From: <cmu...@us...> - 2008-05-15 21:35:01
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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); + } + + +} This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |