfr...@us...> - 2010-03-24 12:59:42
|
Revision: 656
http://treebase.svn.sourceforge.net/treebase/?rev=656&view=rev
Author: sfrgpiel
Date: 2010-03-24 12:59:35 +0000 (Wed, 24 Mar 2010)
Log Message:
-----------
mplaza.jpg pic
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/images/people/mplaza.jpg
Added: trunk/treebase-web/src/main/webapp/images/people/mplaza.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/mplaza.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sfr...@us...> - 2010-03-24 12:59:04
|
Revision: 655
http://treebase.svn.sourceforge.net/treebase/?rev=655&view=rev
Author: sfrgpiel
Date: 2010-03-24 12:58:52 +0000 (Wed, 24 Mar 2010)
Log Message:
-----------
Added Jon Auman and Melanie Plaza
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp 2010-03-24 12:30:11 UTC (rev 654)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp 2010-03-24 12:58:52 UTC (rev 655)
@@ -1,41 +1,75 @@
<div class="gutter">
<h1>People</h1>
<table class="peopleTable">
- <thead><tr><th colspan="6"><h2>Current contributors</h2></th></tr></thead>
- <tr>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Vladimir Gapeyev"/>
- <br/><strong>Vladimir Gapeyev</strong>
- <br/>Deployment Maintainer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Youjun Guo"/>
- <br/><strong>Youjun Guo</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/hlapp.jpeg" width="81" height="108" alt="Hilmar Lapp"/>
- <br/><strong>Hilmar Lapp</strong>
- <br/>Deployment Manager
- </td>
- <td>
- <img src="images/people/bpiel.jpeg" width="81" height="108" alt="William Piel"/>
- <br/><strong>William Piel</strong>
- <br/>Content Editor
- <br />Prototype Dev
- </td>
- <td>
- <img src="images/people/vtannen.jpeg" width="81" height="108" alt="Val Tannen"/>
- <br/><strong>Val Tannen</strong>
- <br/>Development Leader
- </td>
- <td>
- <img src="images/people/rvos.jpg" width="81" height="108" alt="Rutger Vos"/>
- <br/><strong>Rutger Vos</strong>
- <br/>Developer
- <br/>API Design
- </td>
- </tr>
+ <thead><tr><th colspan="6"><h2>Current contributors</h2></th></tr></thead>
+ <tr>
+ <td>
+ <img src="images/people/jauman.jpg" width="81" height="108" alt="Jon Auman"/>
+ <br/><strong>Jon Auman</strong>
+ <br/>
+ DBA &<br/>
+ Systems Administrator
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Vladimir Gapeyev"/>
+ <br/><strong>Vladimir Gapeyev</strong>
+ <br/>Deployment Maintainer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Youjun Guo"/>
+ <br/><strong>Youjun Guo</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/hlapp.jpeg" width="81" height="108" alt="Hilmar Lapp"/>
+ <br/><strong>Hilmar Lapp</strong>
+ <br/>Deployment Manager
+ </td>
+ <td>
+ <img src="images/people/bpiel.jpeg" width="81" height="108" alt="William Piel"/>
+ <br/><strong>William Piel</strong>
+ <br/>Content Editor
+ <br/>Prototype Dev
+ </td>
+ <td>
+ <img src="images/people/mplaza.jpg" width="81" height="108" alt="Melanie Plaza"/>
+ <br/><strong>Melanie Plaza</strong>
+ <br/>Metadata Editor
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <img src="images/people/vtannen.jpeg" width="81" height="108" alt="Val Tannen"/>
+ <br/><strong>Val Tannen</strong>
+ <br/>Development Leader
+ </td>
+ <td>
+ <img src="images/people/rvos.jpg" width="81" height="108" alt="Rutger Vos"/>
+ <br/><strong>Rutger Vos</strong>
+ <br/>Developer
+ <br/>API Design
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Volunteeers"/>
+ <br/><strong>Volunteeers?</strong>
+ <br/>Please sign up!
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Volunteeers"/>
+ <br/><strong>Volunteeers?</strong>
+ <br/>Please sign up!
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Volunteeers"/>
+ <br/><strong>Volunteeers?</strong>
+ <br/>Please sign up!
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Volunteeers"/>
+ <br/><strong>Volunteeers?</strong>
+ <br/>Please sign up!
+ </td>
+ </tr>
</table>
<table class="peopleTable">
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sfr...@us...> - 2010-03-24 12:30:18
|
Revision: 654
http://treebase.svn.sourceforge.net/treebase/?rev=654&view=rev
Author: sfrgpiel
Date: 2010-03-24 12:30:11 +0000 (Wed, 24 Mar 2010)
Log Message:
-----------
jauman.jpg pic added
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/images/people/jauman.jpg
Added: trunk/treebase-web/src/main/webapp/images/people/jauman.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/jauman.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <hl...@us...> - 2010-03-23 22:56:30
|
Revision: 653
http://treebase.svn.sourceforge.net/treebase/?rev=653&view=rev
Author: hlapp
Date: 2010-03-23 22:56:16 +0000 (Tue, 23 Mar 2010)
Log Message:
-----------
Canonicalized URLs.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-23 18:15:11 UTC (rev 652)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-23 22:56:16 UTC (rev 653)
@@ -10,11 +10,11 @@
<li>The ability to visualize and edit trees using Phylowidget</li>
<li>The ability to search on tree topology</li>
<li>Persistent and resolvable URIs for data objects in TreeBASE (i.e. studies, trees, matrices) serve as both globally unique identification numbers and resource locators. These can be included in articles and on researcher's websites, making access to TreeBASE data only a click away</li>
- <li>Data are delivered in several serializations, including <a href="https://www.nescent.org/wg_phyloinformatics/Supporting_NEXUS_Documentation" target="_blank">NEXUS</a> and <a href="http://www.nexml.org" target="_blank">NeXML</a></li>
+ <li>Data are delivered in several serializations, including <a href="http:/hackathon.nescent.org/Supporting_NEXUS_Documentation" target="_blank">NEXUS</a> and <a href="http://www.nexml.org" target="_blank">NeXML</a></li>
<li> A special URL gives journal editors and reviewers anonymous advanced access to data</li>
- <li>Programmatic access to the data using the <a href="https://www.nescent.org/wg_evoinfo/PhyloWS" target="_blank">PhyloWS API</a>. Queries are expressed in URLs using PhyloWS syntax and can return results in RDF as RSS 1.0 feeds, which means that users can set their favorite RSS Reader to fetch all new TreeBASE studies that satisfy a particular query (e.g. return all studies published in "Systematic Biology," or return all trees that include "Homo sapiens," etc)</li>
+ <li>Programmatic access to the data using the <a href="http://evoinfo.nescent.org/PhyloWS" target="_blank">PhyloWS API</a>. Queries are expressed in URLs using PhyloWS syntax and can return results in RDF as RSS 1.0 feeds, which means that users can set their favorite RSS Reader to fetch all new TreeBASE studies that satisfy a particular query (e.g. return all studies published in "Systematic Biology," or return all trees that include "Homo sapiens," etc)</li>
</ul>
<p>
As of early 2010, TreeBASE contains 6,500 trees in 2,500 publications written by 4,500 different authors. These trees have 135,000 distinct taxon labels that map to approximately 60,000 distinct taxa. </p>
</div>
-</div>
\ No newline at end of file
+</div>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-03-23 18:15:18
|
Revision: 652
http://treebase.svn.sourceforge.net/treebase/?rev=652&view=rev
Author: rvos
Date: 2010-03-23 18:15:11 +0000 (Tue, 23 Mar 2010)
Log Message:
-----------
IE fixes
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsListControls.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp
trunk/treebase-web/src/main/webapp/common/header.jsp
trunk/treebase-web/src/main/webapp/common/meta.jsp
trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp
trunk/treebase-web/src/main/webapp/scripts/common.js
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/scripts/prototype/prototype-1.6.1.js
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -1,6 +1,6 @@
<div id="contentRight">
<div class="gutter">
- <h1>Welcome to TreeBASE</h1>
+ <h1>Welcome to TreeBASE</h1>
<p>
TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but are only available to the publication editors or reviewers using a special access code. </p>
<p>The current release includes a host of new features and improvements over the previous TreeBASE prototype. New features include:</p>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -2,11 +2,6 @@
<form id="searchSimple" method="post">
<fieldset>
Search: <input type="hidden" name="formName" value="matrixSimple"/>
- <script type="text/javascript">
- //<![CDATA[
- TreeBASE.register( function() { $('keyword').focus(); } );
- //]]>
- </script>
<input type=text class="textCell" style="width:150px" name="searchTerm" id="keyword" value="${searchTerm}"/>
<button type="submit" name="searchButton" value="matrixID">Matrix ID</button>
<button type="submit" name="searchButton" value="matrixTitle">Title</button>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsListControls.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsListControls.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsListControls.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -1,5 +1,5 @@
<%@ include file="/common/taglibs.jsp"%>
-<script type="text/javascript" src="/treebase-web/scripts/prototype/prototype-1.6.0.3.js"></script>
+<%-- script type="text/javascript" src="/treebase-web/scripts/prototype/prototype-1.6.0.3.js"></script --%>
<c:if test="${! isEmpty }">
<script type="text/javascript">
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -2,11 +2,6 @@
<form id="searchSimple" method="post">
<fieldset>
Search: <input type="hidden" name="formName" value="searchKeyword"/>
- <script type="text/javascript">
- //<![CDATA[
- TreeBASE.register( function() { $('keyword').focus(); } );
- //]]>
- </script>
<input type="text" class="textCell" style="width:150px" name="searchTerm" id="keyword" value="${searchTerm}"/>
<button type="submit" name="searchButton" value="studyID">Study ID</button>
<button type="submit" name="searchButton" value="legacyStudyID">Legacy Study ID</button>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -1,12 +1,7 @@
<%@ include file="/common/taglibs.jsp"%>
<form id="searchSimple" method="post">
<fieldset>
- Search: <input type="hidden" name="formName" value="treeSimple"/>
- <script type="text/javascript">
- //<![CDATA[
- TreeBASE.register( function() { $('keyword').focus(); } );
- //]]>
- </script>
+ Search: <input type="hidden" name="formName" value="treeSimple"/>
<input type="text" class="textCell" style="width:150px" name="searchTerm" id="keyword" value="${searchTerm}"/>
<button type="submit" name="searchButton" value="treeID">Tree ID</button>
<button type="submit" name="searchButton" value="treeTitle">Title</button>
Modified: trunk/treebase-web/src/main/webapp/common/header.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/header.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/common/header.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -1,8 +1,17 @@
<%@ include file="/common/taglibs.jsp"%>
-<h1>
+<h1 style="padding-bottom:0px !important;margin-bottom:0px !important">
<a href="<c:url value="/home.html"/>">
- <img src="<c:url value="/images/logo.gif"/>" alt="TreeBase Logo" width="523" height="112" border="0" />
+ <img
+ src="<c:url value="/images/logo.gif"/>"
+ alt="TreeBase Logo"
+ width="523"
+ height="112"
+ border="0" />
</a>
+ <img
+ src="<c:url value="/images/gradient.jpg"/>"
+ style="width:100%;height:10px;padding:0px !important;margin:0px !important"
+ height="10"
+ alt="" />
</h1>
-<img src="images/gradient.jpg" style="width:100%;height:10px" alt="" />
Modified: trunk/treebase-web/src/main/webapp/common/meta.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/meta.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/common/meta.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -7,3 +7,22 @@
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"/>
<meta name="author" content="Rutger A. Vos (rut...@gm...)"/>
<link rel="icon" href="<c:url value="/images/favicon.ico"/>"/>
+<%
+ String ua = request.getHeader( "User-Agent" );
+ boolean isMSIE = ( ua != null && ua.indexOf( "MSIE" ) != -1 );
+ boolean isOldMSIE = false;
+ if ( isMSIE ) {
+ isOldMSIE = ua.indexOf("MSIE 8.0") == -1;
+
+ }
+%>
+<!-- <%= ua %> -->
+<% if( isOldMSIE ){ %>
+ <script type="text/javascript">
+ alert("Please upgrade your browser!\n\n"+
+ "The TreeBASE team simply do not have the resources to support\n"+
+ "old versions of Internet Explorer. There are many good, free\n"+
+ "browsers available (IE8, FireFox, Safari, Chrome, Opera, etc.),\n"+
+ "please use one of those instead.");
+ </script>
+<% } %>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -29,8 +29,9 @@
<script type="text/javascript" src="<c:url value='/dwr/engine.js'/>"> </script>
<script type="text/javascript" src="<c:url value='/dwr/util.js'/>"></script>
-<script type="text/javascript" src="<c:url value='/scripts/prototype/prototype.js'/>"></script>
+<!-- script type="text/javascript" src="<c:url value='/scripts/prototype/prototype.js'/>"></script-->
<script type="text/javascript" src="<c:url value='/scripts/prototype/prototype-1.6.0.3.js'/>"></script>
+<!-- script type="text/javascript" src="<c:url value='/scripts/prototype/prototype-1.6.1.js'/>"></script-->
<script type="text/javascript" src="<c:url value='/scripts/script.aculo.us/effects.js'/>"></script>
<script type="text/javascript" src="<c:url value='/scripts/script.aculo.us/controls.js'/>"></script>
Modified: trunk/treebase-web/src/main/webapp/scripts/common.js
===================================================================
--- trunk/treebase-web/src/main/webapp/scripts/common.js 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/scripts/common.js 2010-03-23 18:15:11 UTC (rev 652)
@@ -1,223 +1,224 @@
-var newwindow
-
-function popup_new_window(url)
-{
- newwindow=window.open(url,'help','width=800,height=400,scrollbars=yes,menubar=no,resizable=yes,toolbar=no,status=no');
-}
-function popup(url) {
- if (newwindow)
- newwindow.close();
-
- newwindow=window.open(url,'help','width=600,height=400,scrollbars=yes,menubar=no,resizable=yes,toolbar=no,status=no');
- newwindow.moveTo(220, 100)
-}
-function popupWithSizes(url, width, height) {
- if (newwindow) newwindow.close();
- newwindow=window.open(url,'help','width=' + width + ',height=' + height + ',scrollbars=yes,menubar=no,resizable=yes,toolbar=no,status=no');
-}
-function openHelp(tag) {
- var url = '/treebase-web/help.html?helpTag=' + tag;
- var req = new Ajax.Request(url, {
- 'method':'get',
- 'onSuccess':function(response){
- top.consoleRef=window.open('','help',
- 'width=400,height=350'
- +',menubar=no'
- +',toolbar=no'
- +',location=no'
- +',status=no'
- +',top=100'
- +',left=100'
- +',scrollbars=yes'
- +',resizable=yes');
- if ( top.consoleRef == null || top.consoleRef.closed ) {
- alert("Couldn't open window! The help system requires that popups are allowed for the TreeBASE site.");
- }
- top.consoleRef.document.writeln(response.responseText);
- top.consoleRef.document.close();
- }
- });
-}
-
-/*
- The TreeBASE object has three functions:
- 1. it provides for a way to scope our javascript code within the TreeBASE
- namespace so it doesn't clash with all the other libraries we're using
- 2. it allows you to register callbacks with it
- 3. it implements a TreeBASE.initialize() method that executes those
- registered callbacks. Typically we would call this from within the
- body tag, i.e. <body onload="TreeBASE.initialize()"/>, as is done in the
- main template. This allows us to write more unobtrusive javascript.
-*/
-var TreeBASE = {
- 'init' : [],
- 'initialize' : function () {
- for ( var i = 0; i < TreeBASE.init.length; i++ ) {
- TreeBASE.init[i]();
- }
- },
- 'register' : function(func) {
- TreeBASE.init.push(func);
- }
-};
-
-/*
- Here we register a function that fetches all table headers for columns that
- contain icon buttons (i.e. of class "iconColumn"). It sets the background of
- those header cells to pink, and places a link to the icon legend in the first
- of these header cells.
-*/
-TreeBASE.register(
- function () {
- var headers = document.getElementsByTagName('th');
- var iconColumnHeaders = new Array();
- for ( var i = 0; i < headers.length; i++ ) {
- if ( headers[i].className == 'iconColumn' ) {
- iconColumnHeaders.push(headers[i]);
- }
- }
- if ( iconColumnHeaders.length > 0 ) {
- iconColumnHeaders[0].innerHTML = '<a href="/treebase-web/help/iconLegend.jsp"><img src="/treebase-web/images/icons/help.png" class="iconButton" alt="Icon Legend" title="Icon Legend"/></a>';
- for ( var i = 0; i < iconColumnHeaders.length; i++ ) {
- iconColumnHeaders[i].style.backgroundColor = 'pink';
- }
- }
- }
-);
-
-/*
- Here we register a function that fetches all input elements for text of class
- "textCell", to which we add the following behaviours:
- 1. onfocus (i.e. we click in the input) it selects the text it contains
- 2. onfocus we change the border to soft blue
- 3. onblur (i.e. we leave the input) we go back to the previous border
-*/
-TreeBASE.register(
- function() {
- var inputs = $(document).getElementsByClassName('textCell');
- for ( var i = 0; i < inputs.length; i++ ) {
- if ( inputs[i] ) {
- var currentColor = inputs[i].style.borderColor;
- inputs[i].onfocus = function () {
- this.style.borderColor = '#3863A4';
- this.select();
- }
- inputs[i].onblur = function () {
- this.style.borderColor = currentColor;
- }
- }
- }
- }
-);
-
-TreeBASE.register(
- function () {
- if ( document.getElementsByClassName ) {
- var checkBoxCells = document.getElementsByClassName('checkBoxColumn');
- var buttonContainer = $('buttonContainer');
- if ( checkBoxCells.length > 0 && buttonContainer ) {
- var checkButton = new Element('input',{'type':'button','value':'Check all'});
- checkButton.observe('click',function () {
- for ( var i = 0; i < checkBoxCells.length; i++ ) {
- if ( checkBoxCells[i] ) {
- var checkBoxes = $(checkBoxCells[i]).select('input');
- for ( var j = 0; j < checkBoxes.length; j++ ) {
- if ( checkBoxes[j] && checkBoxes[j].type == 'checkbox' || checkBoxes[j].type == 'radio' ) {
- if ( ! checkBoxes[j].disabled ) {
- checkBoxes[j].checked = 'checked';
- }
- }
- }
- }
- }
- });
- var uncheckButton = new Element('input',{'type':'button','value':'Uncheck all'});
- uncheckButton.observe('click',function () {
- for ( var i = 0; i < checkBoxCells.length; i++ ) {
- if ( checkBoxCells[i] ) {
- var checkBoxes = $(checkBoxCells[i]).select('input');
- for ( var j = 0; j < checkBoxes.length; j++ ) {
- if ( checkBoxes[j] && checkBoxes[j].type == 'checkbox' || checkBoxes[j].type == 'radio' ) {
- if ( ! checkBoxes[j].disabled ) {
- checkBoxes[j].checked = null;
- }
- }
- }
- }
- }
- });
- var invertButton = new Element('input',{'type':'button','value':'Invert'});
- invertButton.observe('click',function () {
- for ( var i = 0; i < checkBoxCells.length; i++ ) {
- if ( checkBoxCells[i] ) {
- var checkBoxes = $(checkBoxCells[i]).select('input');
- for ( var j = 0; j < checkBoxes.length; j++ ) {
- if ( checkBoxes[j] && checkBoxes[j].type == 'checkbox' || checkBoxes[j].type == 'radio' ) {
- if ( ! checkBoxes[j].disabled ) {
- if ( checkBoxes[j].checked ) {
- checkBoxes[j].checked = null;
- }
- else {
- checkBoxes[j].checked = 'checked';
- }
- }
- }
- }
- }
- }
- });
- buttonContainer.insertBefore(invertButton,buttonContainer.firstChild);
- buttonContainer.insertBefore(uncheckButton,buttonContainer.firstChild);
- buttonContainer.insertBefore(checkButton,buttonContainer.firstChild);
- }
- }
- }
-);
-
-/* add a tooltip for the help buttons */
-TreeBASE.register(
- function() {
- var links = document.getElementsByTagName('a');
- for ( var i = 0; i < links.length; i++ ) {
- var link = $(links[i]);
- if ( link.hasClassName('openHelp') ) {
- if ( link.title == null || link.title == '' ) {
- link.title = 'Open help popup';
- }
- }
- }
- }
-);
-
-/*
- Collapse/expands elements (identified by id), where
- the expanded version is shown as 'displayAs' (i.e.
- 'block' or 'inline'). This behaviour is added to
- 'link', such that:
- <a onclick="TreeBASE.collapseExpand('foo','block',this)">
- <img src="/treebase-web/images/plus.gif"/>
- </a>
- <div id="foo">
- <!-- this will be collapsed/expanded -->
- </div>
-*/
-TreeBASE.collapseExpand = function(id,displayAs,link) {
- var objToExpand = $(id);
- var img = $(link).firstDescendant();
- if ( img == null ) {
- img = document.createElement(img);
- link.appendChild(img);
- }
- if ( objToExpand.style.display == 'none' ) {
- objToExpand.style.display = displayAs;
- img.src='/treebase-web/images/minus.gif';
- img.alt='collapse'
- link.title='collapse';
- }
- else {
- objToExpand.style.display = 'none';
- img.src='/treebase-web/images/plus.gif';
- img.alt='expand';
- link.title='expand';
- }
-}
+var newwindow
+
+function popup_new_window(url)
+{
+ newwindow=window.open(url,'help','width=800,height=400,scrollbars=yes,menubar=no,resizable=yes,toolbar=no,status=no');
+}
+function popup(url) {
+ if (newwindow)
+ newwindow.close();
+
+ newwindow=window.open(url,'help','width=600,height=400,scrollbars=yes,menubar=no,resizable=yes,toolbar=no,status=no');
+ newwindow.moveTo(220, 100)
+}
+function popupWithSizes(url, width, height) {
+ if (newwindow) newwindow.close();
+ newwindow=window.open(url,'help','width=' + width + ',height=' + height + ',scrollbars=yes,menubar=no,resizable=yes,toolbar=no,status=no');
+}
+function openHelp(tag) {
+ var url = '/treebase-web/help.html?helpTag=' + tag;
+ var req = new Ajax.Request(url, {
+ 'method':'get',
+ 'onSuccess':function(response){
+ top.consoleRef=window.open('','help',
+ 'width=400,height=350'
+ +',menubar=no'
+ +',toolbar=no'
+ +',location=no'
+ +',status=no'
+ +',top=100'
+ +',left=100'
+ +',scrollbars=yes'
+ +',resizable=yes');
+ if ( top.consoleRef == null || top.consoleRef.closed ) {
+ alert("Couldn't open window! The help system requires that popups are allowed for the TreeBASE site.");
+ }
+ top.consoleRef.document.writeln(response.responseText);
+ top.consoleRef.document.close();
+ }
+ });
+}
+
+/*
+ The TreeBASE object has three functions:
+ 1. it provides for a way to scope our javascript code within the TreeBASE
+ namespace so it doesn't clash with all the other libraries we're using
+ 2. it allows you to register callbacks with it
+ 3. it implements a TreeBASE.initialize() method that executes those
+ registered callbacks. Typically we would call this from within the
+ body tag, i.e. <body onload="TreeBASE.initialize()"/>, as is done in the
+ main template. This allows us to write more unobtrusive javascript.
+*/
+var TreeBASE = {
+ 'init' : [],
+ 'initialize' : function () {
+ for ( var i = 0; i < TreeBASE.init.length; i++ ) {
+ TreeBASE.init[i]();
+ }
+ },
+ 'register' : function(func) {
+ TreeBASE.init.push(func);
+ }
+};
+
+/*
+ Here we register a function that fetches all table headers for columns that
+ contain icon buttons (i.e. of class "iconColumn"). It sets the background of
+ those header cells to pink, and places a link to the icon legend in the first
+ of these header cells.
+*/
+TreeBASE.register(
+ function () {
+ var headers = document.getElementsByTagName('th');
+ var iconColumnHeaders = new Array();
+ for ( var i = 0; i < headers.length; i++ ) {
+ if ( headers[i].className == 'iconColumn' ) {
+ iconColumnHeaders.push(headers[i]);
+ }
+ }
+ if ( iconColumnHeaders.length > 0 ) {
+ iconColumnHeaders[0].innerHTML = '<a href="/treebase-web/help/iconLegend.jsp"><img src="/treebase-web/images/icons/help.png" class="iconButton" alt="Icon Legend" title="Icon Legend"/></a>';
+ for ( var i = 0; i < iconColumnHeaders.length; i++ ) {
+ iconColumnHeaders[i].style.backgroundColor = 'pink';
+ }
+ }
+ }
+);
+
+/*
+ Here we register a function that fetches all input elements for text of class
+ "textCell", to which we add the following behaviours:
+ 1. onfocus (i.e. we click in the input) it selects the text it contains
+ 2. onfocus we change the border to soft blue
+ 3. onblur (i.e. we leave the input) we go back to the previous border
+*/
+
+TreeBASE.register(
+ function() {
+ var inputs = $$('.textCell');
+ for ( var i = 0; i < inputs.length; i++ ) {
+ if ( inputs[i] ) {
+ var currentColor = inputs[i].style.borderColor;
+ inputs[i].onfocus = function () {
+ this.style.borderColor = '#3863A4';
+ this.select();
+ }
+ inputs[i].onblur = function () {
+ this.style.borderColor = currentColor;
+ }
+ }
+ }
+ }
+);
+
+TreeBASE.register(
+ function () {
+ if ( document.getElementsByClassName ) {
+ var checkBoxCells = $$('.checkBoxColumn');
+ var buttonContainer = $('buttonContainer');
+ if ( checkBoxCells.length > 0 && buttonContainer ) {
+ var checkButton = new Element('input',{'type':'button','value':'Check all'});
+ checkButton.observe('click',function () {
+ for ( var i = 0; i < checkBoxCells.length; i++ ) {
+ if ( checkBoxCells[i] ) {
+ var checkBoxes = $(checkBoxCells[i]).select('input');
+ for ( var j = 0; j < checkBoxes.length; j++ ) {
+ if ( checkBoxes[j] && checkBoxes[j].type == 'checkbox' || checkBoxes[j].type == 'radio' ) {
+ if ( ! checkBoxes[j].disabled ) {
+ checkBoxes[j].checked = 'checked';
+ }
+ }
+ }
+ }
+ }
+ });
+ var uncheckButton = new Element('input',{'type':'button','value':'Uncheck all'});
+ uncheckButton.observe('click',function () {
+ for ( var i = 0; i < checkBoxCells.length; i++ ) {
+ if ( checkBoxCells[i] ) {
+ var checkBoxes = $(checkBoxCells[i]).select('input');
+ for ( var j = 0; j < checkBoxes.length; j++ ) {
+ if ( checkBoxes[j] && checkBoxes[j].type == 'checkbox' || checkBoxes[j].type == 'radio' ) {
+ if ( ! checkBoxes[j].disabled ) {
+ checkBoxes[j].checked = null;
+ }
+ }
+ }
+ }
+ }
+ });
+ var invertButton = new Element('input',{'type':'button','value':'Invert'});
+ invertButton.observe('click',function () {
+ for ( var i = 0; i < checkBoxCells.length; i++ ) {
+ if ( checkBoxCells[i] ) {
+ var checkBoxes = $(checkBoxCells[i]).select('input');
+ for ( var j = 0; j < checkBoxes.length; j++ ) {
+ if ( checkBoxes[j] && checkBoxes[j].type == 'checkbox' || checkBoxes[j].type == 'radio' ) {
+ if ( ! checkBoxes[j].disabled ) {
+ if ( checkBoxes[j].checked ) {
+ checkBoxes[j].checked = null;
+ }
+ else {
+ checkBoxes[j].checked = 'checked';
+ }
+ }
+ }
+ }
+ }
+ }
+ });
+ buttonContainer.insertBefore(invertButton,buttonContainer.firstChild);
+ buttonContainer.insertBefore(uncheckButton,buttonContainer.firstChild);
+ buttonContainer.insertBefore(checkButton,buttonContainer.firstChild);
+ }
+ }
+ }
+);
+
+/* add a tooltip for the help buttons */
+TreeBASE.register(
+ function() {
+ var links = document.getElementsByTagName('a');
+ for ( var i = 0; i < links.length; i++ ) {
+ var link = $(links[i]);
+ if ( link.hasClassName('openHelp') ) {
+ if ( link.title == null || link.title == '' ) {
+ link.title = 'Open help popup';
+ }
+ }
+ }
+ }
+);
+
+/*
+ Collapse/expands elements (identified by id), where
+ the expanded version is shown as 'displayAs' (i.e.
+ 'block' or 'inline'). This behaviour is added to
+ 'link', such that:
+ <a onclick="TreeBASE.collapseExpand('foo','block',this)">
+ <img src="/treebase-web/images/plus.gif"/>
+ </a>
+ <div id="foo">
+ <!-- this will be collapsed/expanded -->
+ </div>
+*/
+TreeBASE.collapseExpand = function(id,displayAs,link) {
+ var objToExpand = $(id);
+ var img = $(link).firstDescendant();
+ if ( img == null ) {
+ img = document.createElement(img);
+ link.appendChild(img);
+ }
+ if ( objToExpand.style.display == 'none' ) {
+ objToExpand.style.display = displayAs;
+ img.src='/treebase-web/images/minus.gif';
+ img.alt='collapse'
+ link.title='collapse';
+ }
+ else {
+ objToExpand.style.display = 'none';
+ img.src='/treebase-web/images/plus.gif';
+ img.alt='expand';
+ link.title='expand';
+ }
+}
Added: trunk/treebase-web/src/main/webapp/scripts/prototype/prototype-1.6.1.js
===================================================================
--- trunk/treebase-web/src/main/webapp/scripts/prototype/prototype-1.6.1.js (rev 0)
+++ trunk/treebase-web/src/main/webapp/scripts/prototype/prototype-1.6.1.js 2010-03-23 18:15:11 UTC (rev 652)
@@ -0,0 +1,4874 @@
+/* Prototype JavaScript framework, version 1.6.1
+ * (c) 2005-2009 Sam Stephenson
+ *
+ * Prototype is freely distributable under the terms of an MIT-style license.
