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From: <yo...@us...> - 2010-04-01 21:05:19
|
Revision: 665
http://treebase.svn.sourceforge.net/treebase/?rev=665&view=rev
Author: youjun
Date: 2010-04-01 21:05:13 +0000 (Thu, 01 Apr 2010)
Log Message:
-----------
fix the servername always be localhost issue
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp 2010-04-01 20:20:37 UTC (rev 664)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp 2010-04-01 21:05:13 UTC (rev 665)
@@ -23,7 +23,14 @@
<!--c:param name="treeid" value="${tree.id}" /-->
<!--c:param name="id" value="${tree.study.id}" /-->
</c:url>
- <a href="http://www.phylowidget.org/full/?tree='http://<%=request.getServerName()%>:<%=request.getServerPort()%>${url}TB2:Tr${tree.id}'" target="myplwidget">Tr${tree.id}</a>
+ <script type="text/javascript">
+ function openPhylowidget(tree_id)
+ {
+ var realURL = "http://www.phylowidget.org/full/?tree='http://"+location.host+"${url}"+"TB2:Tr"+tree_id+"'";
+ window.open(realURL,'myplwidget')
+ }
+ </script>
+ <a href="javascript:void(0)" onClick="openPhylowidget(${tree.id}">Tr${tree.id}</a>
</display:column>
<display:column
@@ -123,7 +130,8 @@
<!--c:param name="treeid" value="${tree.id}" /-->
<!--c:param name="id" value="${tree.study.id}" /-->
</c:url>
- <a href="http://www.phylowidget.org/full/?tree='http://<%=request.getServerName()%>:<%=request.getServerPort()%>${url}TB2:Tr${tree.id}'" target="myplwidget">
+
+ <a href="javascript:void(0)" onClick="openPhylowidget(${tree.id}">
<img
class="iconButton"
src="<fmt:message key="icons.list"/>"
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp 2010-04-01 20:20:37 UTC (rev 664)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp 2010-04-01 21:05:13 UTC (rev 665)
@@ -5,6 +5,7 @@
<body id="trees"/ --%>
+
<display:table name="${resultSet.results}"
requestURI=""
class="list"
@@ -17,9 +18,17 @@
<c:url var="url" value="/tree_for_phylowidget/">
<!--c:param name="treeid" value="${tree.id}" /-->
<!--c:param name="id" value="${tree.study.id}" /-->
- </c:url>
+ </c:url>
+ <script type="text/javascript">
+ function openPhylowidget(tree_id)
+ {
+ var realURL = "http://www.phylowidget.org/full/?tree='http://"+location.host+"${url}"+"TB2:Tr"+tree_id+"'";
+ window.open(realURL,'myplwidget')
+ }
+
+ </script>
<input type="checkbox" id="s-${tree.id }" name="selection" value="${tree.id }" />
- <a href="http://www.phylowidget.org/full/?tree='http://<%=request.getServerName()%>:<%=request.getServerPort()%>${url}TB2:Tr${tree.id}'" target="myplwidget">Tr${tree.id}</a>
+ <a href="javascript:void(0)" onClick="openPhylowidget(${tree.id})">Tr${tree.id}</a>
</display:column>
@@ -85,7 +94,7 @@
<!--c:param name="treeid" value="${tree.id}" /-->
<!--c:param name="id" value="${tree.study.id}" /-->
</c:url>
- <a href="http://www.phylowidget.org/full/?tree='http://<%=request.getServerName()%>:<%=request.getServerPort()%>${url}TB2:Tr${tree.id}'" target="myplwidget">
+ <a href="javascript:void(0)" onClick="openPhylowidget(${tree.id})">
<img
class="iconButton"
src="<fmt:message key="icons.list"/>"
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <vga...@us...> - 2010-04-01 20:20:44
|
Revision: 664
http://treebase.svn.sourceforge.net/treebase/?rev=664&view=rev
Author: vgapeyev
Date: 2010-04-01 20:20:37 +0000 (Thu, 01 Apr 2010)
Log Message:
-----------
Introducing JNDI parameters (to be used in Tomcat config in treebase-web.xml)
PurlBase - instead of a compile-time parameter in treebase.properties; this fixes SF#2978838
SiteUrl - as requested recently, to support redirection to phylowidget.org
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/PhyloWSPath.java
trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
trunk/treebase-core/src/main/resources/treebase.properties
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnyObjectAsRDFController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchResultsAsRDFController.java
trunk/treebase-web/src/main/webapp/META-INF/context.xml.example
trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/PhyloWSPath.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/PhyloWSPath.java 2010-03-31 18:46:29 UTC (rev 663)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/PhyloWSPath.java 2010-04-01 20:20:37 UTC (rev 664)
@@ -24,13 +24,12 @@
}
/**
- * This method constructs a permanent url based on the
- * treebase.purl.domain property (as computed by TreebaseUtil.getPurlDomain()),
+ * Constructs a PURL, based on the base URL of the PURL service (looked up through JNDI)
* the phylows path and the namespaced GUID for the object.
- * @return the permanent url for the object
+ * @return the PURL for the object
*/
public URL getPurl () {
- StringBuilder sb = new StringBuilder(TreebaseUtil.getPurlDomain());
+ StringBuilder sb = new StringBuilder(TreebaseUtil.getPurlBase());
sb = getPath(sb).append(mNamespacedGUID.toString());
LOGGER.info(sb);
URL url = null;
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-03-31 18:46:29 UTC (rev 663)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-04-01 20:20:37 UTC (rev 664)
@@ -16,6 +16,9 @@
import java.util.Properties;
import java.util.TimeZone;
+import javax.naming.InitialContext;
+import javax.naming.NamingException;
+
import org.apache.log4j.Logger;
import org.cipres.treebase.domain.study.Citation;
import org.cipres.treebase.domain.study.Study;
@@ -40,7 +43,8 @@
public static final String LINESEP = System.getProperty("line.separator");
public static final int citationMaxLength = 5000;
private static final Logger LOGGER = Logger.getLogger(TreebaseUtil.class);
- private static String mPurlDomain;
+ private static String mPurlBase;
+ private static String mSiteUrl;
private TreebaseUtil() {
super();
@@ -435,7 +439,8 @@
*
* @return domain name
*/
- public static String getPurlDomain() {
+ /*--
+ public static String getPurlBase() {
if ( null == mPurlDomain ) {
Properties properties = new Properties();
try {
@@ -459,8 +464,54 @@
return mPurlDomain;
}
}
+*/
+
+ /**
+ * Returns the base URL of the PURL service associated with this Treebase instance,
+ * which can be used to construct full PURLs by suffixing with a PhyloWS command, e.g. "/study/TB2:S1925"
+ *
+ * @return the base URL of the PURL service
+ */
+ public static String getPurlBase() {
+ if (null != mPurlBase)
+ return mPurlBase;
+ else {
+ try {
+ mPurlBase = "http://DUMMY_PURL_BASE/";
+ InitialContext ic = new InitialContext();
+ mPurlBase = (String) ic.lookup("java:comp/env/tb2/PurlBase");
+ } catch (NamingException e) {
+ LOGGER.info("Failure looking up tb2/PurlBase via JNDI");
+ e.printStackTrace();
+ }
+ return mPurlBase;
+ }
+ }
+
/**
+ * Returns the base URL of this Treebase instance, by looking it up in Tomcat via JNDI.
+ *
+ * @return the base URL of of this Treebase instance
+ */
+ public static String getSiteUrl() {
+ if (null != mSiteUrl)
+ return mSiteUrl;
+ else {
+ try {
+ mSiteUrl = "http://DUMMY_SITE_URL/";
+ InitialContext ic = new InitialContext();
+ mSiteUrl = (String) ic.lookup("java:comp/env/tb2/SiteUrl");
+ } catch (NamingException e) {
+ LOGGER.info("Failure looking up tb2/SiteUrl via JNDI");
+ e.printStackTrace();
+ }
+ return mSiteUrl;
+ }
+ }
+
+
+ /**
* This method appends header information upon formatting to the nexus file.
*
* @param pStudy Study is needed to extract the citation information
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2010-03-31 18:46:29 UTC (rev 663)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2010-04-01 20:20:37 UTC (rev 664)
@@ -113,7 +113,7 @@
// This is called by child classes using super.getAnnotations()
// to get the common annotations out of the way
List<Annotation> annotations = new ArrayList<Annotation>();
- URI uri = URI.create(TreebaseUtil.getPurlDomain()+getPhyloWSPath());
+ URI uri = URI.create(TreebaseUtil.getPurlBase()+getPhyloWSPath());
annotations.add(new Annotation(Constants.OWLURI,"owl:sameAs",uri));
return annotations;
}
Modified: trunk/treebase-core/src/main/resources/treebase.properties
===================================================================
--- trunk/treebase-core/src/main/resources/treebase.properties 2010-03-31 18:46:29 UTC (rev 663)
+++ trunk/treebase-core/src/main/resources/treebase.properties 2010-04-01 20:20:37 UTC (rev 664)
@@ -1,3 +1,2 @@
#options are: NexusServiceMesquite | NexusServiceNCL
nexus.parser.impl=NexusServiceMesquite
-treebase.purl.domain=http://purl.org/phylo/treebase/phylows/
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java 2010-03-31 18:46:29 UTC (rev 663)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java 2010-04-01 20:20:37 UTC (rev 664)
@@ -49,7 +49,7 @@
// .append(':')
// .append(request.getServerPort())
// .append("/treebase-web/phylows/");
- properties.setProperty("nexml.uri.base", TreebaseUtil.getPurlDomain());
+ properties.setProperty("nexml.uri.base", TreebaseUtil.getPurlBase());
return properties;
}
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnyObjectAsRDFController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnyObjectAsRDFController.java 2010-03-31 18:46:29 UTC (rev 663)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnyObjectAsRDFController.java 2010-04-01 20:20:37 UTC (rev 664)
@@ -91,7 +91,7 @@
request.getSession().setAttribute("namespacedGUID", namespacedGUID.toString());
// <c:set var="baseURL" value="http://localhost:8080/treebase-web/PhyloWS"/>
// treebase.purl.domain=http://purl.org/phylo/treebase/phylows/
- request.getSession().setAttribute("baseURL", TreebaseUtil.getPurlDomain());
+ request.getSession().setAttribute("baseURL", TreebaseUtil.getPurlBase());
request.getSession().setAttribute("phyloWSPath", phyloWSPath);
return new ModelAndView("anyObjectAsRDF");
}
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchResultsAsRDFController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchResultsAsRDFController.java 2010-03-31 18:46:29 UTC (rev 663)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchResultsAsRDFController.java 2010-04-01 20:20:37 UTC (rev 664)
@@ -35,7 +35,7 @@
request.getSession().setAttribute("searchResultsThawed", searchResults);
request.getSession().setAttribute("recordSchema", request.getSession().getAttribute("recordSchema"));
request.getSession().setAttribute("format", "rss1");
- request.getSession().setAttribute("baseURL", TreebaseUtil.getPurlDomain());
+ request.getSession().setAttribute("baseURL", TreebaseUtil.getPurlBase());
request.getSession().setAttribute("phyloWSPath", phyloWSPath);
if ( null != request.getParameter("query") ) {
String query = request.getParameter("query");
Modified: trunk/treebase-web/src/main/webapp/META-INF/context.xml.example
===================================================================
--- trunk/treebase-web/src/main/webapp/META-INF/context.xml.example 2010-03-31 18:46:29 UTC (rev 663)
+++ trunk/treebase-web/src/main/webapp/META-INF/context.xml.example 2010-04-01 20:20:37 UTC (rev 664)
@@ -16,7 +16,7 @@
<Context reloadable="true">
- <Resource name="jdbc/TreebaseDB" auth="Container"
+ <Resource name="jdbc/TreebaseDB" auth="Container"
type="javax.sql.DataSource"
description="The JNDI DataSource for the Treebase postgres instance."
