treebase-guts

[Treebase-guts] SF.net SVN: treebase:[794] trunk/treebase-core/src/test/java/org/cipres/ treebase/domain/nexus/NexmlSerializationTest.java

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

Revision: 794
          http://treebase.svn.sourceforge.net/treebase/?rev=794&view=rev
Author:   rvos
Date:     2011-04-19 11:23:21 +0000 (Tue, 19 Apr 2011)

Log Message:
-----------
Adding simple test for NeXML serialization.

Added Paths:
-----------
    trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlSerializationTest.java

Added: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlSerializationTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlSerializationTest.java	                        (rev 0)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlSerializationTest.java	2011-04-19 11:23:21 UTC (rev 794)
@@ -0,0 +1,60 @@
+package org.cipres.treebase.domain.nexus;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.Writer;
+
+import junit.framework.Assert;
+
+import org.cipres.treebase.Constants;
+import org.cipres.treebase.dao.AbstractDAOTest;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentConverter;
+import org.nexml.model.DocumentFactory;
+import org.nexml.model.Document;
+
+public class NexmlSerializationTest extends AbstractDAOTest  {
+	private TaxonLabelHome mTaxonLabelHome;
+
+	public void testSerializeStudy() {
+		long studyId = 1787;
+		Study study = (Study)loadObject(Study.class, studyId);
+		Document doc = DocumentFactory.safeCreateDocument();
+		NexmlDocumentConverter conv = new NexmlDocumentConverter(study,getTaxonLabelHome(),doc);
+		String xml = conv.fromTreeBaseToXml(study).getXmlString();
+//		File file = new File("/Users/rvosa/Desktop/NexmlSerializationTest.xml");
+//		try {
+//			Writer output = new BufferedWriter(new FileWriter(file));
+//			output.write(xml);
+//		} catch (FileNotFoundException e) {
+//			// TODO Auto-generated catch block
+//			e.printStackTrace();
+//		} catch (IOException e) {
+//			// TODO Auto-generated catch block
+//			e.printStackTrace();
+//		}		
+		System.out.println(xml);
+		Assert.assertNotNull(xml);
+	}
+	
+	/**
+	 * Return the TaxonLabelHome field.
+	 * 
+	 * @return TaxonLabelHome mTaxonLabelHome
+	 */
+	public TaxonLabelHome getTaxonLabelHome() {
+		return mTaxonLabelHome;
+	}
+
+	/**
+	 * Set the TaxonLabelHome field.
+	 */
+	public void setTaxonLabelHome(TaxonLabelHome pNewTaxonLabelHome) {
+		mTaxonLabelHome = pNewTaxonLabelHome;
+	}	
+}


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[Treebase-guts] SF.net SVN: treebase:[859] trunk/treebase-core/src/test/java/org/cipres/ treebase/domain/nexus/NexmlSerializationTest.java

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

Revision: 859
          http://treebase.svn.sourceforge.net/treebase/?rev=859&view=rev
Author:   rvos
Date:     2011-05-12 20:32:51 +0000 (Thu, 12 May 2011)

Log Message:
-----------
Added test case to check tree serialization

Modified Paths:
--------------
    trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlSerializationTest.java

Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlSerializationTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlSerializationTest.java	2011-05-12 20:00:14 UTC (rev 858)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlSerializationTest.java	2011-05-12 20:32:51 UTC (rev 859)
@@ -14,6 +14,9 @@
 import org.cipres.treebase.dao.AbstractDAOTest;
 import org.cipres.treebase.domain.study.Study;
 import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.cipres.treebase.domain.tree.PhyloTree;
+import org.cipres.treebase.domain.tree.TreeBlock;
 import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentConverter;
 import org.nexml.model.DocumentFactory;
 import org.nexml.model.Document;
@@ -26,22 +29,28 @@
 		Study study = (Study)loadObject(Study.class, studyId);
 		Document doc = DocumentFactory.safeCreateDocument();
 		NexmlDocumentConverter conv = new NexmlDocumentConverter(study,getTaxonLabelHome(),doc);
-		String xml = conv.fromTreeBaseToXml(study).getXmlString();
-//		File file = new File("/Users/rvosa/Desktop/NexmlSerializationTest.xml");
-//		try {
-//			Writer output = new BufferedWriter(new FileWriter(file));
-//			output.write(xml);
-//		} catch (FileNotFoundException e) {
-//			// TODO Auto-generated catch block
-//			e.printStackTrace();
-//		} catch (IOException e) {
-//			// TODO Auto-generated catch block
-//			e.printStackTrace();
-//		}		
+		String xml = conv.fromTreeBaseToXml(study).getXmlString();		
 		System.out.println(xml);
 		Assert.assertNotNull(xml);
 	}
 	
+	public void testSerializeTree() {
+		long treeId = 4816;
+		Document doc = DocumentFactory.safeCreateDocument();		
+		PhyloTree tree = (PhyloTree)loadObject(PhyloTree.class,treeId);
+		TaxonLabelSet tls = tree.getTreeBlock().getTaxonLabelSet();
+		NexusDataSet nds = new NexusDataSet();
+		nds.getTaxonLabelSets().add(tls);
+		TreeBlock treeBlock = new TreeBlock();
+		treeBlock.setTaxonLabelSet(tls);
+		treeBlock.addPhyloTree(tree);
+		nds.getTreeBlocks().add(treeBlock);
+		NexmlDocumentConverter conv = new NexmlDocumentConverter(tree.getStudy(),getTaxonLabelHome(),doc);
+		String xml = conv.fromTreeBaseToXml(nds).getXmlString();
+		System.out.println(xml);
+		Assert.assertNotNull(xml);
+	}
+	
 	/**
 	 * Return the TaxonLabelHome field.
 	 * 


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