[Treebase-guts] SF.net SVN: treebase:[1038] trunk/treebase-core/src/test/java/org/cipres/ treebase/domain/nexus/NexmlTreeConverterTest.java

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

Revision: 1038
          http://treebase.svn.sourceforge.net/treebase/?rev=1038&view=rev
Author:   rvos
Date:     2012-02-01 21:45:39 +0000 (Wed, 01 Feb 2012)
Log Message:
-----------
test to show that @rdmpage's bug no longer occurs.

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

Added: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlTreeConverterTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlTreeConverterTest.java	                        (rev 0)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlTreeConverterTest.java	2012-02-01 21:45:39 UTC (rev 1038)
@@ -0,0 +1,113 @@
+package org.cipres.treebase.domain.nexus;
+
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import junit.framework.Assert;
+
+import org.cipres.treebase.dao.AbstractDAOTest;
+import org.cipres.treebase.domain.TBPersistable;
+import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter;
+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.nexml.model.Document;
+import org.nexml.model.DocumentFactory;
+import org.nexml.model.Network;
+import org.nexml.model.Node;
+import org.nexml.model.OTU;
+
+public class NexmlTreeConverterTest extends AbstractDAOTest {
+	private TaxonLabelHome mTaxonLabelHome;
+	
+	public void testNexmlTreeConverter() {
+		String testName = "testNexmlTreeConverter";
+		//signal beginning of test
+		if (logger.isInfoEnabled()) {
+			logger.info("Running Test: " + testName);
+		}
+		
+		// this study had mismatching taxon labels, according to @rdmpage
+		long studyId = 2048;  
+		
+		// this is the full study as it is stored by the database
+		Study tbStudy = (Study)loadObject(Study.class, studyId);
+
+		// this becomes an object representation of a NeXML document
+		Document nexDoc = DocumentFactory.safeCreateDocument();
+		
+		// the converter populates the NeXML document with the contents of the treebase study
+		NexmlDocumentWriter ndc = new NexmlDocumentWriter(tbStudy,getTaxonLabelHome(),nexDoc);
+		ndc.fromTreeBaseToXml(tbStudy); // here is where the conversion happens
+				
+		// these are the NeXML tree blocks that were created from the study  		
+		List<org.nexml.model.TreeBlock> nexTreeBlocks = nexDoc.getTreeBlockList();
+		
+		// there most be more than zero tree blocks in this study
+		Assert.assertTrue(nexTreeBlocks.size() != 0 );
+		
+		// now we're going to match up the NeXML taxa in trees with their equivalent treebase ones
+		for ( org.nexml.model.TreeBlock nexTreeBlock : nexTreeBlocks ) {
+			
+			// get the equivalent taxa block in treebase for the NeXML tree block's OTU set
+			TaxonLabelSet tbTls = (TaxonLabelSet)findEquivalentObject(nexTreeBlock.getOTUs().getId(),"Tls",tbStudy.getTaxonLabelSets());
+			
+			// now iterate over all nodes in all trees in the focal tree block
+			for ( Network<?> nexTree : nexTreeBlock ) {
+				for ( Node nexNode : nexTree.getNodes() ) {
+					
+					// check to see if there is a taxon; this may be null because we also visit internal nodes
+					OTU nexOTU = nexNode.getOTU();
+					if ( null != nexOTU ) {
+						
+						// populate a set to pass into findEquivalentObject()
+						Set<TaxonLabel> tbTlset = new HashSet<TaxonLabel>(); 
+						tbTlset.addAll(tbTls.getTaxonLabelsReadOnly());
+						
+						// this must not be null, though
+						TaxonLabel tbTl = (TaxonLabel)findEquivalentObject(nexOTU.getId(),"Tl",tbTlset);
+						Assert.assertNotNull("Have to find taxon "+nexNode.getId()+" for node "+nexNode.getId(), tbTl);
+					}
+				}
+			}		
+		}
+	}
+	
+	/**
+	 * 
+	 * @param id - a NeXML id attribute's value
+	 * @param prefix - a prefix as defined by TreebaseIDString 
+	 * @param objects - a set of TBPersistable objects, one of which has a matching id
+	 * @return the TBPersistable object whose prefix + primary key == id
+	 */
+	private TBPersistable findEquivalentObject(String id,String prefix,Set<?> objects) {
+		TBPersistable result = null;
+		for ( Object oObject : objects ) {
+			TBPersistable object = (TBPersistable)oObject; 
+			if ( id.equals(prefix + object.getId()) ) {
+				result = object;
+				break;
+			}
+		}
+		Assert.assertNotNull("Found object with id "+id, result);
+		return result;
+	}
+	
+	/**
+	 * 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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