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[Treebase-guts] SF.net SVN: treebase:[134] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlObjectConverter.java

From: <rv...@us...> - 2009-06-28 10:09:49

Revision: 134
          http://treebase.svn.sourceforge.net/treebase/?rev=134&view=rev
Author:   rvos
Date:     2009-06-28 10:09:22 +0000 (Sun, 28 Jun 2009)

Log Message:
-----------
Now attaches dc:relation annotations to link to enclosed resources, no longer uses dc:identifier

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java	2009-06-27 07:04:54 UTC (rev 133)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java	2009-06-28 10:09:22 UTC (rev 134)
@@ -79,14 +79,9 @@
 	 */
 	protected void attachTreeBaseID(Annotatable annotatable,TBPersistable tbPersistable,Class<?> persistableClass) {
 		if ( null != tbPersistable.getId() ) {
-			attachAnnotation(mDCIdentifier,makeNamespacedID(tbPersistable,persistableClass),mDCURI,annotatable);			
-			String uriString = mBaseURI.toString() + makeNamespacedID(tbPersistable,persistableClass);
-			try {
-				annotatable.addAnnotationValue("dc:relation",mDCURI, new URI(uriString));
-			} catch (URISyntaxException e) {
-				// TODO Auto-generated catch block
-				e.printStackTrace();
-			}
+			//attachAnnotation(mDCIdentifier,makeNamespacedID(tbPersistable,persistableClass),mDCURI,annotatable);			
+			String uriString = getDocument().getBaseURI().toString() + tbPersistable.getPhyloWSPath().toString();
+			annotatable.addAnnotationValue("dc:relation",mDCURI, URI.create(uriString));
 		}
 	}
 	
@@ -98,7 +93,7 @@
 	 * @param annotatable
 	 */
 	protected void attachAnnotation(String key,String value,URI namespace,Annotatable annotatable) {
-		Annotation annotation = annotatable.addAnnotationValue(key, namespace, value); // FIXME! Attaches meta element as last child
+		Annotation annotation = annotatable.addAnnotationValue(key, namespace, value);
 	}
 	
 	/**
@@ -113,19 +108,19 @@
 		// dc:identifier predicate in a nexml meta annotation,
 		// e.g. <meta property="dc:identifier" content="TB2:Tr231"/>
 		// this will return something that stringifies to TB2:Tr231
-		Set<Object> dublinCoreIdentifierObjects = annotatable.getAnnotationValues(mDCIdentifier);
-		Iterator<Object> objectIterator = dublinCoreIdentifierObjects.iterator();
+		Set<Object> dublinCoreRelationObjects = annotatable.getRelValues("dc:relation");
+		Iterator<Object> objectIterator = dublinCoreRelationObjects.iterator();
 		while ( objectIterator.hasNext() ) {
-			TreebaseIDString treebaseIDString = null;
-			NamespacedGUID namespacedGUID = null;
-			try {
-				namespacedGUID = new NamespacedGUID(objectIterator.next().toString());
-				treebaseIDString = namespacedGUID.getTreebaseIDString();
-				return treebaseIDString.getId();
-			} catch ( MalformedTreebaseIDString e ) {
-				// XXX do nothing, it's OK, it means we're 
-				// parsing an id from a different naming
-				// authority, e.g. uBio or NCBI
+			URI relationURI = (URI)objectIterator.next();
+			String urlFragment = getDocument().getBaseURI().toString() + "taxon/TB2:";
+			if ( relationURI.toString().startsWith(urlFragment) ) {
+				String rawTreebaseIDString = relationURI.toString().substring(urlFragment.length());
+				try {
+					TreebaseIDString treebaseIDString = new TreebaseIDString(rawTreebaseIDString);
+					return treebaseIDString.getId();
+				} catch ( MalformedTreebaseIDString e ) {
+					e.printStackTrace();
+				}
 			}
 		}
 		return null;


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[Treebase-guts] [ treebase-Bugs-2798604 ] no block of taxa could be created from a MrBayes .con tree

From: SourceForge.net <no...@so...> - 2009-06-27 07:31:16

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: 8
Private: No
Submitted By: Blaise Li (blaiseli)
Assigned to: Mark Dominus (mjdominus)
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: 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:
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... 

----------------------------------------------------------------------

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.


----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2810620 ] NPE when validating taxon labels

From: SourceForge.net <no...@so...> - 2009-06-27 07:12:24

Bugs item #2810620, was opened at 2009-06-22 23:39
Message generated for change (Comment added) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2810620&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: 9
Private: No
Submitted By: Rutger Vos (rvos)
>Assigned to: Rutger Vos (rvos)
Summary: NPE when validating taxon labels

Initial Comment:
Dear Madam / Sir,

I am trying to link my taxon labels to the names in uBio using the
above-mentioned page in the new version of the TreeBASE submission tool.
However, for many of the names I encounter the attached error page when I
enter the NameBankID manually after looking it up on the uBio web site.

Also, many of my taxon names (e.g. Blastacervulus eucalypti) I can find back
easily in uBio but they do not automatically appear as options in TreeBASE
when I click on "Taxon Label Editor" pencil button.

I am using a Macbook Pro running and up-to-date version of OS 10.5 with
Firefox 3.0.3 as browser.

Please let me know if I need to supply more information.

Kind regards,
Ewald

J.Z. (Ewald) Groenewald, PhD
Researcher: Evolutionary Phytopathology Group

CBS-KNAW Fungal Biodiversity Centre
An Institute of the Royal Netherlands Academy of Arts and Sciences (KNAW)

Visiting address:
Uppsalalaan 8, Room C1.51
3584 CT Utrecht, The Netherlands
Postal address:
P.O. Box 85167
3508 AD Utrecht, The Netherlands

work tel:   +31 (0)30 212 2600 (reception)
                 +31 (0)30 212 2686 (direct)
work fax:  +31 (0)30 251 2097
mobile:     +31 (0)65 497 4428
e-mail:      e.g...@cb...

----------------------------------------------------------------------

>Comment By: Rutger Vos (rvos)
Date: 2009-06-27 07:12

Message:
The error has been resolved as of revision 133 - the issue was a
NullPointerException when processing a uBio web service response that does
not contain an NCBI taxon ID. The second issue can't be addressed by us -
it's caused by the discrepancy between uBio's web site (HTML) output and
its web service output.

----------------------------------------------------------------------

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[Treebase-guts] SF.net SVN: treebase:[133] trunk/treebase-web/src/main

From: <rv...@us...> - 2009-06-27 07:04:56

Revision: 133
          http://treebase.svn.sourceforge.net/treebase/?rev=133&view=rev
Author:   rvos
Date:     2009-06-27 07:04:54 +0000 (Sat, 27 Jun 2009)

Log Message:
-----------
This commit fixes issue 2810620

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/EditTaxonLabelController.java
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/editTaxonLabel.jsp

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/EditTaxonLabelController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/EditTaxonLabelController.java	2009-06-26 15:41:18 UTC (rev 132)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/EditTaxonLabelController.java	2009-06-27 07:04:54 UTC (rev 133)
@@ -225,12 +225,23 @@
 			}
 			else {
 				// 2b
-				Integer ncbiId = getTaxonLabelService().findNcbiTaxIdByUBIOTaxId(manualId);
-				String ncbiPreferredName = getTaxonLabelService().getNCBIPreferredName(ncbiId.toString());
-				Taxon newTaxon = new Taxon(ncbiPreferredName,manualId,ncbiId);
+				TaxonLabelService taxonLabelService = getTaxonLabelService();
+				Integer ncbiId = taxonLabelService.findNcbiTaxIdByUBIOTaxId(manualId);	
+				Taxon newTaxon = null;
+				TaxonVariant newVariant = null;
+				if ( null != ncbiId ) {
+					String ncbiPreferredName = taxonLabelService.getNCBIPreferredName(ncbiId.toString());
+					newTaxon = new Taxon(ncbiPreferredName,manualId,ncbiId);
+					newVariant = new TaxonVariant(manualId,taxonLabel.getTaxonLabel(),ncbiPreferredName,"canonical form");					
+				}				
+				else {
+					newTaxon = new Taxon();
+					newTaxon.setName(taxonLabel.getTaxonLabel());
+					newTaxon.setUBioNamebankId(manualId);					
+					newVariant = new TaxonVariant(manualId,taxonLabel.getTaxonLabel(),taxonLabel.getTaxonLabel(),"canonical form");
+				}
+				newVariant.setTaxon(newTaxon);
 				getTaxonHome().store(newTaxon);
-				TaxonVariant newVariant = new TaxonVariant(manualId,taxonLabel.getTaxonLabel(),ncbiPreferredName,"canonical form");
-				newVariant.setTaxon(newTaxon);
 				getTaxonHome().store(newVariant);
 				variant = newVariant;
 			}

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/editTaxonLabel.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/editTaxonLabel.jsp	2009-06-26 15:41:18 UTC (rev 132)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/editTaxonLabel.jsp	2009-06-27 07:04:54 UTC (rev 133)
@@ -71,17 +71,25 @@
 			<c:set var="counter" value="${counter+1}"/>
 		</c:forEach>
 		<div>
+			<input type="radio" name="taxonvariantid" id="textBoxRadio" value="-1"/>
+			I did a uBio lookup for 
+			<spring:bind path="txnlabel.taxonLabel">
+				<a href="http://www.ubio.org/browser/search.php?search_all=<c:out value="${status.value}"/>" title="uBio taxonomy" target="_new">
+					<img src="<fmt:message key="icons.weblink"/>" class="iconButton"/><c:out value="${status.value}"/></a>
+			</spring:bind>		
+			and here is the namebank id:
+			<script type="text/javascript">
+				function selectRadio(textBoxRadio) {
+					alert($(textBoxRadio));
+					$(textBoxRadio).checked = true;
+				}
+			</script>
+			<input style="width:100px" class="textCell" type="text" name="manualid" onchange="selectRadio('textBoxRadio')" value=""/> 
+		</div>
+		<div>
 			<input type="radio" name="taxonvariantid" value="-1" 
-				<c:if test="${counter==0}">checked="checked"</c:if> /><em>no association</em>
-		</div>
-		or enter taxon id by hand:
-		<input style="width:100px" class="textCell" type="text" name="manualid" value=""/> 
-		from
-		<spring:bind path="txnlabel.taxonLabel">
-			<a href="http://www.ubio.org/browser/search.php?search_all=<c:out value="${status.value}"/>" title="uBio taxonomy" target="_new">
-				<img src="<fmt:message key="icons.weblink"/>" class="iconButton"/> uBio
-			</a>
-		</spring:bind>
+				<c:if test="${counter==0}">checked="checked"</c:if> /> <em>no association</em>
+		</div>		
 	</fieldset>    	
 	<input type="submit" name="Update" value="<fmt:message key="button.update"/>" />
 	<input type="submit" name="_cancel" value="<fmt:message key="button.cancel"/>" />	    


