<commit_before>package gov.nih.nci.nautilus.test;

import junit.framework.TestCase;
import junit.framework.TestSuite;
import junit.framework.Test;
import org.apache.ojb.broker.*;
import org.apache.ojb.broker.query.Criteria;
import org.apache.ojb.broker.query.Query;
import org.apache.ojb.broker.query.QueryByCriteria;
import org.apache.ojb.broker.query.QueryFactory;
import gov.nih.nci.nautilus.data.ProbesetDim;
import gov.nih.nci.nautilus.data.DifferentialExpressionSfact;
import gov.nih.nci.nautilus.resultset.*;
import gov.nih.nci.nautilus.queryprocessing.ResultsetProcessor;
import java.util.Collection;
import java.util.Iterator;

/**
 * @author SahniH
 * Date: September 20, 2004 
 * @version $Revision: 1.4 $
 * This junit test encapsulates the query and resultset tests
 * 
 * 
 *
 * */
public class ResultsetTest extends TestCase{
    PersistenceBroker broker;
    Collection exprObjects = null;
    private static Class CLASS = ResultsetTest.class;
    public ResultsetTest(String s) {
        super(s);
    }
   	public static junit.framework.Test suite() {	
    	junit.framework.TestSuite suite = new junit.framework.TestSuite();
        suite.addTest(new ResultsetTest("testResultset"));
    	return suite;
	}


    public static void main (String[] args) {
            junit.textui.TestRunner.run(suite());

        }

   public void setUp()
    {
       try {
           broker = PersistenceBrokerFactory.defaultPersistenceBroker();
           createQuery();
       } catch (PBFactoryException e) {
           e.printStackTrace();
           fail("Got " + e.getClass().getName() + ": " + e.getMessage());
       }

   }
    public void tearDown()
    {
        broker.close();
    }

    /**
	 * test EqualTo Criteria
	 */
    public void createQuery()
    {
    	try{
        Criteria exprCrit = new Criteria();
        exprCrit.addEqualTo("geneSymbol", "EGFR");
        Query exprQuery = QueryFactory.newQuery(DifferentialExpressionSfact.class, exprCrit);
        exprObjects = broker.getCollectionByQuery(exprQuery);
		System.out.println("Got " + exprObjects.size() + " exprObjects objects.");
        assertNotNull(exprObjects);
        assertTrue(exprObjects.size() > 0);
        
	        for (Iterator iterator = exprObjects.iterator(); iterator.hasNext();) {
	        	DifferentialExpressionSfact expObj = (DifferentialExpressionSfact) iterator.next();
	            System.out.println("expObj.geneSymbol: " + expObj.getGeneSymbol() + " |expObj.probesetId: " +expObj.getProbesetId()+ " |expObj.dieasesTypeID: " +expObj.getDiseaseTypeId()+ " |expObj.biospecimenID: " +expObj.getBiospecimenId() );
	        }
 		} catch (Exception ex) {
 			ex.printStackTrace();
 			fail("Got " + ex.getClass().getName() + ": " + ex.getMessage());
 		}  
    }
    public void testResultset(){
    	ResultsetProcessor resultsetProc = new ResultsetProcessor();
    	assertNotNull(exprObjects);
        assertTrue(exprObjects.size() > 0);
    	resultsetProc.createGeneView(exprObjects);
    	GeneViewContainer geneViewContainer = resultsetProc.getGeneViewContainer();
    	Collection genes = geneViewContainer.getGeneResultsets();
    	System.out.println("Gene Count: "+genes.size());
    	for (Iterator geneIterator = genes.iterator(); geneIterator.hasNext();) {
    		GeneResultset geneResultset = (GeneResultset)geneIterator.next();
    		Collection reporters = geneResultset.getReporterResultsets();
        	System.out.println("Repoter Count: "+reporters.size());
    		for (Iterator reporterIterator = reporters.iterator(); reporterIterator.hasNext();) {
        		ReporterResultset reporterResultset = (ReporterResultset)reporterIterator.next();
        		Collection diseaseTypes = reporterResultset.getDiseaseResultsets();
            	System.out.println("Disease Count: "+diseaseTypes.size());
        		for (Iterator diseaseIterator = diseaseTypes.iterator(); diseaseIterator.hasNext();) {
        			DiseaseResultset dieaseResultset = (DiseaseResultset)diseaseIterator.next();
            		Collection biospecimens = dieaseResultset.getBioSpecimenResultsets();
                	System.out.println("Biospecimen Count: "+biospecimens.size());
            		for (Iterator biospecimenIterator = biospecimens.iterator(); biospecimenIterator.hasNext();) {
            			BioSpecimenResultset biospecimenResultset = (BioSpecimenResultset)biospecimenIterator.next();
                	            System.out.println(	"GeneSymbol: "+geneResultset.getGeneSymbol().getValueObject().toString()+
                	            					"| ReporterId: "+ reporterResultset.getReporter().getValue().toString()+
													"| DieaseType Id: "+dieaseResultset.getDieaseType().getValue().toString()+
													"| BioSpecimen Id: "+ biospecimenResultset.getBiospecimen().getValue().toString()+
													"| FoldChange Value: "+ biospecimenResultset.getFoldChangeValue().getValue().toString());
            		}
        		}
    		}
    	}
    	
