A B C D E F G H I J L M N O P Q R S T U V W
All Classes All Packages

A

AbstractArrayDesignProcessingTest - Class in ubic.gemma.core.loader.expression.arrayDesign

Base test for tests that need persistent array design with sequences.

AbstractArrayDesignProcessingTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.AbstractArrayDesignProcessingTest

AbstractDaoIntegrationTest - Class in ubic.gemma.persistence.service

AbstractDaoIntegrationTest() - Constructor for class ubic.gemma.persistence.service.AbstractDaoIntegrationTest

AbstractDaoTest - Class in ubic.gemma.persistence.service

AbstractDaoTest() - Constructor for class ubic.gemma.persistence.service.AbstractDaoTest

AbstractDaoTest.MyDao - Class in ubic.gemma.persistence.service

AbstractDaoTest.MyEntity - Class in ubic.gemma.persistence.service

AbstractFetcherTest - Class in ubic.gemma.core.loader.util.fetcher

AbstractFetcherTest() - Constructor for class ubic.gemma.core.loader.util.fetcher.AbstractFetcherTest

AbstractGeoServiceTest - Class in ubic.gemma.core.loader.expression.geo

AbstractGeoServiceTest() - Constructor for class ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest

AbstractTsvFileServiceTest - Class in ubic.gemma.core.analysis.service

AbstractTsvFileServiceTest() - Constructor for class ubic.gemma.core.analysis.service.AbstractTsvFileServiceTest

AclAdviceTest - Class in ubic.gemma.core.security.authorization.acl

Tests of ACL management: adding and removing from objects during CRUD operations.

AclAdviceTest() - Constructor for class ubic.gemma.core.security.authorization.acl.AclAdviceTest

AclAuthorizationTest - Class in ubic.gemma.core.security.authorization.acl

AclAuthorizationTest() - Constructor for class ubic.gemma.core.security.authorization.acl.AclAuthorizationTest

AclCollectionBeforeTest - Class in ubic.gemma.core.security.authorization.acl

Test the AclCollectionEntryVoter.

AclCollectionBeforeTest() - Constructor for class ubic.gemma.core.security.authorization.acl.AclCollectionBeforeTest

AclCriteriaUtilsTest - Class in ubic.gemma.persistence.util

AclCriteriaUtilsTest() - Constructor for class ubic.gemma.persistence.util.AclCriteriaUtilsTest

AclQueryUtilsTest - Class in ubic.gemma.persistence.util

AclQueryUtilsTest() - Constructor for class ubic.gemma.persistence.util.AclQueryUtilsTest

AclTestUtils - Class in ubic.gemma.core.security.authorization.acl

Methods for checking ACLs.

AclTestUtils() - Constructor for class ubic.gemma.core.security.authorization.acl.AclTestUtils

addTestAnalyses(ExpressionExperiment) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Create test Analysis for the given expression experiment.

addTestAnalyses(ExpressionExperiment) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

AffyChipTypeExtractorTest - Class in ubic.gemma.core.loader.expression.arrayDesign

AffyChipTypeExtractorTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractorTest

AffyPowerToolsProbesetSummarizeTest - Class in ubic.gemma.core.loader.expression

AffyPowerToolsProbesetSummarizeTest() - Constructor for class ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarizeTest

AffyProbeReaderTest - Class in ubic.gemma.core.loader.expression.arrayDesign

AffyProbeReaderTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReaderTest

AffyScanDateExtractorTest - Class in ubic.gemma.core.analysis.preprocess.batcheffects

AffyScanDateExtractorTest() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractorTest

after() - Method in class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceTest

after() - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceTest

after() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVectorServiceTest

afterPropertiesSet() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

afterPropertiesSet() - Method in class ubic.gemma.core.util.test.TestAuthenticationUtilsImpl

afterPropertiesSet() - Method in class ubic.gemma.persistence.retry.RetryTest

afterPropertiesSet() - Method in class ubic.gemma.web.services.rest.util.BaseJerseyTest

AgilentScanDateExtractorTest - Class in ubic.gemma.core.analysis.preprocess.batcheffects

Tests of parsing various flat file formats used for Agilent slides (and possibly other types)

AgilentScanDateExtractorTest() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractorTest

AllenBrainAtlasServiceTest - Class in ubic.gemma.core.image.aba

Alan brain Atlas service test.

