[Obo-svn-commit] SF.net SVN: obo: [1794] phenote/trunk/test/java/phenote

[<cmu...@us...>]

Revision: 1794
          http://obo.svn.sourceforge.net/obo/?rev=1794&view=rev
Author:   cmungall
Date:     2008-05-15 14:34:38 -0700 (Thu, 15 May 2008)

Log Message:
-----------


Modified Paths:
--------------
    phenote/trunk/test/java/phenote/dataadapter/annotation/OBDSavePhenotypeTest.java

Added Paths:
-----------
    phenote/trunk/test/java/phenote/dataadapter/annotation/SaveAnnotationsAsOBOFormatTest.java
    phenote/trunk/test/java/phenote/datamodel/EnvironmentalAssociationDriverTest.java

Modified: phenote/trunk/test/java/phenote/dataadapter/annotation/OBDSavePhenotypeTest.java
===================================================================
--- phenote/trunk/test/java/phenote/dataadapter/annotation/OBDSavePhenotypeTest.java	2008-05-15 15:03:19 UTC (rev 1793)
+++ phenote/trunk/test/java/phenote/dataadapter/annotation/OBDSavePhenotypeTest.java	2008-05-15 21:34:38 UTC (rev 1794)
@@ -79,7 +79,13 @@
 	}
 
 	@Test public void saveAnnotations()   {
+		// first translate all annotation objects to statements
+		// and store them in the graph
 		Graph g = OBOBridge.getAnnotationGraph(session);
+		
+		// next find "orphan" objects in the session:
+		// this can include OBOClasses such as PATO-based dynamic
+		// composed classes
 		for (IdentifiedObject io : session.getObjects()) {
 			if (io.isBuiltIn())
 				continue;

Added: phenote/trunk/test/java/phenote/dataadapter/annotation/SaveAnnotationsAsOBOFormatTest.java
===================================================================
--- phenote/trunk/test/java/phenote/dataadapter/annotation/SaveAnnotationsAsOBOFormatTest.java	                        (rev 0)
+++ phenote/trunk/test/java/phenote/dataadapter/annotation/SaveAnnotationsAsOBOFormatTest.java	2008-05-15 21:34:38 UTC (rev 1794)
@@ -0,0 +1,82 @@
+package phenote.dataadapter.annotation;
+
+import java.io.File;
+import java.io.IOException;
+import java.sql.SQLException;
+import java.util.Collection;
+
+import org.bbop.dataadapter.DataAdapterException;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.obd.model.Graph;
+import org.obd.model.Statement;
+import org.obd.model.bridge.OBOBridge;
+import org.obd.query.Shard;
+import org.obd.query.impl.OBDSQLShard;
+import org.obo.annotation.datamodel.Annotation;
+import org.obo.datamodel.IdentifiedObject;
+import org.obo.util.AnnotationUtil;
+import org.obo.util.TermUtil;
+
+import phenote.config.Config;
+import phenote.config.ConfigException;
+import phenote.dataadapter.delimited.DelimitedFileAdapter;
+import phenote.datamodel.AbstractAnnotationModelTest;
+import phenote.datamodel.CharFieldManager;
+import phenote.datamodel.CharacterI;
+import phenote.datamodel.CharField;
+import phenote.datamodel.CharacterListI;
+import phenote.main.Phenote;
+
+public class SaveAnnotationsAsOBOFormatTest extends AbstractAnnotationModelTest {
+
+
+	AnnotationOBOFileAdapter adapter = new AnnotationOBOFileAdapter();
+	static CharacterListI clist;
+
+	protected static String getConfigFileName() { return "ncbo-test.cfg"; }
+	protected static String getDataFilePath() { return "test/testfiles/Sox9-human-bbop.tab";}
+
+	@BeforeClass public static void initialize() throws ConfigException {
+		Phenote.resetAllSingletons();
+		Config.inst().setConfigFile("ncbo-test.cfg");
+		Phenote phenote = Phenote.getPhenote();
+		phenote.initOntologies();
+		phenote.initGui();
+		DelimitedFileAdapter ad = new DelimitedFileAdapter();
+		clist = 
+			ad.load(new File(getDataFilePath()));
+		System.err.println("clist size: "+clist.size());
+		testCharacterList(clist);
+		session = CharFieldManager.inst().getOboSession();
+	}
+
+	@BeforeClass public static void setUp() throws Exception  {
+
+	}
+
+	public static void testCharacterList(CharacterListI clist) {
+		for (CharacterI c : clist.getList()) {
+			System.out.println("character ="+c);
+			for (CharField cf : c.getAllCharFields()) {
+				System.out.println("  "+cf.getName()+" "+c.getValueString(cf));
+			}
+
+		}
+	}
+
+	@Before public void setup() {
+	}
+
+	@Test public void saveAnnotations()   {
+		adapter.setAdapterValue("/tmp/foo.obo");
+		adapter.commit(clist);
+
+
+	}
+
+
+
+}

Added: phenote/trunk/test/java/phenote/datamodel/EnvironmentalAssociationDriverTest.java
===================================================================
--- phenote/trunk/test/java/phenote/datamodel/EnvironmentalAssociationDriverTest.java	                        (rev 0)
+++ phenote/trunk/test/java/phenote/datamodel/EnvironmentalAssociationDriverTest.java	2008-05-15 21:34:38 UTC (rev 1794)
@@ -0,0 +1,55 @@
+package phenote.datamodel;
+
+import java.io.File;
+import java.util.Collection;
+
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.obo.annotation.datamodel.Annotation;
+import org.obo.datamodel.OBOSession;
+import org.obo.util.AnnotationUtil;
+
+import phenote.config.Config;
+import phenote.config.ConfigException;
+import phenote.dataadapter.delimited.DelimitedFileAdapter;
+import phenote.main.Phenote;
+
+public class EnvironmentalAssociationDriverTest extends AbstractAnnotationModelTest {
+
+
+
+	protected static OBOSession session;
+
+	protected static String getConfigFileName() { return "ncbo-test.cfg"; }
+	protected static String getDataFilePath() { return "test/testfiles/Sox9-human-bbop.tab";}
+
+	@BeforeClass public static void initialize() throws ConfigException {
+		Phenote.resetAllSingletons();
+		Config.inst().setConfigFile("ncbo-test.cfg");
+		Phenote phenote = Phenote.getPhenote();
+		phenote.initOntologies();
+		phenote.initGui();
+		DelimitedFileAdapter ad = new DelimitedFileAdapter();
+		CharacterListI clist = 
+			ad.load(new File("test/testfiles/Sox9-human-bbop.tab"));
+		System.err.println("clist size: "+clist.size());
+		session = CharFieldManager.inst().getOboSession();
+	}
+
+	@Before public void setup() {
+	}
+
+	@Test public void checkAnnotations()   {
+		Collection<Annotation> annots = AnnotationUtil.getAnnotations(session);
+		System.err.println("# annots = "+annots.size());
+		for (Annotation annot : annots) {
+			System.err.println("annot: "+annot+":: "+annot.getSubject()+" -"+annot.getRelationship()+"-> "+annot.getObject());
+
+		}
+		Assert.assertTrue(annots.size() > 0);
+	}
+
+
+}


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