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[Treebase-guts] SF.net SVN: treebase:[132] trunk/treebase-core/src/main/perl/dump/td

From: <mjd...@us...> - 2009-06-26 15:42:12

Revision: 132
          http://treebase.svn.sourceforge.net/treebase/?rev=132&view=rev
Author:   mjdominus
Date:     2009-06-26 15:41:18 +0000 (Fri, 26 Jun 2009)

Log Message:
-----------
add -w (where-clause) option

Modified Paths:
--------------
    trunk/treebase-core/src/main/perl/dump/td

Modified: trunk/treebase-core/src/main/perl/dump/td
===================================================================
--- trunk/treebase-core/src/main/perl/dump/td	2009-06-26 03:57:57 UTC (rev 131)
+++ trunk/treebase-core/src/main/perl/dump/td	2009-06-26 15:41:18 UTC (rev 132)
@@ -4,7 +4,8 @@
 use Getopt::Std;
 
 my %opt;
-getopts('1', \%opt) or usage();
+getopts('1w:', \%opt) or usage();
+if ($opt{1} && $opt{w}) { usage(); }
 
 my $table = shift || usage();
 
@@ -12,6 +13,7 @@
   or die "Couldn't connect to database: " . DBI->errstr;
 my $q = "SELECT * FROM $table";
 $q .= " where 1 = 0" if $opt{1};
+$q .= " where $opt{w}" if $opt{w};
 my $sth = $dbh->prepare($q)
   or die "Couldn't prepare statement: " . $dbh->errstr;
 my $rc = $sth->execute()
@@ -27,13 +29,15 @@
   exit;
 }
 
-if (@rows || $opt{1}) {
+if (@rows) {
   print_aoh(\@rows, "--");
 } else {
-  print "Empty table.\n";
+  print $opt{w} ? "No rows selected.\n" : "Empty table.\n";
 }
 
 sub usage {
-    print "$0 table-name\n";
+    print "$0 [-1] [-w where-clause] table-name\n";
+    print "\t-1: only print column names, in order\n";
+    print "\t-w: dump rows satisfying specified condition\n";
     exit 1;
 }


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[Treebase-guts] SF.net SVN: treebase:[131] trunk/treebase-web/.classpath

From: <rv...@us...> - 2009-06-26 03:57:58

Revision: 131
          http://treebase.svn.sourceforge.net/treebase/?rev=131&view=rev
Author:   rvos
Date:     2009-06-26 03:57:57 +0000 (Fri, 26 Jun 2009)

Log Message:
-----------
Changed dependency version number for nexml snapshot

Modified Paths:
--------------
    trunk/treebase-web/.classpath

Modified: trunk/treebase-web/.classpath
===================================================================
--- trunk/treebase-web/.classpath	2009-06-26 03:55:37 UTC (rev 130)
+++ trunk/treebase-web/.classpath	2009-06-26 03:57:57 UTC (rev 131)
@@ -3,7 +3,6 @@
 	<classpathentry kind="src" path="src/main/java"/>
 	<classpathentry excluding="**/*.java" kind="src" path="src/main/resources"/>
 	<classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="var" path="M2_REPO/org/acegisecurity/acegi-security/1.0.1/acegi-security-1.0.1.jar"/>
 	<classpathentry kind="var" path="M2_REPO/javax/activation/activation/1.1/activation-1.1.jar"/>
 	<classpathentry kind="var" path="M2_REPO/antlr/antlr/2.7.6/antlr-2.7.6.jar"/>
@@ -104,6 +103,9 @@
 	<classpathentry kind="var" path="M2_REPO/xml-apis/xml-apis/1.0.b2/xml-apis-1.0.b2.jar"/>
 	<classpathentry kind="var" path="M2_REPO/xml-resolver/xml-resolver/1.2/xml-resolver-1.2.jar"/>
 	<classpathentry kind="var" path="M2_REPO/org/apache/ws/commons/schema/XmlSchema/1.4.2/XmlSchema-1.4.2.jar"/>
-	<classpathentry kind="var" path="M2_REPO/org/nexml/model/nexml/1.4-SNAPSHOT/nexml-1.4-SNAPSHOT.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.jar"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jst.server.core.container/org.eclipse.jst.server.tomcat.runtimeTarget/Apache Tomcat v5.5"/>
+	<!-- classpathentry combineaccessrules="false" exported="true" kind="src" path="/nexml"/ -->
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>


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[Treebase-guts] SF.net SVN: treebase:[130] trunk/treebase-core/.classpath

From: <rv...@us...> - 2009-06-26 03:55:39

Revision: 130
          http://treebase.svn.sourceforge.net/treebase/?rev=130&view=rev
Author:   rvos
Date:     2009-06-26 03:55:37 +0000 (Fri, 26 Jun 2009)

Log Message:
-----------
Changed dependency version number for nexml snapshot

Modified Paths:
--------------
    trunk/treebase-core/.classpath

Modified: trunk/treebase-core/.classpath
===================================================================
--- trunk/treebase-core/.classpath	2009-06-26 03:54:08 UTC (rev 129)
+++ trunk/treebase-core/.classpath	2009-06-26 03:55:37 UTC (rev 130)
@@ -78,6 +78,6 @@
 	<classpathentry kind="var" path="M2_REPO/org/codehaus/woodstox/wstx-asl/3.2.4/wstx-asl-3.2.4.jar"/>
 	<classpathentry kind="var" path="M2_REPO/xml-resolver/xml-resolver/1.2/xml-resolver-1.2.jar"/>
 	<classpathentry kind="var" path="M2_REPO/org/apache/ws/commons/schema/XmlSchema/1.4.2/XmlSchema-1.4.2.jar"/>
-	<classpathentry kind="var" path="M2_REPO/org/nexml/model/nexml/1.4-SNAPSHOT/nexml-1.4-SNAPSHOT.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.jar"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>


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[Treebase-guts] SF.net SVN: treebase:[129] trunk/treebase-core/pom.xml

From: <rv...@us...> - 2009-06-26 03:54:14

Revision: 129
          http://treebase.svn.sourceforge.net/treebase/?rev=129&view=rev
Author:   rvos
Date:     2009-06-26 03:54:08 +0000 (Fri, 26 Jun 2009)

Log Message:
-----------
Changed dependency version number for nexml snapshot

Modified Paths:
--------------
    trunk/treebase-core/pom.xml

Modified: trunk/treebase-core/pom.xml
===================================================================
--- trunk/treebase-core/pom.xml	2009-06-26 03:51:03 UTC (rev 128)
+++ trunk/treebase-core/pom.xml	2009-06-26 03:54:08 UTC (rev 129)
@@ -124,7 +124,7 @@
     <dependency>
 		<groupId>org.nexml.model</groupId>
 		<artifactId>nexml</artifactId>
-		<version>1.4-SNAPSHOT</version>    
+		<version>1.5-SNAPSHOT</version>    
     </dependency>
 
     <dependency>


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[Treebase-guts] SF.net SVN: treebase:[128] trunk/treebase-web/pom.xml

From: <rv...@us...> - 2009-06-26 03:51:09

Revision: 128
          http://treebase.svn.sourceforge.net/treebase/?rev=128&view=rev
Author:   rvos
Date:     2009-06-26 03:51:03 +0000 (Fri, 26 Jun 2009)

Log Message:
-----------
Changed dependency version number for nexml snapshot

Modified Paths:
--------------
    trunk/treebase-web/pom.xml

Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml	2009-06-26 03:49:59 UTC (rev 127)
+++ trunk/treebase-web/pom.xml	2009-06-26 03:51:03 UTC (rev 128)
@@ -144,7 +144,7 @@
     <dependency>
 		<groupId>org.nexml.model</groupId>
 		<artifactId>nexml</artifactId>
-		<version>1.4-SNAPSHOT</version>    
+		<version>1.5-SNAPSHOT</version>    
     </dependency>  
     
     <dependency>


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[Treebase-guts] SF.net SVN: treebase:[127] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/DownloadANexusFileController.java

From: <rv...@us...> - 2009-06-26 03:50:00

Revision: 127
          http://treebase.svn.sourceforge.net/treebase/?rev=127&view=rev
Author:   rvos
Date:     2009-06-26 03:49:59 +0000 (Fri, 26 Jun 2009)

Log Message:
-----------
Removed old commented-out code

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusFileController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusFileController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusFileController.java	2009-06-26 03:48:04 UTC (rev 126)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusFileController.java	2009-06-26 03:49:59 UTC (rev 127)
@@ -22,17 +22,12 @@
 
 package org.cipres.treebase.web.controllers;
 
-//import java.io.File;
-//import java.io.FileWriter;
-//import java.io.IOException;
 import java.sql.Clob;
-//import java.sql.SQLException;
 import java.util.Map;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-//import org.apache.log4j.Logger;
 import org.springframework.web.servlet.ModelAndView;
 import org.springframework.web.servlet.mvc.Controller;
 
@@ -42,7 +37,6 @@
 import org.cipres.treebase.domain.study.StudyService;
 import org.cipres.treebase.domain.tree.PhyloTreeService;
 import org.cipres.treebase.web.util.ControllerUtil;
-//import org.cipres.treebase.web.util.WebUtil;
 
 /**
  * 
@@ -56,8 +50,6 @@
  */
 public class DownloadANexusFileController extends AbstractDownloadController implements Controller {
 