AllenBrainAtlasServiceTest() - Constructor for class ubic.gemma.core.image.aba.AllenBrainAtlasServiceTest

AllenBrainAtlasTest - Interface in ubic.gemma.core.util.test.category

Mark tests that require the Allen Brain Atlas RESTful API.

AllTests - Class in ubic.gemma.core.util.test.suite

Test suite consisting of all the tests in the current classpath.

AllTests() - Constructor for class ubic.gemma.core.util.test.suite.AllTests

AnalysisResultSetsJerseyTest - Class in ubic.gemma.web.services.rest

Integration test for the result sets endpoint.

AnalysisResultSetsJerseyTest() - Constructor for class ubic.gemma.web.services.rest.AnalysisResultSetsJerseyTest

AnalysisResultSetsWebServiceTest - Class in ubic.gemma.web.services.rest

AnalysisResultSetsWebServiceTest() - Constructor for class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

AncovaTest - Class in ubic.gemma.core.analysis.expression.diff

Tests of ANCOVA: using linear models with mixtures of fixed level and continuous parameters.

AncovaTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.AncovaTest

annotationsWebService(OntologyService, SearchService, CharacteristicService, ExpressionExperimentService, TaxonService) - Method in class ubic.gemma.web.services.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

AnnotationsWebServiceContextConfiguration() - Constructor for class ubic.gemma.web.services.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

AnnotationsWebServiceTest - Class in ubic.gemma.web.services.rest

AnnotationsWebServiceTest() - Constructor for class ubic.gemma.web.services.rest.AnnotationsWebServiceTest

AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration - Class in ubic.gemma.web.services.rest

Api() - Constructor for class ubic.gemma.web.services.rest.args.StringArrayArgTest.Api

applicationContext - Variable in class ubic.gemma.web.services.rest.util.BaseJerseyTest

The WebApplicationContext that is being used by the container.

applicationContext - Variable in class ubic.gemma.web.util.BaseSpringWebTest

ArrayDesignControllerTest - Class in ubic.gemma.web.controller.expression.arrayDesign

ArrayDesignControllerTest() - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerTest

arrayDesignMergeCli() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration

ArrayDesignMergeCliTest - Class in ubic.gemma.core.apps

ArrayDesignMergeCliTest() - Constructor for class ubic.gemma.core.apps.ArrayDesignMergeCliTest

ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration - Class in ubic.gemma.core.apps

ArrayDesignMergeCliTestContextConfiguration() - Constructor for class ubic.gemma.core.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration

arrayDesignMergeService() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration

ArrayDesignMergeServiceTest - Class in ubic.gemma.core.loader.expression.arrayDesign

ArrayDesignMergeServiceTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeServiceTest

arrayDesignReportService() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration

ArrayDesignReportServiceTest - Class in ubic.gemma.core.analysis.report

ArrayDesignReportServiceTest() - Constructor for class ubic.gemma.core.analysis.report.ArrayDesignReportServiceTest

ArrayDesignSequenceAlignmentandMappingTest - Class in ubic.gemma.core.loader.expression.arrayDesign

ArrayDesignSequenceAlignmentandMappingTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentandMappingTest

ArrayDesignSequenceProcessorFastacmdTest - Class in ubic.gemma.core.loader.expression.arrayDesign

Test exercises the fastacmd - requires executable.

ArrayDesignSequenceProcessorFastacmdTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorFastacmdTest

ArrayDesignSequenceProcessorTest - Class in ubic.gemma.core.loader.expression.arrayDesign

ArrayDesignSequenceProcessorTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorTest

arrayDesignService() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration

arrayDesignService() - Method in class ubic.gemma.web.services.rest.SearchWebServiceTest.SearchWebServiceTestContextConfiguration

ArrayDesignServiceTest - Class in ubic.gemma.model.expression.arrayDesign

ArrayDesignServiceTest() - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

assertBAs(ExpressionExperiment, ArrayDesign, String, int) - Static method in class ubic.gemma.core.loader.util.TestUtils

Checks the BioAssays in the given EE match the given properties.

AuditAdviceTest - Class in ubic.gemma.core.security.audit

Test of adding audit events when objects are created, updated or deleted.

