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[Treebase-guts] SF.net SVN: treebase:[933] trunk/treebase-core/src/test/java/org/cipres/ treebase/domain/nexus/NexmlMatrixConverterTest.java
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From: <lol...@us...> - 2011-07-20 14:54:51
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Revision: 933
http://treebase.svn.sourceforge.net/treebase/?rev=933&view=rev
Author: loloyohe
Date: 2011-07-20 14:54:45 +0000 (Wed, 20 Jul 2011)
Log Message:
-----------
Wrote unit test to help track down issue of bug #3303002. Unit test added was testNexmlEmptyMatrix()
Modified Paths:
--------------
trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java
Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java 2011-07-19 21:21:03 UTC (rev 932)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java 2011-07-20 14:54:45 UTC (rev 933)
@@ -6,25 +6,47 @@
import junit.framework.Assert;
+import mesquite.lib.Annotatable;
+
import org.cipres.treebase.dao.AbstractDAOTest;
+import org.cipres.treebase.dao.jdbc.DiscreteMatrixElementJDBC;
+import org.cipres.treebase.dao.jdbc.MatrixColumnJDBC;
+import org.cipres.treebase.domain.Annotation;
import org.cipres.treebase.domain.matrix.CharSet;
import org.cipres.treebase.domain.matrix.CharacterMatrix;
import org.cipres.treebase.domain.matrix.ColumnRange;
+import org.cipres.treebase.domain.matrix.ContinuousMatrixElement;
+import org.cipres.treebase.domain.matrix.DiscreteChar;
+import org.cipres.treebase.domain.matrix.DiscreteMatrix;
+import org.cipres.treebase.domain.matrix.DiscreteMatrixElement;
+import org.cipres.treebase.domain.matrix.MatrixColumn;
+import org.cipres.treebase.domain.matrix.MatrixElement;
+import org.cipres.treebase.domain.matrix.MatrixRow;
import org.cipres.treebase.domain.matrix.PhyloChar;
+import org.cipres.treebase.domain.matrix.RowSegment;
import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentConverter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlObjectConverter;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.TaxonLabelHome;
import org.nexml.model.CategoricalMatrix;
+import org.nexml.model.Character;
+import org.nexml.model.CharacterState;
import org.nexml.model.ContinuousMatrix;
import org.nexml.model.DocumentFactory;
import org.nexml.model.Document;
import org.nexml.model.Matrix;
+import org.nexml.model.MatrixCell;
import org.nexml.model.MolecularMatrix;
+import org.nexml.model.OTU;
+import org.nexml.model.OTUs;
import org.nexml.model.Subset;
public class NexmlMatrixConverterTest extends AbstractDAOTest {
private TaxonLabelHome mTaxonLabelHome;
+ private static final int MAX_GRANULAR_NCHAR = 1000;
+ private static final int MAX_GRANULAR_NTAX = 30;
+
/**
* Test for {@link org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter#fromTreeBaseToXml(CharacterMatrix)}.
* Finds an equivalent, created NexmlMatrix within a NeXML document to go with the matrix
@@ -52,6 +74,7 @@
NexmlDocumentConverter ndc = new NexmlDocumentConverter(tbStudy,getTaxonLabelHome(),nexDoc);
ndc.fromTreeBaseToXml(tbStudy); // here is where the conversion happens
+
// these are the NeXML matrices that were created from the study
List<Matrix<?>> nexMatrices = nexDoc.getMatrices();
@@ -125,7 +148,87 @@
}
}
+
+
/**
+ * Test for {@link org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter#}.
+ * This verfies that all row-segment annotation are expressed for a particular study.