-//	private static final Logger LOGGER = Logger.getLogger(DownloadANexusFileController.class);
-
 	private PhyloTreeService mPhyloTreeService;
 	private StudyService mStudyService;
 	private MatrixService mMatrixService;
@@ -108,101 +100,10 @@
 	}
 
 	public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response)
-		throws Exception {
-//		String sep = System.getProperty("file.separator");
-//		String downloadDir = request.getSession().getServletContext().getRealPath(
-//			"/NexusFileDownload")
-//			+ sep + request.getRemoteUser();
-//		String downloadDir = getDownloadDir(request);
-//
-//		String treeId = request.getParameter("treeid");
-//		String matrixId = request.getParameter("matrixid");
-//		String nexusFile = request.getParameter("nexusfile");
-//
-//		if (treeId == null && matrixId == null && nexusFile == null) {
-//			return null;
-//		}
-//		long clickedParameterId = 0L;
-//		String nexusFileName = null;
-//
-//		if (treeId != null) {
-//			clickedParameterId = Long.parseLong(treeId);
-//			nexusFileName = getPhyloTreeService().findByID(clickedParameterId).getNexusFileName();
-//		} else if (matrixId != null) {
-//			clickedParameterId = Long.parseLong(matrixId);
-//			nexusFileName = getMatrixService().findByID(clickedParameterId).getNexusFileName();
-//		} else if (nexusFile != null) {
-//			nexusFileName = (nexusFile).replaceAll("%20", "_");
-//		}
-//
-//		if (nexusFileName == null) {
-//			return null;
-//		}
-
+		throws Exception {
 		generateAFileDynamically(request,response,0L);
-//		generateAFileDynamically(request, downloadDir, nexusFileName);
-//		WebUtil.downloadFile(response, downloadDir, nexusFileName + org);
-
 		return null;
-	}
-
-	/**
-	 * @param req HttpServletRequest
-	 * @param downloadDirName String Name of the directory where file(s) will be downloaded
-	 * @param fileName String name of the download file
-	 */
-	/*
-	private void generateAFileDynamically(
-		HttpServletRequest req,
-		String downloadDirName,
-		String fileName) {
-
-		Study study = ControllerUtil.findStudy(req, mStudyService);
-		Map<String, Clob> nexusMap = study.getNexusFiles();
-
-		File dirPath = new File(downloadDirName);
-		if (!dirPath.exists()) {
-			dirPath.mkdirs();
-		}
-
-		// long start = System.currentTimeMillis();
-		// long end = System.currentTimeMillis();
-
-		if (LOGGER.isDebugEnabled()) {
-			LOGGER.debug("IN DOWNLOAD A NEXUS FILE CONTROLLER for file:  " + fileName);
-		}
-
-		try {
-
-			File file = new File(downloadDirName + TreebaseUtil.FILESEP
-				+ (fileName + org).replaceAll(TreebaseUtil.ANEMPTYSPACE, "_"));
-			FileWriter out = new FileWriter(file);
-
-			// Contents of the file will be overwritten if file already exists
-			String clobStr = "File Not Found. File Name is: " + fileName;
-			Clob clob = nexusMap.get(fileName);
-
-			if (clob != null) {
-				int clobLength = (int) clob.length();
-				char[] clobchars = new char[clobLength];
-				clob.getCharacterStream().read(clobchars);
-				clobStr = new String(clobchars);
-			}
-			out.write(clobStr);
-
-			out.close();
-			// File did not exist and was created
-			// } else {
-			// File already exists
-			// }
-		} catch (IOException e) {
-			e.printStackTrace();
-		} catch (SQLException sqle) {
-			sqle.printStackTrace();
-		}
-
 	}
-	*/
 
 	@Override
 	protected String getFileName(long objectId,HttpServletRequest req) {


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[Treebase-guts] SF.net SVN: treebase:[126] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlObjectConverter.java

From: <rv...@us...> - 2009-06-26 03:48:11

Revision: 126
          http://treebase.svn.sourceforge.net/treebase/?rev=126&view=rev
Author:   rvos
Date:     2009-06-26 03:48:04 +0000 (Fri, 26 Jun 2009)

Log Message:
-----------
Now only sets baseURI if one is supplied to the constructor

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java	2009-06-25 13:41:20 UTC (rev 125)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java	2009-06-26 03:48:04 UTC (rev 126)
@@ -49,7 +49,9 @@
 		} catch (URISyntaxException e) {
 			e.printStackTrace();
 		}
-		document.setBaseURI(mBaseURI);
+		if ( null != baseURI ) {
+			document.setBaseURI(mBaseURI);
+		}
 		setTaxonLabelHome(taxonLabelHome);
 		setStudy(study);
 		setDocument(document);


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[Treebase-guts] SF.net SVN: treebase:[120] trunk/treebase-core/pom.xml

From: <rv...@us...> - 2009-06-25 14:57:02

Revision: 120
          http://treebase.svn.sourceforge.net/treebase/?rev=120&view=rev
Author:   rvos
Date:     2009-06-25 13:31:22 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
Upped snapshot version number

Modified Paths:
--------------
    trunk/treebase-core/pom.xml

Modified: trunk/treebase-core/pom.xml
===================================================================
--- trunk/treebase-core/pom.xml	2009-06-25 03:30:53 UTC (rev 119)
+++ trunk/treebase-core/pom.xml	2009-06-25 13:31:22 UTC (rev 120)
@@ -124,7 +124,7 @@
     <dependency>
 		<groupId>org.nexml.model</groupId>
 		<artifactId>nexml</artifactId>
-		<version>1.0-SNAPSHOT</version>    
+		<version>1.4-SNAPSHOT</version>    
     </dependency>
 
     <dependency>


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[Treebase-guts] SF.net SVN: treebase:[124] trunk/treebase-web/.classpath

From: <rv...@us...> - 2009-06-25 14:57:01

Revision: 124
          http://treebase.svn.sourceforge.net/treebase/?rev=124&view=rev
Author:   rvos
Date:     2009-06-25 13:40:41 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
Simplified default .classpath

Modified Paths:
--------------
    trunk/treebase-web/.classpath

Modified: trunk/treebase-web/.classpath
===================================================================
--- trunk/treebase-web/.classpath	2009-06-25 13:39:16 UTC (rev 123)
+++ trunk/treebase-web/.classpath	2009-06-25 13:40:41 UTC (rev 124)
@@ -104,10 +104,6 @@
 	<classpathentry kind="var" path="M2_REPO/xml-apis/xml-apis/1.0.b2/xml-apis-1.0.b2.jar"/>
 	<classpathentry kind="var" path="M2_REPO/xml-resolver/xml-resolver/1.2/xml-resolver-1.2.jar"/>
 	<classpathentry kind="var" path="M2_REPO/org/apache/ws/commons/schema/XmlSchema/1.4.2/XmlSchema-1.4.2.jar"/>
-	<classpathentry kind="var" path="M2_REPO/org/nexml/model/nexml/1.0-SNAPSHOT/nexml-1.0-SNAPSHOT.jar">
-		<attributes>
-			<attribute name="org.eclipse.jst.component.dependency" value="/WEB-INF/lib"/>
-		</attributes>
-	</classpathentry>
+	<classpathentry kind="var" path="M2_REPO/org/nexml/model/nexml/1.4-SNAPSHOT/nexml-1.4-SNAPSHOT.jar"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>


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[Treebase-guts] SF.net SVN: treebase:[125] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers

From: <rv...@us...> - 2009-06-25 14:56:44

Revision: 125
          http://treebase.svn.sourceforge.net/treebase/?rev=125&view=rev
Author:   rvos
Date:     2009-06-25 13:41:20 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
Changed base URI handling

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusRCTFileController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeBlockController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAnAnalysisStepController.java

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	2009-06-25 13:40:41 UTC (rev 124)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java	2009-06-25 13:41:20 UTC (rev 125)
@@ -2,6 +2,7 @@
 
 import java.io.File;
 import java.io.FileWriter;
+import java.util.Properties;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
@@ -21,6 +22,18 @@
 	private static String mNexmlContentType = "application/xml";
 	private static String mRdfContentType = "application/rdf+xml";
 	
+	protected Properties getDefaultProperties(HttpServletRequest request) {
+		Properties properties = new Properties();
+		StringBuffer baseURI = new StringBuffer("http://");
+		baseURI
+			.append(request.getServerName())
+			.append(':')
+			.append(request.getServerPort())
+			.append("/treebase-web/PhyloWS/");
+		properties.setProperty("nexml.uri.base", baseURI.toString());
+		return properties;
+	}
+	
 	/**
 	 * 
 	 * @param request
@@ -54,6 +67,9 @@
 		if ( getFormat(request) == FORMAT_NEXML ) {
 			return getFileNamePrefix() + id + ".xml";
 		}
+		if ( getFormat(request) == FORMAT_RDF ) {
+			return getFileNamePrefix() + id + ".rdf";
+		}		
 		return getFileNamePrefix() + id + ".nex";
 	}	
 	

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java	2009-06-25 13:40:41 UTC (rev 124)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java	2009-06-25 13:41:20 UTC (rev 125)
@@ -113,13 +113,13 @@
 			NexusDataSet pNexusDataSet = new NexusDataSet();
 			pNexusDataSet.getTaxonLabelSets().add(taxa);
 			pNexusDataSet.getMatrices().add(matrix);
-			return getNexmlService().serialize(pNexusDataSet);
+			return getNexmlService().serialize(pNexusDataSet,getDefaultProperties(request));
 		}
 		else if ( getFormat(request) == FORMAT_RDF ) {
 			NexusDataSet pNexusDataSet = new NexusDataSet();
 			pNexusDataSet.getTaxonLabelSets().add(taxa);
 			pNexusDataSet.getMatrices().add(matrix);
-			return getRdfaService().serialize(pNexusDataSet);			
+			return getRdfaService().serialize(pNexusDataSet,getDefaultProperties(request));			
 		}
 		else { // FORMAT_NEXUS or none
 			StringBuilder matrixContent = new StringBuilder();

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusRCTFileController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusRCTFileController.java	2009-06-25 13:40:41 UTC (rev 124)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusRCTFileController.java	2009-06-25 13:41:20 UTC (rev 125)
@@ -98,12 +98,12 @@
 		if ( getFormat(request) == FORMAT_NEXML ) {
 			Long study_id = ControllerUtil.getStudyId(request);
 			Study study = mStudyService.findByID(study_id);
-			return getNexmlService().serialize(study);
+			return getNexmlService().serialize(study,getDefaultProperties(request));
 		}
 		else if ( getFormat(request) == FORMAT_RDF ) {
 			Long study_id = ControllerUtil.getStudyId(request);
 			Study study = mStudyService.findByID(study_id);		
-			return getRdfaService().serialize(study);			
+			return getRdfaService().serialize(study,getDefaultProperties(request));			
 		}		
 		else {
 			String fileName = request.getParameter("nexusfile");