driverClassName="org.postgresql.Driver"
@@ -25,10 +25,18 @@
maxActive="20" maxIdle="10" maxWait="-1"
/>
- <Environment name="tb2/MesquiteFolder" value="/PATH/TO/YOUR/mesquite-2.01.tb"
+ <Environment name="tb2/MesquiteFolder" value="/PATH/TO/YOUR/mesquite-2.01.tb"
type="java.lang.String" override="false"
description="Absolute path to the directory where headless Mesquite is unpacked on the host system."/>
+ <Environment name="tb2/SiteUrl" value="http://YOUR-HOST/treebase-web/"
+ type="java.lang.String" override="false"
+ description="The base URL from which this Treebase instance is served."/>
+
+ <Environment name="tb2/PurlBase" value="http://purl.org/YOUR/PURL/DOMAIN/phylows/"
+ type="java.lang.String" override="false"
+ description="The base URL of a PURL service that redirects to this Treebase instance."/>
+
</Context>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2010-03-31 18:46:29 UTC (rev 663)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2010-04-01 20:20:37 UTC (rev 664)
@@ -1,3 +1,6 @@
+<%@page import="org.cipres.treebase.TreebaseUtil"%>
+<% String purlBase = TreebaseUtil.getPurlBase(); %>
+
<div class="gutter">
<h1>Journals</h1>
<p>In addition to providing a digital library, TreeBASE serves the
@@ -34,9 +37,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DEvolution"
+ href="<%=purlBase%>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
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3DEvolution
</a></p>
</td>
</tr>
@@ -52,9 +55,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22"
+ href="<%=purlBase%>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
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22
</a></p>
</td>
</tr>
@@ -70,9 +73,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22"
+ href="<%=purlBase%>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
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22
</a></p>
</td>
</tr>
@@ -88,9 +91,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22"
+ href="<%=purlBase%>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
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22
</a></p>
</td>
</tr>
@@ -101,9 +104,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycologia"
+ href="<%=purlBase%>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>
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3DMycologia</a>
</p>
</td>
</tr>
@@ -116,9 +119,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22"
+ href="<%=purlBase%>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>
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22</a>
</p>
</td>
</tr>
@@ -132,9 +135,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22"
+ href="<%=purlBase%>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>
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22</a></p>
</td>
</tr>
<tr>
@@ -146,9 +149,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycoscience"
+ href="<%=purlBase%>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>
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3DMycoscience</a></p>
</td>
</tr>
<tr>
@@ -158,9 +161,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycosphere"
+ href="<%=purlBase%>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>
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3DMycosphere</a></p>
</td>
</tr>
<tr>
@@ -173,9 +176,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22"
+ href="<%=purlBase%>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>
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22</a></p>
</td>
</tr>
<tr>
@@ -185,9 +188,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPersoonia"
+ href="<%=purlBase%>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>
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3DPersoonia</a></p>
</td>
</tr>
<tr>
@@ -203,9 +206,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPhytopahology"
+ href="<%=purlBase%>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>
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3DPhytopahology</a></p>
</td>
</tr>
<tr>
@@ -216,9 +219,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22"
+ href="<%=purlBase%>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>
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22</a></p>
</td>
</tr>
<tr>
@@ -229,9 +232,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DRhodora"
+ href="<%=purlBase%>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>
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3DRhodora</a></p>
</td>
</tr>
<tr>
@@ -243,9 +246,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMuelleria"
+ href="<%=purlBase%>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>
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3DMuelleria</a></p>
</td>
</tr>
<tr>
@@ -256,9 +259,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22"
+ href="<%=purlBase%>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>
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22</a></p>
</td>
</tr>
<tr>
@@ -269,9 +272,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22"
+ href="<%=purlBase%>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>
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22</a></p>
</td>
</tr>
<tr>
@@ -282,9 +285,9 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22"
+ href="<%=purlBase%>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>
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22</a></p>
</td>
</tr>
<tr>
@@ -295,56 +298,56 @@
</td>
<td>
<p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22"
+ href="<%=purlBase%>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>
+ <%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>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"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DZootaxa"
title="Zootaxa">Zootaxa</a></p>
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2010-03-31 18:46:29 UTC (rev 663)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2010-04-01 20:20:37 UTC (rev 664)
@@ -1,4 +1,7 @@
+<%@page import="org.cipres.treebase.TreebaseUtil"%>
+<% String purlBase = TreebaseUtil.getPurlBase(); %>
<%@ include file="/common/taglibs.jsp"%>
+
<head>
<title>Summary Information</title>
<content tag="heading">Summary for current study</content>
@@ -28,10 +31,10 @@
</a>
<br/>
<br/>
-<a href="<c:out value="http://purl.org/phylo/treebase/phylows/study/TB2:S"/><c:out value="${submission.study.id}"/>">
+<a href="<c:out value="${submission.study.phyloWSPath.purl}"/>">
<img class="iconButton" alt="link" src="<fmt:message key="icons.weblink"/>" />
Study Accession URL:<br/>
- <c:out value="http://purl.org/phylo/treebase/phylows/study/TB2:S"/><c:out value="${submission.study.id}"/>
+ <c:out value="${submission.study.phyloWSPath.purl}"/>
</a>
<div><strong>You can cite this URL in your manuscript. It will become the permanent and resolvable resource locator after your submission has been approved and the data are made public.</strong></div>
<br/>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp 2010-03-31 18:46:29 UTC (rev 663)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp 2010-04-01 20:20:37 UTC (rev 664)
@@ -1,3 +1,6 @@
+<%@page import="org.cipres.treebase.TreebaseUtil"%>
+<% String purlBase = TreebaseUtil.getPurlBase(); %>
+
<div class="gutter">
<h1>Data Access</h1>
<h2>Web Browser User Interface</h2>
@@ -41,11 +44,11 @@
</p>
<dl>
<dt>URI to a study</dt>
- <dd>http://purl.org/phylo/treebase/phylows/study/TB2:S1925</dd>
+ <dd><%=purlBase%>study/TB2:S1925</dd>
<dt>URI to a matrix</dt>
- <dd>http://purl.org/phylo/treebase/phylows/matrix/TB2:M2610</dd>
+ <dd><%=purlBase%>matrix/TB2:M2610</dd>
<dt>URI to a tree</dt>
- <dd>http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2026</dd>
+ <dd><%=purlBase%>tree/TB2:Tr2026</dd>
</dl>
<h2>RSS Feeds</h2>
<p>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2010-03-31 18:46:29 UTC (rev 663)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2010-04-01 20:20:37 UTC (rev 664)
@@ -54,8 +54,26 @@
<env-entry-name>tb2/MesquiteFolder</env-entry-name>
<env-entry-type>java.lang.String</env-entry-type>
</env-entry>
-
+
+ <env-entry>
+ <description>The base URL from which this Treebase instance is served.
+ Most likely, it has the form "http://your.server.xxx/treebase-web/".
+ Trailing slash is required.</description>
+ <env-entry-name>tb2/SiteUrl</env-entry-name>
+ <env-entry-type>java.lang.String</env-entry-type>
+ </env-entry>
+
+ <env-entry>
+ <description>The base URL of a PURL service that redirects to this Treebase instance.
+ The PURL service should resolve tb2/PurlBase value into something
+ like "http://your.server.xxx/..../treebase-web/phylows/",
+ which must be the valid PhyloWS URL of this Treebase instance.