+ * For details, see the Prototype web site: http://www.prototypejs.org/
+ *
+ *--------------------------------------------------------------------------*/
+
+var Prototype = {
+ Version: '1.6.1',
+
+ Browser: (function(){
+ var ua = navigator.userAgent;
+ var isOpera = Object.prototype.toString.call(window.opera) == '[object Opera]';
+ return {
+ IE: !!window.attachEvent && !isOpera,
+ Opera: isOpera,
+ WebKit: ua.indexOf('AppleWebKit/') > -1,
+ Gecko: ua.indexOf('Gecko') > -1 && ua.indexOf('KHTML') === -1,
+ MobileSafari: /Apple.*Mobile.*Safari/.test(ua)
+ }
+ })(),
+
+ BrowserFeatures: {
+ XPath: !!document.evaluate,
+ SelectorsAPI: !!document.querySelector,
+ ElementExtensions: (function() {
+ var constructor = window.Element || window.HTMLElement;
+ return !!(constructor && constructor.prototype);
+ })(),
+ SpecificElementExtensions: (function() {
+ if (typeof window.HTMLDivElement !== 'undefined')
+ return true;
+
+ var div = document.createElement('div');
+ var form = document.createElement('form');
+ var isSupported = false;
+
+ if (div['__proto__'] && (div['__proto__'] !== form['__proto__'])) {
+ isSupported = true;
+ }
+
+ div = form = null;
+
+ return isSupported;
+ })()
+ },
+
+ ScriptFragment: '<script[^>]*>([\\S\\s]*?)<\/script>',
+ JSONFilter: /^\/\*-secure-([\s\S]*)\*\/\s*$/,
+
+ emptyFunction: function() { },
+ K: function(x) { return x }
+};
+
+if (Prototype.Browser.MobileSafari)
+ Prototype.BrowserFeatures.SpecificElementExtensions = false;
+
+
+var Abstract = { };
+
+
+var Try = {
+ these: function() {
+ var returnValue;
+
+ for (var i = 0, length = arguments.length; i < length; i++) {
+ var lambda = arguments[i];
+ try {
+ returnValue = lambda();
+ break;
+ } catch (e) { }
+ }
+
+ return returnValue;
+ }
+};
+
+/* Based on Alex Arnell's inheritance implementation. */
+
+var Class = (function() {
+ function subclass() {};
+ function create() {
+ var parent = null, properties = $A(arguments);
+ if (Object.isFunction(properties[0]))
+ parent = properties.shift();
+
+ function klass() {
+ this.initialize.apply(this, arguments);
+ }
+
+ Object.extend(klass, Class.Methods);
+ klass.superclass = parent;
+ klass.subclasses = [];
+
+ if (parent) {
+ subclass.prototype = parent.prototype;
+ klass.prototype = new subclass;
+ parent.subclasses.push(klass);
+ }
+
+ for (var i = 0; i < properties.length; i++)
+ klass.addMethods(properties[i]);
+
+ if (!klass.prototype.initialize)
+ klass.prototype.initialize = Prototype.emptyFunction;
+
+ klass.prototype.constructor = klass;
+ return klass;
+ }
+
+ function addMethods(source) {
+ var ancestor = this.superclass && this.superclass.prototype;
+ var properties = Object.keys(source);
+
+ if (!Object.keys({ toString: true }).length) {
+ if (source.toString != Object.prototype.toString)
+ properties.push("toString");
+ if (source.valueOf != Object.prototype.valueOf)
+ properties.push("valueOf");
+ }
+
+ for (var i = 0, length = properties.length; i < length; i++) {
+ var property = properties[i], value = source[property];
+ if (ancestor && Object.isFunction(value) &&
+ value.argumentNames().first() == "$super") {
+ var method = value;
+ value = (function(m) {
+ return function() { return ancestor[m].apply(this, arguments); };
+ })(property).wrap(method);
+
+ value.valueOf = method.valueOf.bind(method);
+ value.toString = method.toString.bind(method);
+ }
+ this.prototype[property] = value;
+ }
+
+ return this;
+ }
+
+ return {
+ create: create,
+ Methods: {
+ addMethods: addMethods
+ }
+ };
+})();
+(function() {
+
+ var _toString = Object.prototype.toString;
+
+ function extend(destination, source) {
+ for (var property in source)
+ destination[property] = source[property];
+ return destination;
+ }
+
+ function inspect(object) {
+ try {
+ if (isUndefined(object)) return 'undefined';
+ if (object === null) return 'null';
+ return object.inspect ? object.inspect() : String(object);
+ } catch (e) {
+ if (e instanceof RangeError) return '...';
+ throw e;
+ }
+ }
+
+ function toJSON(object) {
+ var type = typeof object;
+ switch (type) {
+ case 'undefined':
+ case 'function':
+ case 'unknown': return;
+ case 'boolean': return object.toString();
+ }
+
+ if (object === null) return 'null';
+ if (object.toJSON) return object.toJSON();
+ if (isElement(object)) return;
+
+ var results = [];
+ for (var property in object) {
+ var value = toJSON(object[property]);
+ if (!isUndefined(value))
+ results.push(property.toJSON() + ': ' + value);
+ }
+
+ return '{' + results.join(', ') + '}';
+ }
+
+ function toQueryString(object) {
+ return $H(object).toQueryString();
+ }
+
+ function toHTML(object) {
+ return object && object.toHTML ? object.toHTML() : String.interpret(object);
+ }
+
+ function keys(object) {
+ var results = [];
+ for (var property in object)
+ results.push(property);
+ return results;
+ }
+
+ function values(object) {
+ var results = [];
+ for (var property in object)
+ results.push(object[property]);
+ return results;
+ }
+
+ function clone(object) {
+ return extend({ }, object);
+ }
+
+ function isElement(object) {
+ return !!(object && object.nodeType == 1);
+ }
+
+ function isArray(object) {
+ return _toString.call(object) == "[object Array]";
+ }
+
+
+ function isHash(object) {
+ return object instanceof Hash;
+ }
+
+ function isFunction(object) {
+ return typeof object === "function";
+ }
+
+ function isString(object) {
+ return _toString.call(object) == "[object String]";
+ }
+
+ function isNumber(object) {
+ return _toString.call(object) == "[object Number]";
+ }
+
+ function isUndefined(object) {
+ return typeof object === "undefined";
+ }
+
+ extend(Object, {
+ extend: extend,
+ inspect: inspect,
+ toJSON: toJSON,
+ toQueryString: toQueryString,
+ toHTML: toHTML,
+ keys: keys,
+ values: values,
+ clone: clone,
+ isElement: isElement,
+ isArray: isArray,
+ isHash: isHash,
+ isFunction: isFunction,
+ isString: isString,
+ isNumber: isNumber,
+ isUndefined: isUndefined
+ });
+})();
+Object.extend(Function.prototype, (function() {
+ var slice = Array.prototype.slice;
+
+ function update(array, args) {
+ var arrayLength = array.length, length = args.length;
+ while (length--) array[arrayLength + length] = args[length];
+ return array;
+ }
+
+ function merge(array, args) {
+ array = slice.call(array, 0);
+ return update(array, args);
+ }
+
+ function argumentNames() {
+ var names = this.toString().match(/^[\s\(]*function[^(]*\(([^)]*)\)/)[1]
+ .replace(/\/\/.*?[\r\n]|\/\*(?:.|[\r\n])*?\*\//g, '')
+ .replace(/\s+/g, '').split(',');
+ return names.length == 1 && !names[0] ? [] : names;
+ }
+
+ function bind(context) {
+ if (arguments.length < 2 && Object.isUndefined(arguments[0])) return this;
+ var __method = this, args = slice.call(arguments, 1);
+ return function() {
+ var a = merge(args, arguments);
+ return __method.apply(context, a);
+ }
+ }
+
+ function bindAsEventListener(context) {
+ var __method = this, args = slice.call(arguments, 1);
+ return function(event) {
+ var a = update([event || window.event], args);
+ return __method.apply(context, a);
+ }
+ }
+
+ function curry() {
+ if (!arguments.length) return this;
+ var __method = this, args = slice.call(arguments, 0);
+ return function() {
+ var a = merge(args, arguments);
+ return __method.apply(this, a);
+ }
+ }
+
+ function delay(timeout) {
+ var __method = this, args = slice.call(arguments, 1);
+ timeout = timeout * 1000
+ return window.setTimeout(function() {
+ return __method.apply(__method, args);
+ }, timeout);
+ }
+
+ function defer() {
+ var args = update([0.01], arguments);
+ return this.delay.apply(this, args);
+ }
+
+ function wrap(wrapper) {
+ var __method = this;
+ return function() {
+ var a = update([__method.bind(this)], arguments);
+ return wrapper.apply(this, a);
+ }
+ }
+
+ function methodize() {
+ if (this._methodized) return this._methodized;
+ var __method = this;
+ return this._methodized = function() {
+ var a = update([this], arguments);
+ return __method.apply(null, a);
+ };
+ }
+
+ return {
+ argumentNames: argumentNames,
+ bind: bind,
+ bindAsEventListener: bindAsEventListener,
+ curry: curry,
+ delay: delay,
+ defer: defer,
+ wrap: wrap,
+ methodize: methodize
+ }
+})());
+
+
+Date.prototype.toJSON = function() {
+ return '"' + this.getUTCFullYear() + '-' +
+ (this.getUTCMonth() + 1).toPaddedString(2) + '-' +
+ this.getUTCDate().toPaddedString(2) + 'T' +
+ this.getUTCHours().toPaddedString(2) + ':' +
+ this.getUTCMinutes().toPaddedString(2) + ':' +
+ this.getUTCSeconds().toPaddedString(2) + 'Z"';
+};
+
+
+RegExp.prototype.match = RegExp.prototype.test;
+
+RegExp.escape = function(str) {
+ return String(str).replace(/([.*+?^=!:${}()|[\]\/\\])/g, '\\$1');
+};
+var PeriodicalExecuter = Class.create({
+ initialize: function(callback, frequency) {
+ this.callback = callback;
+ this.frequency = frequency;
+ this.currentlyExecuting = false;
+
+ this.registerCallback();
+ },
+
+ registerCallback: function() {
+ this.timer = setInterval(this.onTimerEvent.bind(this), this.frequency * 1000);
+ },
+
+ execute: function() {
+ this.callback(this);
+ },
+
+ stop: function() {
+ if (!this.timer) return;
+ clearInterval(this.timer);
+ this.timer = null;
+ },
+
+ onTimerEvent: function() {
+ if (!this.currentlyExecuting) {
+ try {
+ this.currentlyExecuting = true;
+ this.execute();
+ this.currentlyExecuting = false;
+ } catch(e) {
+ this.currentlyExecuting = false;
+ throw e;
+ }
+ }
+ }
+});
+Object.extend(String, {
+ interpret: function(value) {
+ return value == null ? '' : String(value);
+ },
+ specialChar: {
+ '\b': '\\b',
+ '\t': '\\t',
+ '\n': '\\n',
+ '\f': '\\f',
+ '\r': '\\r',
+ '\\': '\\\\'
+ }
+});
+
+Object.extend(String.prototype, (function() {
+
+ function prepareReplacement(replacement) {
+ if (Object.isFunction(replacement)) return replacement;
+ var template = new Template(replacement);
+ return function(match) { return template.evaluate(match) };
+ }
+
+ function gsub(pattern, replacement) {
+ var result = '', source = this, match;
+ replacement = prepareReplacement(replacement);
+
+ if (Object.isString(pattern))
+ pattern = RegExp.escape(pattern);
+
+ if (!(pattern.length || pattern.source)) {
+ replacement = replacement('');
+ return replacement + source.split('').join(replacement) + replacement;
+ }
+
+ while (source.length > 0) {
+ if (match = source.match(pattern)) {
+ result += source.slice(0, match.index);
+ result += String.interpret(replacement(match));
+ source = source.slice(match.index + match[0].length);
+ } else {
+ result += source, source = '';
+ }
+ }
+ return result;
+ }
+
+ function sub(pattern, replacement, count) {
+ replacement = prepareReplacement(replacement);
+ count = Object.isUndefined(count) ? 1 : count;
+
+ return this.gsub(pattern, function(match) {
+ if (--count < 0) return match[0];
+ return replacement(match);
+ });
+ }
+
+ function scan(pattern, iterator) {
+ this.gsub(pattern, iterator);
+ return String(this);
+ }
+
+ function truncate(length, truncation) {
+ length = length || 30;
+ truncation = Object.isUndefined(truncation) ? '...' : truncation;
+ return this.length > length ?
+ this.slice(0, length - truncation.length) + truncation : String(this);
+ }
+
+ function strip() {
+ return this.replace(/^\s+/, '').replace(/\s+$/, '');
+ }
+
+ function stripTags() {
+ return this.replace(/<\w+(\s+("[^"]*"|'[^']*'|[^>])+)?>|<\/\w+>/gi, '');
+ }
+
+ function stripScripts() {
+ return this.replace(new RegExp(Prototype.ScriptFragment, 'img'), '');
+ }
+
+ function extractScripts() {
+ var matchAll = new RegExp(Prototype.ScriptFragment, 'img');
+ var matchOne = new RegExp(Prototype.ScriptFragment, 'im');
+ return (this.match(matchAll) || []).map(function(scriptTag) {
+ return (scriptTag.match(matchOne) || ['', ''])[1];
+ });
+ }
+
+ function evalScripts() {
+ return this.extractScripts().map(function(script) { return eval(script) });
+ }
+
+ function escapeHTML() {
+ return this.replace(/&/g,'&').replace(/</g,'<').replace(/>/g,'>');
+ }
+
+ function unescapeHTML() {
+ return this.stripTags().replace(/</g,'<').replace(/>/g,'>').replace(/&/g,'&');
+ }
+
+
+ function toQueryParams(separator) {
+ var match = this.strip().match(/([^?#]*)(#.*)?$/);
+ if (!match) return { };
+
+ return match[1].split(separator || '&').inject({ }, function(hash, pair) {
+ if ((pair = pair.split('='))[0]) {
+ var key = decodeURIComponent(pair.shift());
+ var value = pair.length > 1 ? pair.join('=') : pair[0];
+ if (value != undefined) value = decodeURIComponent(value);
+
+ if (key in hash) {
+ if (!Object.isArray(hash[key])) hash[key] = [hash[key]];
+ hash[key].push(value);
+ }
+ else hash[key] = value;
+ }
+ return hash;
+ });
+ }
+
+ function toArray() {
+ return this.split('');
+ }
+
+ function succ() {
+ return this.slice(0, this.length - 1) +
+ String.fromCharCode(this.charCodeAt(this.length - 1) + 1);
+ }
+
+ function times(count) {
+ return count < 1 ? '' : new Array(count + 1).join(this);
+ }
+
+ function camelize() {
+ var parts = this.split('-'), len = parts.length;
+ if (len == 1) return parts[0];
+
+ var camelized = this.charAt(0) == '-'
+ ? parts[0].charAt(0).toUpperCase() + parts[0].substring(1)
+ : parts[0];
+
+ for (var i = 1; i < len; i++)
+ camelized += parts[i].charAt(0).toUpperCase() + parts[i].substring(1);
+
+ return camelized;
+ }
+
+ function capitalize() {
+ return this.charAt(0).toUpperCase() + this.substring(1).toLowerCase();
+ }
+
+ function underscore() {
+ return this.replace(/::/g, '/')
+ .replace(/([A-Z]+)([A-Z][a-z])/g, '$1_$2')
+ .replace(/([a-z\d])([A-Z])/g, '$1_$2')
+ .replace(/-/g, '_')
+ .toLowerCase();
+ }
+
+ function dasherize() {
+ return this.replace(/_/g, '-');
+ }
+
+ function inspect(useDoubleQuotes) {
+ var escapedString = this.replace(/[\x00-\x1f\\]/g, function(character) {
+ if (character in String.specialChar) {
+ return String.specialChar[character];
+ }
+ return '\\u00' + character.charCodeAt().toPaddedString(2, 16);
+ });
+ if (useDoubleQuotes) return '"' + escapedString.replace(/"/g, '\\"') + '"';
+ return "'" + escapedString.replace(/'/g, '\\\'') + "'";
+ }
+
+ function toJSON() {
+ return this.inspect(true);
+ }
+
+ function unfilterJSON(filter) {
+ return this.replace(filter || Prototype.JSONFilter, '$1');
+ }
+
+ function isJSON() {
+ var str = this;
+ if (str.blank()) return false;
+ str = this.replace(/\\./g, '@').replace(/"[^"\\\n\r]*"/g, '');
+ return (/^[,:{}\[\]0-9.\-+Eaeflnr-u \n\r\t]*$/).test(str);
+ }
+
+ function evalJSON(sanitize) {
+ var json = this.unfilterJSON();
+ try {
+ if (!sanitize || json.isJSON()) return eval('(' + json + ')');
+ } catch (e) { }
+ throw new SyntaxError('Badly formed JSON string: ' + this.inspect());
+ }
+
+ function include(pattern) {
+ return this.indexOf(pattern) > -1;
+ }
+
+ function startsWith(pattern) {
+ return this.indexOf(pattern) === 0;
+ }
+
+ function endsWith(pattern) {
+ var d = this.length - pattern.length;
+ return d >= 0 && this.lastIndexOf(pattern) === d;
+ }
+
+ function empty() {
+ return this == '';
+ }
+
+ function blank() {
+ return /^\s*$/.test(this);
+ }
+
+ function interpolate(object, pattern) {
+ return new Template(this, pattern).evaluate(object);
+ }
+
+ return {
+ gsub: gsub,
+ sub: sub,
+ scan: scan,
+ truncate: truncate,
+ strip: String.prototype.trim ? String.prototype.trim : strip,
+ stripTags: stripTags,
+ stripScripts: stripScripts,
+ extractScripts: extractScripts,
+ evalScripts: evalScripts,
+ escapeHTML: escapeHTML,
+ unescapeHTML: unescapeHTML,
+ toQueryParams: toQueryParams,
+ parseQuery: toQueryParams,
+ toArray: toArray,
+ succ: succ,
+ times: times,
+ camelize: camelize,
+ capitalize: capitalize,
+ underscore: underscore,
+ dasherize: dasherize,
+ inspect: inspect,
+ toJSON: toJSON,
+ unfilterJSON: unfilterJSON,
+ isJSON: isJSON,
+ evalJSON: evalJSON,
+ include: include,
+ startsWith: startsWith,
+ endsWith: endsWith,
+ empty: empty,
+ blank: blank,
+ interpolate: interpolate
+ };
+})());
+
+var Template = Class.create({
+ initialize: function(template, pattern) {
+ this.template = template.toString();
+ this.pattern = pattern || Template.Pattern;
+ },
+
+ evaluate: function(object) {
+ if (object && Object.isFunction(object.toTemplateReplacements))
+ object = object.toTemplateReplacements();
+
+ return this.template.gsub(this.pattern, function(match) {
+ if (object == null) return (match[1] + '');
+
+ var before = match[1] || '';
+ if (before == '\\') return match[2];
+
+ var ctx = object, expr = match[3];
+ var pattern = /^([^.[]+|\[((?:.*?[^\\])?)\])(\.|\[|$)/;
+ match = pattern.exec(expr);
+ if (match == null) return before;
+
+ while (match != null) {
+ var comp = match[1].startsWith('[') ? match[2].replace(/\\\\]/g, ']') : match[1];
+ ctx = ctx[comp];
+ if (null == ctx || '' == match[3]) break;
+ expr = expr.substring('[' == match[3] ? match[1].length : match[0].length);
+ match = pattern.exec(expr);
+ }
+
+ return before + String.interpret(ctx);
+ });
+ }
+});
+Template.Pattern = /(^|.|\r|\n)(#\{(.*?)\})/;
+
+var $break = { };
+
+var Enumerable = (function() {
+ function each(iterator, context) {
+ var index = 0;
+ try {
+ this._each(function(value) {
+ iterator.call(context, value, index++);
+ });
+ } catch (e) {
+ if (e != $break) throw e;
+ }
+ return this;
+ }
+
+ function eachSlice(number, iterator, context) {
+ var index = -number, slices = [], array = this.toArray();
+ if (number < 1) return array;
+ while ((index += number) < array.length)
+ slices.push(array.slice(index, index+number));
+ return slices.collect(iterator, context);
+ }
+
+ function all(iterator, context) {
+ iterator = iterator || Prototype.K;
+ var result = true;
+ this.each(function(value, index) {
+ result = result && !!iterator.call(context, value, index);
+ if (!result) throw $break;
+ });
+ return result;
+ }
+
+ function any(iterator, context) {
+ iterator = iterator || Prototype.K;
+ var result = false;
+ this.each(function(value, index) {
+ if (result = !!iterator.call(context, value, index))
+ throw $break;
+ });
+ return result;
+ }
+
+ function collect(iterator, context) {
+ iterator = iterator || Prototype.K;
+ var results = [];
+ this.each(function(value, index) {
+ results.push(iterator.call(context, value, index));
+ });
+ return results;
+ }
+
+ function detect(iterator, context) {
+ var result;
+ this.each(function(value, index) {
+ if (iterator.call(context, value, index)) {
+ result = value;
+ throw $break;
+ }
+ });
+ return result;
+ }
+
+ function findAll(iterator, context) {
+ var results = [];
+ this.each(function(value, index) {
+ if (iterator.call(context, value, index))
+ results.push(value);
+ });
+ return results;
+ }
+
+ function grep(filter, iterator, context) {
+ iterator = iterator || Prototype.K;
+ var results = [];
+
+ if (Object.isString(filter))
+ filter = new RegExp(RegExp.escape(filter));
+
+ this.each(function(value, index) {
+ if (filter.match(value))
+ results.push(iterator.call(context, value, index));
+ });
+ return results;
+ }
+
+ function include(object) {
+ if (Object.isFunction(this.indexOf))
+ if (this.indexOf(object) != -1) return true;
+
+ var found = false;
+ this.each(function(value) {
+ if (value == object) {
+ found = true;
+ throw $break;
+ }
+ });
+ return found;
+ }
+
+ function inGroupsOf(number, fillWith) {
+ fillWith = Object.isUndefined(fillWith) ? null : fillWith;
+ return this.eachSlice(number, function(slice) {
+ while(slice.length < number) slice.push(fillWith);
+ return slice;
+ });
+ }
+
+ function inject(memo, iterator, context) {
+ this.each(function(value, index) {
+ memo = iterator.call(context, memo, value, index);
+ });
+ return memo;
+ }
+
+ function invoke(method) {
+ var args = $A(arguments).slice(1);
+ return this.map(function(value) {
+ return value[method].apply(value, args);
+ });
+ }
+
+ function max(iterator, context) {
+ iterator = iterator || Prototype.K;
+ var result;
+ this.each(function(value, index) {
+ value = iterator.call(context, value, index);
+ if (result == null || value >= result)
+ result = value;
+ });
+ return result;
+ }
+
+ function min(iterator, context) {
+ iterator = iterator || Prototype.K;
+ var result;
+ this.each(function(value, index) {
+ value = iterator.call(context, value, index);
+ if (result == null || value < result)
+ result = value;
+ });
+ return result;
+ }
+
+ function partition(iterator, context) {
+ iterator = iterator || Prototype.K;
+ var trues = [], falses = [];
+ this.each(function(value, index) {
+ (iterator.call(context, value, index) ?