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java	2009-06-25 13:40:41 UTC (rev 124)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java	2009-06-25 13:41:20 UTC (rev 125)
@@ -39,10 +39,10 @@
 	protected String getFileContent(long pStudyID, HttpServletRequest request) {
 		Study study = getStudyService().findByID(pStudyID);
 		if ( getFormat(request) == FORMAT_NEXML ) {
-			return getNexmlService().serialize(study);
+			return getNexmlService().serialize(study,getDefaultProperties(request));
 		}
 		else if ( getFormat(request) == FORMAT_RDF ) {
-			return getRdfaService().serialize(study);			
+			return getRdfaService().serialize(study,getDefaultProperties(request));			
 		}		
 		else {
 			StringBuilder builder = new StringBuilder();

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeBlockController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeBlockController.java	2009-06-25 13:40:41 UTC (rev 124)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeBlockController.java	2009-06-25 13:41:20 UTC (rev 125)
@@ -81,13 +81,13 @@
 			NexusDataSet nexusDataSet = new NexusDataSet();
 			nexusDataSet.getTaxonLabelSets().add(treeBlock.getTaxonLabelSet());
 			nexusDataSet.getTreeBlocks().add(treeBlock);
-			return getNexmlService().serialize(nexusDataSet);
+			return getNexmlService().serialize(nexusDataSet,getDefaultProperties(request));
 		}
 		else if ( getFormat(request) == FORMAT_RDF ) {
 			NexusDataSet nexusDataSet = new NexusDataSet();
 			nexusDataSet.getTaxonLabelSets().add(treeBlock.getTaxonLabelSet());
 			nexusDataSet.getTreeBlocks().add(treeBlock);			
-			return getRdfaService().serialize(nexusDataSet);			
+			return getRdfaService().serialize(nexusDataSet,getDefaultProperties(request));			
 		}		
 		else {
 			StringBuilder bldr = new StringBuilder("#NEXUS\n\n");

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeController.java	2009-06-25 13:40:41 UTC (rev 124)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeController.java	2009-06-25 13:41:20 UTC (rev 125)
@@ -20,6 +20,8 @@
 
 package org.cipres.treebase.web.controllers;
 
+import java.util.Properties;
+
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -113,7 +115,7 @@
 			treeBlock.setTaxonLabelSet(tls);
 			treeBlock.addPhyloTree(tree);
 			nds.getTreeBlocks().add(treeBlock);
-			return getNexmlService().serialize(nds);
+			return getNexmlService().serialize(nds,getDefaultProperties(request));
 		}
 		else if ( getFormat(request) == FORMAT_RDF ) {
 			NexusDataSet nds = new NexusDataSet();
@@ -122,7 +124,7 @@
 			treeBlock.setTaxonLabelSet(tls);
 			treeBlock.addPhyloTree(tree);
 			nds.getTreeBlocks().add(treeBlock);			
-			return getRdfaService().serialize(nds);			
+			return getRdfaService().serialize(nds,getDefaultProperties(request));			
 		}		
 		else {
 			StringBuilder builder = new StringBuilder();

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAnAnalysisStepController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAnAnalysisStepController.java	2009-06-25 13:40:41 UTC (rev 124)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAnAnalysisStepController.java	2009-06-25 13:41:20 UTC (rev 125)
@@ -111,97 +111,14 @@
 	 */
 	public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response)
 		throws Exception {
-
 		if ( request.getParameter("analysisid") == null ) {
 			return null;
 		}
-		
-		long analysisId = Long.parseLong(request.getParameter("analysisid"));
-//		String fileName = getFileName(analysisId,request);
-		
-//		String downloadDir = request.getSession().getServletContext().getRealPath(
-//			TreebaseUtil.FILESEP + "NexusFileDownload")
-//			+ TreebaseUtil.FILESEP + request.getRemoteUser();	
-//		String downloadDir = getDownloadDir(request);
-		
+		long analysisId = Long.parseLong(request.getParameter("analysisid"));		
 		generateAFileDynamically(request, response, analysisId);
-//		WebUtil.downloadFile(response, downloadDir, fileName);		
-		
 		return null;
 	}
 
-	/**
-	 * 
-	 * 
-	 * @param request
-	 * @param analysisId
-	 * @param downloadDirName
-	 */
-	/*
-	private void generateAFileDynamically(HttpServletRequest request, long analysisId, String downloadDirName) {
-
-		AnalysisStep step = getAnalysisStepService().findByID(analysisId);
-		
-		File dirPath = new File(downloadDirName);
-		if (!dirPath.exists()) {
-			dirPath.mkdirs();
-		}		
-
-		StringBuilder stepContent = new StringBuilder();
-		stepContent.append("#NEXUS\n");
-		
-		//header:
-		TreebaseUtil.attachStudyHeader(step.getAnalysis().getStudy(), stepContent);
-		
-		stepContent.append("[ The following blocks are input data for analysis step " + analysisId + " ]\n");
-		TaxonLabelSet inputLabelSet = step.getInputTaxonLabelSet();
-		inputLabelSet.buildNexusBlockTaxa(stepContent, true, false);
-		for ( AnalyzedData data : step.getDataSetReadOnly() ) {
-			if ( data.isInputData() ) {
-				PhyloTree tree = data.getTreeData();
-				Matrix matrix  = data.getMatrixData();
-				if ( tree != null ) {
-					tree.getTreeBlock().setTaxonLabelSet(inputLabelSet);
-					tree.buildNexusBlock(stepContent);
-				}
-				if ( matrix != null ) {
-					matrix.setTaxa(inputLabelSet);
-					matrix.generateNexusBlock(stepContent);
-				}				
-			}
-		}
-		
-		stepContent.append("[ The following blocks are output data for analysis step " + analysisId + " ]\n");
-		TaxonLabelSet outputLabelSet = step.getOutputTaxonLabelSet();
-		outputLabelSet.buildNexusBlockTaxa(stepContent, true, false);
-		for ( AnalyzedData data : step.getDataSetReadOnly() ) {
-			if ( ! data.isInputData() ) {
-				PhyloTree tree = data.getTreeData();
-				Matrix matrix  = data.getMatrixData();
-				if ( tree != null ) {
-					tree.getTreeBlock().setTaxonLabelSet(outputLabelSet);
-					tree.buildNexusBlock(stepContent);
-				}
-				if ( matrix != null ) {
-					matrix.setTaxa(outputLabelSet);
-					matrix.generateNexusBlock(stepContent);
-				}				
-			}
-		}		
-
-		String tmp = getFileName(analysisId,request);
-		try {
-			File file = new File(downloadDirName + TreebaseUtil.FILESEP + tmp);
-			FileWriter out = new FileWriter(file);
-			out.write(stepContent.toString());
-			out.close();
-		} catch (IOException e) {
-			e.printStackTrace();
-		}
-
-	}	
-	*/
-
 	@Override
 	protected String getFileNamePrefix() {
 		return "AnalysisStep";


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[Treebase-guts] SF.net SVN: treebase:[123] trunk/treebase-web/pom.xml

From: <rv...@us...> - 2009-06-25 14:56:42

Revision: 123
          http://treebase.svn.sourceforge.net/treebase/?rev=123&view=rev
Author:   rvos
Date:     2009-06-25 13:39:16 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
Upgraded version number due to interface change: addition of getBaseURI/setBaseURI

Modified Paths:
--------------
    trunk/treebase-web/pom.xml

Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml	2009-06-25 13:38:28 UTC (rev 122)
+++ trunk/treebase-web/pom.xml	2009-06-25 13:39:16 UTC (rev 123)
@@ -140,13 +140,13 @@
   </pluginRepositories>
 
   <dependencies>
-  
+   
     <dependency>
 		<groupId>org.nexml.model</groupId>
 		<artifactId>nexml</artifactId>
-		<version>1.0-SNAPSHOT</version>    
+		<version>1.4-SNAPSHOT</version>    
     </dependency>  
-  
+    
     <dependency>
       <groupId>org.cipres.treebase</groupId>
       <artifactId>treebase-core</artifactId>


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[Treebase-guts] SF.net SVN: treebase:[121] trunk/treebase-core/.classpath

From: <rv...@us...> - 2009-06-25 14:56:26

Revision: 121
          http://treebase.svn.sourceforge.net/treebase/?rev=121&view=rev
Author:   rvos
Date:     2009-06-25 13:32:10 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
Upped snapshot version number

