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[Treebase-guts] SF.net SVN: treebase:[664] trunk
|
From: <vga...@us...> - 2010-04-01 20:20:44
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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 -->
<!-- ========================================================== -->
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