AuditAdviceTest() - Constructor for class ubic.gemma.core.security.audit.AuditAdviceTest

AuditControllerTest - Class in ubic.gemma.web.remote

AuditControllerTest() - Constructor for class ubic.gemma.web.remote.AuditControllerTest

AuditEventDaoImplTest - Class in ubic.gemma.model.common.auditAndSecurity

AuditEventDaoImplTest() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEventDaoImplTest

auditEventService() - Method in class ubic.gemma.core.util.test.BaseCliTest.BaseCliTestContextConfiguration

AuditTrailDaoTest - Class in ubic.gemma.model.common.auditAndSecurity

AuditTrailDaoTest() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditTrailDaoTest

auditTrailService() - Method in class ubic.gemma.core.util.test.BaseCliTest.BaseCliTestContextConfiguration

AuditTrailServiceImplTest - Class in ubic.gemma.model.common.auditAndSecurity

AuditTrailServiceImplTest() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest

authenticationManager() - Method in class ubic.gemma.core.util.test.BaseCliTest.BaseCliTestContextConfiguration

B

Bar(EntityUtilsTest.Foo) - Constructor for class ubic.gemma.persistence.util.EntityUtilsTest.Bar

BaseAnalyzerConfigurationTest - Class in ubic.gemma.core.analysis.expression.diff

Other tests can extend this class if they want an expression experiment with complete block design and biological replicates.

BaseAnalyzerConfigurationTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.BaseAnalyzerConfigurationTest

BaseCliTest - Class in ubic.gemma.core.util.test

Minimal setup

BaseCliTest() - Constructor for class ubic.gemma.core.util.test.BaseCliTest

BaseCliTest.BaseCliTestContextConfiguration - Class in ubic.gemma.core.util.test

Basic context configuration

BaseCliTestContextConfiguration() - Constructor for class ubic.gemma.core.util.test.BaseCliTest.BaseCliTestContextConfiguration

BaseJerseyIntegrationTest - Class in ubic.gemma.web.services.rest.util

Base class for Jersey-based integration tests.

BaseJerseyIntegrationTest() - Constructor for class ubic.gemma.web.services.rest.util.BaseJerseyIntegrationTest

BaseJerseyTest - Class in ubic.gemma.web.services.rest.util

Base class for Jersey-based tests that needs a WebApplicationContext for loading and configuring or mocking Spring components.

BaseJerseyTest() - Constructor for class ubic.gemma.web.services.rest.util.BaseJerseyTest

BaselineDetectionTest - Class in ubic.gemma.core.analysis.expression.diff

BaselineDetectionTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.BaselineDetectionTest

BaseSpringContextTest - Class in ubic.gemma.core.util.test

subclass for tests that need the container and use the database

BaseSpringContextTest() - Constructor for class ubic.gemma.core.util.test.BaseSpringContextTest

BaseSpringWebTest - Class in ubic.gemma.web.util

Class to extend for tests of controllers et al. that need a spring context.

BaseSpringWebTest() - Constructor for class ubic.gemma.web.util.BaseSpringWebTest

BatchInfoPopulationServiceIntegrationTest - Class in ubic.gemma.core.analysis.preprocess.batcheffects

Test fetching and loading the batch information from raw files.

BatchInfoPopulationServiceIntegrationTest() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceIntegrationTest

BatchInfoPopulationServiceTest - Class in ubic.gemma.core.analysis.preprocess.batcheffects

Unit tests.

BatchInfoPopulationServiceTest() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceTest

before() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceTest

before() - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationProcessingTest

before() - Method in class ubic.gemma.core.security.principal.PrincipalTest

before() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVectorServiceTest

BibliographicReferenceServiceImplTest - Class in ubic.gemma.core.annotation.reference

BibliographicReferenceServiceImplTest() - Constructor for class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImplTest

BibliographicReferenceServiceTest - Class in ubic.gemma.core.annotation.reference

This class tests the bibliographic reference data access object.

BibliographicReferenceServiceTest() - Constructor for class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceTest

BibRefControllerTest - Class in ubic.gemma.web.controller.common.description.bibref

Tests the BibliographicReferenceController

BibRefControllerTest() - Constructor for class ubic.gemma.web.controller.common.description.bibref.BibRefControllerTest

BioAssayServiceTest - Class in ubic.gemma.model.expression.bioAssay

BioAssayServiceTest() - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayServiceTest

BioMartEnsemblNcbiFetcherTest - Class in ubic.gemma.core.util.biomart

Tests that biomart fetcher works correctly.