Modified Paths:
--------------
    trunk/treebase-core/.classpath

Modified: trunk/treebase-core/.classpath
===================================================================
--- trunk/treebase-core/.classpath	2009-06-25 13:31:22 UTC (rev 120)
+++ trunk/treebase-core/.classpath	2009-06-25 13:32:10 UTC (rev 121)
@@ -1,82 +1,83 @@
-<classpath>
-  <classpathentry kind="src" path="src/main/java"/>
-  <classpathentry kind="src" path="src/main/resources" excluding="**/*.java"/>
-  <classpathentry kind="src" path="src/test/java" output="target/test-classes"/>
-  <classpathentry kind="src" path="src/test/resources" output="target/test-classes" excluding="**/*.java"/>
-  <classpathentry kind="output" path="target/classes"/>
-  <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-  <classpathentry kind="var" path="M2_REPO/org/acegisecurity/acegi-security/1.0.1/acegi-security-1.0.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/antlr/antlr/2.7.6/antlr-2.7.6.jar"/>
-  <classpathentry kind="var" path="M2_REPO/aopalliance/aopalliance/1.0/aopalliance-1.0.jar"/>
-  <classpathentry kind="var" path="M2_REPO/apple/apple-java-extensions/1.2/apple-java-extensions-1.2.jar"/>
-  <classpathentry kind="var" path="M2_REPO/c3p0/c3p0/0.9.1.2/c3p0-0.9.1.2.jar"/>
-  <classpathentry kind="var" path="M2_REPO/cglib/cglib-nodep/2.1_3/cglib-nodep-2.1_3.jar"/>
-  <classpathentry kind="var" path="M2_REPO/commons-codec/commons-codec/1.3/commons-codec-1.3.jar"/>
-  <classpathentry kind="var" path="M2_REPO/commons-collections/commons-collections/3.1/commons-collections-3.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/commons-lang/commons-lang/2.1/commons-lang-2.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/commons-logging/commons-logging/1.0.4/commons-logging-1.0.4.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-api/2.1.1/cxf-api-2.1.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-common-schemas/2.1.1/cxf-common-schemas-2.1.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-common-utilities/2.1.1/cxf-common-utilities-2.1.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-bindings-soap/2.1.1/cxf-rt-bindings-soap-2.1.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-bindings-xml/2.1.1/cxf-rt-bindings-xml-2.1.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-core/2.1.1/cxf-rt-core-2.1.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-databinding-jaxb/2.1.1/cxf-rt-databinding-jaxb-2.1.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-frontend-jaxws/2.1.1/cxf-rt-frontend-jaxws-2.1.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-frontend-simple/2.1.1/cxf-rt-frontend-simple-2.1.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-transports-http/2.1.1/cxf-rt-transports-http-2.1.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-transports-http-jetty/2.1.1/cxf-rt-transports-http-jetty-2.1.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-ws-addr/2.1.1/cxf-rt-ws-addr-2.1.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-tools-common/2.1.1/cxf-tools-common-2.1.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/ibm/db2jcc/2.6.80/db2jcc-2.6.80.jar"/>
-  <classpathentry kind="var" path="M2_REPO/ibm/db2jcc_license_cu/2.6.80/db2jcc_license_cu-2.6.80.jar"/>
-  <classpathentry kind="var" path="M2_REPO/dom4j/dom4j/1.6.1/dom4j-1.6.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/net/sf/ehcache/ehcache/1.2.3/ehcache-1.2.3.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/hibernate/ejb3-persistence/1.0.1.GA/ejb3-persistence-1.0.1.GA.jar"/>
-  <classpathentry kind="var" path="M2_REPO/com/sun/xml/fastinfoset/FastInfoset/1.2.2/FastInfoset-1.2.2.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/cipres/framework/1.0.1/framework-1.0.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-activation_1.1_spec/1.0.2/geronimo-activation_1.1_spec-1.0.2.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-annotation_1.0_spec/1.1.1/geronimo-annotation_1.0_spec-1.1.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-javamail_1.4_spec/1.3/geronimo-javamail_1.4_spec-1.3.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-jaxws_2.1_spec/1.0/geronimo-jaxws_2.1_spec-1.0.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-servlet_2.5_spec/1.2/geronimo-servlet_2.5_spec-1.2.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-stax-api_1.0_spec/1.0.1/geronimo-stax-api_1.0_spec-1.0.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-ws-metadata_2.0_spec/1.1.2/geronimo-ws-metadata_2.0_spec-1.1.2.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/hibernate/hibernate/3.2.6.ga/hibernate-3.2.6.ga.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/hibernate/hibernate-annotations/3.3.1.GA/hibernate-annotations-3.3.1.GA.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/hibernate/hibernate-commons-annotations/3.0.0.ga/hibernate-commons-annotations-3.0.0.ga.jar"/>
-  <classpathentry kind="var" path="M2_REPO/com/lowagie/itext/1.3/itext-1.3.jar"/>
-  <classpathentry kind="var" path="M2_REPO/jama/jama/1.0.1/jama-1.0.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/javax/xml/bind/jaxb-api/2.1/jaxb-api-2.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/com/sun/xml/bind/jaxb-impl/2.1.6/jaxb-impl-2.1.6.jar"/>
-  <classpathentry kind="var" path="M2_REPO/com/sun/xml/bind/jaxb-xjc/2.1.6/jaxb-xjc-2.1.6.jar"/>
-  <classpathentry kind="var" path="M2_REPO/javax/sql/jdbc-stdext/2.0/jdbc-stdext-2.0.jar"/>
-  <classpathentry kind="var" path="M2_REPO/jdom/jdom/1.1/jdom-1.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/mortbay/jetty/jetty/6.1.9/jetty-6.1.9.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/mortbay/jetty/jetty-util/6.1.9/jetty-util-6.1.9.jar"/>
-  <classpathentry kind="var" path="M2_REPO/jsci/jsci/mesquite/jsci-mesquite.jar"/>
-  <classpathentry kind="var" path="M2_REPO/javax/transaction/jta/1.0.1B/jta-1.0.1B.jar"/>
-  <classpathentry kind="var" path="M2_REPO/junit/junit/3.8.1/junit-3.8.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/log4j/log4j/1.2.13/log4j-1.2.13.jar"/>
-  <classpathentry kind="var" path="M2_REPO/mesquite/mesquite/2.01.tb/mesquite-2.01.tb.jar"/>
-  <classpathentry kind="var" path="M2_REPO/mrj/MRJToolkitStubs/1.0/MRJToolkitStubs-1.0.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/neethi/neethi/2.0.4/neethi-2.0.4.jar"/>
-  <classpathentry kind="var" path="M2_REPO/oro/oro/2.0.8/oro-2.0.8.jar"/>
-  <classpathentry kind="var" path="M2_REPO/pal/pal/mesquite-201/pal-mesquite-201.jar"/>
-  <classpathentry kind="var" path="M2_REPO/javax/xml/soap/saaj-api/1.3/saaj-api-1.3.jar"/>
-  <classpathentry kind="var" path="M2_REPO/com/sun/xml/messaging/saaj/saaj-impl/1.3/saaj-impl-1.3.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/springframework/spring/2.0.7/spring-2.0.7.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/springframework/spring-beans/2.0.8/spring-beans-2.0.8.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/springframework/spring-context/2.0.8/spring-context-2.0.8.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/springframework/spring-core/2.0.8/spring-core-2.0.8.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/springframework/spring-mock/2.0.7/spring-mock-2.0.7.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/springframework/spring-web/2.0.8/spring-web-2.0.8.jar"/>
-  <classpathentry kind="var" path="M2_REPO/tolbaseclasses/tolbaseclasses/mesquite/tolbaseclasses-mesquite.jar"/>
-  <classpathentry kind="var" path="M2_REPO/velocity/velocity/1.4/velocity-1.4.jar"/>
-  <classpathentry kind="var" path="M2_REPO/velocity/velocity-dep/1.4/velocity-dep-1.4.jar"/>
-  <classpathentry kind="var" path="M2_REPO/wsdl4j/wsdl4j/1.6.1/wsdl4j-1.6.1.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/codehaus/woodstox/wstx-asl/3.2.4/wstx-asl-3.2.4.jar"/>
-  <classpathentry kind="var" path="M2_REPO/xml-resolver/xml-resolver/1.2/xml-resolver-1.2.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/apache/ws/commons/schema/XmlSchema/1.4.2/XmlSchema-1.4.2.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/nexml/model/nexml/1.0-SNAPSHOT/nexml-1.0-SNAPSHOT.jar"/>
-</classpath>
\ No newline at end of file
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src/main/java"/>
+	<classpathentry excluding="**/*.java" kind="src" path="src/main/resources"/>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
+	<classpathentry excluding="**/*.java" kind="src" output="target/test-classes" path="src/test/resources"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="var" path="M2_REPO/org/acegisecurity/acegi-security/1.0.1/acegi-security-1.0.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/antlr/antlr/2.7.6/antlr-2.7.6.jar"/>
+	<classpathentry kind="var" path="M2_REPO/aopalliance/aopalliance/1.0/aopalliance-1.0.jar"/>
+	<classpathentry kind="var" path="M2_REPO/apple/apple-java-extensions/1.2/apple-java-extensions-1.2.jar"/>
+	<classpathentry kind="var" path="M2_REPO/c3p0/c3p0/0.9.1.2/c3p0-0.9.1.2.jar"/>
+	<classpathentry kind="var" path="M2_REPO/cglib/cglib-nodep/2.1_3/cglib-nodep-2.1_3.jar"/>
+	<classpathentry kind="var" path="M2_REPO/commons-codec/commons-codec/1.3/commons-codec-1.3.jar"/>
+	<classpathentry kind="var" path="M2_REPO/commons-collections/commons-collections/3.1/commons-collections-3.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/commons-lang/commons-lang/2.1/commons-lang-2.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/commons-logging/commons-logging/1.0.4/commons-logging-1.0.4.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-api/2.1.1/cxf-api-2.1.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-common-schemas/2.1.1/cxf-common-schemas-2.1.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-common-utilities/2.1.1/cxf-common-utilities-2.1.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-bindings-soap/2.1.1/cxf-rt-bindings-soap-2.1.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-bindings-xml/2.1.1/cxf-rt-bindings-xml-2.1.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-core/2.1.1/cxf-rt-core-2.1.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-databinding-jaxb/2.1.1/cxf-rt-databinding-jaxb-2.1.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-frontend-jaxws/2.1.1/cxf-rt-frontend-jaxws-2.1.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-frontend-simple/2.1.1/cxf-rt-frontend-simple-2.1.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-transports-http/2.1.1/cxf-rt-transports-http-2.1.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-transports-http-jetty/2.1.1/cxf-rt-transports-http-jetty-2.1.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-rt-ws-addr/2.1.1/cxf-rt-ws-addr-2.1.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/cxf/cxf-tools-common/2.1.1/cxf-tools-common-2.1.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/ibm/db2jcc/2.6.80/db2jcc-2.6.80.jar"/>
+	<classpathentry kind="var" path="M2_REPO/ibm/db2jcc_license_cu/2.6.80/db2jcc_license_cu-2.6.80.jar"/>
+	<classpathentry kind="var" path="M2_REPO/dom4j/dom4j/1.6.1/dom4j-1.6.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/net/sf/ehcache/ehcache/1.2.3/ehcache-1.2.3.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/hibernate/ejb3-persistence/1.0.1.GA/ejb3-persistence-1.0.1.GA.jar"/>
+	<classpathentry kind="var" path="M2_REPO/com/sun/xml/fastinfoset/FastInfoset/1.2.2/FastInfoset-1.2.2.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/cipres/framework/1.0.1/framework-1.0.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-activation_1.1_spec/1.0.2/geronimo-activation_1.1_spec-1.0.2.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-annotation_1.0_spec/1.1.1/geronimo-annotation_1.0_spec-1.1.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-javamail_1.4_spec/1.3/geronimo-javamail_1.4_spec-1.3.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-jaxws_2.1_spec/1.0/geronimo-jaxws_2.1_spec-1.0.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-servlet_2.5_spec/1.2/geronimo-servlet_2.5_spec-1.2.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-stax-api_1.0_spec/1.0.1/geronimo-stax-api_1.0_spec-1.0.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-ws-metadata_2.0_spec/1.1.2/geronimo-ws-metadata_2.0_spec-1.1.2.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/hibernate/hibernate/3.2.6.ga/hibernate-3.2.6.ga.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/hibernate/hibernate-annotations/3.3.1.GA/hibernate-annotations-3.3.1.GA.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/hibernate/hibernate-commons-annotations/3.0.0.ga/hibernate-commons-annotations-3.0.0.ga.jar"/>
+	<classpathentry kind="var" path="M2_REPO/com/lowagie/itext/1.3/itext-1.3.jar"/>
+	<classpathentry kind="var" path="M2_REPO/jama/jama/1.0.1/jama-1.0.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/javax/xml/bind/jaxb-api/2.1/jaxb-api-2.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/com/sun/xml/bind/jaxb-impl/2.1.6/jaxb-impl-2.1.6.jar"/>
+	<classpathentry kind="var" path="M2_REPO/com/sun/xml/bind/jaxb-xjc/2.1.6/jaxb-xjc-2.1.6.jar"/>
+	<classpathentry kind="var" path="M2_REPO/javax/sql/jdbc-stdext/2.0/jdbc-stdext-2.0.jar"/>
+	<classpathentry kind="var" path="M2_REPO/jdom/jdom/1.1/jdom-1.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/mortbay/jetty/jetty/6.1.9/jetty-6.1.9.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/mortbay/jetty/jetty-util/6.1.9/jetty-util-6.1.9.jar"/>
+	<classpathentry kind="var" path="M2_REPO/jsci/jsci/mesquite/jsci-mesquite.jar"/>
+	<classpathentry kind="var" path="M2_REPO/javax/transaction/jta/1.0.1B/jta-1.0.1B.jar"/>
+	<classpathentry kind="var" path="M2_REPO/junit/junit/3.8.1/junit-3.8.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/log4j/log4j/1.2.13/log4j-1.2.13.jar"/>
+	<classpathentry kind="var" path="M2_REPO/mesquite/mesquite/2.01.tb/mesquite-2.01.tb.jar"/>
+	<classpathentry kind="var" path="M2_REPO/mrj/MRJToolkitStubs/1.0/MRJToolkitStubs-1.0.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/neethi/neethi/2.0.4/neethi-2.0.4.jar"/>
+	<classpathentry kind="var" path="M2_REPO/oro/oro/2.0.8/oro-2.0.8.jar"/>
+	<classpathentry kind="var" path="M2_REPO/pal/pal/mesquite-201/pal-mesquite-201.jar"/>
+	<classpathentry kind="var" path="M2_REPO/javax/xml/soap/saaj-api/1.3/saaj-api-1.3.jar"/>
+	<classpathentry kind="var" path="M2_REPO/com/sun/xml/messaging/saaj/saaj-impl/1.3/saaj-impl-1.3.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/springframework/spring/2.0.7/spring-2.0.7.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/springframework/spring-beans/2.0.8/spring-beans-2.0.8.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/springframework/spring-context/2.0.8/spring-context-2.0.8.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/springframework/spring-core/2.0.8/spring-core-2.0.8.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/springframework/spring-mock/2.0.7/spring-mock-2.0.7.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/springframework/spring-web/2.0.8/spring-web-2.0.8.jar"/>
+	<classpathentry kind="var" path="M2_REPO/tolbaseclasses/tolbaseclasses/mesquite/tolbaseclasses-mesquite.jar"/>
+	<classpathentry kind="var" path="M2_REPO/velocity/velocity/1.4/velocity-1.4.jar"/>
+	<classpathentry kind="var" path="M2_REPO/velocity/velocity-dep/1.4/velocity-dep-1.4.jar"/>
+	<classpathentry kind="var" path="M2_REPO/wsdl4j/wsdl4j/1.6.1/wsdl4j-1.6.1.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/codehaus/woodstox/wstx-asl/3.2.4/wstx-asl-3.2.4.jar"/>
+	<classpathentry kind="var" path="M2_REPO/xml-resolver/xml-resolver/1.2/xml-resolver-1.2.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/apache/ws/commons/schema/XmlSchema/1.4.2/XmlSchema-1.4.2.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/nexml/model/nexml/1.4-SNAPSHOT/nexml-1.4-SNAPSHOT.jar"/>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>