+ */
+ public void testNexmlEmptyMatrix() {
+ String testName = "testNexmlEmptyMatrix()";
+ //signal beginning of test
+ if (logger.isInfoEnabled()) {
+ logger.info("Running Test: " + testName);
+ }
+
+ long studyId = 586; //this study is known to output an empty Nexml matrix
+
+ // this is the full study as it is stored by the database
+ Study tbStudy = (Study)loadObject(Study.class, studyId);
+
+ // these are the character state matrices that are part of the study
+ Set<org.cipres.treebase.domain.matrix.Matrix> tbMatrices = tbStudy.getMatrices();
+
+
+ // this is an object representation of a NeXML document
+ Document nexDoc = DocumentFactory.safeCreateDocument();
+
+ // the converter populates the NeXML document with the contents of the treebase study
+ NexmlDocumentConverter ndc = new NexmlDocumentConverter(tbStudy,getTaxonLabelHome(),nexDoc);
+
+ ndc.fromTreeBaseToXml(tbStudy); // here is where the conversion happens
+
+
+ // these are the NeXML matrices that were created from the study
+ List<Matrix<?>> nexMatrices = nexDoc.getMatrices();
+
+ //returns true if matrix contains no elements
+ boolean nexTest = nexMatrices.isEmpty();
+
+ //should be false if the matrix contains elements
+ Assert.assertFalse(nexTest);
+
+ // there most be more than zero matrices because every treebase study has at least one matrix
+ Assert.assertTrue(nexMatrices.size() != 0 );
+
+ // now we're going to match up the NeXML matrices with their equivalent treebase ones
+ for ( Matrix<?> nexMatrix : nexMatrices ) {
+
+ // the xml id is the same as the primary key of the equivalent matrix stored by treebase
+ String nexId = nexMatrix.getId();
+
+ for ( org.cipres.treebase.domain.matrix.Matrix tbMatrix : tbMatrices ) {
+ String tbId = "M" + tbMatrix.getId();
+ // if true, the matrices are equivalent
+
+ System.out.println(tbMatrix.getClass());
+ System.out.println(nexMatrix.getClass().toString() + "hi");
+
+ if ( nexId.equals(tbId) ) {
+ Assert.assertTrue("NeXML matrix "+nexId+ " is one of the known subclasses",
+ nexMatrix instanceof CategoricalMatrix || nexMatrix instanceof MolecularMatrix || nexMatrix instanceof ContinuousMatrix);
+
+ Assert.assertNotNull(nexMatrix);
+ Assert.assertNotNull(tbMatrix);
+
+
+ for ( MatrixRow tbRow : ((CharacterMatrix) tbMatrix).getRowsReadOnly() ) {
+ System.out.println (tbRow.buildElementAsString());
+ }
+ }
+ //print out the rows of the nexml matrix to see if there are sequences
+
+ }
+
+ }
+
+ //System.out.println(nexDoc.getXmlString());
+ }
+
+
+
+
+ /**
* Test for {@link org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter#}.
* It verifies that NexmlCharSets have the same name and coordinates as those in the
* TreeBASE matrix.
@@ -166,7 +269,7 @@
// iterate over all treebase matrices for the study
for ( org.cipres.treebase.domain.matrix.Matrix tbMatrix : tbMatrices ) {
String tbId = "M" + tbMatrix.getId();
-
+
// if true, the matrices are equivalent
if ( nexId.equals(tbId) ) {
Assert.assertTrue("NeXML matrix "+nexId+ " is one of the known subclasses",
@@ -191,7 +294,7 @@
//get names of TreeBASE and NeXML character set
String tbCharSetName = tbCharSet.getLabel();
String nexCharSetName = nexSubset.getLabel();
-
+
//verify that the names are the same
Assert.assertEquals("The NeXML character set must have copied the label of the TreeBASE character set",tbCharSetName,nexCharSetName);
@@ -230,6 +333,7 @@
PhyloChar tbCharacter = tbCharacterMatrix.getCharacter(i);
Assert.assertNotNull("The TreeBASE PhyloChar should not be null if there as an index into it in this set", tbCharacter);
Assert.assertEquals("If the TreeBASE character has a label, then the NeXML character's label should match it", tbCharacter.getLabel(), nexCharacter.getLabel());
+
}
}
else {
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