Class RNASeqBatchInfoPopulationTest

java.lang.Object

ubic.gemma.core.util.test.BaseTest5

ubic.gemma.core.util.test.BaseIntegrationTest5

ubic.gemma.core.util.test.BaseSpringContextTest5

ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest5

ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

@DirtiesContext
@ExtendWith(NetworkAvailableExtension.class)
public class RNASeqBatchInfoPopulationTest
extends AbstractGeoServiceTest5

Author:

paul

Field Summary

Fields inherited from class BaseSpringContextTest5

arrayDesignPersister, externalDatabaseService, log, persisterHelper, taxonService, testHelper

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 AbstractGeoServiceTest5

getTestFileBasePath, getTestFileBasePath

Methods inherited from class BaseSpringContextTest5

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 BaseIntegrationTest5

setUpAuthentication, tearDownSecurityContext

Methods inherited from class Object

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

Constructor Details

RNASeqBatchInfoPopulationTest

public RNASeqBatchInfoPopulationTest()

Method Details

setUp

@BeforeEach
public void setUp()
           throws Exception

Throws:

Exception

testParseHeaders

@Test
public void testParseHeaders()

testGetBatches

@Test
@Tag("slow")
@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

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

Throws:

Exception

testGSE156689NoBatchinfo

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

Throws:

Exception

testBatchA

@Test
public void testBatchA()
                throws Exception

Throws:

Exception

testBatchB

@Test
public void testBatchB()
                throws Exception

Throws:

Exception

testBatchC

@Test
public void testBatchC()
                throws Exception

Throws:

Exception

testBatchD

@Test
public void testBatchD()
                throws Exception

Throws:

Exception

testBatchDX

@Test
public void testBatchDX()
                 throws Exception

Throws:

Exception

testBatchMixedHeaders

@Test
public void testBatchMixedHeaders()
                           throws Exception

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

Throws:

Exception

testBatchMixedHeadersSinglePlatformSingleton

@Test
public void testBatchMixedHeadersSinglePlatformSingleton()
                                                  throws Exception

Throws:

Exception

testBatchMixedHeadersSinglePlatform

@Test
public void testBatchMixedHeadersSinglePlatform()
                                         throws Exception

Throws:

Exception

testBatchE

@Test
public void testBatchE()
                throws Exception

Throws:

Exception

testBatchF

@Test
public void testBatchF()
                throws Exception

Throws:

Exception

testBatchG

@Test
public void testBatchG()
                throws Exception

Throws:

Exception

testBatchH

@Test
public void testBatchH()
                throws Exception

Throws:

Exception

testBatchI

@Test
public void testBatchI()
                throws Exception

Throws:

Exception

testBatchJ

@Test
public void testBatchJ()
                throws Exception

Throws:

Exception

testBatchK

@Test
public void testBatchK()
                throws Exception

Throws:

Exception

testBatchL

@Test
public void testBatchL()
                throws Exception

Throws:

Exception

testBatchM

@Test
public void testBatchM()
                throws Exception

Throws:

Exception

testBatchO

@Test
public void testBatchO()
                throws Exception

Throws:

Exception

testBatchP

@Test
public void testBatchP()
                throws Exception

Throws:

Exception

testBatchQ

@Test
public void testBatchQ()
                throws Exception

Throws:

Exception

testBatchR

@Test
public void testBatchR()
                throws Exception

Throws:

Exception

testBatchS

@Test
public void testBatchS()
                throws Exception

Throws:

Exception

teardown

@AfterEach
public void teardown()