+ Trailing slash is required.</description>
+ <env-entry-name>tb2/PurlBase</env-entry-name>
+ <env-entry-type>java.lang.String</env-entry-type>
+ </env-entry>
+
<!-- ========================================================== -->
<!-- List of Filters -->
<!-- ========================================================== -->
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2010-03-31 18:46:36
|
Revision: 663
http://treebase.svn.sourceforge.net/treebase/?rev=663&view=rev
Author: youjun
Date: 2010-03-31 18:46:29 +0000 (Wed, 31 Mar 2010)
Log Message:
-----------
bring in urlrewrite tool, re-direct "view tree" to phylowidget.org
Modified Paths:
--------------
trunk/treebase-web/pom.xml
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/WEB-INF/urlrewrite.xml
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2010-03-31 14:49:01 UTC (rev 662)
+++ trunk/treebase-web/pom.xml 2010-03-31 18:46:29 UTC (rev 663)
@@ -77,6 +77,10 @@
<name>NeXML Remote Repository</name>
<url>http://nexml-dev.nescent.org/.m2/repository/</url>
</repository>
+ <repository>
+ <id>org.tuckey.urlrewritefilter</id>
+ <url>http://repository.jboss.org/maven2/org/tuckey/urlrewritefilter/</url>
+ </repository>
</repositories>
@@ -316,6 +320,11 @@
<version>1.0</version>
</dependency>
+ <dependency>
+ <groupId>org.tuckey</groupId>
+ <artifactId>urlrewritefilter</artifactId>
+ <version>3.0.4</version>
+ </dependency>
</dependencies>
</project>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp 2010-03-31 14:49:01 UTC (rev 662)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp 2010-03-31 18:46:29 UTC (rev 663)
@@ -19,11 +19,11 @@
export="false">
<display:column sortable="false" title="ID">
- <c:url var="treeURL" value="tree.html">
- <c:param name="id" value="${study.id}" />
- <c:param name="treeid" value="${tree.id}" />
- </c:url>
- <a href="javascript:popupWithSizes('${treeURL}',1000,900,'1')">Tr${tree.id}</a>
+ <c:url var="url" value="/tree_for_phylowidget/">
+ <!--c:param name="treeid" value="${tree.id}" /-->
+ <!--c:param name="id" value="${tree.study.id}" /-->
+ </c:url>
+ <a href="http://www.phylowidget.org/full/?tree='http://<%=request.getServerName()%>:<%=request.getServerPort()%>${url}TB2:Tr${tree.id}'" target="myplwidget">Tr${tree.id}</a>
</display:column>
<display:column
@@ -119,11 +119,11 @@
sortable="false"
class="iconColumn"
headerClass="iconColumn">
- <c:url var="treeURL" value="tree.html">
- <c:param name="id" value="${study.id}" />
- <c:param name="treeid" value="${tree.id}" />
- </c:url>
- <a href="javascript:popupWithSizes('${treeURL}',1000,900,'1')">
+ <c:url var="url" value="/tree_for_phylowidget/">
+ <!--c:param name="treeid" value="${tree.id}" /-->
+ <!--c:param name="id" value="${tree.study.id}" /-->
+ </c:url>
+ <a href="http://www.phylowidget.org/full/?tree='http://<%=request.getServerName()%>:<%=request.getServerPort()%>${url}TB2:Tr${tree.id}'" target="myplwidget">
<img
class="iconButton"
src="<fmt:message key="icons.list"/>"
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp 2010-03-31 14:49:01 UTC (rev 662)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp 2010-03-31 18:46:29 UTC (rev 663)
@@ -14,12 +14,12 @@
export = "false">
<display:column title="" sortable="true" class="checkBoxColumn">
- <c:url var="url" value="study/tree.html">
- <c:param name="treeid" value="${tree.id}" />
- <c:param name="id" value="${tree.study.id}" />
+ <c:url var="url" value="/tree_for_phylowidget/">
+ <!--c:param name="treeid" value="${tree.id}" /-->
+ <!--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}" target="myplwidget">Tr${tree.id}</a>
+ <a href="http://www.phylowidget.org/full/?tree='http://<%=request.getServerName()%>:<%=request.getServerPort()%>${url}TB2:Tr${tree.id}'" target="myplwidget">Tr${tree.id}</a>
</display:column>
@@ -81,11 +81,11 @@
sortable="false"
class="iconColumn"
headerClass="iconColumn">
- <c:url var="url" value="study/tree.html">
- <c:param name="treeid" value="${tree.id}" />
- <c:param name="id" value="${tree.study.id}" />
+ <c:url var="url" value="/tree_for_phylowidget/">
+ <!--c:param name="treeid" value="${tree.id}" /-->
+ <!--c:param name="id" value="${tree.study.id}" /-->
</c:url>
- <a href="${url}" target="myplwidget">
+ <a href="http://www.phylowidget.org/full/?tree='http://<%=request.getServerName()%>:<%=request.getServerPort()%>${url}TB2:Tr${tree.id}'" target="myplwidget">
<img
class="iconButton"
src="<fmt:message key="icons.list"/>"
Added: trunk/treebase-web/src/main/webapp/WEB-INF/urlrewrite.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/urlrewrite.xml (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/urlrewrite.xml 2010-03-31 18:46:29 UTC (rev 663)
@@ -0,0 +1,97 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE urlrewrite PUBLIC "-//tuckey.org//DTD UrlRewrite 3.2//EN"
+ "http://tuckey.org/res/dtds/urlrewrite3.2.dtd">
+
+<!--
+
+ Configuration file for UrlRewriteFilter
+ http://tuckey.org/urlrewrite/
+
+-->
+<urlrewrite>
+
+ <rule>
+ <note>
+ The rule means that requests to /test/status/ will be redirected to /rewrite-status
+ the url will be rewritten.
+ </note>
+ <from>/tree_for_phylowidget/(.*)</from>
+ <to>/phylows/tree/$1?format=nexus</to>
+ </rule>
+
+ <!--
+ <outbound-rule>
+ <note>
+ The outbound-rule specifies that when response.encodeURL is called (if you are using JSTL c:url)
+ the url /rewrite-status will be rewritten to /test/status/.
+
+ The above rule and this outbound-rule means that end users should never see the
+ url /rewrite-status only /test/status/ both in thier location bar and in hyperlinks
+ in your pages.
+ </note>
+ <from>/rewrite-status</from>
+ <to>/test/status/</to>
+ </outbound-rule>
+ -->
+
+ <!--
+
+ INSTALLATION
+
+ in your web.xml add...
+
+ <filter>
+ <filter-name>UrlRewriteFilter</filter-name>
+ <filter-class>org.tuckey.web.filters.urlrewrite.UrlRewriteFilter</filter-class>
+ <init-param>
+ <param-name>logLevel</param-name>
+ <param-value>WARN</param-value>
+ </init-param>
+ </filter>
+ <filter-mapping>
+ <filter-name>UrlRewriteFilter</filter-name>
+ <url-pattern>/*</url-pattern>
+ </filter-mapping>
+
+ EXAMPLES
+
+ Redirect one url
+ <rule>
+ <from>/some/old/page.html</from>
+ <to type="redirect">/very/new/page.html</to>
+ </rule>
+
+ Redirect a directory
+ <rule>
+ <from>/some/olddir/(.*)</from>
+ <to type="redirect">/very/newdir/$1</to>
+ </rule>
+
+ Clean a url
+ <rule>
+ <from>/products/([0-9]+)</from>
+ <to>/products/index.jsp?product_id=$1</to>
+ </rule>
+ eg, /products/1234 will be passed on to /products/index.jsp?product_id=1234 without the user noticing.
+
+ Browser detection
+ <rule>
+ <condition name="user-agent">Mozilla/[1-4]</condition>
+ <from>/some/page.html</from>
+ <to>/some/page-for-old-browsers.html</to>
+ </rule>
+ eg, will pass the request for /some/page.html on to /some/page-for-old-browsers.html only for older
+ browsers whose user agent srtings match Mozilla/1, Mozilla/2, Mozilla/3 or Mozilla/4.
+
+ Centralised browser detection
+ <rule>
+ <condition name="user-agent">Mozilla/[1-4]</condition>
+ <set type="request" name="browser">moz</set>
+ </rule>
+ eg, all requests will be checked against the condition and if matched
+ request.setAttribute("browser", "moz") will be called.
+
+ -->
+
+</urlrewrite>
+
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2010-03-31 14:49:01 UTC (rev 662)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2010-03-31 18:46:29 UTC (rev 663)
@@ -85,8 +85,12 @@
<filter-class>org.displaytag.filter.ResponseOverrideFilter</filter-class>
</filter>
-
-
+ <filter>
+ <filter-name>UrlRewriteFilter</filter-name>
+ <filter-class>org.tuckey.web.filters.urlrewrite.UrlRewriteFilter</filter-class>
+ </filter>
+
+
<!-- ========================================================== -->
<!-- Mappings for Filters defined aboved -->
@@ -114,8 +118,13 @@
<filter-name>ResponseOverrideFilter</filter-name>
<url-pattern>*.html</url-pattern>
</filter-mapping>
+
+ <filter-mapping>
+ <filter-name>UrlRewriteFilter</filter-name>
+ <url-pattern>/*</url-pattern>
+ </filter-mapping>
-
+
<!-- ========================================================== -->
<!-- define the listener -->
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From: SourceForge.net <no...@so...> - 2010-03-31 17:39:34
|
Bugs item #2978838, was opened at 2010-03-29 17:19 Message generated for change (Comment added) made by vgapeyev You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2978838&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: internals Group: None Status: Open Priority: 8 Private: No Submitted By: Vladimir Gapeyev (vgapeyev) Assigned to: Vladimir Gapeyev (vgapeyev) Summary: Move PURL prefix value from build to Tomcat config Initial Comment: Currently, the value of a PURL prefix is specified at compile time in the source code. Instead, it should come at run time as a parameter from Tomcat, e.g., should be specified as a JNDI parameter in treebase-web.xml config file in Tomcat. Fixing this is essential for restoring proper functionality of the development instance (and any other non-production instance). Make sure to modify installation instructions on the wiki: mention the need to set up a PURL account and define purl redirection there. ---------------------------------------------------------------------- Comment By: Vladimir Gapeyev (vgapeyev) Date: 2010-03-31 13:39 Message: On Mar 19, 2010, at 10:34 AM, Hilmar Lapp wrote: I created the following alternative base URLs, with obvious redirection: http://purl.org/phylo/treebase/dev/phylows/ http://purl.org/phylo/treebase/stage/phylows/ ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2978838&group_id=248804 |
|
From: <vga...@us...> - 2010-03-31 14:49:07
|
Revision: 662
http://treebase.svn.sourceforge.net/treebase/?rev=662&view=rev
Author: vgapeyev
Date: 2010-03-31 14:49:01 +0000 (Wed, 31 Mar 2010)
Log Message:
-----------
Fixed a typo in a log message.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java 2010-03-31 13:54:49 UTC (rev 661)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java 2010-03-31 14:49:01 UTC (rev 662)
@@ -132,7 +132,7 @@
InitialContext ic = new InitialContext();
mJndiMesquiteFolder = (String) ic.lookup("java:comp/env/tb2/MesquiteFolder");
} catch (NamingException e) {
- LOGGER.info("Failure looking up tb/MesquiteFolder via JNDI");
+ LOGGER.info("Failure looking up tb2/MesquiteFolder via JNDI");
}
String mesquiteFolder;
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|
From: <vga...@us...> - 2010-03-31 13:54:57
|
Revision: 661
http://treebase.svn.sourceforge.net/treebase/?rev=661&view=rev
Author: vgapeyev
Date: 2010-03-31 13:54:49 +0000 (Wed, 31 Mar 2010)
Log Message:
-----------
Putting the date on the last pre-release data cleaning patch.
