Package ubic.gemma.core.loader.expression.geo.service

Class GeoDatasetServiceTest

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.loader.expression.geo.service.GeoDatasetServiceTest

All Implemented Interfaces:

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

@NetworkAvailable(url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi")
public class GeoDatasetServiceTest
extends AbstractGeoServiceTest

Test full procedure of loading GEO data, focus on corner cases. Tests deletion of data sets as well.

Author:

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
GeoDatasetServiceTest()

Method Summary

Modifier and Type	Method	Description
void	setUp()
void	tearDown()
void	testFetchAndLoadGSE1133()
void	testFetchAndLoadGSE12135EXON()
void	testFetchAndLoadGSE13657()
void	testFetchAndLoadGSE16035()
void	testFetchAndLoadGSE18707()
void	testFetchAndLoadGSE37646RNASEQ()
void	testFetchAndLoadGSE5949()
void	testFetchAndLoadGSE9048()
void	testFetchAndLoadMultiChipPerSeriesShort()
void	testLoadGSE28383ExonArray()
void	testLoadGSE30521ExonArray()

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

GeoDatasetServiceTest

public GeoDatasetServiceTest()

Method Details

setUp

public void setUp()
           throws URISyntaxException

Throws:

URISyntaxException

tearDown

public void tearDown()

testFetchAndLoadGSE1133

public void testFetchAndLoadGSE1133()
                             throws Exception

Throws:

Exception

testFetchAndLoadGSE37646RNASEQ

public void testFetchAndLoadGSE37646RNASEQ()

testFetchAndLoadGSE16035

public void testFetchAndLoadGSE16035()

testFetchAndLoadGSE12135EXON

public void testFetchAndLoadGSE12135EXON()

testFetchAndLoadGSE13657

public void testFetchAndLoadGSE13657()

testFetchAndLoadGSE9048

public void testFetchAndLoadGSE9048()
                             throws Exception

Throws:

Exception

testFetchAndLoadGSE18707

public void testFetchAndLoadGSE18707()
                              throws QuantitationTypeConversionException

Throws:

QuantitationTypeConversionException

testFetchAndLoadGSE5949

public void testFetchAndLoadGSE5949()
                             throws Exception

Throws:

Exception

testFetchAndLoadMultiChipPerSeriesShort

public void testFetchAndLoadMultiChipPerSeriesShort()
                                             throws Exception

Throws:

Exception

testLoadGSE30521ExonArray

public void testLoadGSE30521ExonArray()

testLoadGSE28383ExonArray

public void testLoadGSE28383ExonArray()