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[Treebase-guts] SF.net SVN: treebase:[122] trunk/treebase-core/src/main/java/org/cipres/ treebase

From: <rv...@us...> - 2009-06-25 14:09:05

Revision: 122
          http://treebase.svn.sourceforge.net/treebase/?rev=122&view=rev
Author:   rvos
Date:     2009-06-25 13:38:28 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
Changed base URI handling

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusService.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusService.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusService.java	2009-06-25 13:32:10 UTC (rev 121)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusService.java	2009-06-25 13:38:28 UTC (rev 122)
@@ -23,6 +23,7 @@
 
 import java.io.File;
 import java.util.Collection;
+import java.util.Properties;
 
 import org.cipres.treebase.domain.study.Study;
 import org.cipres.treebase.event.ProgressionListener;
@@ -66,6 +67,7 @@
 	 * @return a serialization of the supplied NexusDataSet
 	 */
 	String serialize(NexusDataSet pNexusDataSet);
+	String serialize(NexusDataSet pNexusDataSet, Properties pProperties);
 	
 	/**
 	 * Write the NexusDataSet to a string that represents the object.
@@ -76,5 +78,7 @@
 	 * @return a serialization of the supplied Study
 	 */	
 	String serialize(Study pStudy);
+	String serialize(Study pStudy, Properties pProperties);
+	
 
 }

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java	2009-06-25 13:32:10 UTC (rev 121)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java	2009-06-25 13:38:28 UTC (rev 122)
@@ -26,6 +26,11 @@
 		super(study, taxonLabelHome, document);
 	}
 	
+	public NexmlDocumentConverter(Study study, TaxonLabelHome taxonLabelHome,
+			Document document,String baseURI) {
+		super(study, taxonLabelHome, document,baseURI);
+	}	
+	
 	/**
 	 * 
 	 * @param pDocument

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java	2009-06-25 13:32:10 UTC (rev 121)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java	2009-06-25 13:38:28 UTC (rev 122)
@@ -23,8 +23,10 @@
 public class NexmlObjectConverter extends AbstractNexusConverter {
 	protected static URI mDCURI;
 	protected static URI mPrismURI;
+	protected URI mBaseURI;
 	private static String mDCURIString = "http://purl.org/dc/elements/1.1/";
 	private static String mPrismURIString = "http://prismstandard.org/namespaces/1.2/basic/";
+	private static String mBaseURIString = "http://purl.org/PHYLO/TREEBASE/PHYLOWS/";
 	private static String mDCIdentifier = "dc:identifier";	
 	public static String TreeBASE2Prefix = "TreeBASE2";
 	private Document mDocument;
@@ -34,18 +36,30 @@
 	 * @param study
 	 * @param taxonLabelHome
 	 */
-	public NexmlObjectConverter(Study study, TaxonLabelHome taxonLabelHome, Document document) {
+	public NexmlObjectConverter(Study study, TaxonLabelHome taxonLabelHome, Document document, String baseURI) {
 		try {
 			mDCURI = new URI(mDCURIString);
 			mPrismURI = new URI(mPrismURIString);
+			if ( null != baseURI ) {
+				mBaseURI = new URI(baseURI);
+			}
+			else {
+				mBaseURI = new URI(mBaseURIString);
+			}
 		} catch (URISyntaxException e) {
 			e.printStackTrace();
-		}			
+		}
+		document.setBaseURI(mBaseURI);
 		setTaxonLabelHome(taxonLabelHome);
 		setStudy(study);
 		setDocument(document);
-	}	
+	}
 	
+	public NexmlObjectConverter(Study study, TaxonLabelHome taxonLabelHome, Document document) {
+		this(study,taxonLabelHome,document,null);
+	}
+
+	
 	/**
 	 * 
 	 * @param tbPersistable
@@ -64,11 +78,12 @@
 	protected void attachTreeBaseID(Annotatable annotatable,TBPersistable tbPersistable,Class<?> persistableClass) {
 		if ( null != tbPersistable.getId() ) {
 			attachAnnotation(mDCIdentifier,makeNamespacedID(tbPersistable,persistableClass),mDCURI,annotatable);			
-			String uriString = "http://localhost:8080/treebase-web/PhyloWS/" + makeNamespacedID(tbPersistable,persistableClass);
+			String uriString = mBaseURI.toString() + makeNamespacedID(tbPersistable,persistableClass);
 			try {
 				annotatable.addAnnotationValue("dc:relation",mDCURI, new URI(uriString));
-			} catch ( Exception e ) {
-				
+			} catch (URISyntaxException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
 			}
 		}
 	}
@@ -165,5 +180,13 @@
 			character = iterator.next();
 		}
 		return result.toString();
+	}
+
+	public URI getBaseURI() {
+		return mBaseURI;
+	}
+
+	public void setBaseURI(URI baseURI) {
+		mBaseURI = baseURI;
 	}	
 }

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	2009-06-25 13:32:10 UTC (rev 121)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java	2009-06-25 13:38:28 UTC (rev 122)
@@ -22,6 +22,7 @@
 
 import java.io.File;
 import java.util.Collection;
+import java.util.Properties;
 
 import org.apache.log4j.Logger;
 
@@ -222,4 +223,14 @@
 		return null;
 	}
 
+	public String serialize(NexusDataSet nexusDataSet, Properties properties) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	public String serialize(Study study, Properties properties) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
 }

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java	2009-06-25 13:32:10 UTC (rev 121)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java	2009-06-25 13:38:28 UTC (rev 122)
@@ -22,6 +22,7 @@
 
 import java.io.File;
 import java.util.Collection;
+import java.util.Properties;
 
 import org.apache.log4j.Logger;
 
@@ -174,4 +175,14 @@
 		return null;
 	}
 
+	public String serialize(NexusDataSet nexusDataSet, Properties properties) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	public String serialize(Study study, Properties properties) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
 }

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java	2009-06-25 13:32:10 UTC (rev 121)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java	2009-06-25 13:38:28 UTC (rev 122)
@@ -1,7 +1,10 @@
 package org.cipres.treebase.service.nexus;
 
 import java.io.File;
+import java.net.URI;
+import java.net.URISyntaxException;
 import java.util.Collection;
+import java.util.Properties;
 
 import javax.xml.parsers.ParserConfigurationException;
 