Modified Paths:
--------------
trunk/treebase-core/db/cleaning/2010-03-20_pre-release_hotfixes/README.txt
Added Paths:
-----------
trunk/treebase-core/db/cleaning/2010-03-20_pre-release_hotfixes/
Removed Paths:
-------------
trunk/treebase-core/db/cleaning/pre-release_hotfixes/
Modified: trunk/treebase-core/db/cleaning/2010-03-20_pre-release_hotfixes/README.txt
===================================================================
--- trunk/treebase-core/db/cleaning/pre-release_hotfixes/README.txt 2010-03-19 21:44:13 UTC (rev 630)
+++ trunk/treebase-core/db/cleaning/2010-03-20_pre-release_hotfixes/README.txt 2010-03-31 13:54:49 UTC (rev 661)
@@ -2,6 +2,7 @@
detects TaxonLabelSets whose study_id still refers to a dummy study used for loading from TB1 dumps
and updates it to the proper real study.
+This was applied to the production DB at treebase.nescent.org by Jon on 2010-03-20.
=============================================================
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|
|
From: <yo...@us...> - 2010-03-30 15:54:56
|
Revision: 660
http://treebase.svn.sourceforge.net/treebase/?rev=660&view=rev
Author: youjun
Date: 2010-03-30 15:54:49 +0000 (Tue, 30 Mar 2010)
Log Message:
-----------
clean taxonlabels after delete a tree
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/tree/PhyloTreeDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/tree/PhyloTreeDAO.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/tree/PhyloTreeDAO.java 2010-03-29 19:34:59 UTC (rev 659)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/tree/PhyloTreeDAO.java 2010-03-30 15:54:49 UTC (rev 660)
@@ -18,6 +18,7 @@
import org.cipres.treebase.domain.study.SubmissionHome;
import org.cipres.treebase.domain.taxon.TaxonLabel;
import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
import org.cipres.treebase.domain.taxon.TaxonVariant;
import org.cipres.treebase.domain.tree.PhyloTree;
import org.cipres.treebase.domain.tree.PhyloTreeHome;
@@ -124,7 +125,9 @@
block.removePhyloTree(pTree);
if (block.isEmpty()) {
+ TaxonLabelSet tSet=block.getTaxonLabelSet();
deleteTreeBlock(block);
+ getTaxonLabelHome().clean(tSet);
}
}
@@ -149,16 +152,18 @@
// getHibernateTemplate().delete(data);
}
-
+
+ Set<TaxonLabel> tSet=pTree.getAllTaxonLabels();
// Delete by direct JDBC:
// * Tree nodes
// ** for each tree node, node attribute.
// ** (TODO) NodeEdge
- PhyloTreeJDBC.deletePhyloTreeNodeSQL(pTree, getSession());
+ //PhyloTreeJDBC.deletePhyloTreeNodeSQL(pTree, getSession());
// cascade delete by hibernate:
// * tree atrribute
getHibernateTemplate().delete(pTree);
+ getTaxonLabelHome().clean(new ArrayList<TaxonLabel>(tSet));
}
/**
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2010-03-29 19:34:59 UTC (rev 659)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2010-03-30 15:54:49 UTC (rev 660)
@@ -1,6 +1,7 @@
package org.cipres.treebase.domain.taxon;
import java.net.URI;
+import java.util.Collections;
import java.util.List;
import java.util.Set;
@@ -30,6 +31,7 @@
import org.hibernate.annotations.Fetch;
import org.hibernate.annotations.FetchMode;
import org.hibernate.annotations.Index;
+import org.hibernate.annotations.IndexColumn;
/**
* TaxonLabel usually associates with one Taxon. If it does not, it usually means the referred
@@ -57,7 +59,7 @@
private TaxonVariant mTaxonVariant;
private Study mStudy;
private Submission mSubmission;
-
+ private Set<TaxonLabelSet> mTaxonLabelSet;
/**
* Constructor.
*/
@@ -207,8 +209,28 @@
}
return null;
}
+
+ /**
+ * Return the TaxonLabelSet field.
+ *
+ * @return List<PhyloTaxonLabel>
+ */
+ @ManyToMany(cascade = {CascadeType.MERGE, CascadeType.PERSIST, CascadeType.REFRESH})
+ @JoinTable(name = "TaxonLabelSET_TaxonLabel", joinColumns = {@JoinColumn(name = "TaxonLabel_ID")}, inverseJoinColumns = @JoinColumn(name = "TaxonLabelSet_ID"))
+ protected Set<TaxonLabelSet> getTaxonLabelSet() {
+ return mTaxonLabelSet;
+ }
+
/**
+ * Set the TaxonLabelSet field.
+ */
+ protected void setTaxonLabelSet(Set<TaxonLabelSet> pTaxonLabelSet) {
+ mTaxonLabelSet = pTaxonLabelSet;
+ }
+
+
+ /**
* Return the taxon name if it available.
*/
@Transient
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2010-03-29 19:34:59 UTC (rev 659)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2010-03-30 15:54:49 UTC (rev 660)
@@ -407,7 +407,7 @@
* @return Set<TreeNode>
*/
//@OneToMany(mappedBy = "tree", cascade = {CascadeType.MERGE, CascadeType.PERSIST}, fetch = FetchType.LAZY)
- @OneToMany(mappedBy = "tree", cascade = {CascadeType.MERGE, CascadeType.PERSIST})
+ @OneToMany(mappedBy = "tree", cascade = {CascadeType.ALL})
//@Fetch(FetchMode.SUBSELECT)
@Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE, region = "treeCache")
//@Loader(namedQuery="loadNodes")
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|
From: SourceForge.net <no...@so...> - 2010-03-30 13:26:54
|
Bugs item #2978845, was opened at 2010-03-29 17:35 Message generated for change (Comment added) made by vgapeyev You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2978845&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: internals Group: None Status: Open Priority: 8 Private: No Submitted By: Vladimir Gapeyev (vgapeyev) Assigned to: Nobody/Anonymous (nobody) Summary: Timestamps on builds Initial Comment: (Some?) pages of the treebase-dev site should contain a timestamp of the build (ex. Version: 2.2.1 Built: 03/26/2010 12:43 PM ), as an indication what version is being run on a given instance. Ideally, this should include source code version from SVN. To make the timestamp invisible on production, there are a couple options: - Put it inside an <!-- --> HTML comment. - Make it's JSP rendering conditional depending on the value of the parameter like amIProduction that comes from Tomcat via JNDI. ---------------------------------------------------------------------- Comment By: Vladimir Gapeyev (vgapeyev) Date: 2010-03-30 09:26 Message: From: rut...@gm... Subject: Re: [Treebase-devel] Is TreeBASE down? Date: March 29, 2010 6:00:48 PM EDT To: vla...@du... Cc: tre...@li... If you look in the html source of any page and you scroll all the way down to 'p class="footerLogo"' it will show the SVN revision of that deployment. At least, this used to work back when MJD and I were using the 'publish' script, which used ${TREEBASE_HOME}/treebase-core/src/main/java/org/cipres/treebase/Version.java as a little servlet to embed the SVN revision in the footer.jsp (this is done by deleting and then updating this version file). Perhaps this can be re-instated? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2978845&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-03-30 10:29:51
|
Bugs item #2977247, was opened at 2010-03-26 16:01 Message generated for change (Settings changed) made by youjun You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2977247&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: Zoom and hand tools missing for PhyloWidget in search side Initial Comment: The new fix for PhyloWidget on the search side (ie without the "Save to Database") seems to be missing the arrow, hand, and magnifying glass tools which allow the user to explore the tree. This needs to be added back in. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2977247&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-03-29 21:35:10
|
Bugs item #2978845, was opened at 2010-03-29 17:35 Message generated for change (Tracker Item Submitted) made by vgapeyev You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2978845&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: internals Group: None Status: Open Priority: 8 Private: No Submitted By: Vladimir Gapeyev (vgapeyev) Assigned to: Nobody/Anonymous (nobody) Summary: Timestamps on builds Initial Comment: (Some?) pages of the treebase-dev site should contain a timestamp of the build (ex. Version: 2.2.1 Built: 03/26/2010 12:43 PM ), as an indication what version is being run on a given instance. Ideally, this should include source code version from SVN. To make the timestamp invisible on production, there are a couple options: - Put it inside an <!-- --> HTML comment. - Make it's JSP rendering conditional depending on the value of the parameter like amIProduction that comes from Tomcat via JNDI. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2978845&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-03-29 21:24:45
|
Bugs item #2978840, was opened at 2010-03-29 17:24 Message generated for change (Tracker Item Submitted) made by vgapeyev You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2978840&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: internals Group: None Status: Open Priority: 8 Private: No Submitted By: Vladimir Gapeyev (vgapeyev) Assigned to: Vladimir Gapeyev (vgapeyev) Summary: Set up a build server at treebase-dev.nescent.org Initial Comment: A new SVN check in should initiate an automated build and deployment on treebase-dev. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2978840&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-03-29 21:19:57
|
Bugs item #2978838, was opened at 2010-03-29 17:19 Message generated for change (Tracker Item Submitted) made by vgapeyev You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2978838&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: internals Group: None Status: Open Priority: 8 Private: No Submitted By: Vladimir Gapeyev (vgapeyev) Assigned to: Vladimir Gapeyev (vgapeyev) Summary: Move PURL prefix value from build to Tomcat config Initial Comment: Currently, the value of a PURL prefix is specified at compile time in the source code. Instead, it should come at run time as a parameter from Tomcat, e.g., should be specified as a JNDI parameter in treebase-web.xml config file in Tomcat. Fixing this is essential for restoring proper functionality of the development instance (and any other non-production instance). Make sure to modify installation instructions on the wiki: mention the need to set up a PURL account and define purl redirection there. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2978838&group_id=248804 |
|
From: <yo...@us...> - 2010-03-29 19:35:09
|
Revision: 659
http://treebase.svn.sourceforge.net/treebase/?rev=659&view=rev
Author: youjun
Date: 2010-03-29 19:34:59 +0000 (Mon, 29 Mar 2010)
Log Message:
-----------
fix delete matrix, fix limitedphylowidget zooming tool
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/MatrixDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelHome.java
trunk/treebase-core/src/main/resources/applicationContext-dao.xml
trunk/treebase-phylowidget/build.properties
trunk/treebase-web/src/main/resources/ApplicationResources.properties
trunk/treebase-web/src/main/webapp/test/phylowidget/PhyloWidget.jar
Added Paths:
-----------
trunk/treebase-phylowidget/data/menus/limited-menus.xml
Removed Paths:
-------------
trunk/treebase-phylowidget/data/menus/nondb-menus.xml
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java 2010-03-29 19:34:59 UTC (rev 659)
@@ -124,6 +124,28 @@
}
/**
+ * Delete all rows and associated objects using direct SQL.