+ trues : falses).push(value);
+ });
+ return [trues, falses];
+ }
+
+ function pluck(property) {
+ var results = [];
+ this.each(function(value) {
+ results.push(value[property]);
+ });
+ return results;
+ }
+
+ function reject(iterator, context) {
+ var results = [];
+ this.each(function(value, index) {
+ if (!iterator.call(context, value, index))
+ results.push(value);
+ });
+ return results;
+ }
+
+ function sortBy(iterator, context) {
+ return this.map(function(value, index) {
+ return {
+ value: value,
+ criteria: iterator.call(context, value, index)
+ };
+ }).sort(function(left, right) {
+ var a = left.criteria, b = right.criteria;
+ return a < b ? -1 : a > b ? 1 : 0;
+ }).pluck('value');
+ }
+
+ function toArray() {
+ return this.map();
+ }
+
+ function zip() {
+ var iterator = Prototype.K, args = $A(arguments);
+ if (Object.isFunction(args.last()))
+ iterator = args.pop();
+
+ var collections = [this].concat(args).map($A);
+ return this.map(function(value, index) {
+ return iterator(collections.pluck(index));
+ });
+ }
+
+ function size() {
+ return this.toArray().length;
+ }
+
+ function inspect() {
+ return '#<Enumerable:' + this.toArray().inspect() + '>';
+ }
+
+
+
+
+
+
+
+
+
+ return {
+ each: each,
+ eachSlice: eachSlice,
+ all: all,
+ every: all,
+ any: any,
+ some: any,
+ collect: collect,
+ map: collect,
+ detect: detect,
+ findAll: findAll,
+ select: findAll,
+ filter: findAll,
+ grep: grep,
+ include: include,
+ member: include,
+ inGroupsOf: inGroupsOf,
+ inject: inject,
+ invoke: invoke,
+ max: max,
+ min: min,
+ partition: partition,
+ pluck: pluck,
+ reject: reject,
+ sortBy: sortBy,
+ toArray: toArray,
+ entries: toArray,
+ zip: zip,
+ size: size,
+ inspect: inspect,
+ find: detect
+ };
+})();
+function $A(iterable) {
+ if (!iterable) return [];
+ if ('toArray' in Object(iterable)) return iterable.toArray();
+ var length = iterable.length || 0, results = new Array(length);
+ while (length--) results[length] = iterable[length];
+ return results;
+}
+
+function $w(string) {
+ if (!Object.isString(string)) return [];
+ string = string.strip();
+ return string ? string.split(/\s+/) : [];
+}
+
+Array.from = $A;
+
+
+(function() {
+ var arrayProto = Array.prototype,
+ slice = arrayProto.slice,
+ _each = arrayProto.forEach; // use native browser JS 1.6 implementation if available
+
+ function each(iterator) {
+ for (var i = 0, length = this.length; i < length; i++)
+ iterator(this[i]);
+ }
+ if (!_each) _each = each;
+
+ function clear() {
+ this.length = 0;
+ return this;
+ }
+
+ function first() {
+ return this[0];
+ }
+
+ function last() {
+ return this[this.length - 1];
+ }
+
+ function compact() {
+ return this.select(function(value) {
+ return value != null;
+ });
+ }
+
+ function flatten() {
+ return this.inject([], function(array, value) {
+ if (Object.isArray(value))
+ return array.concat(value.flatten());
+ array.push(value);
+ return array;
+ });
+ }
+
+ function without() {
+ var values = slice.call(arguments, 0);
+ return this.select(function(value) {
+ return !values.include(value);
+ });
+ }
+
+ function reverse(inline) {
+ return (inline !== false ? this : this.toArray())._reverse();
+ }
+
+ function uniq(sorted) {
+ return this.inject([], function(array, value, index) {
+ if (0 == index || (sorted ? array.last() != value : !array.include(value)))
+ array.push(value);
+ return array;
+ });
+ }
+
+ function intersect(array) {
+ return this.uniq().findAll(function(item) {
+ return array.detect(function(value) { return item === value });
+ });
+ }
+
+
+ function clone() {
+ return slice.call(this, 0);
+ }
+
+ function size() {
+ return this.length;
+ }
+
+ function inspect() {
+ return '[' + this.map(Object.inspect).join(', ') + ']';
+ }
+
+ function toJSON() {
+ var results = [];
+ this.each(function(object) {
+ var value = Object.toJSON(object);
+ if (!Object.isUndefined(value)) results.push(value);
+ });
+ return '[' + results.join(', ') + ']';
+ }
+
+ function indexOf(item, i) {
+ i || (i = 0);
+ var length = this.length;
+ if (i < 0) i = length + i;
+ for (; i < length; i++)
+ if (this[i] === item) return i;
+ return -1;
+ }
+
+ function lastIndexOf(item, i) {
+ i = isNaN(i) ? this.length : (i < 0 ? this.length + i : i) + 1;
+ var n = this.slice(0, i).reverse().indexOf(item);
+ return (n < 0) ? n : i - n - 1;
+ }
+
+ function concat() {
+ var array = slice.call(this, 0), item;
+ for (var i = 0, length = arguments.length; i < length; i++) {
+ item = arguments[i];
+ if (Object.isArray(item) && !('callee' in item)) {
+ for (var j = 0, arrayLength = item.length; j < arrayLength; j++)
+ array.push(item[j]);
+ } else {
+ array.push(item);
+ }
+ }
+ return array;
+ }
+
+ Object.extend(arrayProto, Enumerable);
+
+ if (!arrayProto._reverse)
+ arrayProto._reverse = arrayProto.reverse;
+
+ Object.extend(arrayProto, {
+ _each: _each,
+ clear: clear,
+ first: first,
+ last: last,
+ compact: compact,
+ flatten: flatten,
+ without: without,
+ reverse: reverse,
+ uniq: uniq,
+ intersect: intersect,
+ clone: clone,
+ toArray: clone,
+ size: size,
+ inspect: inspect,
+ toJSON: toJSON
+ });
+
+ var CONCAT_ARGUMENTS_BUGGY = (function() {
+ return [].concat(arguments)[0][0] !== 1;
+ })(1,2)
+
+ if (CONCAT_ARGUMENTS_BUGGY) arrayProto.concat = concat;
+
+ if (!arrayProto.indexOf) arrayProto.indexOf = indexOf;
+ if (!arrayProto.lastIndexOf) arrayProto.lastIndexOf = lastIndexOf;
+})();
+function $H(object) {
+ return new Hash(object);
+};
+
+var Hash = Class.create(Enumerable, (function() {
+ function initialize(object) {
+ this._object = Object.isHash(object) ? object.toObject() : Object.clone(object);
+ }
+
+ function _each(iterator) {
+ for (var key in this._object) {
+ var value = this._object[key], pair = [key, value];
+ pair.key = key;
+ pair.value = value;
+ iterator(pair);
+ }
+ }
+
+ function set(key, value) {
+ return this._object[key] = value;
+ }
+
+ function get(key) {
+ if (this._object[key] !== Object.prototype[key])
+ return this._object[key];
+ }
+
+ function unset(key) {
+ var value = this._object[key];
+ delete this._object[key];
+ return value;
+ }
+
+ function toObject() {
+ return Object.clone(this._object);
+ }
+
+ function keys() {
+ return this.pluck('key');
+ }
+
+ function values() {
+ return this.pluck('value');
+ }
+
+ function index(value) {
+ var match = this.detect(function(pair) {
+ return pair.value === value;
+ });
+ return match && match.key;
+ }
+
+ function merge(object) {
+ return this.clone().update(object);
+ }
+
+ function update(object) {
+ return new Hash(object).inject(this, function(result, pair) {
+ result.set(pair.key, pair.value);
+ return result;
+ });
+ }
+
+ function toQueryPair(key, value) {
+ if (Object.isUndefined(value)) return key;
+ return key + '=' + encodeURIComponent(String.interpret(value));
+ }
+
+ function toQueryString() {
+ return this.inject([], function(results, pair) {
+ var key = encodeURIComponent(pair.key), values = pair.value;
+
+ if (values && typeof values == 'object') {
+ if (Object.isArray(values))
+ return results.concat(values.map(toQueryPair.curry(key)));
+ } else results.push(toQueryPair(key, values));
+ return results;
+ }).join('&');
+ }
+
+ function inspect() {
+ return '#<Hash:{' + this.map(function(pair) {
+ return pair.map(Object.inspect).join(': ');
+ }).join(', ') + '}>';
+ }
+
+ function toJSON() {
+ return Object.toJSON(this.toObject());
+ }
+
+ function clone() {
+ return new Hash(this);
+ }
+
+ return {
+ initialize: initialize,
+ _each: _each,
+ set: set,
+ get: get,
+ unset: unset,
+ toObject: toObject,
+ toTemplateReplacements: toObject,
+ keys: keys,
+ values: values,
+ index: index,
+ merge: merge,
+ update: update,
+ toQueryString: toQueryString,
+ inspect: inspect,
+ toJSON: toJSON,
+ clone: clone
+ };
+})());
+
+Hash.from = $H;
+Object.extend(Number.prototype, (function() {
+ function toColorPart() {
+ return this.toPaddedString(2, 16);
+ }
+
+ function succ() {
+ return this + 1;
+ }
+
+ function times(iterator, context) {
+ $R(0, this, true).each(iterator, context);
+ return this;
+ }
+
+ function toPaddedString(length, radix) {
+ var string = this.toString(radix || 10);
+ return '0'.times(length - string.length) + string;
+ }
+
+ function toJSON() {
+ return isFinite(this) ? this.toString() : 'null';
+ }
+
+ function abs() {
+ return Math.abs(this);
+ }
+
+ function round() {
+ return Math.round(this);
+ }
+
+ function ceil() {
+ return Math.ceil(this);
+ }
+
+ function floor() {
+ return Math.floor(this);
+ }
+
+ return {
+ toColorPart: toColorPart,
+ succ: succ,
+ times: times,
+ toPaddedString: toPaddedString,
+ toJSON: toJSON,
+ abs: abs,
+ round: round,
+ ceil: ceil,
+ floor: floor
+ };
+})());
+
+function $R(start, end, exclusive) {
+ return new ObjectRange(start, end, exclusive);
+}
+
+var O...
[truncated message content] |
|
From: <sfr...@us...> - 2010-03-23 17:45:03
|
Revision: 651
http://treebase.svn.sourceforge.net/treebase/?rev=651&view=rev
Author: sfrgpiel
Date: 2010-03-23 17:44:56 +0000 (Tue, 23 Mar 2010)
Log Message:
-----------
Added verbiage to the splash page
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-23 14:50:54 UTC (rev 650)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-23 17:44:56 UTC (rev 651)
@@ -2,21 +2,19 @@
<div class="gutter">
<h1>Welcome to TreeBASE</h1>
<p>
- TreeBASE is a repository of phylogenetic information, specifically
- user-submitted phylogenetic trees and the data used to generate them.
- TreeBASE accepts all types of phylogenetic data (e.g., trees of species,
- trees of populations, trees of genes) representing all biotic taxa.
- Data in TreeBASE are exposed to the public if they are used in a
- publication that is in press or published in a peer-reviewed
- scientific journal, book, conference proceedings, or thesis.
- Data used in publications that are in preparation or in review can be
- submitted to TreeBASE but are only available to the publication
- editors or reviewers using a special access code.
- </p>
- <p>
- As of early 2010, TreeBASE contains 6,500 trees in 2,500 publications
- written by 4,500 different authors. These trees have 135,000 distinct
- taxon labels that map to approximately 60,000 distinct taxa.
- </p>
+ TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but are only available to the publication editors or reviewers using a special access code. </p>
+ <p>The current release includes a host of new features and improvements over the previous TreeBASE prototype. New features include:</p>
+ <ul>
+ <li>Richer annotation of metadata (journal DOIs, specimen georeferences, Genbank accession numbers, etc) </li>
+ <li>A mapping between taxon labels and taxonomic names in uBio and NCBI for improved normalization of names</li>
+ <li>The ability to visualize and edit trees using Phylowidget</li>
+ <li>The ability to search on tree topology</li>
+ <li>Persistent and resolvable URIs for data objects in TreeBASE (i.e. studies, trees, matrices) serve as both globally unique identification numbers and resource locators. These can be included in articles and on researcher's websites, making access to TreeBASE data only a click away</li>
+ <li>Data are delivered in several serializations, including <a href="https://www.nescent.org/wg_phyloinformatics/Supporting_NEXUS_Documentation" target="_blank">NEXUS</a> and <a href="http://www.nexml.org" target="_blank">NeXML</a></li>
+ <li> A special URL gives journal editors and reviewers anonymous advanced access to data</li>
+ <li>Programmatic access to the data using the <a href="https://www.nescent.org/wg_evoinfo/PhyloWS" target="_blank">PhyloWS API</a>. Queries are expressed in URLs using PhyloWS syntax and can return results in RDF as RSS 1.0 feeds, which means that users can set their favorite RSS Reader to fetch all new TreeBASE studies that satisfy a particular query (e.g. return all studies published in "Systematic Biology," or return all trees that include "Homo sapiens," etc)</li>
+ </ul>
+ <p>
+ As of early 2010, TreeBASE contains 6,500 trees in 2,500 publications written by 4,500 different authors. These trees have 135,000 distinct taxon labels that map to approximately 60,000 distinct taxa. </p>
</div>
</div>
\ No newline at end of file
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|
|
From: SourceForge.net <no...@so...> - 2010-03-23 14:52:56
|
Bugs item #2973661, was opened at 2010-03-20 00:14 Message generated for change (Settings changed) made by youjun You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973661&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: youjun guo (youjun) Summary: Taxa List has labels listed in duplicates, triplicates, etc Initial Comment: When a user is submitting data and clicks on the taxon list page (http://treebase.nescent.org/treebase-web/user/taxaList.html) the taxon labels are duplicated or triplicated, or quadrupled (etc) depending on the study. This bug appears to have cropped up just recently -- I would have noticed it before. Each distinct taxon label should be listed once. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973661&group_id=248804 |
|
From: <yo...@us...> - 2010-03-23 14:51:01
|
Revision: 650
http://treebase.svn.sourceforge.net/treebase/?rev=650&view=rev
Author: youjun
Date: 2010-03-23 14:50:54 +0000 (Tue, 23 Mar 2010)
Log Message:
-----------
eliminate repeat results return by findByStudy
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-03-23 13:45:53 UTC (rev 649)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-03-23 14:50:54 UTC (rev 650)
@@ -81,7 +81,7 @@
// ALERT: the result might not be unique since mesquite allows duplicated taxonlabels
// in the same tree.
// returnVal = (TaxonLabel) c.uniqueResult();
-
+ c.setResultTransformer(Criteria.DISTINCT_ROOT_ENTITY);
returnVal = c.list();
}
return returnVal;
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|
|
From: <sfr...@us...> - 2010-03-23 13:45:59
|
Revision: 649
http://treebase.svn.sourceforge.net/treebase/?rev=649&view=rev
Author: sfrgpiel
Date: 2010-03-23 13:45:53 +0000 (Tue, 23 Mar 2010)
Log Message:
-----------
Removed the display of DOI because it takes up too much real-estate and so causes title to wrap.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyList.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyList.jsp 2010-03-23 04:37:49 UTC (rev 648)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyList.jsp 2010-03-23 13:45:53 UTC (rev 649)
@@ -49,7 +49,7 @@
<c:set var="DOIResource" value="${DOIResolver}${study.citation.doi}"/>
<a href="${DOIResource}" target="_blank">
<img class="iconButton" src="<fmt:message key="icons.weblink"/>" />
- ${study.citation.doi}</a>
+ <!-- ${study.citation.doi} --></a>
</c:if>
</display:column>
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|
|
From: <sfr...@us...> - 2010-03-23 04:38:02
|
Revision: 648
http://treebase.svn.sourceforge.net/treebase/?rev=648&view=rev
Author: sfrgpiel
Date: 2010-03-23 04:37:49 +0000 (Tue, 23 Mar 2010)
Log Message:
-----------
Edited login page to be xhtml-compliant
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/login.jsp
Modified: trunk/treebase-web/src/main/webapp/login.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/login.jsp 2010-03-22 23:06:27 UTC (rev 647)
+++ trunk/treebase-web/src/main/webapp/login.jsp 2010-03-23 04:37:49 UTC (rev 648)
@@ -5,26 +5,31 @@
<content tag="heading"><fmt:message key="login.title"/>
</content>
-<p>
- A Special Note to Submitters to the Previous Version
- of TreeBASE: If you started a submission in the previous
- version, but that submission remained "in progress,"
- you will need to start the submission all over again
- in this new version of TreeBASE.
