Package ubic.gemma.core.analysis.preprocess

Class TwoChannelExpressionDataDoubleMatrixTest

java.lang.Object

org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests

ubic.gemma.core.util.test.BaseTest

ubic.gemma.core.util.test.BaseIntegrationTest

ubic.gemma.core.util.test.BaseSpringContextTest

ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest

ubic.gemma.core.analysis.preprocess.TwoChannelExpressionDataDoubleMatrixTest

All Implemented Interfaces:

org.springframework.beans.factory.Aware, org.springframework.context.ApplicationContextAware

public class TwoChannelExpressionDataDoubleMatrixTest
extends AbstractGeoServiceTest

Author:

keshav, pavlidis

Field Summary

Fields

Modifier and Type	Field	Description
final NetworkAvailableRule	networkAvailableRule

Fields inherited from class ubic.gemma.core.util.test.BaseSpringContextTest

externalDatabaseService, log, persisterHelper, rule, taxonService, testHelper

Fields inherited from class org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests

applicationContext, logger

Constructor Summary

Constructors

Constructor	Description
TwoChannelExpressionDataDoubleMatrixTest()

Method Summary

Modifier and Type	Method	Description
void	setUp()
void	tearDown()
void	testConstructExpressionDataDoubleMatrix()	Tests the construction of an ExpressionDataDoubleMatrix
void	testConstructExpressionDataDoubleMatrixWithGeoValues()	This is a self-contained test.
void	testMatrixConversion()

Methods inherited from class ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest

getTestFileBasePath, getTestFileBasePath

Methods inherited from class ubic.gemma.core.util.test.BaseSpringContextTest

addTestAnalyses, countRowsInTable, deleteFromTables, getJdbcTemplate, getNewTestPersistentCompleteExpressionExperiment, getTaxon, getTestNonPersistentBioSequence, getTestPersistentArrayDesign, getTestPersistentArrayDesign, getTestPersistentArrayDesign, getTestPersistentBasicExpressionExperiment, getTestPersistentBasicExpressionExperiment, getTestPersistentBibliographicReference, getTestPersistentBioAssay, getTestPersistentBioAssay, getTestPersistentBioMaterial, getTestPersistentBioMaterial, getTestPersistentBioSequence, getTestPersistentBioSequence, getTestPersistentBioSequence2GeneProducts, getTestPersistentBlatResult, getTestPersistentBlatResult, getTestPersistentCompleteExpressionExperiment, getTestPersistentCompleteExpressionExperimentWithSequences, getTestPersistentCompleteExpressionExperimentWithSequences, getTestPersistentContact, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentExpressionExperiment, getTestPersistentExpressionExperiment, getTestPersistentGene, getTestPersistentGene, getTestPersistentGeneProduct, getTestPersistentQuantitationType, randomName, resetTestCollectionSize, runAsAdmin, runAsAgent, runAsAnonymous, runAsUser, runAsUser, setTestCollectionSize

Methods inherited from class ubic.gemma.core.util.test.BaseIntegrationTest

setUpAuthentication, tearDownSecurityContext

Methods inherited from class org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests

setApplicationContext

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

networkAvailableRule

public final NetworkAvailableRule networkAvailableRule

Constructor Details

TwoChannelExpressionDataDoubleMatrixTest

public TwoChannelExpressionDataDoubleMatrixTest()

Method Details

setUp

public void setUp()
           throws Exception

Throws:

Exception

tearDown

public void tearDown()

testConstructExpressionDataDoubleMatrix

public void testConstructExpressionDataDoubleMatrix()

Tests the construction of an ExpressionDataDoubleMatrix

testConstructExpressionDataDoubleMatrixWithGeoValues

public void testConstructExpressionDataDoubleMatrixWithGeoValues()

This is a self-contained test. That is, it does not depend on the setup in onSetUpInTransaction}. It tests creating an ExpressionDataDoubleMatrix using real values from the Gene Expression Omnibus (GEO). That is, we have obtained information from GSE994. The probe sets used are 218120_s_at and 121_at, and the samples used are GSM15697 and GSM15744. Specifically, we the Gemma objects that correspond to the GEO objects are: DesignElement 1 = 218120_s_at, DesignElement 2 = 121_at BioAssay 1 = "Current Smoker 73", BioAssay 2 = "Former Smoker 34" BioMaterial 1 = "GSM15697", BioMaterial 2 = "GSM15744" BioAssayDimension = "GSM15697, GSM15744" (the names of all the biomaterials).

testMatrixConversion

@NetworkAvailable(url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi")
public void testMatrixConversion()
                          throws Exception

Throws:

Exception