+ *
+ * @param pMatrix
+ * @param pSession
+ */
+ public static void deleteMatrixRowSQL(CharacterMatrix pMatrix, Session pSession) {
+ // delete all matrix rows by direct JDBC:
+ // * delete all row segments
+ // * delete all rows
+
+ String query = "DELETE FROM ROWSEGMENT WHERE MATRIXROW_ID in (select row.MATRIXROW_ID from MATRIXROW row where row.MATRIX_ID = :matrixID)";
+ Query q = pSession.createSQLQuery(query);
+ q.setParameter("matrixID", pMatrix.getId());
+ q.executeUpdate();
+
+ query = "DELETE FROM MATRIXROW WHERE MATRIX_ID = :matrixID";
+ q = pSession.createSQLQuery(query);
+ q.setParameter("matrixID", pMatrix.getId());
+ q.executeUpdate();
+
+ }
+ /**
* Delete all elements and associated objects in a matrix using direct SQL.
*
* @param pTree
@@ -153,8 +175,8 @@
q.setParameter("matrixID", pMatrix.getId());
q.executeUpdate();
- query = "delete from matrixelement where matrixelement_id IN "
- + "(select m.matrixelement_id from matrixelement m, MATRIXCOLUMN c where m.MATRIXCOLUMN_ID = c.MATRIXCOLUMN_ID and c.MATRIX_ID = :matrixID)";
+ query = "DELETE FROM matrixelement WHERE matrixcolumn_id IN"
+ + "(SELECT c.matrixcolumn_id FROM matrixcolumn c WHERE c.matrix_id = :matrixID)";
q = pSession.createSQLQuery(query);
q.setParameter("matrixID", pMatrix.getId());
q.executeUpdate();
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/MatrixDAO.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/MatrixDAO.java 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/MatrixDAO.java 2010-03-29 19:34:59 UTC (rev 659)
@@ -28,6 +28,9 @@
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.study.Submission;
import org.cipres.treebase.domain.study.SubmissionHome;
+import org.cipres.treebase.domain.taxon.TaxonLabel;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
import org.apache.log4j.Logger;
import org.hibernate.Criteria;
@@ -50,7 +53,8 @@
private MatrixRowHome mMatrixRowHome;
private SubmissionHome mSubmissionHome;
private AnalyzedDataHome mAnalyzedDataHome;
-
+ private TaxonLabelHome mTaxonLabelHome;
+
/**
* Constructor.
*/
@@ -107,6 +111,25 @@
}
/**
+ * set the TaxonLabelHome field.
+ */
+ public void setTaxonLabelHome(TaxonLabelHome pNewTaxonLabelHome) {
+ mTaxonLabelHome = pNewTaxonLabelHome;
+ }
+
+ /**
+ * Return the TaxonLabelHome field.
+ *
+ *
+ * @return TaxonLabelHome mTaxonLabelHome
+ */
+ private TaxonLabelHome getTaxonLabelHome() {
+ return mTaxonLabelHome;
+ }
+
+
+
+ /**
* Return the SubmissionHome field.
*
* @return SubmissionHome mSubmissionHome
@@ -138,6 +161,35 @@
/**
*
+ * @see org.cipres.treebase.domain.matrix.MatrixHome#cascadeDelete(org.cipres.treebase.domain.matrix.CharacterMatrix)
+ */
+ public void cascadeDelete(CharacterMatrix pMatrix) {
+
+ // bi-directional relationships:
+ // * delete submission-> matrix
+ // * delete analyzedData -> matrix
+ Submission sub = getSubmissionHome().findByMatrix(pMatrix);
+ if (sub != null) {
+ sub.removeMatrix(pMatrix);
+ }
+
+ Collection<AnalyzedData> dataLink = getAnalyzedDataHome().findByMatrix(pMatrix);
+ for (AnalyzedData data : dataLink) {
+ data.getAnalysisStep().removeAnalyzedData(data);
+ }
+
+ TaxonLabelSet tSet = pMatrix.getTaxa();
+ List<TaxonLabel> tList = pMatrix.getAllTaxonLabels();
+
+ getHibernateTemplate().delete(pMatrix);
+
+ getTaxonLabelHome().clean(tSet);
+ getTaxonLabelHome().clean(tList);
+
+ }
+
+ /**
+ *
* @see org.cipres.treebase.domain.matrix.MatrixHome#delete(org.cipres.treebase.domain.matrix.Matrix)
*/
public void delete(Matrix pMatrix) {
@@ -145,21 +197,8 @@
// Use double dispatch.
pMatrix.cascadeDelete(this);
-
- // bi-directional relationships:
- // * delete submission-> matrix
- // * delete analyzedData -> matrix
- Submission sub = getSubmissionHome().findByMatrix(pMatrix);
- if (sub != null) {
- sub.removeMatrix(pMatrix);
- }
-
- Collection<AnalyzedData> dataLink = getAnalyzedDataHome().findByMatrix(pMatrix);
- for (AnalyzedData data : dataLink) {
- data.getAnalysisStep().removeAnalyzedData(data);
- }
-
- getHibernateTemplate().delete(pMatrix);
+
+
}
}
@@ -184,8 +223,17 @@
getMatrixRowHome().deleteRows(pRows);
}
+
/**
*
+ * @see org.cipres.treebase.domain.matrix.MatrixHome#cascadeDeleteRows(java.util.Collection)
+ */
+ public void cascadeDeleteRows(CharacterMatrix pMatrix) {
+ MatrixJDBC.deleteMatrixRowSQL(pMatrix,getSession());
+ }
+
+ /**
+ *
* @see org.cipres.treebase.domain.matrix.MatrixHome#cascadeDeleteAncStateSet(java.util.Set)
*/
public void cascadeDeleteAncStateSet(Set<AncStateSet> pAncStateSets) {
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 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-03-29 19:34:59 UTC (rev 659)
@@ -466,12 +466,12 @@
Query q = getSession()
.createQuery("select count(*) from TreeBlock tb where tb.taxonLabelSet = :ts");
q.setParameter("ts", tSet);
- int count=((Integer)q.iterate().next()).intValue();
+ int count=((Long)q.iterate().next()).intValue();
q = getSession()
.createQuery("select count(*) from Matrix m where m.taxa = :ts");
q.setParameter("ts", tSet);
- count += ((Integer)q.iterate().next()).intValue();
+ count += ((Long)q.iterate().next()).intValue();
if(count==0)deletePersist(tSet);
}
@@ -482,12 +482,12 @@
Query q = getSession()
.createQuery("select count(*) from PhyloTreeNode pn where pn.taxonLabel = :tl");
q.setParameter("tl", tl);
- int count=((Integer)q.iterate().next()).intValue();
+ int count=((Long)q.iterate().next()).intValue();
q = getSession()
.createQuery("select count(*) from MatrixRow mr where mr.taxonLabel = :tl");
q.setParameter("tl", tl);
- count += ((Integer)q.iterate().next()).intValue();
+ count += ((Long)q.iterate().next()).intValue();
if(count==0)deletePersist(tl);
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java 2010-03-29 19:34:59 UTC (rev 659)
@@ -83,7 +83,7 @@
*
* @return CodonPositionSet
*/
- @OneToOne(cascade = {CascadeType.PERSIST, CascadeType.MERGE})
+ @OneToOne(cascade = {CascadeType.ALL})
@JoinColumn(name = "CODONPOSITIONSET_ID", nullable = true)
public CodonPositionSet getDefaultCodonPosSet() {
return mDefaultCodonPosSet;
@@ -111,7 +111,7 @@
*
* @return CharWeightSet
*/
- @OneToOne(cascade = {CascadeType.PERSIST, CascadeType.MERGE})
+ @OneToOne(cascade = {CascadeType.ALL})
@JoinColumn(name = "CHARWEIGHTSET_ID", nullable = true)
public CharWeightSet getDefaultWeightSet() {
return mDefaultWeightSet;
@@ -139,7 +139,7 @@
*
* @return ExcludedCharSet
*/
- @OneToOne(cascade = {CascadeType.PERSIST, CascadeType.MERGE})
+ @OneToOne(cascade = {CascadeType.ALL})
@JoinColumn(name = "CHARSET_ID", nullable = true)
public ExcludedCharSet getDefaultExcludedSet() {
return mDefaultExcludedSet;
@@ -167,7 +167,7 @@
*
* @return TypeSet mDefaultTypeSet
*/
- @OneToOne(cascade = {CascadeType.PERSIST, CascadeType.MERGE})
+ @OneToOne(cascade = {CascadeType.ALL})
@JoinColumn(name = "TYPESET_ID", nullable = true)
public TypeSet getDefaultTypeSet() {
return mDefaultTypeSet;
@@ -332,7 +332,7 @@
*
* @return AncStateSet
*/
- @OneToOne(cascade = {CascadeType.PERSIST, CascadeType.MERGE})
+ @OneToOne(cascade = {CascadeType.ALL})
@JoinColumn(name = "ANCSTATESET_ID", nullable = true)
public AncStateSet getDefaultAncSet() {
return mDefaultAncSet;
@@ -358,7 +358,7 @@
//@OneToMany(cascade = CascadeType.ALL)
// no cascade merge since we do not modify a column ?? Need test.
