Package ubic.gemma.core.analysis.preprocess.batcheffects

Class RNASeqBatchInfoPopulationTest

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.batcheffects.RNASeqBatchInfoPopulationTest

All Implemented Interfaces:

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

@DirtiesContext
public class RNASeqBatchInfoPopulationTest
extends AbstractGeoServiceTest

Author:

paul

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
RNASeqBatchInfoPopulationTest()

Method Summary

Modifier and Type	Method	Description
void	setUp()
void	teardown()
void	testBatchA()
void	testBatchB()
void	testBatchC()
void	testBatchD()
void	testBatchDX()
void	testBatchE()
void	testBatchF()
void	testBatchG()
void	testBatchH()
void	testBatchI()
void	testBatchJ()
void	testBatchK()
void	testBatchL()
void	testBatchM()
void	testBatchMixedHeaders()	See https://github.com/PavlidisLab/GemmaCuration/issues/64
void	testBatchMixedHeadersSinglePlatform()
void	testBatchMixedHeadersSinglePlatformSingleton()
void	testBatchO()
void	testBatchP()
void	testBatchQ()
void	testBatchR()
void	testBatchS()
void	testGetBatches()	Test of creating batch factor.
void	testGSE14285OneBatch()
void	testGSE156689NoBatchinfo()
void	testParseHeaders()

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

RNASeqBatchInfoPopulationTest

public RNASeqBatchInfoPopulationTest()

Method Details

setUp

public void setUp()
           throws Exception

Throws:

Exception

testParseHeaders

public void testParseHeaders()

testGetBatches

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

Test of creating batch factor. GSE71229 has two lanes

Throws:

Exception

testGSE14285OneBatch

@NetworkAvailable(url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi")
public void testGSE14285OneBatch()
                          throws Exception

Throws:

Exception

testGSE156689NoBatchinfo

@NetworkAvailable(url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi")
public void testGSE156689NoBatchinfo()
                              throws Exception

Throws:

Exception

testBatchA

public void testBatchA()
                throws Exception

Throws:

Exception

testBatchB

public void testBatchB()
                throws Exception

Throws:

Exception

testBatchC

public void testBatchC()
                throws Exception

Throws:

Exception

testBatchD

public void testBatchD()
                throws Exception

Throws:

Exception

testBatchDX

public void testBatchDX()
                 throws Exception

Throws:

Exception

testBatchMixedHeaders

public void testBatchMixedHeaders()
                           throws Exception

See https://github.com/PavlidisLab/GemmaCuration/issues/64

Throws:

Exception

testBatchMixedHeadersSinglePlatformSingleton

public void testBatchMixedHeadersSinglePlatformSingleton()
                                                  throws Exception

Throws:

Exception

testBatchMixedHeadersSinglePlatform

public void testBatchMixedHeadersSinglePlatform()
                                         throws Exception

Throws:

Exception

testBatchE

public void testBatchE()
                throws Exception

Throws:

Exception

testBatchF

public void testBatchF()
                throws Exception

Throws:

Exception

testBatchG

public void testBatchG()
                throws Exception

Throws:

Exception

testBatchH

public void testBatchH()
                throws Exception

Throws:

Exception

testBatchI

public void testBatchI()
                throws Exception

Throws:

Exception

testBatchJ

public void testBatchJ()
                throws Exception

Throws:

Exception

testBatchK

public void testBatchK()
                throws Exception

Throws:

Exception

testBatchL

public void testBatchL()
                throws Exception

Throws:

Exception

testBatchM

public void testBatchM()
                throws Exception

Throws:

Exception

testBatchO

public void testBatchO()
                throws Exception

Throws:

Exception

testBatchP

public void testBatchP()
                throws Exception

Throws:

Exception

testBatchQ

public void testBatchQ()
                throws Exception

Throws:

Exception

testBatchR

public void testBatchR()
                throws Exception

Throws:

Exception

testBatchS

public void testBatchS()
                throws Exception

Throws:

Exception

teardown

public void teardown()