-</p>
+
+<table width="501" border="0">
+ <tr>
+ <td width="495"><p><strong>A Special Note to Submitters to the Previous Version
+ of TreeBASE:</strong> If you started a submission in the previous
+ version, but that submission remained "in progress,"
+ you will need to start the submission all over again
+ in this new version of TreeBASE.</p>
+ </td>
+ </tr>
+</table>
+
<h2>The Submission Process</h2>
<p>Typically an author submits a paper to a journal for review
and initiates a TreeBASE submission. At this stage, the
- submission is classified as "in progress." A submission
+ submission is classified as "in progress." A submission
number is issued and the submitter is given a special URL
that can be mailed to the journal editor so that referees
or reviewers can inspect (but not change) the uploaded data.
</p>
-<p>When the journal editor says that the paper is "accepted" or
- "accepted with minor revision," the submitter can return to the
- submission and change its status from "in progress" to "ready."
+<p>When the journal editor says that the paper is "accepted" or
+ "accepted with minor revision," the submitter can return to the
+ submission and change its status from "in progress" to "ready."
At that point, the submitter can cite a URI in his or her paper
that serves as an accession number and as a permanent, resolvable
URL to the data. TreeBASE staff will verify that the submission
@@ -34,7 +39,7 @@
<h2>General Requirements</h2>
<ul>
- <li>The paper must be published in a peer-reviewed journal or book. Data for manuscripts that are "accepted with minor revision," "accepted," or "in press" can be published in TreeBASE. Data for manuscripts that are "submitted" or "in preparation" must not move beyond the initial "in progress" stage of TreeBASE submission.</li>
+ <li>The paper must be published in a peer-reviewed journal or book. Data for manuscripts that are "accepted with minor revision," "accepted," or "in press" can be published in TreeBASE. Data for manuscripts that are "submitted" or "in preparation" must not move beyond the initial "in progress" stage of TreeBASE submission.</li>
<li>The names of all authors listed with the paper must be included.</li>
@@ -51,24 +56,25 @@
<p>Data are uploaded to TreeBASE in the NEXUS format, which is used by many popular phylogenetics software packages (e.g., MacClade and Mesquite: Maddison and Maddison, 1992; PAUP: Swofford, 1993). These programs allow other file formats (e.g. Hennig86, PHYLIP, etc.) to be converted into NEXUS. TreeBASE uses <a href="http://mesquiteproject.org/" title="Mesquite" target="_blank">Mesquite</a> to parse incoming data: <strong>if your data cannot be parsed by Mesquite then they will not be parsed by TreeBASE</strong>, so it's always a good idea to save your data in Mesquite prior to uploading. For example: </p>
<ul>
-<li> Launch <a href="http://mesquiteproject.org/" title="Mesquite" target="_blank">Mesquite</a>
-<li>Under the <em>File Menu</em> select <em>Open File</em> and choose your character matrix
-<li>If your tree(s) are stored in a separate file, under the <em>File Menu</em> select
-<em>Include File...</em> and choose your tree file
+<li> Launch <a href="http://mesquiteproject.org/" title="Mesquite" target="_blank">Mesquite</a> </li>
+<li>Under the <em>File Menu</em> select <em>Open File</em> and choose your character matrix</li>
+<li>If your tree(s) are stored in a separate file, under the <em>File Menu</em> select
+ <em>Include File...</em> and choose your tree file </li>
<li>By clicking on "Taxa," "Character Matrix," or "Trees from treefile.tre" from the project margin on the left, you can rename
them: these names will be carried through into TreeBASE, so it's useful to give them informative names. For example, you could name your matrix "Hymenopteran COI Alignment"
-or your tree block "Set of 5 MP Trees from COI Analysis"
-<li>By clicking on the <em>Tree</em> icon from the project margin on the left, you can examine your trees.
-<ul>
- <li>Use the <em>Reroot at Branch</em> tool to reorient the tree the way it appears in the figures of your paper. </li>
- <li>Under the<em> Drawing Menu</em>,
- you can view the relative branch lengths in your tree by selecting <em>Branches Proportional to Lengths</em> </li>
-</ul>
-<li>To rename your trees, click the <em>List & Manage Trees</em> icon from the project margin on the left. Renaming your trees makes it easy to identify them after uploading to TreeBASE.</li>
+or your tree block "Set of 5 MP Trees from COI Analysis"</li>
+<li>By clicking on the <em>Tree</em> icon from the project margin on the left, you can examine your trees.
+ <ul>
+ <li>Use the <em>Reroot at Branch</em> tool to reorient the tree the way it appears in the figures of your paper</li>
+ <li>Under the<em> Drawing Menu</em>,
+ you can view the relative branch lengths in your tree by selecting <em>Branches Proportional to Lengths</em></li>
+ </ul>
+</li>
+
+ <li>To rename your trees, click the <em>List & Manage Trees</em> icon from the project margin on the left. Renaming your trees makes it easy to identify them after uploading to TreeBASE.</li>
<li>To view or edit the taxon labels, click the <em>Taxa</em> icon from the project margin on the left. Verify that the taxon labels comply with TreeBASE's requirements (see below) and edit as needed</li>
<li>If all looks good, select <em>Save File</em> from the <em>File</em> menu.
- Your NEXUS file is now ready to upload to TreeBASE
- </li>
+ Your NEXUS file is now ready to upload to TreeBASE </li>
</ul>
<p>The most frequent error in submitting data to TreeBASE is when taxon labels in the matrices do not match with taxon labels in the trees. Using the above procedure with Mesquite, however, will avoid the problem. </p>
@@ -76,17 +82,18 @@
<h3>Preparation of taxon labels</h3>
<ul>
- <li>Do not abbreviate taxon names (e.g. write "Homo sapiens", not "H. sapiens")</li>
+ <li>Do not abbreviate taxon names (e.g. write "Homo sapiens", not "H. sapiens")</li>
- <li>The NEXUS file should use underscores ("_") to represent spaces</li>
+ <li>The NEXUS file should use underscores ("_") to represent spaces</li>
<li>Avoid using quotation marks, brackets, parentheses, commas, colons, and semicolons.</li>
- <li>Avoid using codes for non-redundant names (e.g. write "Drosophila melanogaster", not "DMelan45GRX"). However, it is acceptable two write "Drosophila melanogaster 45GRX".</li>
+ <li>Avoid using codes for non-redundant names (e.g. write "Drosophila melanogaster", not "DMelan45GRX"). However, it is acceptable two write "Drosophila melanogaster 45GRX".</li>
- <li>Separate the name of parasites and hosts with "ex.," e.g. "Wolbachia sp. ex. Drosophila melanogaster"</li>
+ <li>Separate the name of parasites and hosts with "ex.," e.g. "Wolbachia sp. ex. Drosophila melanogaster"</li>
</ul>
+
<hr/>
<p>Please fill in following information to login<br/>
<span class="required">* Required Fields</span></p>
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|
|
From: <rv...@us...> - 2010-03-22 23:06:36
|
Revision: 647
http://treebase.svn.sourceforge.net/treebase/?rev=647&view=rev
Author: rvos
Date: 2010-03-22 23:06:27 +0000 (Mon, 22 Mar 2010)
Log Message:
-----------
Made more compatible with IE8, added facility where all but last analysis is collapsed, to reduce scrolling
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/analysisList.jsp
trunk/treebase-web/src/main/webapp/styles/styles.css
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/analysisList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/analysisList.jsp 2010-03-22 23:04:55 UTC (rev 646)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/analysisList.jsp 2010-03-22 23:06:27 UTC (rev 647)
@@ -9,6 +9,9 @@
<jsp:include page="analysisList.jsp"/>
--%>
<script type="text/javascript" src="/treebase-web/scripts/user/analysisEditor.js"></script>
+<script type="text/javascript">
+ var myAnalysisIDs = new Array();
+</script>
<c:set var="analysisStepCounter" value="0" scope="request"/>
<c:set var="redirect" value="redirect:/user/analyses.html" scope="request"/>
<c:forEach var="analysisCommand" items="${studyCommand.analysisCommandList}" varStatus="status_analysis">
@@ -18,6 +21,7 @@
<h2>
<a onclick="TreeBASE.collapseExpand('analysis<c:out value="${analysisCommand.id}"/>','block',this)"
style="border:none"
+ id="analysisCollapser<c:out value="${analysisCommand.id}"/>"
title="collapse">
<img
class="iconButton"
@@ -131,7 +135,10 @@
<fieldset
style="padding-left:20px;padding-right:20px;background-color:#E5E5E5;border:none"
- id="analysis<c:out value="${analysisCommand.id}"/>">
+ id="analysis<c:out value="${analysisCommand.id}"/>">
+ <script type="text/javascript">
+ myAnalysisIDs.push('<c:out value="${analysisCommand.id}"/>');
+ </script>
<!-- EDITABLE -->
<c:if test="${editable}">
@@ -330,3 +337,15 @@
</form>
</div>
</c:if>
+
+<c:if test="${editable}">
+ <script type="text/javascript">
+ for ( var i = 0; i < ( myAnalysisIDs.length - 1 ); i++ ) {
+ TreeBASE.collapseExpand(
+ 'analysis'+myAnalysisIDs[i],
+ 'block',
+ $('analysisCollapser'+myAnalysisIDs[i])
+ );
+ }
+ </script>
+</c:if>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/styles/styles.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/styles.css 2010-03-22 23:04:55 UTC (rev 646)
+++ trunk/treebase-web/src/main/webapp/styles/styles.css 2010-03-22 23:06:27 UTC (rev 647)
@@ -22,7 +22,7 @@
}
#content a:hover, #contentRight a:hover {
- border-bottom: 2px solid orangered;
+ border-bottom: 2px solid #FF4500;
font-weight: bold
}
@@ -308,8 +308,9 @@
img.journal {
width: 121px;
height: 40px;
- border: 0;
- align: bottom
+ border: 1px solid silver;
+ margin: 5px;
+ padding: 5px
}
@@ -572,20 +573,10 @@
border: 1px solid silver
}
input.software {
- width: 100%;
- overflow: scroll
}
select.software {
width: 100%
}
.analysisStep {
background-color:white
-}
-
-/* Home page styles
-*******************************************************************************************/
-#sponsors > img {
- border: 1px solid silver;
- margin: 5px;
- padding: 5px
}
\ No newline at end of file
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|
|
From: <rv...@us...> - 2010-03-22 23:05:06
|
Revision: 646
http://treebase.svn.sourceforge.net/treebase/?rev=646&view=rev
Author: rvos
Date: 2010-03-22 23:04:55 +0000 (Mon, 22 Mar 2010)
Log Message:
-----------
Made more xhtml compliant
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp
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/partnership.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp
trunk/treebase-web/src/main/webapp/common/header.jsp
trunk/treebase-web/src/main/webapp/common/search-nav.jsp
trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp 2010-03-22 19:30:21 UTC (rev 645)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp 2010-03-22 23:04:55 UTC (rev 646)
@@ -1,105 +1,103 @@
-<div id="contentRight">
- <div class="gutter">
- <h1>Overview</h1>
- <p>
- TreeBASE is a relational database designed to manage and explore information on
- phylogenetic relationships (Sanderson et al., 1993, 1994; Piel et al., 1996;
- Morel, 1996; Piel et al., 2000). It includes phylogenetic trees and data
- matrices, together with information about the relevant publication, taxa,
- morphological and sequence-based characters, and published analyses.
- </p>
- <p>
- The database is designed to allow retrieval of trees and data from different
- studies so that existing phylogenetic results may be reassessed, compared,
- combined and reused. Applications include:
- </p>
- <ul>
- <li>
- to locate information on the phylogeny of particular groups of interest.
- </li>
- <li>
- to obtain datasets for studies of character evolution, including general
- patterns across many groups, such as patterns of homoplasy.
- </li>
- <li>
- in studies of biogeography -- to retrieve trees with representatives in
- particular geographical areas.
- </li>
- <li>
- in studies of coevolution -- to retrieve information on host and parasite
- phylogenies.
- </li>
- <li>
- in studies of congruence and combination of data -- to retrieve all molecular
- and morphological phylogenies for particular groups.
- </li>
- <li>
- in studies of phylogenetic methods -- to retrieve all parsimony or maximum
- likelihood reconstructions, for example, or to download datasets of various
- sorts to test methods.
- </li>
- <li>
- to link together trees of particular groups into more inclusive phylogenies.
- </li>
- <li>
- to discover understudied groups -- a resource for students, funding agencies,
- etc.
- </li>
- <li>
- to retrieve phylogenetic information for use in conservation biology and the
- management of natural resources.
- </li>
- </ul>
- <h2>History, Funding, and Governance</h2>
- <p>
- The prototype for TreeBASE was first launched in 1994 (Sanderson et al. 1994,
- Piel et al., 2002) with funding from NSF SGER (NSF DEB 9318325: "A prototype
- database of phylogenetic studies"). The database underwent a complete
- redevelopment and redesign with funding from the <a href="http://www.phylo.org">
- Cyberinfrastructure for Phylogenetic Research project</a> (NSF EF 0331654:
- "Building the Tree of Life -- A National Resource for Phyloinformatics and
- Computational Phylogenetics").
- </p>
- <p>
- TreeBASE was released in March 2010 as one of the main products of The
- Phyloinformatics Research Foundation, Inc., a Connecticut non-profit
- corporation. The Foundation provides direction, governance, and continuity for
- software, data sharing, and communication standards to promote phyloinformatic
- research for the scientific community.
- </p>
- <p>
- The current version of the database is 2.0 (released March 2010), and is hosted
- by the National Evolutionary Synthesis Center (<a href="http://www.nescent.org">
- NESCent</a>). In previous years the database has been hosted by the
- <a href="http://www.peabody.yale.edu/">Yale Peabody Museum</a>, the
- <a href="http://www.sdsc.edu">San Diego Supercomputer Center</a>, the
- <a href="http://www.buffalo.edu">University at Buffalo</a>,
- <a href="http://www.harvard.edu">Harvard University</a>,
- <a href="http://www.leiden.edu">Leiden University</a>, and the
- <a href="http://www.ucdavid.edu">University of California, Davis</a>.
- </p>
- <h2>Related resources</h2>
- <ul>
- <li><a href="http://eol.org">Encyclopedia of Life</a>: A new project to create an
- online reference source and database for every one of the 1.8 million species that
- are named and known on this planet.</li>
- <li><a href="http://tolweb.org">Tree of Life Web Project</a>: A collaborative
- effort of biologists and nature enthusiasts from around the world. On more than
- 10,000 World Wide Web pages, the project provides information about biodiversity,
- the characteristics of different groups of organisms, and their evolutionary history</li>
- <li><a href="http://mesquiteproject.org">Mesquite</a>: Experimental, modular
- software for evolutionary biology, designed to help biologists analyze comparative
- data about organisms in a phylogenetic context.
- </li>
- </ul>
- <h2>Logo</h2>
- <p>
- The logo displayed on the TreeBASE web-application has been adapted to match the
- color style of the website. Please use the logo shown here for linking to or citing
- TreeBASE.
- <center>
- <img src="images/TreeBASE.png" alt="TreeBASE Logo" width="108" height="66" />
- </center>
- </p>
- </div>
+<div class="gutter">
+ <h1>Overview</h1>
+ <p>
+ TreeBASE is a relational database designed to manage and explore information on
+ phylogenetic relationships (Sanderson et al., 1993, 1994; Piel et al., 1996;
+ Morel, 1996; Piel et al., 2000). It includes phylogenetic trees and data
+ matrices, together with information about the relevant publication, taxa,
+ morphological and sequence-based characters, and published analyses.
+ </p>
+ <p>
+ The database is designed to allow retrieval of trees and data from different
+ studies so that existing phylogenetic results may be reassessed, compared,
+ combined and reused. Applications include:
+ </p>
+ <ul>
+ <li>
+ to locate information on the phylogeny of particular groups of interest.
+ </li>
+ <li>
+ to obtain datasets for studies of character evolution, including general
+ patterns across many groups, such as patterns of homoplasy.
+ </li>
+ <li>
+ in studies of biogeography -- to retrieve trees with representatives in
+ particular geographical areas.
+ </li>
+ <li>
+ in studies of coevolution -- to retrieve information on host and parasite
+ phylogenies.
+ </li>
+ <li>
+ in studies of congruence and combination of data -- to retrieve all molecular
+ and morphological phylogenies for particular groups.
+ </li>
+ <li>
+ in studies of phylogenetic methods -- to retrieve all parsimony or maximum
+ likelihood reconstructions, for example, or to download datasets of various
+ sorts to test methods.
+ </li>
+ <li>
+ to link together trees of particular groups into more inclusive phylogenies.
+ </li>
+ <li>
+ to discover understudied groups -- a resource for students, funding agencies,
+ etc.
+ </li>
+ <li>
+ to retrieve phylogenetic information for use in conservation biology and the
+ management of natural resources.
+ </li>
+ </ul>
+ <h2>History, Funding, and Governance</h2>
+ <p>
+ The prototype for TreeBASE was first launched in 1994 (Sanderson et al. 1994,
+ Piel et al., 2002) with funding from NSF SGER (NSF DEB 9318325: "A prototype
+ database of phylogenetic studies"). The database underwent a complete
+ redevelopment and redesign with funding from the <a href="http://www.phylo.org">
+ Cyberinfrastructure for Phylogenetic Research project</a> (NSF EF 0331654:
+ "Building the Tree of Life -- A National Resource for Phyloinformatics and
+ Computational Phylogenetics").