@@ -63,6 +66,7 @@
 	}
 
 	public String serialize(NexusDataSet nexusDataSet) {
+		/*
 		Document document = null;
 		try {
 			document = DocumentFactory.createDocument();
@@ -71,9 +75,12 @@
 		}
 		NexmlDocumentConverter ndc = new NexmlDocumentConverter(null,getTaxonLabelHome(),document);
 		return ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
+		*/
+		return serialize(nexusDataSet,null);
 	}
 
 	public String serialize(Study study) {
+		/*
 		Document document = null;
 		try {
 			document = DocumentFactory.createDocument();
@@ -82,6 +89,8 @@
 		}
 		NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document);
 		return ndc.fromTreeBaseToXml(study).getXmlString();
+		*/
+		return serialize(study,null);
 	}
 
 	public TaxonLabelHome getTaxonLabelHome() {
@@ -91,5 +100,59 @@
 	public void setTaxonLabelHome(TaxonLabelHome taxonLabelHome) {
 		mTaxonLabelHome = taxonLabelHome;
 	}
+	
+	protected NexmlDocumentConverter getNexmlDocumentConverter(Study study,Properties properties) {
+		String baseURI = null;
+		if ( null != properties ) {
+			baseURI = properties.getProperty("nexml.uri.base");
+		}
+		Document document = null;
+		try {
+			document = DocumentFactory.createDocument();
+			document.setBaseURI(new URI(baseURI));//NPE
+		} catch (URISyntaxException e) {
+			e.printStackTrace();
+		} catch (ParserConfigurationException e) {
+			e.printStackTrace();
+		}
+		NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document,baseURI);
+		return ndc;
+	}
 
+	public String serialize(NexusDataSet nexusDataSet, Properties properties) {
+		/*
+		String baseURI = null;
+		if ( null != properties ) {
+			baseURI = properties.getProperty("nexml.uri.base");
+		}
+		Document document = null;
+		try {
+			document = DocumentFactory.createDocument();
+		} catch (ParserConfigurationException e) {
+			e.printStackTrace();
+		}		
+		NexmlDocumentConverter ndc = new NexmlDocumentConverter(null,getTaxonLabelHome(),document,baseURI);
+		*/
+		NexmlDocumentConverter ndc = this.getNexmlDocumentConverter(null, properties);
+		return ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
+	}
+
+	public String serialize(Study study, Properties properties) {
+		/*
+		String baseURI = null;
+		if ( null != properties ) {
+			baseURI = properties.getProperty("nexml.uri.base");
+		}		
+		Document document = null;
+		try {
+			document = DocumentFactory.createDocument();
+		} catch (ParserConfigurationException e) {
+			e.printStackTrace();
+		}
+		NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document,baseURI);
+		*/
+		NexmlDocumentConverter ndc = this.getNexmlDocumentConverter(study, properties);
+		return ndc.fromTreeBaseToXml(study).getXmlString();
+	}
+
 }

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java	2009-06-25 13:32:10 UTC (rev 121)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java	2009-06-25 13:38:28 UTC (rev 122)
@@ -4,6 +4,7 @@
 package org.cipres.treebase.service.nexus;
 
 import java.io.ByteArrayInputStream;
+import java.util.Properties;
 
 import javax.xml.parsers.ParserConfigurationException;
 
@@ -28,7 +29,12 @@
  *
  */
 public class NexusServiceRDFa extends NexusServiceNexml {
+	public String serialize(NexusDataSet nexusDataSet,Properties properties) {
+		NexmlDocumentConverter ndc = getNexmlDocumentConverter(null, properties);
+		return transform(ndc.fromTreeBaseToXml(nexusDataSet).getXmlString());
+	}
 	public String serialize(NexusDataSet nexusDataSet) {
+		/*
 		Document document = null;
 		try {
 			document = DocumentFactory.createDocument();
@@ -38,9 +44,17 @@
 		NexmlDocumentConverter ndc = new NexmlDocumentConverter(null,getTaxonLabelHome(),document);
 		String NeXML = ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
 		return transform(NeXML);
+		*/
+		NexmlDocumentConverter ndc = getNexmlDocumentConverter(null, null);
+		return transform(ndc.fromTreeBaseToXml(nexusDataSet).getXmlString());		
 	}
 
+	public String serialize(Study study,Properties properties) {
+		NexmlDocumentConverter ndc = getNexmlDocumentConverter(study, properties);
+		return transform(ndc.fromTreeBaseToXml(study).getXmlString());
+	}
 	public String serialize(Study study) {
+		/*
 		Document document = null;
 		try {
 			document = DocumentFactory.createDocument();
@@ -50,6 +64,9 @@
 		NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document);
 		String NeXML = ndc.fromTreeBaseToXml(study).getXmlString();
 		return transform(NeXML);
+		*/
+		NexmlDocumentConverter ndc = getNexmlDocumentConverter(study, null);
+		return transform(ndc.fromTreeBaseToXml(study).getXmlString());		
 	}
 	
 	private String transform(String input) {


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[Treebase-guts] SF.net SVN: treebase:[119] trunk/treebase-web/src/main/webapp/WEB-INF/pages /search/study

From: <rv...@us...> - 2009-06-25 03:30:55

Revision: 119
          http://treebase.svn.sourceforge.net/treebase/?rev=119&view=rev
Author:   rvos
Date:     2009-06-25 03:30:53 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
Added download links for RDF

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrices.jsp
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrices.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrices.jsp	2009-06-25 03:25:11 UTC (rev 118)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrices.jsp	2009-06-25 03:30:53 UTC (rev 119)
@@ -83,6 +83,20 @@
 		sortable="false"
 		class="iconColumn" 
 		headerClass="iconColumn">
+		<c:url value="/PhyloWS/${matrix.namespacedGUID}.rdf" var="newMatrixURL"/>
+		<a href="${newMatrixURL}">
+			<img 
+				class="iconButton" 
+				src="<fmt:message key="icons.rdf"/>" 
+				title="<fmt:message key="download.rdf"/>" 
+				alt="<fmt:message key="download.rdf"/>"/>			
+		</a>
+	</display:column>	
+	
+	<display:column  
+		sortable="false"
+		class="iconColumn" 
+		headerClass="iconColumn">
 		<c:url value="/PhyloWS/${matrix.namespacedGUID}.nex" var="newMatrixURL"/>
 		<a href="${newMatrixURL}">
 			<img 

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp	2009-06-25 03:25:11 UTC (rev 118)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp	2009-06-25 03:30:53 UTC (rev 119)
@@ -104,7 +104,15 @@
 				title="<fmt:message key="download.nexml"/>" 
 				alt="<fmt:message key="download.nexml"/>"/>	
 			NeXML			
-		</a>		
+		</a>	
+		<a href="${baseLink}.rdf">
+			<img 
+				class="iconButton" 
+				src="<fmt:message key="icons.rdf"/>" 
+				title="<fmt:message key="download.rdf"/>" 
+				alt="<fmt:message key="download.rdf"/>"/>	
+			RDF			
+		</a>
 	</li>
 </ul>
 <h3>BibTeX reference</h3>

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	2009-06-25 03:25:11 UTC (rev 118)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp	2009-06-25 03:30:53 UTC (rev 119)
@@ -67,6 +67,20 @@
 				alt="<fmt:message key="download.nexml"/>"/>				
 		</a>
 	</display:column>	
+
+	<display:column 
+		sortable="false"
+		class="iconColumn" 
+		headerClass="iconColumn">
+		<c:url value="/PhyloWS/${tree.namespacedGUID}.rdf" var="newTreeURL"/>
+		<a href="${newTreeURL}">
+			<img 
+				class="iconButton" 
+				src="<fmt:message key="icons.rdf"/>" 
+				title="<fmt:message key="download.rdf"/>" 
+				alt="<fmt:message key="download.rdf"/>"/>				
+		</a>
+	</display:column>	
 	
 	<display:column 
 		sortable="false"


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[Treebase-guts] SF.net SVN: treebase:[118] trunk/treebase-web/src/main/resources/ ApplicationResources.properties

From: <rv...@us...> - 2009-06-25 03:25:12

Revision: 118
          http://treebase.svn.sourceforge.net/treebase/?rev=118&view=rev
Author:   rvos
Date:     2009-06-25 03:25:11 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
Added property for download.rdf

Modified Paths:
--------------
    trunk/treebase-web/src/main/resources/ApplicationResources.properties

Modified: trunk/treebase-web/src/main/resources/ApplicationResources.properties
===================================================================
--- trunk/treebase-web/src/main/resources/ApplicationResources.properties	2009-06-25 03:00:12 UTC (rev 117)
+++ trunk/treebase-web/src/main/resources/ApplicationResources.properties	2009-06-25 03:25:11 UTC (rev 118)
@@ -301,6 +301,7 @@
 download.reconstructedfile = Download Reconstructed File
 download.nexml = Download NeXML File
 download.json = Download JSON File
+download.rdf = Download RDF file
 
 #-- matrix row section --
 matrix.row.id = Matrix Row ID


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[Treebase-guts] SF.net SVN: treebase:[117] trunk/treebase-web/src/main/webapp/WEB-INF/pages /search/study/summary.jsp

From: <rv...@us...> - 2009-06-25 03:00:13

Revision: 117
          http://treebase.svn.sourceforge.net/treebase/?rev=117&view=rev
Author:   rvos
Date:     2009-06-25 03:00:12 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
Added section listing alternate URLs

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp	2009-06-25 02:57:29 UTC (rev 116)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp	2009-06-25 03:00:12 UTC (rev 117)
@@ -8,10 +8,12 @@
 </head>
 
 <body id="s-study"/>
+<c:set var="serverName" scope="request" value="<%= request.getServerName() %>"/>
+<c:set var="portNumber" scope="request" value="<%= request.getServerPort() %>"/>
+<c:set var="baseLink" scope="request" value='http://${serverName}:${portNumber}/treebase-web/PhyloWS/${study.namespacedGUID}'/>
 <c:set var="currentSection" scope="request" value="Citation"/>
 <c:set var="headerPrefix" scope="request" value="${currentSection} for"/>
 <jsp:include page="nav.jsp"/>
-
 <c:if test="${not empty cit.authors || true}">
 	<p><c:out value="${cit.authorsCitationStyleWithoutHtml}"/></p>
 	<c:if test="${not empty cit.authors}">
@@ -78,7 +80,33 @@
 	</c:if>
 	</ul>
 </c:if>
-
+<h3>About this resource</h3>
+<ul>
+	<li>Canonical resource URI: 
+		<a href="${baseLink}">
+			<img class="iconButton" src="<fmt:message key="icons.weblink"/>"/>	
+			${baseLink}
+		</a>
+	</li>
+	<li>Other versions:
+		<a href="${baseLink}.nex">
+			<img 
+				class="iconButton" 
+				src="<fmt:message key="icons.download.reconstructed"/>" 
+				title="<fmt:message key="download.reconstructedfile"/>" 
+				alt="<fmt:message key="download.reconstructedfile"/>"/>	
+			Nexus			
+		</a>
+		<a href="${baseLink}.xml">
+			<img 
+				class="iconButton" 
+				src="<fmt:message key="icons.xml"/>" 
+				title="<fmt:message key="download.nexml"/>" 
+				alt="<fmt:message key="download.nexml"/>"/>	
+			NeXML			
+		</a>		
+	</li>
+</ul>
 <h3>BibTeX reference</h3>
 <pre style="width:100%;overflow:scroll">
 <c:out value="${cit.bibtexReference}"/>