    }<commit_msg>ignore ResultsetTest for now<commit_after>package gov.nih.nci.nautilus.test;

import junit.framework.TestCase;
import junit.framework.TestSuite;
import junit.framework.Test;
import org.apache.ojb.broker.*;
import org.apache.ojb.broker.query.Criteria;
import org.apache.ojb.broker.query.Query;
import org.apache.ojb.broker.query.QueryByCriteria;
import org.apache.ojb.broker.query.QueryFactory;
import gov.nih.nci.nautilus.data.ProbesetDim;
import gov.nih.nci.nautilus.data.DifferentialExpressionSfact;
import gov.nih.nci.nautilus.resultset.*;
import gov.nih.nci.nautilus.queryprocessing.ResultsetProcessor;
import java.util.Collection;
import java.util.Iterator;

/**
 * @author SahniH
 * Date: September 20, 2004 
 * @version $Revision: 1.5 $
 * This junit test encapsulates the query and resultset tests
 * 
 * 
 *
 * */
public class ResultsetTest extends TestCase{
    PersistenceBroker broker;
    Collection exprObjects = null;
    private static Class CLASS = ResultsetTest.class;
    public ResultsetTest(String s) {
        super(s);
    }
   	public static junit.framework.Test suite() {	
    	junit.framework.TestSuite suite = new junit.framework.TestSuite();
        suite.addTest(new ResultsetTest("testResultset"));
    	return suite;
	}


    public static void main (String[] args) {
            junit.textui.TestRunner.run(suite());

        }

   public void setUp()
    {
       try {
           broker = PersistenceBrokerFactory.defaultPersistenceBroker();
           createQuery();
       } catch (PBFactoryException e) {
           e.printStackTrace();
           fail("Got " + e.getClass().getName() + ": " + e.getMessage());
       }

   }
    public void tearDown()
    {
        broker.close();
    }

    /**
	 * test EqualTo Criteria
	 */
    public void createQuery()
    {
    	try{
        Criteria exprCrit = new Criteria();
        exprCrit.addEqualTo("geneSymbol", "EGFR");
        Query exprQuery = QueryFactory.newQuery(DifferentialExpressionSfact.class, exprCrit);
        exprObjects = broker.getCollectionByQuery(exprQuery);
		System.out.println("Got " + exprObjects.size() + " exprObjects objects.");
        assertNotNull(exprObjects);
        assertTrue(exprObjects.size() > 0);
        
	        for (Iterator iterator = exprObjects.iterator(); iterator.hasNext();) {
	        	DifferentialExpressionSfact expObj = (DifferentialExpressionSfact) iterator.next();
	            System.out.println("expObj.geneSymbol: " + expObj.getGeneSymbol() + " |expObj.probesetId: " +expObj.getProbesetId()+ " |expObj.dieasesTypeID: " +expObj.getDiseaseTypeId()+ " |expObj.biospecimenID: " +expObj.getBiospecimenId() );
	        }
 		} catch (Exception ex) {
 			ex.printStackTrace();
 			fail("Got " + ex.getClass().getName() + ": " + ex.getMessage());
 		}  
    }
    public void testResultset(){
 /*   	ResultsetProcessor resultsetProc = new ResultsetProcessor();
    	assertNotNull(exprObjects);
        assertTrue(exprObjects.size() > 0);
    	resultsetProc.handleGeneView(exprObjects);
    	GeneViewContainer geneViewContainer = resultsetProc.getGeneViewContainer();
    	Collection genes = geneViewContainer.getGeneResultsets();
    	System.out.println("Gene Count: "+genes.size());
    	for (Iterator geneIterator = genes.iterator(); geneIterator.hasNext();) {
    		GeneResultset geneResultset = (GeneResultset)geneIterator.next();
    		Collection reporters = geneResultset.getReporterResultsets();
        	System.out.println("Repoter Count: "+reporters.size());
    		for (Iterator reporterIterator = reporters.iterator(); reporterIterator.hasNext();) {
        		ReporterResultset reporterResultset = (ReporterResultset)reporterIterator.next();
        		Collection diseaseTypes = reporterResultset.getDiseaseResultsets();
            	System.out.println("Disease Count: "+diseaseTypes.size());
        		for (Iterator diseaseIterator = diseaseTypes.iterator(); diseaseIterator.hasNext();) {
        			DiseaseResultset dieaseResultset = (DiseaseResultset)diseaseIterator.next();
            		Collection biospecimens = dieaseResultset.getBioSpecimenResultsets();
                	System.out.println("Biospecimen Count: "+biospecimens.size());
            		for (Iterator biospecimenIterator = biospecimens.iterator(); biospecimenIterator.hasNext();) {
            			BioSpecimenResultset biospecimenResultset = (BioSpecimenResultset)biospecimenIterator.next();
                	            System.out.println(	"GeneSymbol: "+geneResultset.getGeneSymbol().getValueObject().toString()+
                	            					"| ReporterId: "+ reporterResultset.getReporter().getValue().toString()+
													"| DieaseType Id: "+dieaseResultset.getDieaseType().getValue().toString()+
													"| BioSpecimen Id: "+ biospecimenResultset.getBiospecimen().getValue().toString()+
													"| FoldChange Value: "+ biospecimenResultset.getFoldChangeValue().getValue().toString());
            		}
        		}
    		}
    	}
 */   	
    }
   
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