//@OneToMany(cascade = {CascadeType.PERSIST, CascadeType.REMOVE})
- @OneToMany
+ @OneToMany(cascade = {CascadeType.ALL})
@JoinColumn(name = "MATRIX_ID")
@IndexColumn(name = "COLUMN_ORDER")
@Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE, region = "matrixCache")
@@ -445,10 +445,10 @@
// private Set<CodonPositionSet> mCodonPosSets;
// private Set<GeneticCodeSet> mCodeSets;
// private Set<TypeSet> mTypeSets;
-
- pMatrixHome.cascadeDeleteElements(this);
- pMatrixHome.cascadeDeleteRows(getRows());
- pMatrixHome.cascadeDeleteColumns(this);
+ pMatrixHome.cascadeDelete(this);
+ //pMatrixHome.cascadeDeleteElements(this);
+ //pMatrixHome.cascadeDeleteRows(this);
+ //pMatrixHome.cascadeDeleteColumns(this);
// pMatrixHome.cascadeDeleteAncStateSet(getAncStateSets());
// pMatrixHome.cascadeDeleteCharWeightSet(getWeightSets());
@@ -508,7 +508,7 @@
// the one side has to be the owner side, cannot use "mappedby"
// also need to duplicate specify the JoinColumn here.
// @OneToMany(mappedBy = "matrix", cascade = CascadeType.ALL)
- @OneToMany(cascade = {CascadeType.MERGE, CascadeType.PERSIST})
+ @OneToMany(cascade = {CascadeType.ALL})
@JoinColumn(name = "MATRIX_ID")
@IndexColumn(name = "ROW_ORDER")
@Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE, region = "matrixCache")
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixHome.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixHome.java 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixHome.java 2010-03-29 19:34:59 UTC (rev 659)
@@ -55,14 +55,14 @@
* @param pMatrix
*/
void cascadeDeleteColumns(CharacterMatrix pMatrix);
-
+ void cascadeDelete(CharacterMatrix pMatrix);
/**
* Delete a collection of matrix rows.
*
* @param pRows
*/
void cascadeDeleteRows(Collection<MatrixRow> pRows);
-
+ void cascadeDeleteRows(CharacterMatrix pMatrix);
/**
* Delete a collection of ancestral state sets.
*
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2010-03-29 19:34:59 UTC (rev 659)
@@ -10,6 +10,8 @@
import javax.persistence.Entity;
import javax.persistence.FetchType;
import javax.persistence.JoinColumn;
+import javax.persistence.JoinTable;
+import javax.persistence.ManyToMany;
import javax.persistence.ManyToOne;
import javax.persistence.Table;
import javax.persistence.Transient;
@@ -54,6 +56,7 @@
private TaxonVariant mTaxonVariant;
private Study mStudy;
+ private Submission mSubmission;
/**
* Constructor.
@@ -173,14 +176,28 @@
*
* @return the submission
* @author mjd 20080929
+ * modified by Youjun
*/
- @Transient
+ @ManyToOne(cascade = {CascadeType.MERGE, CascadeType.PERSIST, CascadeType.REFRESH})
+ @JoinTable(name = "sub_taxonlabel",
+ joinColumns = @JoinColumn(name = "taxonlabel_id"),
+ inverseJoinColumns = @JoinColumn(name="submission_id")
+
+ )
public Submission getSubmission() {
- Study s = getStudy();
- return s == null ? null : s.getSubmission();
+
+ return mSubmission;
}
/**
+ * Set the Submission field.
+ */
+ public void setSubmission(Submission pNewSubmission) {
+ mSubmission = pNewSubmission;
+ }
+
+
+ /**
* Return the taxon name if it available.
*/
@Transient
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelHome.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelHome.java 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelHome.java 2010-03-29 19:34:59 UTC (rev 659)
@@ -2,6 +2,7 @@
package org.cipres.treebase.domain.taxon;
import java.util.Collection;
+import java.util.List;
import java.util.Set;
import org.cipres.treebase.domain.DomainHome;
@@ -229,4 +230,15 @@
* @return All taxonlabelsets of which this taxonlabel is a member
*/
Set<TaxonLabelSet> findTaxonLabelSets(TaxonLabel tl);
+
+ /**
+ * clean orphan record @ TaxonLabelSet
+ */
+ public void clean(TaxonLabelSet tSet);
+
+ /**
+ * clean orphan record @ TaxonLabel
+ */
+ public void clean(List<TaxonLabel> tList);
+
}
Modified: trunk/treebase-core/src/main/resources/applicationContext-dao.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-dao.xml 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/resources/applicationContext-dao.xml 2010-03-29 19:34:59 UTC (rev 659)
@@ -173,6 +173,7 @@
<property name="matrixRowHome" ref="matrixRowHome" />
<property name="submissionHome" ref="submissionHome" />
<property name="analyzedDataHome" ref="analyzedDataHome" />
+ <property name="taxonLabelHome" ref="taxonLabelHome" />
</bean>
</property>
</bean>
Modified: trunk/treebase-phylowidget/build.properties
===================================================================
--- trunk/treebase-phylowidget/build.properties 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-phylowidget/build.properties 2010-03-29 19:34:59 UTC (rev 659)
@@ -49,7 +49,7 @@
# Whether or not to try and sign the jar.
signjar = true
# Whether or not to generate a new key. Set the value to true if it is the first time to run ant build in this machine.
-signjar.genkey = false
+signjar.genkey = true
# Your keystore alias and password.
signjar.alias = phylowidget
signjar.storepass = birdman
Added: trunk/treebase-phylowidget/data/menus/limited-menus.xml
===================================================================
--- trunk/treebase-phylowidget/data/menus/limited-menus.xml (rev 0)
+++ trunk/treebase-phylowidget/data/menus/limited-menus.xml 2010-03-29 19:34:59 UTC (rev 659)
@@ -0,0 +1,81 @@
+<menuset name="PhyloWidget Menus">
+ <menu type="Toolbar" fontsize="11" x="2" y="2">
+ <item name="File">
+ <!--item name="New Tree" action="treeNew" shortcut="control-n"/-->
+ <!--item name="Load Tree..." action="treeLoad"/-->
+ <item name="Save Tree..." action="treeSave"/>
+ <!--item name="Save Tree To Database" action="treeSaveToDB"/-->
+ <item name="Export Image">
+ <item name="Large (1600x1200)" action="fileOutputBig"/>
+ <item name="Small (640 x 480)" action="fileOutputSmall"/>
+ <item name="PDF" action="fileOutputPDF"/>
+ </item>
+ </item>
+ <item name="View">
+ <item name="Zoom to Full" action="viewZoomToFull" shortcut="control-F"/>
+ <item name="Renderer Type">
+ <item name="Rectangular" action="viewRectangular" shortcut="control-1"/>
+ <item name="Diagonal" action="viewDiagonal" shortcut="control-2"/>
+ <item name="Circular" action="viewCircular" shortcut="control-3"/>
+ </item>
+ <item name="Show/Hide">
+ <item name="Branch Lengths" type="CheckBox" property="showBranchLengths" value="false"/>
+ <item name="Inner Clade Labels" type="CheckBox" property="showCladeLabels" value="false"/>
+ </item>
+ <item name="Style">
+ <item name="Text Angle" type="NumberScroller" property="textRotation" increment=".5" default="0" min="-45" max="45"/>
+ <item name="Node Size" type="NumberScroller" property="nodeSize" increment =".005" default=".2" min="0" max=".5"/>
+ <item name="Line Weight" type="NumberScroller" property="lineSize" increment =".001" default=".1" min="0" max=".5"/>
+ </item>
+ <item name="Render Threshold" type="NumberScroller" property="renderThreshold" increment="5" default="150" min="5" max="1000"/>
+ <item name="Minimum Text Size" type="NumberScroller" property="minTextSize" increment =".1" default="10" min="0" max="36"/>
+ <!-- <item name="Stretch Tree to Fit" type="CheckBox" property="fitTreeToWindow" /> -->
+ <item name="Use Branch Lengths" type="CheckBox" property="useBranchLengths" shortcut="ctrl-b" />
+ </item>
+ <!--item name="Tree">
+ <item name="Mutate Once" action="treeMutateOnce" shortcut="control-m"/>
+ <item name="Mutate Slow" action="treeMutateSlow"/>
+ <item name="Mutate Fast" action="treeMutateFast"/>
+ <item name="Stop Mutating" action="treeStopMutating" shortcut="control-shift-m"/>
+ </item>
+ <item name="Flip Tree" action="treeFlip" shortcut="control-R"/>
+ <item name="Auto-sort Tree" action="treeAutoSort" shortcut="control-L"/>
+ <item name="Remove Elbows" action="treeRemoveElbows" shortcut="control-E"/>
+ </item-->
+ </menu>
+
+ <menu name="dock" type="ToolDock" width="30" rotation="left">
+ <!-- the "rotation" parameter can have the values: left, right, top, bottom -->
+ <item name="Arrow" tool="arrow" shortcut="a" icon="dock/arrow.png"/>
+ <item name="Scroll" tool="scroll" shortcut="s" icon="dock/grab.png"/>
+ <item name="Zoom" tool="zoom" shortcut="z" icon="dock/zoom.png"/>
+ </menu>
+
+ <menu name="context" type="org.phylowidget.ui.PhyloContextMenu">
+ <!--item name="Tree Edit" hint="t">
+ <item name="Add" hint="a">
+ <item name="Child" action="nodeAddChild" hint="c"/>
+ <item name="Sister" action="nodeAddSister" hint="s"/>
+ </item>
+ <item name="Delete" hint="d">
+ <item name="This node" action="nodeDelete" hint="t"/>
+ <item name="Subtree" action="nodeDeleteSubtree" hint="s"/>
+ </item>
+ </item-->
+ <item name="Layout" hint="a">
+ <item name="Reroot" action="nodeReroot" hint="r"/>
+ <item name="Flip subtree" action="nodeFlipSubtree" hint="f"/>
+ <item name="Switch children" action="nodeSwitchChildren" hint="s"/>
+ </item>
+ <!--item name="Clipboard" hint="c">
+ <item name="Cut" action="nodeCut" hint="x"/>
+ <item name="Copy" action="nodeCopy" hint="c"/>
+ <item name="Paste" action="nodePaste" hint="v"/>
+ <item name="Clear" action="nodeClearClipboard" hint="r"/>
+ </item-->
+ <!--item name="Node Edit" hint="e">
+ <item name="Name" action="nodeEditName" hint="n"/>
+ <item name="Branch length" action="nodeEditBranchLength" hint="b"/>
+ </item-->
+ </menu>
+</menuset>
Deleted: trunk/treebase-phylowidget/data/menus/nondb-menus.xml
===================================================================
--- trunk/treebase-phylowidget/data/menus/nondb-menus.xml 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-phylowidget/data/menus/nondb-menus.xml 2010-03-29 19:34:59 UTC (rev 659)
@@ -1,81 +0,0 @@
-<menuset name="PhyloWidget Menus">
- <menu type="Toolbar" fontsize="11" x="2" y="2">
- <item name="File">
- <!--item name="New Tree" action="treeNew" shortcut="control-n"/-->
- <!--item name="Load Tree..." action="treeLoad"/-->
- <item name="Save Tree..." action="treeSave"/>
- <!--item name="Save Tree To Database" action="treeSaveToDB"/-->
- <item name="Export Image">
- <item name="Large (1600x1200)" action="fileOutputBig"/>
- <item name="Small (640 x 480)" action="fileOutputSmall"/>
- <item name="PDF" action="fileOutputPDF"/>
- </item>
- </item>
- <item name="View">
- <item name="Zoom to Full" action="viewZoomToFull" shortcut="control-F"/>
- <item name="Renderer Type">
- <item name="Rectangular" action="viewRectangular" shortcut="control-1"/>
- <item name="Diagonal" action="viewDiagonal" shortcut="control-2"/>
