treebase-guts

[Treebase-guts] SF.net SVN: treebase:[64] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlOTUConverter.java

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

Revision: 64
          http://treebase.svn.sourceforge.net/treebase/?rev=64&view=rev
Author:   rvos
Date:     2009-06-19 02:15:10 +0000 (Fri, 19 Jun 2009)

Log Message:
-----------
Added NCBI taxonID and uBio namebankID serialization (to metadata attachments)

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	2009-06-19 02:14:12 UTC (rev 63)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java	2009-06-19 02:15:10 UTC (rev 64)
@@ -4,6 +4,7 @@
 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;
@@ -74,6 +75,15 @@
 		OTU xmlOTU = xmlOTUs.createOTU();
 		xmlOTU.setLabel(taxonLabel.getTaxonLabel());
 		attachTreeBaseID(xmlOTU,taxonLabel);
+		if ( null != taxonLabel.getNcbiTaxID() ) {
+			attachAnnotation("dc:identifier", "NCBI:" + taxonLabel.getNcbiTaxID(), mDCURI, xmlOTU);
+		}
+		TaxonVariant tv = taxonLabel.getTaxonVariant();
+		if ( null != tv ) {
+			if ( null != tv.getNamebankID() ) {
+				attachAnnotation("dc:identifier", "uBio:" + tv.getNamebankID(), mDCURI, xmlOTU);
+			}
+		}
 		return xmlOTU;
 	}
 


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[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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[Treebase-guts] SF.net SVN: treebase:[787] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlOTUConverter.java

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

Revision: 787
          http://treebase.svn.sourceforge.net/treebase/?rev=787&view=rev
Author:   rvos
Date:     2011-04-19 10:59:49 +0000 (Tue, 19 Apr 2011)

Log Message:
-----------
Now setting the xml:base attribute to <phylowsPurl>/taxon/TB2: on every taxa block.

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	2011-04-19 10:55:10 UTC (rev 786)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java	2011-04-19 10:59:49 UTC (rev 787)
@@ -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;
@@ -46,6 +48,7 @@
 	 */
 	public OTUs fromTreeBaseToXml(TaxonLabelSet taxonLabelSet) {
 		OTUs xmlOTUs = getDocument().createOTUs();
+		xmlOTUs.setBaseURI(mTaxonBaseURI);
 		xmlOTUs.setLabel(taxonLabelSet.getTitle());
 		attachTreeBaseID(xmlOTUs,taxonLabelSet,TaxonLabelSet.class);
 		for ( TaxonLabel taxonLabel : taxonLabelSet.getTaxonLabelsReadOnly() ) {


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[Treebase-guts] SF.net SVN: treebase:[908] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlOTUConverter.java

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

Revision: 908
          http://treebase.svn.sourceforge.net/treebase/?rev=908&view=rev
Author:   rvos
Date:     2011-06-10 16:47:32 +0000 (Fri, 10 Jun 2011)

Log Message:
-----------
Removed unused import

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	2011-06-10 14:51:54 UTC (rev 907)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java	2011-06-10 16:47:32 UTC (rev 908)
@@ -1,7 +1,5 @@
 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;


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[Treebase-guts] SF.net SVN: treebase:[944] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlOTUConverter.java

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

Revision: 944
          http://treebase.svn.sourceforge.net/treebase/?rev=944&view=rev
Author:   rvos
Date:     2011-08-25 14:31:28 +0000 (Thu, 25 Aug 2011)
Log Message:
-----------
Added skos:historyNote to keep track of which version of the converter we're using

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

Property Changed:
----------------
    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	2011-08-25 14:29:19 UTC (rev 943)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java	2011-08-25 14:31:28 UTC (rev 944)
@@ -1,5 +1,6 @@
 package org.cipres.treebase.domain.nexus.nexml;
 
+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;
@@ -46,7 +47,11 @@
 	 */
 	public OTUs fromTreeBaseToXml(TaxonLabelSet taxonLabelSet) {
 		OTUs xmlOTUs = getDocument().createOTUs();
+		
+		// attach base uri and skos:historyNote
 		xmlOTUs.setBaseURI(mTaxonBaseURI);
+		getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlOTUConverter $Rev$");
+		
 		xmlOTUs.setLabel(taxonLabelSet.getTitle());
 		attachTreeBaseID(xmlOTUs,taxonLabelSet,TaxonLabelSet.class);
 		for ( TaxonLabel taxonLabel : taxonLabelSet.getTaxonLabelsReadOnly() ) {


Property changes on: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
___________________________________________________________________
Added: svn:keywords
   + Rev

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[Treebase-guts] SF.net SVN: treebase:[947] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlOTUConverter.java

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

Revision: 947
          http://treebase.svn.sourceforge.net/treebase/?rev=947&view=rev
Author:   rvos
Date:     2011-08-25 14:40:19 +0000 (Thu, 25 Aug 2011)
Log Message:
-----------
Actually, the skos:historyNote should probably be attached to the taxa, not the study

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	2011-08-25 14:39:44 UTC (rev 946)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java	2011-08-25 14:40:19 UTC (rev 947)
@@ -50,7 +50,7 @@
 		
 		// attach base uri and skos:historyNote
 		xmlOTUs.setBaseURI(mTaxonBaseURI);
-		getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlOTUConverter $Rev$");
+		xmlOTUs.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlOTUConverter $Rev$");
 		
 		xmlOTUs.setLabel(taxonLabelSet.getTitle());
 		attachTreeBaseID(xmlOTUs,taxonLabelSet,TaxonLabelSet.class);

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