+ </p>
+ <p>
+ TreeBASE was released in March 2010 as one of the main products of The
+ Phyloinformatics Research Foundation, Inc., a Connecticut non-profit
+ corporation. The Foundation provides direction, governance, and continuity for
+ software, data sharing, and communication standards to promote phyloinformatic
+ research for the scientific community.
+ </p>
+ <p>
+ The current version of the database is 2.0 (released March 2010), and is hosted
+ by the National Evolutionary Synthesis Center (<a href="http://www.nescent.org">
+ NESCent</a>). In previous years the database has been hosted by the
+ <a href="http://www.peabody.yale.edu/">Yale Peabody Museum</a>, the
+ <a href="http://www.sdsc.edu">San Diego Supercomputer Center</a>, the
+ <a href="http://www.buffalo.edu">University at Buffalo</a>,
+ <a href="http://www.harvard.edu">Harvard University</a>,
+ <a href="http://www.leiden.edu">Leiden University</a>, and the
+ <a href="http://www.ucdavid.edu">University of California, Davis</a>.
+ </p>
+ <h2>Related resources</h2>
+ <ul>
+ <li><a href="http://eol.org">Encyclopedia of Life</a>: A new project to create an
+ online reference source and database for every one of the 1.8 million species that
+ are named and known on this planet.</li>
+ <li><a href="http://tolweb.org">Tree of Life Web Project</a>: A collaborative
+ effort of biologists and nature enthusiasts from around the world. On more than
+ 10,000 World Wide Web pages, the project provides information about biodiversity,
+ the characteristics of different groups of organisms, and their evolutionary history</li>
+ <li><a href="http://mesquiteproject.org">Mesquite</a>: Experimental, modular
+ software for evolutionary biology, designed to help biologists analyze comparative
+ data about organisms in a phylogenetic context.
+ </li>
+ </ul>
+ <h2>Logo</h2>
+ <p>
+ The logo displayed on the TreeBASE web-application has been adapted to match the
+ color style of the website. Please use the logo shown here for linking to or citing
+ TreeBASE.
+ </p>
+ <div style="width:100%;text-align:center">
+ <img src="images/TreeBASE.png" alt="TreeBASE Logo" width="108" height="66" />
+ </div>
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp 2010-03-22 19:30:21 UTC (rev 645)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp 2010-03-22 23:04:55 UTC (rev 646)
@@ -1,46 +1,40 @@
-<div id="contentRight">
- <div class="gutter">
- <h1>Contacts</h1>
- <h2>Help</h2>
- <p>
- For questions about data submission and data content, please
- contact the TreeBASE helpdesk:
- <a href="mailto:help@treebase.org">help@treebase.org</a>
- </p>
+<div class="gutter">
+ <h1>Contacts</h1>
+ <h2>Help</h2>
+ <p>
+ For questions about data submission and data content, please
+ contact the TreeBASE helpdesk:
+ <a href="mailto:help@treebase.org">help@treebase.org</a>
+ </p>
- <h2>Bugs</h2>
- <p>
- To report software bugs, browser conflicts, and ergonomic
- inefficiencies, please email your issue report to the TreeBASE bug queue:
- <a href="mailto:bugs@treebase.org">bugs@treebase.org</a>
- </p>
+ <h2>Bugs</h2>
+ <p>
+ To report software bugs, browser conflicts, and ergonomic
+ inefficiencies, please email your issue report to the TreeBASE bug queue:
+ <a href="mailto:bugs@treebase.org">bugs@treebase.org</a>
+ </p>
- <p>
- Alternatively, you can enter a bug report directly into our
- SourceForge online bug tracker. For that, please follow these steps:
- </p>
- <ol style="list-style-type:upper-roman">
- <li>If you have a SourceForge account, log in to it and
- proceed to (II) below. Otherwise:</li>
-
- <ol>
- <li>Visit <a
- href="http://sourceforge.net/account/registration/">http://sourceforge.net/account/registration/</a>
- and fill in the form.</li>
-
- <li>After you confirm the account creation by email, log in at <a
- href="http://sourceforge.net/account/login.php">http://sourceforge.net/account/login.php</a></li>
- </ol>
-
- <li> Visit <a
- href="https://sourceforge.net/tracker2/?group_id=248804&atid=1126676">
- https://sourceforge.net/tracker2/?group_id=248804&atid=1126676</a>. On this page you can browse the bug database.</li>
+ <p>
+ Alternatively, you can enter a bug report directly into our
+ SourceForge online bug tracker. For that, please follow these steps:
+ </p>
+ <ol style="list-style-type:upper-roman">
+ <li>If you have a SourceForge account, log in to it and
+ proceed to (II) below. Otherwise visit <a
+ href="http://sourceforge.net/account/registration/">
+ http://sourceforge.net/account/registration/</a>
+ and fill in the form. After you confirm the account creation by email, log in at <a
+ href="http://sourceforge.net/account/login.php">http://sourceforge.net/account/login.php
+ </a></li>
+
+ <li> Visit <a
+ href="https://sourceforge.net/tracker2/?group_id=248804&atid=1126676">
+ https://sourceforge.net/tracker2/?group_id=248804&atid=1126676</a>. On this page you can browse the bug database.</li>
- <li>Click the "add new" button. Add the
- description of the bug. Long outputs or error messages can be attached as
- separate files if you prefer. Click "add artifact" to submit the report.</li>
- </ol>
- </div>
+ <li>Click the "add new" button. Add the
+ description of the bug. Long outputs or error messages can be attached as
+ separate files if you prefer. Click "add artifact" to submit the report.</li>
+ </ol>
</div>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2010-03-22 19:30:21 UTC (rev 645)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2010-03-22 23:04:55 UTC (rev 646)
@@ -1,326 +1,350 @@
-<div id="contentRight">
<div class="gutter">
-<h1>Journals</h1>
-<p>In addition to providing a digital library, TreeBASE serves the
-scientific community by offering journal editors and reviewers special
-advanced anonymous access to submitted data. This access improves the
-quality of the review process because reviewers can inspect and evaluate
-the data, and in turn that also improves the quality of data in
-TreeBASE. Below is a list of journals that recommend or require
-submission to TreeBASE as an integral part of their publication
-policies. We encourage other journals and scientific societies to do the
-same because archiving and sharing of scientific data is critical for
-promoting subsequent reuse of published data, leveraging the cumulative
-knowledge of science, and maximizing the impact of scientific
-publications on future research.</p>
-<table>
- <tr>
- <td valign="top">
- <p><b>Journal Hyperlink</b></p>
- </td>
- <td>
- <p><b>PhyloWS URL to Studies in TreeBASE</b><br>
- (note: add "&format=rss1" to the end of each URL to use
- it in your favorite RSS reader)</p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.wiley.com/bw/journal.asp?ref=0014-3820"
- title="Evolution"> <img class="journal"
- src="images/journal_files/image001.gif" alt="Evolution"/> </a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DEvolution"
- title="Find records in TreeBASE for articles published in Evolution">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DEvolution
- </a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a
- href="http://www3.interscience.wiley.com/journal/119423602/home">
- <img class="journal"
- src="images/journal_files/image002.jpg"> </a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22"
- title="Find records in TreeBASE for articles published in Evolutionary Applications">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22
- </a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a
- href="http://www.elsevier.com/wps/find/journaldescription.cws_home/720691/description#description">
+ <h1>Journals</h1>
+ <p>In addition to providing a digital library, TreeBASE serves the
+ scientific community by offering journal editors and reviewers special
+ advanced anonymous access to submitted data. This access improves the
+ quality of the review process because reviewers can inspect and evaluate
+ the data, and in turn that also improves the quality of data in
+ TreeBASE. Below is a list of journals that recommend or require
+ submission to TreeBASE as an integral part of their publication
+ policies. We encourage other journals and scientific societies to do the
+ same because archiving and sharing of scientific data is critical for
+ promoting subsequent reuse of published data, leveraging the cumulative
+ knowledge of science, and maximizing the impact of scientific
+ publications on future research.</p>
+ <table>
+ <tr>
+ <td valign="top">
+ <p><b>Journal Hyperlink</b></p>
+ </td>
+ <td>
+ <p><b>PhyloWS URL to Studies in TreeBASE</b><br/>
+ (note: add "&format=rss1" to the end of each URL to use
+ it in your favorite RSS reader)</p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.wiley.com/bw/journal.asp?ref=0014-3820"
+ title="Evolution">
+ <img class="journal"
+ src="images/journal_files/image001.gif" alt="Evolution"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DEvolution"
+ title="Find records in TreeBASE for articles published in Evolution">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DEvolution
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p>
+ <a
+ href="http://www3.interscience.wiley.com/journal/119423602/home">
+ <img class="journal"
+ src="images/journal_files/image002.jpg" alt="Evolutionary Applications"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22"
+ title="Find records in TreeBASE for articles published in Evolutionary Applications">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p>
+ <a
+ href="http://www.elsevier.com/wps/find/journaldescription.cws_home/720691/description#description">
+ <img class="journal"
+ src="images/journal_files/image003.jpg" alt="Fungal Biology"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22"
+ title="Find records in TreeBASE for articles published in Fungal Biology">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p>
+ <a href="http://www.publish.csiro.au/nid/120.htm">
+ <img class="journal"
+ src="images/journal_files/image004.gif"
+ alt="Invertebrate Systematics" />
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22"
+ title="Find records in TreeBASE for articles published in Invertebrate Systematics">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.msafungi.org/">
+ <img class="journal" src="images/journal_files/image005.gif" alt="Mycologia" /></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycologia"
+ title="Find records in TreeBASE for articles published in Mycologia">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycologia</a>
+ </p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.springer.com/life+sciences/plant+sciences/journal/11557">
<img class="journal"
- src="images/journal_files/image003.jpg" /></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22"
- title="Find records in TreeBASE for articles published in Fungal Biology">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22
- </a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.publish.csiro.au/nid/120.htm">
- <img class="journal"
- src="images/journal_files/image004.gif"
- alt="Invertebrate Systematics" /> </a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22"
- title="Find records in TreeBASE for articles published in Invertebrate Systematics">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22
- </a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.msafungi.org/"> <img class="journal" src="images/journal_files/image005.gif"
- alt="Join MSA" /></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycologia"
- title="Find records in TreeBASE for articles published in Mycologia">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycologia</a>
- </p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a
- href="http://www.springer.com/life+sciences/plant+sciences/journal/11557">
- <img class="journal"
- src="images/journal_files/image006.jpg" alt="Get MycPro"/> </a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22"
- title="Find records in TreeBASE for articles published in Mycologial Progress">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22</a>
- </p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a
- href="http://www.elsevier.com/wps/find/journaldescription.cws_home/707043/description#description">
- <img class="journal"
- src="images/journal_files/image007.gif" alt="Join BMS">
- </a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22"
- title="Find records in TreeBASE for articles published in Mycologial Research">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a
- href="http://www.springer.com/life+sciences/microbiology/journal/10267">
- <img class="journal"
- src="images/journal_files/image008.gif" alt=Mycoscience></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycoscience"
- title="Find records in TreeBASE for articles published in Mycoscience">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycoscience</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.mycosphere.org/"><img class="journal" src="images/journal_files/image009.jpg"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycosphere"
- title="Find records in TreeBASE for articles published in Mycosphere">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycosphere</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a
- href="http://www.elsevier.com/wps/find/journaldescription.cws_home/701789/description#description">
- <img class="journal"
- src="images/journal_files/image010.gif"
- alt="Organisms, Diversity, and Evolution"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22"
- title="Find records in TreeBASE for articles published in Organisms Diversity & Evolution">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.persoonia.org/"><img class="journal" src="images/journal_files/image011.jpg"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPersoonia"
- title="Find records in TreeBASE for articles published in Persoonia">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPersoonia</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://apsjournals.apsnet.org/loi/phyto?cookieSet=1"
- title=link> <img class="journal"
- src="images/journal_files/image012.jpg" alt="Join APS"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPhytopahology"
- title="Find records in TreeBASE for articles published in Phytopahology">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPhytopahology</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.apsnet.org/pd/"><img class="journal" src="images/journal_files/image013.jpg"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22"
- title="Find records in TreeBASE for articles published in Plant Disease">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.rhodora.org/Rhodora.html"><img
- class="journal"
- src="images/journal_files/image014.gif" alt="Rhodora"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DRhodora"
- title="Find records in TreeBASE for articles published in Rhodora">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DRhodora</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a
- href="http://www.rbg.vic.gov.au/science/information-and-resources/science-publications/muelleria">
- <img class="journal"
- src="images/journal_files/image015.jpg"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMuelleria"
- title="Find records in TreeBASE for articles published in Muelleria">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMuelleria</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.studiesinmycology.org/"><img class="journal" src="images/journal_files/image016.gif"
- alt="Studies in Mycology"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22"
- title="Find records in TreeBASE for articles published in Studies in Mycology">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://systbiol.org/"><img class="journal" src="images/journal_files/image017.gif" alt="Join SSB"/>
- </a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22"
- title="Find records in TreeBASE for articles published in Systematic Biology">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.sysbot.org/"><img class="journal" src="images/journal_files/image018.gif"
- alt="Join ASPT"/></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22"
- title="Find records in TreeBASE for articles published in Systematic Botany">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://tropical-bryology.org/"><img class="journal" src="images/journal_files/image019.jpg"/></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22"
- title="Find records in TreeBASE for articles published in Tropical Bryology">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22</a></p>
- </td>
- </tr>
-</table>
+ src="images/journal_files/image006.jpg" alt="Mycologial Progress"/> </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22"
+ title="Find records in TreeBASE for articles published in Mycologial Progress">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22</a>
+ </p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.elsevier.com/wps/find/journaldescription.cws_home/707043/description#description">
+ <img class="journal"
+ src="images/journal_files/image007.gif" alt="Mycologial Research"/>
+ </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22"
+ title="Find records in TreeBASE for articles published in Mycologial Research">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.springer.com/life+sciences/microbiology/journal/10267">
+ <img class="journal"
+ src="images/journal_files/image008.gif" alt="Mycoscience"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycoscience"
+ title="Find records in TreeBASE for articles published in Mycoscience">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycoscience</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.mycosphere.org/">
+ <img class="journal" src="images/journal_files/image009.jpg" alt="Mycosphere"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycosphere"
+ title="Find records in TreeBASE for articles published in Mycosphere">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycosphere</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.elsevier.com/wps/find/journaldescription.cws_home/701789/description#description">
+ <img class="journal"
+ src="images/journal_files/image010.gif"
+ alt="Organisms, Diversity, and Evolution"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22"
+ title="Find records in TreeBASE for articles published in Organisms Diversity & Evolution">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.persoonia.org/">
+ <img class="journal" src="images/journal_files/image011.jpg" alt="Persoonia"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPersoonia"
+ title="Find records in TreeBASE for articles published in Persoonia">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPersoonia</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p>
+ <a href="http://apsjournals.apsnet.org/loi/phyto?cookieSet=1">
+ <img
+ class="journal"
+ src="images/journal_files/image012.jpg"
+ alt="Phytopahology"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPhytopahology"
+ title="Find records in TreeBASE for articles published in Phytopahology">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPhytopahology</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.apsnet.org/pd/">
+ <img class="journal" src="images/journal_files/image013.jpg" alt="Plant Disease"/>
+ </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22"
+ title="Find records in TreeBASE for articles published in Plant Disease">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.rhodora.org/Rhodora.html"><img
+ class="journal"
+ src="images/journal_files/image014.gif" alt="Rhodora"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DRhodora"
+ title="Find records in TreeBASE for articles published in Rhodora">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DRhodora</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.rbg.vic.gov.au/science/information-and-resources/science-publications/muelleria">
+ <img class="journal"
+ src="images/journal_files/image015.jpg" alt="Muelleria"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMuelleria"
+ title="Find records in TreeBASE for articles published in Muelleria">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMuelleria</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.studiesinmycology.org/">
+ <img class="journal" src="images/journal_files/image016.gif"
+ alt="Studies in Mycology"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22"
+ title="Find records in TreeBASE for articles published in Studies in Mycology">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://systbiol.org/">
+ <img class="journal" src="images/journal_files/image017.gif" alt="Systematic Biology"/>
+ </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22"
+ title="Find records in TreeBASE for articles published in Systematic Biology">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.sysbot.org/">
+ <img class="journal" src="images/journal_files/image018.gif"
+ alt="Systematic Botany"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22"
+ title="Find records in TreeBASE for articles published in Systematic Botany">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://tropical-bryology.org/">
+ <img class="journal" src="images/journal_files/image019.jpg" alt="Tropical Bryology"/>
+ </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22"
+ title="Find records in TreeBASE for articles published in Tropical Bryology">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22</a></p>
+ </td>
+ </tr>
+ </table>
+
+ <p><b>Other Journals with a Significant Presence in TreeBASE</b>: <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%2American+Journal+of+Botany%22"
+ title="American Journal of Botany">American Journal of Botany</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Annals+of+the+Missouri+Botanical+Garden%22"
+ title="Annals of the Missouri Botanical Garden">Annals of the
+ Missouri Botanical Garden</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Biological+Journal+of+the+Linnean+Society%22"
+ title="Biological Journal of the Linnean Society">Biological
+ Journal of the Linnean Society</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22BMC+Evolutionary+Biology%22"
+ title="BMC Evolutionary Biology">BMC Evolutionary Biology</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Canadian+Journal+of+Botany%22"
+ title="Canadian Journal of Botany">Canadian Journal of Botany</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DCladistics"
+ title="Cladistics">Cladistics</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Diversity%22"
+ title="Fungal Diversity">Fungal Diversity</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22International+Journal+of+Plant+Sciences%22"
+ title="International Journal of Plant Sciences">International
+ Journal of Plant Sciences</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Journal+of+Phycology%22"
+ title="Journal of Phycology">Journal of Phycology</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Molecular+Biology+and+Evolution%22"
+ title="Molecular Biology and Evolution">Molecular Biology and
+ Evolution</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Molecular+Ecology%22"
+ title="Molecular Ecology">Molecular Ecology</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Molecular+Phylogenetics+and+Evolution%22"
+ title="Molecular Phylogenetics and Evolution">Molecular
+ Phylogenetics and Evolution</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Systematics+and+Evolution%22"
+ title="Plant Systematics and Evolution">Plant Systematics and
+ Evolution</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Proceeding+of+the+National+Academy+of+Sciences+of+the+United+States+of+America%22"
+ title="Proceeding of the National Academy of Sciences of the United States of America">
+ Proceeding of the National Academy of Sciences of the United States of
+ America</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Proceedings+of+the+Royal+Society+B%22"
+ title="Proceedings of the Royal Society B">Proceedings of the Royal
+ Society B</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DTaxon"
+ title="Taxon">Taxon</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DZootaxa"
+ title="Zootaxa">Zootaxa</a></p>
-<p><b>Other Journals with a Significant Presence in TreeBASE</b>: <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%2American+Journal+of+Botany%22"
- title="American Journal of Botany">American Journal of Botany</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Annals+of+the+Missouri+Botanical+Garden%22"
- title="Annals of the Missouri Botanical Garden">Annals of the
-Missouri Botanical Garden</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Biological+Journal+of+the+Linnean+Society%22"
- title="Biological Journal of the Linnean Society">Biological
-Journal of the Linnean Society</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22BMC+Evolutionary+Biology%22"
- title="BMC Evolutionary Biology">BMC Evolutionary Biology</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Canadian+Journal+of+Botany%22"
- title="Canadian Journal of Botany">Canadian Journal of Botany</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DCladistics"
- title="Cladistics">Cladistics</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Diversity%22"
- title="Fungal Diversity">Fungal Diversity</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22International+Journal+of+Plant+Sciences%22"
- title="International Journal of Plant Sciences">International
-Journal of Plant Sciences</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Journal+of+Phycology%22"
- title="Journal of Phycology">Journal of Phycology</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Molecular+Biology+and+Evolution%22"
- title="Molecular Biology and Evolution">Molecular Biology and
-Evolution</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Molecular+Ecology%22"
- title="Molecular Ecology">Molecular Ecology</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Molecular+Phylogenetics+and+Evolution%22"
- title="Molecular Phylogenetics and Evolution">Molecular
-Phylogenetics and Evolution</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Systematics+and+Evolution%22"
- title="Plant Systematics and Evolution">Plant Systematics and
-Evolution</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Proceeding+of+the+National+Academy+of+Sciences+of+the+United+States+of+America%22"
- title="Proceeding of the National Academy of Sciences of the United States of America">
-Proceeding of the National Academy of Sciences of the United States of
-America</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Proceedings+of+the+Royal+Society+B%22"
- title="Proceedings of the Royal Society B">Proceedings of the Royal
-Society B</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DTaxon"
- title="Taxon">Taxon</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DZootaxa"
- title="Zootaxa">Zootaxa</a></p>
-
-</div>
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp 2010-03-22 19:30:21 UTC (rev 645)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp 2010-03-22 23:04:55 UTC (rev 646)
@@ -1,59 +1,62 @@
-<div id="contentRight">
- <div class="gutter">
- <h1>Partnerships</h1>
- <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
- <img
- width="160"
- src="images/nescent_logo.jpg"
- style="display:inline;float:left;margin-right:15px"/>The
- <a
- href="http://www.nescent.org"
- title="National Evolutionary Synthesis Center (NESCent)">National
- Evolutionary Synthesis Center (NESCent)
- </a> is a national center sponsored by NSF with the mission of facilitating
- synthetic research in evolutionary biology. Through a partnership with CIPRES
- and TreeBASE, NESCent is serving to deploy, maintain, and host TreeBASE.