- <item name="Circular" action="viewCircular" shortcut="control-3"/>
- </item>
- <item name="Show/Hide">
- <item name="Branch Lengths" type="CheckBox" property="showBranchLengths" value="false"/>
- <item name="Inner Clade Labels" type="CheckBox" property="showCladeLabels" value="false"/>
- </item>
- <item name="Style">
- <item name="Text Angle" type="NumberScroller" property="textRotation" increment=".5" default="0" min="-45" max="45"/>
- <item name="Node Size" type="NumberScroller" property="nodeSize" increment =".005" default=".2" min="0" max=".5"/>
- <item name="Line Weight" type="NumberScroller" property="lineSize" increment =".001" default=".1" min="0" max=".5"/>
- </item>
- <item name="Render Threshold" type="NumberScroller" property="renderThreshold" increment="5" default="150" min="5" max="1000"/>
- <item name="Minimum Text Size" type="NumberScroller" property="minTextSize" increment =".1" default="10" min="0" max="36"/>
- <!-- <item name="Stretch Tree to Fit" type="CheckBox" property="fitTreeToWindow" /> -->
- <item name="Use Branch Lengths" type="CheckBox" property="useBranchLengths" shortcut="ctrl-b" />
- </item>
- <!--item name="Tree">
- <item name="Mutate Once" action="treeMutateOnce" shortcut="control-m"/>
- <item name="Mutate Slow" action="treeMutateSlow"/>
- <item name="Mutate Fast" action="treeMutateFast"/>
- <item name="Stop Mutating" action="treeStopMutating" shortcut="control-shift-m"/>
- </item>
- <item name="Flip Tree" action="treeFlip" shortcut="control-R"/>
- <item name="Auto-sort Tree" action="treeAutoSort" shortcut="control-L"/>
- <item name="Remove Elbows" action="treeRemoveElbows" shortcut="control-E"/>
- </item-->
- </menu>
-
- <menu name="dock" type="ToolDock" width="30" rotation="left">
- <!-- the "rotation" parameter can have the values: left, right, top, bottom -->
- <item name="Arrow" tool="arrow" shortcut="a" icon="dock/arrow.png"/>
- <item name="Scroll" tool="scroll" shortcut="s" icon="dock/grab.png"/>
- <item name="Zoom" tool="zoom" shortcut="z" icon="dock/zoom.png"/>
- </menu>
-
- <menu name="context" type="org.phylowidget.ui.PhyloContextMenu">
- <!--item name="Tree Edit" hint="t">
- <item name="Add" hint="a">
- <item name="Child" action="nodeAddChild" hint="c"/>
- <item name="Sister" action="nodeAddSister" hint="s"/>
- </item>
- <item name="Delete" hint="d">
- <item name="This node" action="nodeDelete" hint="t"/>
- <item name="Subtree" action="nodeDeleteSubtree" hint="s"/>
- </item>
- </item-->
- <item name="Layout" hint="a">
- <item name="Reroot" action="nodeReroot" hint="r"/>
- <item name="Flip subtree" action="nodeFlipSubtree" hint="f"/>
- <item name="Switch children" action="nodeSwitchChildren" hint="s"/>
- </item>
- <!--item name="Clipboard" hint="c">
- <item name="Cut" action="nodeCut" hint="x"/>
- <item name="Copy" action="nodeCopy" hint="c"/>
- <item name="Paste" action="nodePaste" hint="v"/>
- <item name="Clear" action="nodeClearClipboard" hint="r"/>
- </item-->
- <!--item name="Node Edit" hint="e">
- <item name="Name" action="nodeEditName" hint="n"/>
- <item name="Branch length" action="nodeEditBranchLength" hint="b"/>
- </item-->
- </menu>
-</menuset>
Modified: trunk/treebase-web/src/main/resources/ApplicationResources.properties
===================================================================
--- trunk/treebase-web/src/main/resources/ApplicationResources.properties 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-web/src/main/resources/ApplicationResources.properties 2010-03-29 19:34:59 UTC (rev 659)
@@ -91,6 +91,7 @@
nav.references=References
nav.journals=Journals
+
#-- top navigation menu --
nav.personalinfo = Personal Information
nav.submissions=TreeBASE Submissions
Modified: trunk/treebase-web/src/main/webapp/test/phylowidget/PhyloWidget.jar
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: SourceForge.net <no...@so...> - 2010-03-28 16:56:39
|
Feature Requests item #2978049, was opened at 2010-03-28 16:56 Message generated for change (Tracker Item Submitted) made by You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126677&aid=2978049&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: Open Priority: 5 Private: No Submitted By: https://www.google.com/jhughes () Assigned to: Nobody/Anonymous (nobody) Summary: Unified search feature like entrez NCBI Initial Comment: Currently when searching for something in Treebase, the user needs to select certain boxes like study id or taxon. It would be nice if the search engine could find the most relevant hit without having to tick these boxes in a similar way to NCBI Entrez searches where you can just type in an accession number and Entrez will automatically return all relevant hits so the user doesn't a priori know that the accession corresponds to a protein sequence. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126677&aid=2978049&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-03-28 03:41:53
|
Bugs item #2977860, was opened at 2010-03-27 23:41 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2977860&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: Exception when requesting password Initial Comment: When user forgets password and asks to have it emailed, exception barf returns. Uncaught Exception Encountered javax.mail.SendFailedException: Send failure (javax.mail.SendFailedException: Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. (javax.mail.SendFailedException: Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. )))) at javax.mail.Transport.send(Transport.java:163) at javax.mail.Transport.send(Transport.java:48) at org.cipres.treebase.web.controllers.PasswordFormController.onSubmit(PasswordFormController.java:132) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) 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.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) 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) Caused by: javax.mail.SendFailedException: Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. (javax.mail.SendFailedException: Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. ))) at com.sun.mail.smtp.SMTPTransport.rcptTo(SMTPTransport.java:1196) at com.sun.mail.smtp.SMTPTransport.sendMessage(SMTPTransport.java:584) at javax.mail.Transport.send(Transport.java:95) ... 54 more Caused by: com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. (javax.mail.SendFailedException: Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. )) at com.sun.mail.smtp.SMTPTransport.rcptTo(SMTPTransport.java:1047) ... 56 more Caused by: javax.mail.SendFailedException: Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. ) at com.sun.mail.smtp.SMTPTransport.rcptTo(SMTPTransport.java:1196) ... 56 more Caused by: com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. at com.sun.mail.smtp.SMTPTransport.rcptTo(SMTPTransport.java:1047) ... 56 more Cookies: JSESSIONID=[887390FE613CEE56D2EEFCCE3D7FF91C] __utma=[216002130.839762607.1263756393.1264687215.1264739521.8] __utmz=[216002130.1263756393.1.1.utmccn] ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2977860&group_id=248804 |
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From: <yo...@us...> - 2010-03-27 01:02:57
|
Revision: 658
http://treebase.svn.sourceforge.net/treebase/?rev=658&view=rev
Author: youjun
Date: 2010-03-27 01:02:51 +0000 (Sat, 27 Mar 2010)
Log Message:
-----------
finish modification
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 2010-03-26 20:44:55 UTC (rev 657)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-03-27 01:02:51 UTC (rev 658)
@@ -478,6 +478,18 @@
public void clean(List<TaxonLabel> tList) {
// TODO Auto-generated method stub
-
+ for(TaxonLabel tl : tList){
+ Query q = getSession()
+ .createQuery("select count(*) from PhyloTreeNode pn where pn.taxonLabel = :tl");
+ q.setParameter("tl", tl);
+ int count=((Integer)q.iterate().next()).intValue();
+
+ q = getSession()
+ .createQuery("select count(*) from MatrixRow mr where mr.taxonLabel = :tl");
+ q.setParameter("tl", tl);
+ count += ((Integer)q.iterate().next()).intValue();
+
+ if(count==0)deletePersist(tl);
+ }
}
}
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From: SourceForge.net <no...@so...> - 2010-03-26 21:18:28
|
Bugs item #2977283, was opened at 2010-03-26 14:18 Message generated for change (Tracker Item Submitted) made by tmkeesey You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2977283&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: easy Status: Open Priority: 5 Private: No Submitted By: Mike Keesey (tmkeesey) Assigned to: Nobody/Anonymous (nobody) Summary: crossdomain.xml Initial Comment: In order for Adobe Flash-based web applications to be able to use the PhyloWS API, there needs to be a permissions file at <http://treebase.org/crossdomain.xml>. See, for example, <http://static.flickr.com/crossdomain.xml>. More information on cross-domain policy files can be found here: <http://www.adobe.com/devnet/articles/crossdomain_policy_file_spec.html>. Attahced is an example crossdomain.xml which would allow the fewest retrictions. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2977283&group_id=248804 |
|
From: <yo...@us...> - 2010-03-26 20:45:02
|
Revision: 657
http://treebase.svn.sourceforge.net/treebase/?rev=657&view=rev
Author: youjun
Date: 2010-03-26 20:44:55 +0000 (Fri, 26 Mar 2010)
Log Message:
-----------
add method to clen orphan value in taxonlabel and taxonlabelset
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 2010-03-24 12:59:35 UTC (rev 656)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-03-26 20:44:55 UTC (rev 657)
@@ -460,4 +460,24 @@
}
return result;
}
+
+ public void clean(TaxonLabelSet tSet) {
+ // TODO Auto-generated method stub
+ Query q = getSession()
+ .createQuery("select count(*) from TreeBlock tb where tb.taxonLabelSet = :ts");
+ q.setParameter("ts", tSet);
+ int count=((Integer)q.iterate().next()).intValue();
+
+ q = getSession()
+ .createQuery("select count(*) from Matrix m where m.taxa = :ts");
+ q.setParameter("ts", tSet);
+ count += ((Integer)q.iterate().next()).intValue();
+
+ if(count==0)deletePersist(tSet);
+ }
+
+ public void clean(List<TaxonLabel> tList) {
+ // TODO Auto-generated method stub
+
+ }
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: SourceForge.net <no...@so...> - 2010-03-26 20:01:25
|
