[Treebase-guts] SF.net SVN: treebase:[135] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlOTUConverter.java

[<rv...@us...>]

Revision: 135
          http://treebase.svn.sourceforge.net/treebase/?rev=135&view=rev
Author:   rvos
Date:     2009-06-28 10:10:36 +0000 (Sun, 28 Jun 2009)

Log Message:
-----------
Now attaches uBio and NCBI identifiers as dc:relation annotations

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

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java	2009-06-28 10:09:22 UTC (rev 134)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java	2009-06-28 10:10:36 UTC (rev 135)
@@ -1,5 +1,7 @@
 package org.cipres.treebase.domain.nexus.nexml;
 
+import java.net.URI;
+
 import org.cipres.treebase.domain.study.Study;
 import org.cipres.treebase.domain.taxon.TaxonLabel;
 import org.cipres.treebase.domain.taxon.TaxonLabelHome;
@@ -80,12 +82,16 @@
 		}
 		attachTreeBaseID(xmlOTU,taxonLabel,TaxonLabel.class);
 		if ( null != taxonLabel.getNcbiTaxID() ) {
-			attachAnnotation("dc:identifier", "NCBI:" + taxonLabel.getNcbiTaxID(), mDCURI, xmlOTU);
+			StringBuilder urlString = new StringBuilder(getDocument().getBaseURI().toString());
+			taxonLabel.getPhyloWSPath().getPath(urlString).append("NCBI:").append(taxonLabel.getNcbiTaxID());									
+			xmlOTU.addAnnotationValue("dc:relation", mDCURI, URI.create(urlString.toString()));
 		}
 		TaxonVariant tv = taxonLabel.getTaxonVariant();
 		if ( null != tv ) {
 			if ( null != tv.getNamebankID() ) {
-				attachAnnotation("dc:identifier", "uBio:" + tv.getNamebankID(), mDCURI, xmlOTU);
+				StringBuilder urlString = new StringBuilder(getDocument().getBaseURI().toString());
+				taxonLabel.getPhyloWSPath().getPath(urlString).append("uBio:").append(tv.getNamebankID());					
+				xmlOTU.addAnnotationValue("dc:relation", mDCURI, URI.create(urlString.toString()));
 			}
 		}
 		return xmlOTU;


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