- </p>
- <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
- <img
- width="160"
- height="100"
- src="images/partnership/image002.jpg"
- style="display:inline;float:left;margin-right:15px"/>
- <a
- href="http://www.datadryad.org"
- title="Dryad">Dryad</a> is an open digital repository of author-submitted
- published data which supports many journals in evolutionary biology and ecology.
- Metadata in TreeBASE is being harvested and mirrored by Dryad using the TreeBASE
- OAI-PMH service. Metadata for existing TreeBASE records is being enriched through
- manual and semi-automated mechanisms. Dryad is also forwarding phylogenetic data
- depositions to TreeBASE at the request of the author. These activities are
- funded by NSF DBI 0743720: "A Digital Repository for Preservation and
- Sharing of Data Underlying Published Works in Evolutionary Biology."
- </p>
- <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
- <img
- width="160"
- height="100"
- src="images/partnership/image003.jpg"
- style="display:inline;float:left;margin-right:15px"/>
- TreeBASE currently makes use of <a
- href="http://www.ubio.org/index.php?pagename=services_overview"
- title="uBio's taxonomic name services">uBio's taxonomic name services</a>
- to match taxon labels in submitted trees and matrices against uBio's dictionary
- of nomenclature. TreeBASE further uses this mapping to acquire and store <a
- href="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=howlink"
- title="NCBI taxids">NCBI taxids</a>. In prior years, TreeBASE has provided a bulk list
- of its taxonomy to uBio in order to store links to TreeBASE, and there are plans to
- automate this procedure in the future.
- </p>
- <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
- <img
- width="160"
- height="100"
- src="images/partnership/image004.jpg"
- style="display:inline;float:left;margin-right:15px"/>Many thanks to the National Science Foundation
- for their valuable support.
- </p>
- </div>
+<div class="gutter">
+ <h1>Partnerships</h1>
+ <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
+ <img
+ width="160"
+ src="images/nescent_logo.jpg"
+ style="display:inline;float:left;margin-right:15px"
+ alt="NESCent"/>The
+ <a
+ href="http://www.nescent.org"
+ title="National Evolutionary Synthesis Center (NESCent)">National
+ Evolutionary Synthesis Center (NESCent)
+ </a> is a national center sponsored by NSF with the mission of facilitating
+ synthetic research in evolutionary biology. Through a partnership with CIPRES
+ and TreeBASE, NESCent is serving to deploy, maintain, and host TreeBASE.
+ </p>
+ <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
+ <img
+ width="160"
+ height="100"
+ src="images/partnership/image002.jpg"
+ style="display:inline;float:left;margin-right:15px"
+ alt="Dryad"/>
+ <a
+ href="http://www.datadryad.org"
+ title="Dryad">Dryad</a> is an open digital repository of author-submitted
+ published data which supports many journals in evolutionary biology and ecology.
+ Metadata in TreeBASE is being harvested and mirrored by Dryad using the TreeBASE
+ OAI-PMH service. Metadata for existing TreeBASE records is being enriched through
+ manual and semi-automated mechanisms. Dryad is also forwarding phylogenetic data
+ depositions to TreeBASE at the request of the author. These activities are
+ funded by NSF DBI 0743720: "A Digital Repository for Preservation and
+ Sharing of Data Underlying Published Works in Evolutionary Biology."
+ </p>
+ <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
+ <img
+ width="160"
+ height="100"
+ src="images/partnership/image003.jpg"
+ style="display:inline;float:left;margin-right:15px"
+ alt="uBio"/>
+ TreeBASE currently makes use of <a
+ href="http://www.ubio.org/index.php?pagename=services_overview"
+ title="uBio's taxonomic name services">uBio's taxonomic name services</a>
+ to match taxon labels in submitted trees and matrices against uBio's dictionary
+ of nomenclature. TreeBASE further uses this mapping to acquire and store <a
+ href="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=howlink"
+ title="NCBI taxids">NCBI taxids</a>. In prior years, TreeBASE has provided a bulk list
+ of its taxonomy to uBio in order to store links to TreeBASE, and there are plans to
+ automate this procedure in the future.
+ </p>
+ <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
+ <img
+ width="160"
+ height="100"
+ src="images/partnership/image004.jpg"
+ style="display:inline;float:left;margin-right:15px"
+ alt="NSF"/>
+ Many thanks to the National Science
+ Foundation for their valuable support.
+ </p>
</div>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp 2010-03-22 19:30:21 UTC (rev 645)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp 2010-03-22 23:04:55 UTC (rev 646)
@@ -1,119 +1,117 @@
-<div id="contentRight">
- <div class="gutter">
- <h1>People</h1>
- <table class="peopleTable">
- <thead><tr><th colspan="6"><h2>Current contributors</h2></th></tr></thead>
- <tr>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Vladimir Gapeyev"/>
- <br/><strong>Vladimir Gapeyev</strong>
- <br/>Deployment Maintainer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Youjun Guo"/>
- <br/><strong>Youjun Guo</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/hlapp.jpeg" width="81" height="108" alt="Hilmar Lapp"/>
- <br/><strong>Hilmar Lapp</strong>
- <br/>Deployment Manager
- </td>
- <td>
- <img src="images/people/bpiel.jpeg" width="81" height="108" alt="William Piel"/>
- <br/><strong>William Piel</strong>
- <br/>Content Editor
- <br />Prototype Dev
- </td>
- <td>
- <img src="images/people/vtannen.jpeg" width="81" height="108" alt="Val Tannen"/>
- <br/><strong>Val Tannen</strong>
- <br/>Development Leader
- </td>
- <td>
- <img src="images/people/rvos.jpg" width="81" height="108" alt="Rutger Vos"/>
- <br/><strong>Rutger Vos</strong>
- <br/>Developer
- <br/>API Design
- </td>
- </tr>
- </table>
-
- <table class="peopleTable">
- <thead><tr><th colspan="6"><h2>Past contributors</h2></th></tr></thead>
- <tr>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Lucie Chan"/>
- <br/><strong>Lucie Chan</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Shirley Cohen"/>
- <br/><strong>Shirley Cohen</strong>
- <br/>Student Researcher
- </td>
- <td>
- <img src="images/people/mjdominus.jpeg" width="81" height="108" alt="Mark J. Dominus"/>
- <br/><strong>Mark J. Dominus</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/mdonoghue.gif" width="81" height="108" alt="Michael Donoghue"/>
- <br/><strong>Michael Donoghue</strong>
- <br/>Concept
- </td>
- <td>
- <img src="images/people/teriksson.gif" width="81" height="108" alt="Torsten Eriksson"/>
- <br/><strong>Torsten Eriksson</strong>
- <br/>Prototype Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Madhusudan Gujral"/>
- <br/><strong>Madhusudan Gujral</strong>
- <br/>Developer
- </td>
- </tr>
- <tr>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Chris Henze"/>
- <br/><strong>Chris Henze</strong>
- <br/>Prototype Developer
- </td>
- <td>
- <img src="images/people/krice.gif" width="81" height="108" alt="Ken Rice"/>
- <br/><strong>Ken Rice</strong>
- <br/>Prototype Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Jin Ruan"/>
- <br/><strong>Jin Ruan</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/msanderson.gif" width="81" height="108" alt="Mike Sanderson"/>
- <br/><strong>Mike Sanderson</strong>
- <br/>Concept
- <br/>Prototype Dev
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Can van Tran"/>
- <br/><strong>Can van Tran</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Tracy Zhao"/>
- <br/><strong>Tracy Zhao</strong>
- <br/>Developer
- </td>
- </tr>
- </table>
-
- <h2>Phyloinformatics Research Foundation Inc, Board</h2>
- <ul>
- <li>Michael Donoghue</li>
- <li>David Maddison</li>
- <li>William Piel</li>
- <li>Val Tannen</li>
- </ul>
- </div>
+<div class="gutter">
+ <h1>People</h1>
+ <table class="peopleTable">
+ <thead><tr><th colspan="6"><h2>Current contributors</h2></th></tr></thead>
+ <tr>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Vladimir Gapeyev"/>
+ <br/><strong>Vladimir Gapeyev</strong>
+ <br/>Deployment Maintainer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Youjun Guo"/>
+ <br/><strong>Youjun Guo</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/hlapp.jpeg" width="81" height="108" alt="Hilmar Lapp"/>
+ <br/><strong>Hilmar Lapp</strong>
+ <br/>Deployment Manager
+ </td>
+ <td>
+ <img src="images/people/bpiel.jpeg" width="81" height="108" alt="William Piel"/>
+ <br/><strong>William Piel</strong>
+ <br/>Content Editor
+ <br />Prototype Dev
+ </td>
+ <td>
+ <img src="images/people/vtannen.jpeg" width="81" height="108" alt="Val Tannen"/>
+ <br/><strong>Val Tannen</strong>
+ <br/>Development Leader
+ </td>
+ <td>
+ <img src="images/people/rvos.jpg" width="81" height="108" alt="Rutger Vos"/>
+ <br/><strong>Rutger Vos</strong>
+ <br/>Developer
+ <br/>API Design
+ </td>
+ </tr>
+ </table>
+
+ <table class="peopleTable">
+ <thead><tr><th colspan="6"><h2>Past contributors</h2></th></tr></thead>
+ <tr>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Lucie Chan"/>
+ <br/><strong>Lucie Chan</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Shirley Cohen"/>
+ <br/><strong>Shirley Cohen</strong>
+ <br/>Student Researcher
+ </td>
+ <td>
+ <img src="images/people/mjdominus.jpeg" width="81" height="108" alt="Mark J. Dominus"/>
+ <br/><strong>Mark J. Dominus</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/mdonoghue.gif" width="81" height="108" alt="Michael Donoghue"/>
+ <br/><strong>Michael Donoghue</strong>
+ <br/>Concept
+ </td>
+ <td>
+ <img src="images/people/teriksson.gif" width="81" height="108" alt="Torsten Eriksson"/>
+ <br/><strong>Torsten Eriksson</strong>
+ <br/>Prototype Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Madhusudan Gujral"/>
+ <br/><strong>Madhusudan Gujral</strong>
+ <br/>Developer
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Chris Henze"/>
+ <br/><strong>Chris Henze</strong>
+ <br/>Prototype Developer
+ </td>
+ <td>
+ <img src="images/people/krice.gif" width="81" height="108" alt="Ken Rice"/>
+ <br/><strong>Ken Rice</strong>
+ <br/>Prototype Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Jin Ruan"/>
+ <br/><strong>Jin Ruan</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/msanderson.gif" width="81" height="108" alt="Mike Sanderson"/>
+ <br/><strong>Mike Sanderson</strong>
+ <br/>Concept
+ <br/>Prototype Dev
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Can van Tran"/>
+ <br/><strong>Can van Tran</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Tracy Zhao"/>
+ <br/><strong>Tracy Zhao</strong>
+ <br/>Developer
+ </td>
+ </tr>
+ </table>
+
+ <h2>Phyloinformatics Research Foundation Inc, Board</h2>
+ <ul>
+ <li>Michael Donoghue</li>
+ <li>David Maddison</li>
+ <li>William Piel</li>
+ <li>Val Tannen</li>
+ </ul>
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp 2010-03-22 19:30:21 UTC (rev 645)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp 2010-03-22 23:04:55 UTC (rev 646)
@@ -1,88 +1,86 @@
-<div id="contentRight">
- <div class="gutter">
- <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.
- <em>Syst. Biol.</em> <strong>43</strong>:585-589.
- </p>
- <p>
- <strong>Donoghue, M. J.</strong>
- 1994. Progress and prospects in reconstructing plant phylogeny.
- <em>Ann. Missouri Bot. Gard.</em> <strong>81</strong>:405-418.
- </p>
- <p>
- <strong>Donoghue, M. J. and D. D. Ackerly.</strong>
- 1996. Phylogenetic uncertainties and sensitivity analyses in comparative biology.
- <em>Phil. Trans. R. Soc. London B, 351: 1241-1249.</em>
- </p>
- <p>
- <strong>Maddison, W. P. and D. R. Maddison.</strong>
- 1992.
- <em>MacClade: Interactive Analysis of Phylogeny and Character Evolution, Vers. 3.0.</em>
- Sunderland, MA: Sinauer Assoc.
- </p>
- <p>
- <strong>Morell, V.</strong>
- 1996. TreeBASE: the roots of phylogeny.
- <em>Science</em> <strong>273</strong>: 569.
- </p>
- <p>
- <strong>Piel, W. H.</strong>
- 2003. "Phyloinformatics and Tree Networks." In:
- <strong>Wu, C. H., P. Wang, and J. T. L. Wang,</strong> eds.
- <em>Computational Biology and Genome Informatics</em>. World Scientific Press.
- </p>
- <p>
- <strong>Piel, W. H., M. J. Donoghue, and M. J. Sanderson.</strong>
- 2002. "Tree...
[truncated message content] |
|
From: <sfr...@us...> - 2010-03-22 19:30:28
|
Revision: 645
http://treebase.svn.sourceforge.net/treebase/?rev=645&view=rev
Author: sfrgpiel
Date: 2010-03-22 19:30:21 +0000 (Mon, 22 Mar 2010)
Log Message:
-----------
Made changes to instructions for preparing data with Mesquite.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/login.jsp
Modified: trunk/treebase-web/src/main/webapp/login.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/login.jsp 2010-03-22 16:17:53 UTC (rev 644)
+++ trunk/treebase-web/src/main/webapp/login.jsp 2010-03-22 19:30:21 UTC (rev 645)
@@ -5,36 +5,36 @@
<content tag="heading"><fmt:message key="login.title"/>
</content>
-<P>
+<p>
A Special Note to Submitters to the Previous Version
of TreeBASE: If you started a submission in the previous
version, but that submission remained "in progress,"
you will need to start the submission all over again
in this new version of TreeBASE.