Bugs item #2977247, was opened at 2010-03-26 16:01 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2977247&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: Zoom and hand tools missing for PhyloWidget in search side Initial Comment: The new fix for PhyloWidget on the search side (ie without the "Save to Database") seems to be missing the arrow, hand, and magnifying glass tools which allow the user to explore the tree. This needs to be added back in. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2977247&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-03-26 19:58:53
|
Bugs item #2977244, was opened at 2010-03-26 15:58 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2977244&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: 4 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: NumberFormatException when a string is searched on taxon_id Initial Comment: If someone enters a a bit of text instead of a number for a taxon_id search (e.g. an NCBI id) the result is an exception trace. We need something more elegant. Uncaught Exception Encountered java.lang.NumberFormatException: For input string: "Homo" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:481) at java.lang.Integer.parseInt(Integer.java:514) at org.cipres.treebase.web.controllers.TaxonSearchController.doIdentifierSearch(TaxonSearchController.java:283) at org.cipres.treebase.web.controllers.TaxonSearchController.doTaxonSearch(TaxonSearchController.java:247) at org.cipres.treebase.web.controllers.TaxonSearchController.onSubmit(TaxonSearchController.java:89) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) 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.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) 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) Cookies: JSESSIONID=[A55A42C07C8F552BC9D0FD39AABD281A] __utma=[216002130.839762607.1263756393.1264687215.1264739521.8] __utmz=[216002130.1263756393.1.1.utmccn] ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2977244&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-03-26 11:15:34
|
Bugs item #2948080, was opened at 2010-02-08 21:18 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2948080&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: internals Group: None >Status: Closed Priority: 5 Private: No Submitted By: Ryan Scherle (rscherle) Assigned to: Rutger Vos (rvos) Summary: Make lat/lon available in nexml Initial Comment: Check whether lat/lon information is available in nexml records exported from TreeBASE. If not, add it. ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2010-03-26 11:15 Message: I've implemented this, although there are no records that actually demonstrate this functionality. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2010-03-26 11:15 Message: Your bug has been resolved. Thanks for the report. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2010-02-11 14:48 Message: The lat/long information is currently not available in the NeXML serialization. How would we best add this? Would you say that in this instance it's metadata (i.e. presumably requiring a semantic annotation, perhaps using DarwinCore predicates) or data (requiring a lat/long datatype in core NeXML, perhaps). I think it's the former, what do you think? ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2010-02-11 14:48 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=2948080&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-03-26 11:12:00
|
Bugs item #2846456, was opened at 2009-08-28 19:28 Message generated for change (Settings changed) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2846456&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: data Group: None Status: Open Priority: 6 Private: No Submitted By: William Piel (sfrgpiel) >Assigned to: Rutger Vos (rvos) Summary: Need PhyloWS API search by date-time-stamp Initial Comment: We need to be sure that our API can search using data-time-stamps. i.e. "find all studies that were modified since Jan 23, 2010." (and separately, "find all studies that were made public after Jan 23, 2010"). This may require investigating how and where TreeBASE2 is currently tracking modification stamps. If it does not do so yet, we should probably add modification stamp fields on some key tables -- and it's probably easier to do this with a postgresql-level trigger or part of the schema. At any rate, any of the following modifications should stamped and searchable by the API: modifications to the citation, matrix metadata (including row-segment additions/subtractions), tree metadata (including re-rooting a tree), taxon labels, and mapping between taxon labels and taxon variants, and mapping between taxon variants and taxa. i.e., if a study contains a matrix for which a taxon label gets re-mapped to a different taxon variant or taxon at time/date x, then the whole study should be considered changed at time/date x. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2846456&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-03-26 11:11:16
|
Bugs item #2798604, was opened at 2009-05-29 21:21 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&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: data Group: None Status: Open Priority: 7 Private: No Submitted By: Blaise Li (blaiseli) Assigned to: Rutger Vos (rvos) Summary: no block of taxa could be created from a MrBayes .con tree Initial Comment: The upoad of the attached file fails: it says it cannot generate a block of taxa. This is either a bug or a strong limitation: the file contains a nexus tree obtained from MrBayes; it should not be so special. ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2010-03-26 11:11 Message: I think this needs to be closed: there is simply no way we will ever support all nexus variants. It is a feature of treebase that we support mesquite-compatible files. We state this very clearly. If people decide to upload files that are not compatible with mesquite there's not much we can do. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2009-11-18 18:23 Message: This has been downgraded. We can't fix this unless mesquite gets fixed. If people want to upload mrbayes files they will have to run them through mesquite first on their own machines. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2009-06-27 07:31 Message: The issue is because, although mesquite *can* create a taxa block on the fly while reading a tree block without a translation table, it doesn't want to. It prods the user for feedback, which makes the import hang in headless mode. Bill has emailed the Maddisons about this, and it looks like the issue could certainly be fixed in their code (even if that would make it some sort of treebase special). But - then we have to fold that change into our previous treebase special version of mesquite, which was a snapshot roughly at version 2.1, and we're now at 2.6. I did some testing and some methods have changed or have been removed, so we would need to adapt our code base to that new api. ---------------------------------------------------------------------- Comment By: William Piel (sfrgpiel) Date: 2009-06-23 14:29 Message: Thanks for reporting this bug. We'll look into it as soon as possible. ---------------------------------------------------------------------- Comment By: William Piel (sfrgpiel) Date: 2009-06-23 14:29 Message: This looks like a difficult bug to fix because the problem stems from Mesquite. I'm puzzled why Mesquite cannot create a default taxon block from a tree block that does not use a translation table. I've tried opening trees like this in Mesquite v. 2 with no success... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-03-26 11:08:52
|
Bugs item #2810770, was opened at 2009-06-23 08:16 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2810770&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: data Group: None >Status: Closed Priority: 7 Private: No Submitted By: Blaise Li (blaiseli) Assigned to: Rutger Vos (rvos) Summary: Uncaught Exception for a tree Initial Comment: I get an uncaught exception when I try to see this: http://8ball.sdsc.edu:6666/treebase-web/search/downloadATree.html?id=2345&treeid=1652 (This link was given by a research on trees having 4 taxa. Tree title is Perralderia) ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2010-03-26 11:08 Message: Can't reproduce: the tree downloads correctly. Closing this. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2009-11-20 16:17 Message: Thanks for reporting this bug. We'll look into it as soon as possible. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2009-11-20 16:17 Message: I am still working on this. Initially it seemed like this had to do with other bug reports about incomplete tree loading, but it turns out that's not the case for this report. It looks like there is something idiosyncratic going on with this particular record. The tree structure itself looks sane in the database. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2810770&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-03-26 11:07:01
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Bugs item #2972133, was opened at 2010-03-17 18:52 Message generated for change (Settings changed) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2972133&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: Add to connotea, del.icio.us etc broken due to absolute URL Initial Comment: The code uses an absolute path, which results in things like http://localhost.localdomain:8280/treebase-web/search/study/summary.html?id=1021, which obviously won't work. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2010-03-26 11:07 Message: Thanks for reporting this bug. We'll look into it as soon as possible. ---------------------------------------------------------------------- Comment By: Hilmar Lapp (hlapp) Date: 2010-03-17 19:02 Message: Turns out I do have a CiteULike account. The code adds an entry to the library but w/o a link back to the TreeBASE URL (or the article URL). Is that intended? ---------------------------------------------------------------------- Comment By: Hilmar Lapp (hlapp) Date: 2010-03-17 18:57 Message: This may only affect Connotea actually. The add to Del.icio.us code works, can't test CiteULike as a I don't have an account. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2972133&group_id=248804 |
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