Class GeoDatasetServiceTest

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.loader.expression.geo.service.GeoDatasetServiceTest

@Tag("geo")
@NetworkAvailable(url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi")
@ExtendWith(NetworkAvailableExtension.class)
public class GeoDatasetServiceTest
extends AbstractGeoServiceTest5

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

Author:

pavlidis

Field Summary

Fields inherited from class BaseSpringContextTest5

arrayDesignPersister, externalDatabaseService, log, persisterHelper, taxonService, testHelper

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 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

GeoDatasetServiceTest

public GeoDatasetServiceTest()

Method Details

setUp

@BeforeEach
public void setUp()
           throws URISyntaxException

Throws:

URISyntaxException

tearDown

@AfterEach
public void tearDown()

testFetchAndLoadGSE1133

@Test
@Tag("slow")
public void testFetchAndLoadGSE1133()
                             throws Exception

Throws:

Exception

testFetchAndLoadGSE37646RNASEQ

@Test
public void testFetchAndLoadGSE37646RNASEQ()

testFetchAndLoadGSE16035

@Test
@Tag("slow")
public void testFetchAndLoadGSE16035()

testFetchAndLoadGSE12135EXON

@Test
@Tag("slow")
public void testFetchAndLoadGSE12135EXON()

testFetchAndLoadGSE13657

@Test
public void testFetchAndLoadGSE13657()

testFetchAndLoadGSE9048

@Test
@Tag("slow")
public void testFetchAndLoadGSE9048()
                             throws Exception

Throws:

Exception

testFetchAndLoadGSE18707

@Test
public void testFetchAndLoadGSE18707()
                              throws QuantitationTypeConversionException

Throws:

QuantitationTypeConversionException

testFetchAndLoadGSE5949

@Test
public void testFetchAndLoadGSE5949()
                             throws Exception

Throws:

Exception

testFetchAndLoadMultiChipPerSeriesShort

@Test
@Disabled("This test fails randomly on the CI.")
public void testFetchAndLoadMultiChipPerSeriesShort()
                                             throws Exception

Throws:

Exception

testLoadGSE30521ExonArray

@Test
@Tag("slow")
public void testLoadGSE30521ExonArray()

testLoadGSE28383ExonArray

@Test
@Tag("slow")
public void testLoadGSE28383ExonArray()