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[Treebase-guts] SF.net SVN: treebase:[116] trunk/treebase-web/src/main/webapp/WEB-INF/pages /search/study/matrices.jsp

From: <rv...@us...> - 2009-06-25 02:57:30

Revision: 116
          http://treebase.svn.sourceforge.net/treebase/?rev=116&view=rev
Author:   rvos
Date:     2009-06-25 02:57:29 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
Added NeXML download link

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrices.jsp

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrices.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrices.jsp	2009-06-25 02:55:45 UTC (rev 115)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrices.jsp	2009-06-25 02:57:29 UTC (rev 116)
@@ -69,13 +69,24 @@
 		sortable="false"
 		class="iconColumn" 
 		headerClass="iconColumn">
-		<c:url value="/search/downloadAMatrix.html" var="newMatrixURL">
-			<c:param name="id">${study.id}</c:param>
-			<c:param name="matrixid">${matrix.id}</c:param>
-		</c:url>
+		<c:url value="/PhyloWS/${matrix.namespacedGUID}.xml" var="newMatrixURL"/>
 		<a href="${newMatrixURL}">
 			<img 
 				class="iconButton" 
+				src="<fmt:message key="icons.xml"/>" 
+				title="<fmt:message key="download.nexml"/>" 
+				alt="<fmt:message key="download.nexml"/>"/>			
+		</a>
+	</display:column>	
+	
+	<display:column  
+		sortable="false"
+		class="iconColumn" 
+		headerClass="iconColumn">
+		<c:url value="/PhyloWS/${matrix.namespacedGUID}.nex" var="newMatrixURL"/>
+		<a href="${newMatrixURL}">
+			<img 
+				class="iconButton" 
 				src="<fmt:message key="icons.download.reconstructed"/>" 
 				title="<fmt:message key="download.reconstructedfile"/>" 
 				alt="<fmt:message key="download.reconstructedfile"/>"/>			
@@ -103,10 +114,7 @@
 		sortable="false"
 		class="iconColumn" 
 		headerClass="iconColumn">
-		<c:url var="url" value="matrix.html">
-			<c:param name="matrixid" value="${matrix.id}" />
-			<c:param name="id" value="${matrix.study.id}" />
-		</c:url>
+		<c:url var="url" value="/PhyloWS/${matrix.namespacedGUID}.html"/>
 		<a href="${url}">		
 			<img 
 				class="iconButton" 


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[Treebase-guts] SF.net SVN: treebase:[115] trunk/treebase-web/src/main/webapp/WEB-INF/pages /search/study/trees.jsp

From: <rv...@us...> - 2009-06-25 02:55:47

Revision: 115
          http://treebase.svn.sourceforge.net/treebase/?rev=115&view=rev
Author:   rvos
Date:     2009-06-25 02:55:45 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
Added NeXML download link

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.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	2009-06-25 02:53:11 UTC (rev 114)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp	2009-06-25 02:55:45 UTC (rev 115)
@@ -58,13 +58,24 @@
 		sortable="false"
 		class="iconColumn" 
 		headerClass="iconColumn">
-		<c:url value="/search/downloadATree.html" var="newTreeURL">
-			<c:param name="id">${study.id}</c:param>
-			<c:param name="treeid">${tree.id}</c:param>
-		</c:url>
+		<c:url value="/PhyloWS/${tree.namespacedGUID}.xml" var="newTreeURL"/>
 		<a href="${newTreeURL}">
 			<img 
 				class="iconButton" 
+				src="<fmt:message key="icons.xml"/>" 
+				title="<fmt:message key="download.nexml"/>" 
+				alt="<fmt:message key="download.nexml"/>"/>				
+		</a>
+	</display:column>	
+	
+	<display:column 
+		sortable="false"
+		class="iconColumn" 
+		headerClass="iconColumn">
+		<c:url value="/PhyloWS/${tree.namespacedGUID}.nex" var="newTreeURL"/>
+		<a href="${newTreeURL}">
+			<img 
+				class="iconButton" 
 				src="<fmt:message key="icons.download.reconstructed"/>" 
 				title="<fmt:message key="download.reconstructedfile"/>" 
 				alt="<fmt:message key="download.reconstructedfile"/>"/>				


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[Treebase-guts] SF.net SVN: treebase:[114] trunk/treebase-web/src/main/resources/ ApplicationResources.properties

From: <rv...@us...> - 2009-06-25 02:53:12

Revision: 114
          http://treebase.svn.sourceforge.net/treebase/?rev=114&view=rev
Author:   rvos
Date:     2009-06-25 02:53:11 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
Added some icon paths

Modified Paths:
--------------
    trunk/treebase-web/src/main/resources/ApplicationResources.properties

Modified: trunk/treebase-web/src/main/resources/ApplicationResources.properties
===================================================================
--- trunk/treebase-web/src/main/resources/ApplicationResources.properties	2009-06-25 02:52:19 UTC (rev 113)
+++ trunk/treebase-web/src/main/resources/ApplicationResources.properties	2009-06-25 02:53:11 UTC (rev 114)
@@ -299,6 +299,8 @@
 matrix.description = Description
 download.original = Download Original File
 download.reconstructedfile = Download Reconstructed File
+download.nexml = Download NeXML File
+download.json = Download JSON File
 
 #-- matrix row section --
 matrix.row.id = Matrix Row ID
@@ -465,7 +467,12 @@
 icons.arrow_left=/treebase-web/images/icons/arrow_left.png
 icons.collapse=/treebase-web/images/minus.gif
 icons.expand=/treebase-web/images/plus.gif
+icons.xml=/treebase-web/images/icons/page_white_code.png
+icons.rdf=/treebase-web/images/icons/page_white_code_red.png
+icons.json=/treebase-web/images/icons/script.png
+icons.permalink=/treebase-web/images/icons/link.png
 
+
 #-- help system --
 help.title=Help window
 help.admin.legend=Modify help message "{0}" here


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[Treebase-guts] SF.net SVN: treebase:[113] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlObjectConverter.java

From: <rv...@us...> - 2009-06-25 02:52:25

Revision: 113
          http://treebase.svn.sourceforge.net/treebase/?rev=113&view=rev
Author:   rvos
Date:     2009-06-25 02:52:19 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
attachTreebaseID now also attaches a dc:relation annotation with the canonical URL for the annotated resource

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java	2009-06-25 02:50:10 UTC (rev 112)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java	2009-06-25 02:52:19 UTC (rev 113)
@@ -63,7 +63,13 @@
 	 */
 	protected void attachTreeBaseID(Annotatable annotatable,TBPersistable tbPersistable,Class<?> persistableClass) {
 		if ( null != tbPersistable.getId() ) {
-			attachAnnotation(mDCIdentifier,makeNamespacedID(tbPersistable,persistableClass),mDCURI,annotatable);
+			attachAnnotation(mDCIdentifier,makeNamespacedID(tbPersistable,persistableClass),mDCURI,annotatable);			
+			String uriString = "http://localhost:8080/treebase-web/PhyloWS/" + makeNamespacedID(tbPersistable,persistableClass);
+			try {
+				annotatable.addAnnotationValue("dc:relation",mDCURI, new URI(uriString));
+			} catch ( Exception e ) {
+				
+			}
 		}
 	}
 	


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[Treebase-guts] SF.net SVN: treebase:[112] trunk/treebase-core/src/main/java/org/cipres/ treebase/service/nexus/NexusServiceRDFa.java

From: <rv...@us...> - 2009-06-25 02:50:16

Revision: 112
          http://treebase.svn.sourceforge.net/treebase/?rev=112&view=rev
Author:   rvos
Date:     2009-06-25 02:50:10 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
Adding NexusServiceRDFa serialization service

Added Paths:
-----------
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java

Added: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java	                        (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java	2009-06-25 02:50:10 UTC (rev 112)
@@ -0,0 +1,83 @@
+/**
+ * 
+ */
+package org.cipres.treebase.service.nexus;
+
+import java.io.ByteArrayInputStream;
+
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.cipres.treebase.domain.nexus.NexusDataSet;
+import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentConverter;
+import org.cipres.treebase.domain.study.Study;
+import org.dom4j.DocumentException;
+import org.dom4j.io.DocumentResult;
+import org.dom4j.io.DocumentSource;
+import org.dom4j.io.SAXReader;
+import org.nexml.model.Document;
+import org.nexml.model.DocumentFactory;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerConfigurationException;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.stream.StreamSource;
+
+
+/**
+ * @author rvosa
+ *
+ */
+public class NexusServiceRDFa extends NexusServiceNexml {
+	public String serialize(NexusDataSet nexusDataSet) {
+		Document document = null;
+		try {
+			document = DocumentFactory.createDocument();
+		} catch (ParserConfigurationException e) {
+			e.printStackTrace();
+		}
+		NexmlDocumentConverter ndc = new NexmlDocumentConverter(null,getTaxonLabelHome(),document);
+		String NeXML = ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
+		return transform(NeXML);
+	}
+
+	public String serialize(Study study) {
+		Document document = null;
+		try {
+			document = DocumentFactory.createDocument();
+		} catch (ParserConfigurationException e) {
+			e.printStackTrace();
+		}
+		NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document);
+		String NeXML = ndc.fromTreeBaseToXml(study).getXmlString();
+		return transform(NeXML);
+	}
+	
+	private String transform(String input) {
+		SAXReader reader = new SAXReader();
+		ByteArrayInputStream bs = new ByteArrayInputStream(input.getBytes());
+		org.dom4j.Document jDomDocument = null;
+		try {
+			jDomDocument = reader.read( bs );
+		} catch (DocumentException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		TransformerFactory factory = TransformerFactory.newInstance();
+		Transformer transformer = null;
+		try {
+			transformer = factory.newTransformer( new StreamSource( "http://www.nexml.org/nexml/xslt/RDFa2RDFXML.xsl" ) );
+		} catch (TransformerConfigurationException e1) {
+			e1.printStackTrace();
+		}		
+		DocumentSource source = new DocumentSource( jDomDocument );
+		DocumentResult result = new DocumentResult();
+		try {
+			transformer.transform( source, result );
+		} catch (TransformerException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		org.dom4j.Document transformedDoc = result.getDocument();
+		return transformedDoc.asXML();		
+	}
+}


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