-</P>
+</p>
<h2>The Submission Process</h2>
-<P>Typically an author submits a paper to a journal for review
+<p>Typically an author submits a paper to a journal for review
and initiates a TreeBASE submission. At this stage, the
submission is classified as "in progress." A submission
number is issued and the submitter is given a special URL
that can be mailed to the journal editor so that referees
or reviewers can inspect (but not change) the uploaded data.
-</P>
+</p>
-<P>When the journal editor says that the paper is "accepted" or
+<p>When the journal editor says that the paper is "accepted" or
"accepted with minor revision," the submitter can return to the
submission and change its status from "in progress" to "ready."
At that point, the submitter can cite a URI in his or her paper
that serves as an accession number and as a permanent, resolvable
URL to the data. TreeBASE staff will verify that the submission
is complete, and if so, the data are made public.
-</P>
+</p>
<h2>General Requirements</h2>
<ul>
- <li>The paper must be published in a peer-reviewed journal or book. Data for manuscripts that are "accepted with minor revision," "accepted," or "in press" can be included in TreeBASE. Data for manuscripts that are "submitted" or "in preparation" must not move beyond the initial "in progress" stage of TreeBASE submission.</li>
+ <li>The paper must be published in a peer-reviewed journal or book. Data for manuscripts that are "accepted with minor revision," "accepted," or "in press" can be published in TreeBASE. Data for manuscripts that are "submitted" or "in preparation" must not move beyond the initial "in progress" stage of TreeBASE submission.</li>
<li>The names of all authors listed with the paper must be included.</li>
@@ -49,29 +49,36 @@
<h2>Preparation of NEXUS files</h2>
-<P>
- Data are uploaded to TreeBASE in the NEXUS format, which is
- used by many popular phylogenetics software packages (e.g.,
- MacClade and Mesquite: Maddison and Maddison, 1992; PAUP:
- Swofford, 1993). These programs allow other file formats (e.g.
- Hennig86, PHYLIP, etc.) to be converted into NEXUS. TreeBASE
- uses Mesquite to parse incoming data: if your data cannot be
- parsed by Mesquite then they will not be parsed by TreeBASE,
- so it's always a good idea to open and then save your data in
- Mesquite prior to uploading. To be sure that the data are free
- of syntax errors, please prepare them with MacClade or Mesquite,
- and have these programs write the characters and trees in the
- same NEXUS file. The most frequent error is when taxon labels
- in the character block do not match perfectly with taxon labels
- in the trees block.
-</P>
+<p>Data are uploaded to TreeBASE in the NEXUS format, which is used by many popular phylogenetics software packages (e.g., MacClade and Mesquite: Maddison and Maddison, 1992; PAUP: Swofford, 1993). These programs allow other file formats (e.g. Hennig86, PHYLIP, etc.) to be converted into NEXUS. TreeBASE uses <a href="http://mesquiteproject.org/" title="Mesquite" target="_blank">Mesquite</a> to parse incoming data: <strong>if your data cannot be parsed by Mesquite then they will not be parsed by TreeBASE</strong>, so it's always a good idea to save your data in Mesquite prior to uploading. For example: </p>
+<ul>
+<li> Launch <a href="http://mesquiteproject.org/" title="Mesquite" target="_blank">Mesquite</a>
+<li>Under the <em>File Menu</em> select <em>Open File</em> and choose your character matrix
+<li>If your tree(s) are stored in a separate file, under the <em>File Menu</em> select
+<em>Include File...</em> and choose your tree file
+<li>By clicking on "Taxa," "Character Matrix," or "Trees from treefile.tre" from the project margin on the left, you can rename
+ them: these names will be carried through into TreeBASE, so it's useful to give them informative names. For example, you could name your matrix "Hymenopteran COI Alignment"
+or your tree block "Set of 5 MP Trees from COI Analysis"
+<li>By clicking on the <em>Tree</em> icon from the project margin on the left, you can examine your trees.
+<ul>
+ <li>Use the <em>Reroot at Branch</em> tool to reorient the tree the way it appears in the figures of your paper. </li>
+ <li>Under the<em> Drawing Menu</em>,
+ you can view the relative branch lengths in your tree by selecting <em>Branches Proportional to Lengths</em> </li>
+</ul>
+<li>To rename your trees, click the <em>List & Manage Trees</em> icon from the project margin on the left. Renaming your trees makes it easy to identify them after uploading to TreeBASE.</li>
+ <li>To view or edit the taxon labels, click the <em>Taxa</em> icon from the project margin on the left. Verify that the taxon labels comply with TreeBASE's requirements (see below) and edit as needed</li>
+ <li>If all looks good, select <em>Save File</em> from the <em>File</em> menu.
+ Your NEXUS file is now ready to upload to TreeBASE
+ </li>
+ </ul>
+<p>The most frequent error in submitting data to TreeBASE is when taxon labels in the matrices do not match with taxon labels in the trees. Using the above procedure with Mesquite, however, will avoid the problem. </p>
-<P>Preparation of taxon labels</P>
+<h3>Preparation of taxon labels</h3>
+
<ul>
<li>Do not abbreviate taxon names (e.g. write "Homo sapiens", not "H. sapiens")</li>
- <li>In the NEXUS file, use underscores ("_") to represent spaces</li>
+ <li>The NEXUS file should use underscores ("_") to represent spaces</li>
<li>Avoid using quotation marks, brackets, parentheses, commas, colons, and semicolons.</li>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: SourceForge.net <no...@so...> - 2010-03-22 18:59:10
|
Bugs item #2974771, was opened at 2010-03-22 14:59 Message generated for change (Tracker Item Submitted) made by hlapp You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974771&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: Hilmar Lapp (hlapp) Assigned to: Nobody/Anonymous (nobody) Summary: Accessing phyloWS URLs yields exception for HTML view Initial Comment: For example the following works: http://www.treebase.org/treebase-web/phylows/tree/TB2:Tr6917?format=rdf whereas removing the format= parameter (i.e., the HTML view) results in the following YIKES. I suspect that this means that depending on the path from which you access a page, the phyloWSPath (and possibly other page or request parameters) are not properly initialized. javax.servlet.jsp.el.ELException: An error occurred while getting property "phyloWSPath" from an instance of class org.cipres.treebase.domain.study.Study$$EnhancerByCGLIB$$4d099cbc at org.apache.commons.el.Logger.logError(Logger.java:484) at org.apache.commons.el.Logger.logError(Logger.java:588) at org.apache.commons.el.ArraySuffix.evaluate(ArraySuffix.java:318) at org.apache.commons.el.ComplexValue.evaluate(ComplexValue.java:145) at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:263) at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:190) at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:924) at org.apache.jsp.WEB_002dINF.pages.anyObjectAsRDF_jsp._jspx_meth_c_005fout_005f1(anyObjectAsRDF_jsp.java:224) at org.apache.jsp.WEB_002dINF.pages.anyObjectAsRDF_jsp._jspx_meth_c_005fif_005f0(anyObjectAsRDF_jsp.java:199) at org.apache.jsp.WEB_002dINF.pages.anyObjectAsRDF_jsp._jspService(anyObjectAsRDF_jsp.java:100) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:39) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679) at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461) at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399) at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301) at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142) at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:239) at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1142) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:879) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974771&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-03-22 18:57:12
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Bugs item #2974738, was opened at 2010-03-22 14:18 Message generated for change (Settings changed) made by youjun You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974738&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) >Assigned to: youjun guo (youjun) Summary: listing studies causes exception Initial Comment: When admin person wants to get a list of all "in progress" studies, a "yikes" message is returned. http://www.treebase.org/treebase-web/admin/selectStudies.html ============ Yikes! javax.servlet.jsp.el.ELException: An error occurred while getting property "emailAddressString" from an instance of class org.cipres.treebase.domain.admin.User$$EnhancerByCGLIB$$6ece7264 at org.apache.commons.el.Logger.logError(Logger.java:484) at org.apache.commons.el.Logger.logError(Logger.java:588) at org.apache.commons.el.ArraySuffix.evaluate(ArraySuffix.java:318) at org.apache.commons.el.ComplexValue.evaluate(ComplexValue.java:145) at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:263) at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:190) at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:924) at org.apache.jsp.WEB_002dINF.pages.changeStudyStatus_jsp._jspx_meth_display_005fcolumn_005f1(changeStudyStatus_jsp.java:456) at org.apache.jsp.WEB_002dINF.pages.changeStudyStatus_jsp._jspService(changeStudyStatus_jsp.java:160) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:39) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679) at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461) at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399) at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301) at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142) at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:239) at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1142) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:879) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974738&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-03-22 18:18:02
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Bugs item #2974738, was opened at 2010-03-22 14:18 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974738&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: listing studies causes exception Initial Comment: When admin person wants to get a list of all "in progress" studies, a "yikes" message is returned. http://www.treebase.org/treebase-web/admin/selectStudies.html ============ Yikes! javax.servlet.jsp.el.ELException: An error occurred while getting property "emailAddressString" from an instance of class org.cipres.treebase.domain.admin.User$$EnhancerByCGLIB$$6ece7264 at org.apache.commons.el.Logger.logError(Logger.java:484) at org.apache.commons.el.Logger.logError(Logger.java:588) at org.apache.commons.el.ArraySuffix.evaluate(ArraySuffix.java:318) at org.apache.commons.el.ComplexValue.evaluate(ComplexValue.java:145) at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:263) at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:190) at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:924) at org.apache.jsp.WEB_002dINF.pages.changeStudyStatus_jsp._jspx_meth_display_005fcolumn_005f1(changeStudyStatus_jsp.java:456) at org.apache.jsp.WEB_002dINF.pages.changeStudyStatus_jsp._jspService(changeStudyStatus_jsp.java:160) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:39) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679) at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461) at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399) at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301) at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142) at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:239) at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1142) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:879) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974738&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-03-22 18:05:12
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Bugs item #2973661, was opened at 2010-03-20 00:14 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973661&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) >Assigned to: youjun guo (youjun) Summary: Taxa List has labels listed in duplicates, triplicates, etc Initial Comment: When a user is submitting data and clicks on the taxon list page (http://treebase.nescent.org/treebase-web/user/taxaList.html) the taxon labels are duplicated or triplicated, or quadrupled (etc) depending on the study. This bug appears to have cropped up just recently -- I would have noticed it before. Each distinct taxon label should be listed once. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973661&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-03-22 18:01:23
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Bugs item #2973932, was opened at 2010-03-20 18:46 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973932&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Hilmar Lapp (hlapp) Summary: Broken link in Advanced Search box Initial Comment: Under each tab in the search page there is a link to "TreeBASE help page about searching" which points to http://www.treebase.org/treebase-web/help/urlAPI.jsp. The correct URL is actually "http://www.treebase.org/treebase-web/urlAPI.html" -- but I suggest instead that our text say "visit the description of TreeBASE's PhyloWS implementation." and then provide "http://sourceforge.net/apps/mediawiki/treebase/index.php?title=API" as the hyperlink. ---------------------------------------------------------------------- Comment By: Hilmar Lapp (hlapp) Date: 2010-03-20 18:59 Message: I fixed this in the source code, svn commit# 639. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973932&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-03-22 18:00:11
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Bugs item #2974156, was opened at 2010-03-21 13:24 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974156&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: youjun guo (youjun) Summary: PhyloWidget Crashes FireFox Initial Comment: TreeBASE's version of PhyloWidget seems to cause FireFox to hang (forever). This is FireFox 3.0.18 on Mac 10.6. The latest version of PhyloWidget (www.phylowidget.org) does not cause this problem. Best is to upgrade our version to the latest one, adding in the extra code for committing changes to the database. The instance on the Search side can have all default PhyloWidget menus available. The instance on the Submit side should avoid all menu items that allow the user to change a taxon label name -- but rerooted, flipping, etc, should be retained. (basically, as it is currently implemented). ---------------------------------------------------------------------- Comment By: youjun guo (youjun) Date: 2010-03-21 14:09 Message: could this be a browser cache issue? The applet will hang if the verification of jar signature didn't get passed. So if the browser cache the signature from last version it will stop loading the new version, youjun ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974156&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-03-22 17:59:48
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Bugs item #2968156, was opened at 2010-03-10 13:38 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2968156&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Priority: 9 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: youjun guo (youjun) Summary: Update Web Page Initial Comment: The html on TreeBASE splash page, etc, needs updating based on text that we are working on here: http://docs.google.com/Doc?docid=0AXEQpupFgwYiZGg4bXF6bl82NmZwdm50cmRz&hl=en ---------------------------------------------------------------------- Comment By: Hilmar Lapp (hlapp) Date: 2010-03-10 15:28 Message: Also add text to status change to 'Ready' that tells user that data will become public after review (and acceptance of the publication?). Confirm exact language with Bill. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2968156&group_id=248804 |
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From: <yo...@us...> - 2010-03-22 16:17:59
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Revision: 644
http://treebase.svn.sourceforge.net/treebase/?rev=644&view=rev
Author: youjun
Date: 2010-03-22 16:17:53 +0000 (Mon, 22 Mar 2010)
Log Message:
-----------
re-sign the phylowidget.jar
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp
trunk/treebase-web/src/main/webapp/test/phylowidget/PhyloWidget.jar
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp 2010-03-21 13:45:31 UTC (rev 643)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp 2010-03-22 16:17:53 UTC (rev 644)
@@ -119,7 +119,7 @@
<param name="showBranchLengths" value="true"/>
<param name="useBranchLengths" value="true"/>
-->
- <param name="menuFile" value="nondb-menus.xml" />
+ <param name="menuFile" value="limited-menus.xml" />
<param name="image" value="loading.gif" />
<param name="boxmessage" value="Loading PhyloWidget software..." />
<param name="boxbgcolor" value="#FFFFFF" />
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp 2010-03-21 13:45:31 UTC (rev 643)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp 2010-03-22 16:17:53 UTC (rev 644)
@@ -19,7 +19,7 @@
<c:param name="id" value="${tree.study.id}" />
</c:url>
<input type="checkbox" id="s-${tree.id }" name="selection" value="${tree.id }" />
- <a href="${url}">Tr${tree.id }</a>
+ <a href="${url}" target="myplwidget">Tr${tree.id}</a>
</display:column>
@@ -85,7 +85,7 @@
<c:param name="treeid" value="${tree.id}" />
<c:param name="id" value="${tree.study.id}" />
</c:url>
- <a href="${url}" target="_blank">
+ <a href="${url}" target="myplwidget">
<img
class="iconButton"
src="<fmt:message key="icons.list"/>"
Modified: trunk/treebase-web/src/main/webapp/test/phylowidget/PhyloWidget.jar
===================================================================
(Binary files differ)
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From: SourceForge.net <no...@so...> - 2010-03-21 18:09:24
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Bugs item #2974156, was opened at 2010-03-21 13:24 Message generated for change (Comment added) made by youjun You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974156&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: youjun guo (youjun) Summary: PhyloWidget Crashes FireFox Initial Comment: TreeBASE's version of PhyloWidget seems to cause FireFox to hang (forever). This is FireFox 3.0.18 on Mac 10.6. The latest version of PhyloWidget (www.phylowidget.org) does not cause this problem. Best is to upgrade our version to the latest one, adding in the extra code for committing changes to the database. The instance on the Search side can have all default PhyloWidget menus available. The instance on the Submit side should avoid all menu items that allow the user to change a taxon label name -- but rerooted, flipping, etc, should be retained. (basically, as it is currently implemented). ---------------------------------------------------------------------- >Comment By: youjun guo (youjun) Date: 2010-03-21 14:09 Message: could this be a browser cache issue? The applet will hang if the verification of jar signature didn't get passed. So if the browser cache the signature from last version it will stop loading the new version, youjun ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974156&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-03-21 17:24:37
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Bugs item #2974156, was opened at 2010-03-21 13:24 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974156&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: youjun guo (youjun) Summary: PhyloWidget Crashes FireFox Initial Comment: TreeBASE's version of PhyloWidget seems to cause FireFox to hang (forever). This is FireFox 3.0.18 on Mac 10.6. The latest version of PhyloWidget (www.phylowidget.org) does not cause this problem. Best is to upgrade our version to the latest one, adding in the extra code for committing changes to the database. The instance on the Search side can have all default PhyloWidget menus available. The instance on the Submit side should avoid all menu items that allow the user to change a taxon label name -- but rerooted, flipping, etc, should be retained. (basically, as it is currently implemented). ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974156&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-03-21 13:50:42
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Bugs item #2973950, was opened at 2010-03-20 20:17 Message generated for change (Settings changed) made by youjun You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973950&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) >Assigned to: youjun guo (youjun) Summary: View Tree Keeps Opening New Windows Initial Comment: When a user in the Search side clicks on a tree to view it in PhyloWidget, the result is that a new window opens (this is good). But if the user then returns to the list of trees and clicks on another tree, we get another new window instead of opening up into the existing phylowidget window. Let's change this so that the target of the popup window uses a standard name (eg "PhyloWidget") and then all subsequent clicks on trees point to this same target. Also, please change the hover-over label from "Tree Section" to "View Tree" ---------------------------------------------------------------------- >Comment By: youjun guo (youjun) Date: 2010-03-21 09:50 Message: fix the link, it will open in its own window ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973950&group_id=248804 |
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