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[Treebase-guts] SF.net SVN: treebase:[1097] branches/simple-search-UI
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From: <hl...@us...> - 2013-01-22 13:00:32
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Revision: 1097
http://treebase.svn.sourceforge.net/treebase/?rev=1097&view=rev
Author: hlapp
Date: 2013-01-22 13:00:20 +0000 (Tue, 22 Jan 2013)
Log Message:
-----------
Rolling back revisions 1092 through 1095 on the simple-search-UI branch so that from its branching point onward it doesn't have changes that are also on the main trunk.
Modified Paths:
--------------
branches/simple-search-UI/treebase-core/pom.xml
branches/simple-search-UI/treebase-web/pom.xml
branches/simple-search-UI/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java
branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp
branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/web.xml
Removed Paths:
-------------
branches/simple-search-UI/treebase-web/src/main/webapp/images/paypalsub.jpg
Modified: branches/simple-search-UI/treebase-core/pom.xml
===================================================================
--- branches/simple-search-UI/treebase-core/pom.xml 2013-01-22 01:17:59 UTC (rev 1096)
+++ branches/simple-search-UI/treebase-core/pom.xml 2013-01-22 13:00:20 UTC (rev 1097)
@@ -127,7 +127,7 @@
<dependency>
<groupId>postgresql</groupId>
<artifactId>postgresql</artifactId>
- <version>8.4-702.jdbc3</version>
+ <version>8.3-603.jdbc3</version>
</dependency>
<dependency>
@@ -171,8 +171,6 @@
<groupId>org.slf4j</groupId>
<artifactId>slf4j-jdk14</artifactId>
</exclusion>
-
-
</exclusions>
</dependency>
<dependency>
@@ -188,10 +186,6 @@
<groupId>org.slf4j</groupId>
<artifactId>slf4j-jdk14</artifactId>
</exclusion>
- <exclusion>
- <groupId>org.apache.geronimo.specs</groupId>
- <artifactId>geronimo-servlet_2.5_spec</artifactId>
- </exclusion>
</exclusions>
</dependency>
<dependency>
Modified: branches/simple-search-UI/treebase-web/pom.xml
===================================================================
--- branches/simple-search-UI/treebase-web/pom.xml 2013-01-22 01:17:59 UTC (rev 1096)
+++ branches/simple-search-UI/treebase-web/pom.xml 2013-01-22 13:00:20 UTC (rev 1097)
@@ -115,6 +115,12 @@
<dependency>
<groupId>javax.servlet</groupId>
+ <artifactId>servlet-api</artifactId>
+ <version>2.4</version>
+ </dependency>
+
+ <dependency>
+ <groupId>javax.servlet</groupId>
<artifactId>jstl</artifactId>
<version>1.1.2</version>
</dependency>
@@ -413,6 +419,13 @@
</exclusion>
</exclusions>
</dependency>
+
+ <dependency>
+ <groupId>opensymphony</groupId>
+ <artifactId>oscache</artifactId>
+ <version>2.4.1</version>
+ </dependency>
+
</dependencies>
</project>
Modified: branches/simple-search-UI/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java
===================================================================
--- branches/simple-search-UI/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java 2013-01-22 01:17:59 UTC (rev 1096)
+++ branches/simple-search-UI/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java 2013-01-22 13:00:20 UTC (rev 1097)
@@ -248,7 +248,7 @@
errors.add(label.getTaxonLabel() + " has not been linked to the external taxonomy");
}
else if ( label.getAttemptedLinking() && label.getNcbiTaxID() == null ) {
- errors.add(label.getTaxonLabel() + " - an unsuccessful attempt has been made to link this to the external taxonomy");
+ errors.add(label.getTaxonLabel() + " - an unsuccesful attempt has been made to link this to the external taxonomy");
}
}
Modified: branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp
===================================================================
--- branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp 2013-01-22 01:17:59 UTC (rev 1096)
+++ branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp 2013-01-22 13:00:20 UTC (rev 1097)
@@ -18,8 +18,8 @@
<p>TreeBASE provides an advanced access URL for anonymous reviewers and referees to provide additional quality control before the data are made public. Although additional NSF requirements relating to provenance and how data were generated are not normally required or scrutinized by TreeBASE staff, submitters who flag their submission (in the submission notes section) as NSF-sponsored data will receive special attention by our staff. In these cases, TreeBASE staff will check to make sure that provenance and analysis metadata are adequately provided, and, as needed, communicate with the submitter and assist in properly formatting and ingesting these data. </p>
<h2>Data Standards and Dissemination</h2>
