[Treebase-guts] SF.net SVN: treebase:[578] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/taxon/TaxonLabel.java

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

Revision: 578
          http://treebase.svn.sourceforge.net/treebase/?rev=578&view=rev
Author:   rvos
Date:     2010-03-15 01:14:03 +0000 (Mon, 15 Mar 2010)

Log Message:
-----------
Added getAnnotations() and getLabel() for nexml and rdf serialization.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java	2010-03-15 01:13:21 UTC (rev 577)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java	2010-03-15 01:14:03 UTC (rev 578)
@@ -1,5 +1,9 @@
 package org.cipres.treebase.domain.taxon;
 
+import java.net.URI;
+import java.util.List;
+import java.util.Set;
+
 import javax.persistence.AttributeOverride;
 import javax.persistence.CascadeType;
 import javax.persistence.Column;
@@ -10,8 +14,12 @@
 import javax.persistence.Table;
 import javax.persistence.Transient;
 
+import org.cipres.treebase.Constants;
+import org.cipres.treebase.TreebaseUtil;
 import org.cipres.treebase.domain.AbstractPersistedObject;
+import org.cipres.treebase.domain.Annotation;
 import org.cipres.treebase.domain.TBPersistable;
+import org.cipres.treebase.domain.admin.Person;
 import org.cipres.treebase.domain.study.Study;
 import org.cipres.treebase.domain.study.Submission;
 import org.hibernate.annotations.BatchSize;
@@ -194,4 +202,35 @@
 		}
 		return result;
 	}
+	
+	@Transient
+	public List<Annotation> getAnnotations() {
+		List<Annotation> annotations = super.getAnnotations();
+		if ( null != getNcbiTaxID() ) {
+			StringBuilder urlString = new StringBuilder(TreebaseUtil.getPurlDomain());
+			getPhyloWSPath().getPath(urlString).append("NCBI:").append(getNcbiTaxID());									
+			annotations.add(new Annotation(Constants.DCTermsURI, "dc:relation", URI.create(urlString.toString())));
+			annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.ncbi", "NCBI:" + getNcbiTaxID()));
+			annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxon", getTaxonVariant().getTaxon().getId()));
+			annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxonLabel", getId()));
+			annotations.add(new Annotation(Constants.TBTermsURI, "tb:title.taxon", getTaxonVariant().getTaxon().getName()));
+		}
+		TaxonVariant tv = getTaxonVariant();
+		if ( null != tv ) {
+			if ( null != tv.getNamebankID() ) {
+				StringBuilder urlString = new StringBuilder(TreebaseUtil.getPurlDomain());
+				getPhyloWSPath().getPath(urlString).append("uBio:").append(tv.getNamebankID());					
+				annotations.add(new Annotation(Constants.DCTermsURI, "dc:relation", URI.create(urlString.toString())));
+				annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.ubio", "uBio:" + tv.getNamebankID()));
+				annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxonVariant", tv.getId()));
+				annotations.add(new Annotation(Constants.TBTermsURI, "tb:title.taxonVariant", tv.getFullName()));
+			}
+		}	
+		return annotations;
+	}	
+	
+	@Transient
+	public String getLabel() {
+		return getTaxonLabel();
+	}
 }


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