[Treebase-guts] SF.net SVN: treebase:[574] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml

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

Revision: 574
          http://treebase.svn.sourceforge.net/treebase/?rev=574&view=rev
Author:   rvos
Date:     2010-03-15 01:08:05 +0000 (Mon, 15 Mar 2010)

Log Message:
-----------
Now calls getAnnotations() to let the object decide what metadata to add as opposed to fiddling with the object here.

Modified Paths:
--------------
    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/NexmlTreeBlockConverter.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	2010-03-15 01:07:17 UTC (rev 573)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java	2010-03-15 01:08:05 UTC (rev 574)
@@ -1,12 +1,9 @@
 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;
 import org.cipres.treebase.domain.taxon.TaxonLabelSet;
-import org.cipres.treebase.domain.taxon.TaxonVariant;
 import org.nexml.model.Document;
 import org.nexml.model.OTU;
 import org.nexml.model.OTUs;
@@ -81,26 +78,6 @@
 			xmlOTU.setLabel(taxonLabel.getTaxonLabel());
 		}
 		attachTreeBaseID(xmlOTU,taxonLabel,TaxonLabel.class);
-		if ( null != taxonLabel.getNcbiTaxID() ) {
-			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()));
-			xmlOTU.addAnnotationValue("tb:identifier.ncbi", mTBTermsURI, "NCBI:" + taxonLabel.getNcbiTaxID());
-			xmlOTU.addAnnotationValue("tb:identifier.taxon", mTBTermsURI, taxonLabel.getTaxonVariant().getTaxon().getId());
-			xmlOTU.addAnnotationValue("tb:identifier.taxonLabel", mTBTermsURI, taxonLabel.getId());
-			xmlOTU.addAnnotationValue("tb:title.taxon", mTBTermsURI, taxonLabel.getTaxonVariant().getTaxon().getName());
-		}
-		TaxonVariant tv = taxonLabel.getTaxonVariant();
-		if ( null != tv ) {
-			if ( null != tv.getNamebankID() ) {
-				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()));
-				xmlOTU.addAnnotationValue("tb:identifier.ubio", mTBTermsURI, "uBio:" + tv.getNamebankID());
-				xmlOTU.addAnnotationValue("tb:identifier.taxonVariant", mTBTermsURI, tv.getId());
-				xmlOTU.addAnnotationValue("tb:title.taxonVariant", mTBTermsURI, tv.getFullName());
-			}
-		}
 		return xmlOTU;
 	}
 

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java	2010-03-15 01:07:17 UTC (rev 573)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java	2010-03-15 01:08:05 UTC (rev 574)
@@ -3,6 +3,7 @@
 import java.util.Iterator;
 import java.util.Set;
 
+import org.cipres.treebase.Constants;
 import org.cipres.treebase.domain.study.Study;
 import org.cipres.treebase.domain.taxon.TaxonLabel;
 import org.cipres.treebase.domain.taxon.TaxonLabelHome;
@@ -84,21 +85,6 @@
 		if ( null != phyloTree.getLabel() ) {
 			xmlTree.setLabel(phyloTree.getLabel());
 		}
-		if ( null != phyloTree.getId() ) { 
-			xmlTree.addAnnotationValue("tb:identifier.tree", mTBTermsURI, phyloTree.getId());
-		}
-		if ( null != phyloTree.getKindDescription() ) {
-			xmlTree.addAnnotationValue("tb:kind.tree", mTBTermsURI, phyloTree.getKindDescription());
-		}
-		if ( null != phyloTree.getTypeDescription() ) {
-			xmlTree.addAnnotationValue("tb:type.tree", mTBTermsURI, phyloTree.getTypeDescription());
-		}
-		if ( null != phyloTree.getQualityDescription() ) {
-			xmlTree.addAnnotationValue("tb:quality.tree", mTBTermsURI, phyloTree.getQualityDescription());
-		}
-		if ( null != phyloTree.getnTax() ) {
-			xmlTree.addAnnotationValue("tb:ntax.tree", mTBTermsURI, phyloTree.getnTax());
-		}
 		attachTreeBaseID(xmlTree, phyloTree,PhyloTree.class);
 		copyTreeBaseTree(phyloTree, xmlTree);
 		return xmlTree;


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