<p>TreeBASE plans to remain in compliance with the emerging, but still evolving, standard of Minimal Information for a Phylogenetic Analysis (<a href="http://www.nescent.org/sites/evoio/MIAPA" target="_blank">MIAPA</a>). In addition, TreeBASE publishes persistant and resolvable globally unique identifiers (GUIDs) for all major data objects and disseminates data and metadata using commonly accepted standards. A Restful <a href="http://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS" target="_blank">PhyloWS</a> API exposes metadata using RSS feeds in RDF; a <a href="http://www.nexml.org/" target="_blank">NeXML</a> serialization exposes data marked up with metadata using published vocabularies and fully qualified URIs in compliance with <a href="http://linkeddata.org/" target="_blank">Linked Data</a> standards. Basic record metadata are published through an OIA-PMH service, and TreeBASE records are mirrored by Dryad, which provides a secondary Dryad <a href="http://www.datacite.org" target="_blank">DataCite DOI</a>. However, for most people in the scientific community, data will be retrieved using the web user interface and downloaded in the NEXUS format, while metadata can be downloaded separately in a tab-separated text format. </p>
-<h2>Data Persistence</h2>
-<p>Although no data service can guarantee indefinite persistence, TreeBASE will make every effort to preserve its services as long as possible. Additionally, the Articles of Incorporation of the <a href="http://www.phylofoundation.org" target="_blank">Phyloinformatics Research Foundation</a>, which oversees TreeBASE activities, specify that if dissolution is ever required the assets will be transferred to a similar entity with a comparable mission. </p>
+<h2>Data Persistance</h2>
+<p>Although no data service can guarantee indefinite persistance, TreeBASE will make every effort to preserve its services as long as possible. Additionally, the Articles of Incorporation of the <a href="http://www.phylofoundation.org" target="_blank">Phyloinformatics Research Foundation</a>, which oversees TreeBASE activities, specify that if dissolution is ever required the assets will be transferred to a similar entity with a comparable mission. </p>
<h2>Preparing a Data Management Plan for NSF</h2>
<p>Scientists are welcome to designate TreeBASE as their selected repository and dissemination service for phylogenetic data generated by sponsored research. In their Data Management Plan, we suggest that the following be mentioned:</p>
<ul>
@@ -43,7 +43,7 @@
<table>
<tr><td><input type="hidden" name="on0" value="TreeBASE Study URI:">TreeBASE Study URI:</td></tr><tr><td><input type="text" name="os0" maxlength="60"></td></tr>
</table>
-<input type="image" src="images/paypalsub.jpg" border="0" name="submit" alt="PayPal - The safer, easier way to pay online!">
+<input type="image" src="http://www.phylofoundation.org/icns/sub.jpg" border="0" name="submit" alt="PayPal - The safer, easier way to pay online!">
<img alt="" border="0" src="https://www.paypalobjects.com/WEBSCR-640-20110401-1/en_US/i/scr/pixel.gif" width="1" height="1">
</form></td>
<td><form action="https://www.paypal.com/cgi-bin/webscr" method="post">
Modified: branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/web.xml 2013-01-22 01:17:59 UTC (rev 1096)
+++ branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/web.xml 2013-01-22 13:00:20 UTC (rev 1097)
@@ -58,7 +58,47 @@
<listener>
<listener-class>net.bull.javamelody.SessionListener</listener-class>
</listener>
+
+ <filter>
+ <filter-name>CacheFilter</filter-name>
+ <filter-class>com.opensymphony.oscache.web.filter.CacheFilter</filter-class>
+ <init-param>
+ <param-name>expires</param-name>
+ <param-value>time</param-value>
+ </init-param>
+ <init-param>
+ <param-name>time</param-name>
+ <param-value>2592000</param-value> <!-- one month -->
+ </init-param>
+ </filter>
+ <filter-mapping>
+ <filter-name>CacheFilter</filter-name>
+ <url-pattern>/search/downloadAStudy.html</url-pattern>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>CacheFilter</filter-name>
+ <url-pattern>/search/study/anyObjectAsRDF.rdf</url-pattern>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>CacheFilter</filter-name>
+ <url-pattern>/search/downloadANexusFile.html</url-pattern>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>CacheFilter</filter-name>
+ <url-pattern>/search/downloadAMatrix.html</url-pattern>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>CacheFilter</filter-name>
+ <url-pattern>/search/downloadATree.html</url-pattern>
+ </filter-mapping>
+
+
+
<!-- =================================================================== -->
<!-- Declarations of JNDI Resources expected from the Tomcat container -->
<!-- =================================================================== -->
Deleted: branches/simple-search-UI/treebase-web/src/main/webapp/images/paypalsub.jpg
===================================================================
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![http://www.phylofoundation.org/icns/sub.jpg"](http://www.phylofoundation.org/icns/sub.jpg"){kind=link}
![https://www.paypalobjects.com/WEBSCR-640-20110401-1/en_US/i/scr/pixel.gif"](https://www.paypalobjects.com/WEBSCR-640-20110401-1/en_US/i/scr/pixel.gif"){kind=link}