[Treebase-guts] SF.net SVN: treebase:[1040] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml

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

Revision: 1040
          http://treebase.svn.sourceforge.net/treebase/?rev=1040&view=rev
Author:   rvos
Date:     2012-02-01 23:15:59 +0000 (Wed, 01 Feb 2012)
Log Message:
-----------
This revision places attachTreeBaseID() earlier in the NeXML object creation, before any annotations are attached. This so that the about attribute is set correctly, by computing it from the TreeBASE ID instead of the internal object ID from the NeXML API.

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

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUWriter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUWriter.java	2012-02-01 21:52:11 UTC (rev 1039)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUWriter.java	2012-02-01 23:15:59 UTC (rev 1040)
@@ -30,13 +30,12 @@
 	 */
 	public OTUs fromTreeBaseToXml(TaxonLabelSet taxonLabelSet) {
 		OTUs xmlOTUs = getDocument().createOTUs();
+		attachTreeBaseID(xmlOTUs,taxonLabelSet,TaxonLabelSet.class);
 		
-		// attach base uri and skos:historyNote
 		xmlOTUs.setBaseURI(mTaxonBaseURI);
-		xmlOTUs.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using "+this.toString()+" $Rev$");
-		
+		xmlOTUs.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using "+this.toString()+" $Rev$");		
 		xmlOTUs.setLabel(taxonLabelSet.getTitle());
-		attachTreeBaseID(xmlOTUs,taxonLabelSet,TaxonLabelSet.class);
+		
 		for ( TaxonLabel taxonLabel : taxonLabelSet.getTaxonLabelsReadOnly() ) {
 			fromTreeBaseToXml(taxonLabel,xmlOTUs);
 		}

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockWriter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockWriter.java	2012-02-01 21:52:11 UTC (rev 1039)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockWriter.java	2012-02-01 23:15:59 UTC (rev 1040)
@@ -52,15 +52,17 @@
 		TaxonLabelSet taxonLabelSet = treeBlock.getTaxonLabelSet();
 		OTUs xmlOTUs = getOTUsById(taxonLabelSet.getId());
 		org.nexml.model.TreeBlock xmlTreeBlock = getDocument().createTreeBlock(xmlOTUs);
+		attachTreeBaseID((Annotatable)xmlTreeBlock,treeBlock,TreeBlock.class);
 		
 		// attach base uri and skos:historyNote
 		xmlTreeBlock.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using "+this.toString()+" $Rev$");
 		xmlTreeBlock.setBaseURI(mTreeBaseURI);
+		xmlTreeBlock.setLabel(treeBlock.getLabel());
 		
 		if ( null != treeBlock.getTitle() ) {
 			xmlTreeBlock.setLabel(treeBlock.getTitle());
 		}
-		attachTreeBaseID((Annotatable)xmlTreeBlock,treeBlock,TreeBlock.class);
+		
 		for ( PhyloTree phyloTree : treeBlock.getTreeList() ) {
 			fromTreeBaseToXml(phyloTree,xmlTreeBlock);
 		}

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