BioMartEnsemblNcbiFetcherTest() - Constructor for class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiFetcherTest

BioMartEnsemblNcbiObjectGeneratorTest - Class in ubic.gemma.core.util.biomart

Class to test BioMartEnsemblNcbiObjectGeneration.

BioMartEnsemblNcbiObjectGeneratorTest() - Constructor for class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiObjectGeneratorTest

BioMartEnsemblNcbiParserTest - Class in ubic.gemma.core.util.biomart

Tests the parsing of a BioMart file.

BioMartEnsemblNcbiParserTest() - Constructor for class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiParserTest

BioMaterialServiceTest - Class in ubic.gemma.model.expression.biomaterial

BioMaterialServiceTest() - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterialServiceTest

BioSequencePersistTest - Class in ubic.gemma.model.genome

BioSequencePersistTest() - Constructor for class ubic.gemma.model.genome.BioSequencePersistTest

BioSequenceTest - Class in ubic.gemma.model.genome.biosequence

BioSequenceTest() - Constructor for class ubic.gemma.model.genome.biosequence.BioSequenceTest

BlacklistTest - Class in ubic.gemma.model.expression

BlacklistTest() - Constructor for class ubic.gemma.model.expression.BlacklistTest

BlatAssociationScorerTest - Class in ubic.gemma.core.analysis.sequence

BlatAssociationScorer tests

BlatAssociationScorerTest() - Constructor for class ubic.gemma.core.analysis.sequence.BlatAssociationScorerTest

BlatAssociationServiceTest - Class in ubic.gemma.model.genome.sequenceAnalysis

BlatAssociationServiceTest() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociationServiceTest

BlatResultParserTest - Class in ubic.gemma.core.loader.genome

BlatResultParserTest() - Constructor for class ubic.gemma.core.loader.genome.BlatResultParserTest

BlatResultServiceTest - Class in ubic.gemma.model.genome.sequenceAnalysis

BlatResultServiceTest() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatResultServiceTest

BlatResultTest - Class in ubic.gemma.model.genome

BlatResultTest() - Constructor for class ubic.gemma.model.genome.BlatResultTest

C

CharacteristicDaoImplTest - Class in ubic.gemma.persistence.service.common.description

CharacteristicDaoImplTest() - Constructor for class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest

characteristicService() - Method in class ubic.gemma.web.services.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

CharacteristicServiceTest - Class in ubic.gemma.model.common.description

CharacteristicServiceTest() - Constructor for class ubic.gemma.model.common.description.CharacteristicServiceTest

CharacteristicSortTest - Class in ubic.gemma.core.ontology

CharacteristicSortTest() - Constructor for class ubic.gemma.core.ontology.CharacteristicSortTest

CharacteristicValueObjectTest - Class in ubic.gemma.model.genome.gene.phenotype.valueObject

CharacteristicValueObjectTest() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest

checkDeletedAcl(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclTestUtils

Make sure object f has no ACLs

checkDeleteEEAcls(ExpressionExperiment) - Method in class ubic.gemma.core.security.authorization.acl.AclTestUtils

CHeck the entire entity graph of an ee for ACL deletion.

checkEEAcls(ExpressionExperiment) - Method in class ubic.gemma.core.security.authorization.acl.AclTestUtils

Validate ACLs on EE

checkEESubSetAcls(ExpressionExperimentSubSet) - Method in class ubic.gemma.core.security.authorization.acl.AclTestUtils

checkHasAces(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclTestUtils

checkHasAcl(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclTestUtils

checkHasAclParent(Object, Object) - Method in class ubic.gemma.core.security.authorization.acl.AclTestUtils

checkLacksAces(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclTestUtils

checkLacksAcl(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclTestUtils

checkResults(DifferentialExpressionAnalysis) - Method in class ubic.gemma.core.analysis.expression.diff.LowVarianceDataTest

checkResults(DifferentialExpressionAnalysis) - Method in class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionTest2

cleanup() - Method in class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperServiceTest

Cleanup() - Method in class ubic.gemma.core.image.aba.AllenBrainAtlasServiceTest

CliTest - Class in ubic.gemma.core.apps

CliTest() - Constructor for class ubic.gemma.core.apps.CliTest

CoexpressionNodeDegreeValueObjectTest - Class in ubic.gemma.model.analysis.expression.coexpression

CoexpressionNodeDegreeValueObjectTest() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.CoexpressionNodeDegreeValueObjectTest

ComBatTest - Class in ubic.gemma.core.analysis.preprocess.batcheffects

ComBatTest() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.ComBatTest

CompassSearchSourceTest - Class in ubic.gemma.core.search.source

CompassSearchSourceTest() - Constructor for class ubic.gemma.core.search.source.CompassSearchSourceTest

CompositeSequenceGeneMapperServiceTest - Class in ubic.gemma.core.analysis.service

This test makes use of the ArrayDesignProbeMapperServiceImpl.

CompositeSequenceGeneMapperServiceTest() - Constructor for class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperServiceTest

CompositeSequenceParserTest - Class in ubic.gemma.core.loader.expression.arrayDesign

CompositeSequenceParserTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParserTest

CompositeSequenceServiceTest - Class in ubic.gemma.persistence.service.expression.designElement

CompositeSequenceServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceTest

ConfigurationCookieTest - Class in ubic.gemma.web.util

ConfigurationCookieTest() - Constructor for class ubic.gemma.web.util.ConfigurationCookieTest

configure() - Method in class ubic.gemma.web.services.rest.providers.WebApplicationExceptionMapperTest

configure() - Method in class ubic.gemma.web.services.rest.util.BaseJerseyTest

ContinuousVariableDiffExTest - Class in ubic.gemma.core.analysis.expression.diff

ContinuousVariableDiffExTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.ContinuousVariableDiffExTest

CorsFilterTest - Class in ubic.gemma.web.services.rest.servlet

CorsFilterTest() - Constructor for class ubic.gemma.web.services.rest.servlet.CorsFilterTest

countRowsInTable(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Count the rows in the given table.

CuratableValueObjectTest - Class in ubic.gemma.web.controller.expression

CuratableValueObjectTest() - Constructor for class ubic.gemma.web.controller.expression.CuratableValueObjectTest

CustomResource() - Constructor for class ubic.gemma.web.services.rest.providers.WebApplicationExceptionMapperTest.CustomResource

D

DatabaseEntryDaoImplTest - Class in ubic.gemma.model.common.description

DatabaseEntryDaoImplTest() - Constructor for class ubic.gemma.model.common.description.DatabaseEntryDaoImplTest

DatabaseSearchSourceTest - Class in ubic.gemma.core.search.source

DatabaseSearchSourceTest() - Constructor for class ubic.gemma.core.search.source.DatabaseSearchSourceTest

DatasetCombinerTest - Class in ubic.gemma.core.loader.expression.geo

DatasetCombinerTest() - Constructor for class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

DatasetsRestTest - Class in ubic.gemma.web.services.rest

DatasetsRestTest() - Constructor for class ubic.gemma.web.services.rest.DatasetsRestTest

DatasetsWebServiceTest - Class in ubic.gemma.web.services.rest

DatasetsWebServiceTest() - Constructor for class ubic.gemma.web.services.rest.DatasetsWebServiceTest

DataUpdaterTest - Class in ubic.gemma.core.loader.expression

DataUpdaterTest() - Constructor for class ubic.gemma.core.loader.expression.DataUpdaterTest

deleteFromTables(String...) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Convenience method for deleting all rows from the specified tables.

DesignElementDataVectorServiceTest - Class in ubic.gemma.model.expression.bioAssayData

DesignElementDataVectorServiceTest() - Constructor for class ubic.gemma.model.expression.bioAssayData.DesignElementDataVectorServiceTest

DetectFactorBaselineTest - Class in ubic.gemma.core.datastructure.matrix

DetectFactorBaselineTest() - Constructor for class ubic.gemma.core.datastructure.matrix.DetectFactorBaselineTest

DifferentialExpressionAnalysisHelperServiceTest - Class in ubic.gemma.core.analysis.expression.diff

DifferentialExpressionAnalysisHelperServiceTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperServiceTest

DifferentialExpressionAnalysisServiceTest - Class in ubic.gemma.model.analysis

DifferentialExpressionAnalysisServiceTest() - Constructor for class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest

DifferentialExpressionAnalyzerServiceTest - Class in ubic.gemma.core.analysis.expression.diff

DifferentialExpressionAnalyzerServiceTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest

DifferentialExpressionAnalyzerTest - Class in ubic.gemma.core.analysis.expression.diff

DifferentialExpressionAnalyzerTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerTest

DiffExMetaAnalyzerServiceTest - Class in ubic.gemma.core.analysis.expression.diff

This is a test that requires complex setup: loading several data sets, information on genes, array design annotations, conducting differential expression, and finally the meta-analysis.

DiffExMetaAnalyzerServiceTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceTest

DiffExTest - Class in ubic.gemma.core.analysis.expression.diff

Tests added to check various cases of differential expression analysis.

DiffExTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.DiffExTest

DiffExWithInvalidInteraction2Test - Class in ubic.gemma.core.analysis.expression.diff

for bug 3927

DiffExWithInvalidInteraction2Test() - Constructor for class ubic.gemma.core.analysis.expression.diff.DiffExWithInvalidInteraction2Test

DiffExWithInvalidInteractionTest - Class in ubic.gemma.core.analysis.expression.diff

DiffExWithInvalidInteractionTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.DiffExWithInvalidInteractionTest

E

EntityUtilsTest - Class in ubic.gemma.persistence.util

EntityUtilsTest() - Constructor for class ubic.gemma.persistence.util.EntityUtilsTest

EntityUtilsTest.Bar - Class in ubic.gemma.persistence.util

ESearchXMLParserTest - Class in ubic.gemma.core.loader.entrez.pubmed

ESearchXMLParserTest() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.ESearchXMLParserTest

EutilFetchTest - Class in ubic.gemma.core.loader.entrez

EutilFetchTest() - Constructor for class ubic.gemma.core.loader.entrez.EutilFetchTest

executeSqlScript(String, boolean) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Execute the given SQL script.

ExecutingTaskTest - Class in ubic.gemma.core.job

ExecutingTaskTest() - Constructor for class ubic.gemma.core.job.ExecutingTaskTest

ExonArrayDataAddIntegrationTest - Class in ubic.gemma.core.loader.expression

Uses the Affy Power Tools, and full-sized data sets.

ExonArrayDataAddIntegrationTest() - Constructor for class ubic.gemma.core.loader.expression.ExonArrayDataAddIntegrationTest

ExperimentalDesignControllerTest - Class in ubic.gemma.web.controller.expression.experiment

ExperimentalDesignControllerTest() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest

ExperimentalDesignImportDuplicateValueTest - Class in ubic.gemma.core.loader.expression.simple

Test for import that results in multiple factor values for the same factor on a single biomaterial.

ExperimentalDesignImportDuplicateValueTest() - Constructor for class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImportDuplicateValueTest

ExperimentalDesignImporterTest - Class in ubic.gemma.core.loader.expression.simple

ExperimentalDesignImporterTest() - Constructor for class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterTest

ExperimentalDesignWriterTest - Class in ubic.gemma.core.datastructure.matrix

ExperimentalDesignWriterTest() - Constructor for class ubic.gemma.core.datastructure.matrix.ExperimentalDesignWriterTest

ExpressionAnalysisResultSetServiceTest - Class in ubic.gemma.persistence.service.analysis.expression.diff

This implementation is using the Hibernate Criteria API, so we want to minimally test the logic of translating Filters and Sort into proper Criteria queries.

ExpressionAnalysisResultSetServiceTest() - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceTest

ExpressionDataDoubleMatrixTest - Class in ubic.gemma.core.datastructure.matrix

ExpressionDataDoubleMatrixTest() - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixTest

ExpressionDataMatrixColumnSortTest - Class in ubic.gemma.core.datastructure.matrix

ExpressionDataMatrixColumnSortTest() - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSortTest

expressionDataMatrixService - Variable in class ubic.gemma.core.analysis.expression.diff.BaseAnalyzerConfigurationTest

ExpressionDataSVDTest - Class in ubic.gemma.core.analysis.preprocess

ExpressionDataSVDTest() - Constructor for class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest

ExpressionDataTestMatrix - Class in ubic.gemma.core.datastructure.matrix

Creates a sample small test matrix, not persistent.

ExpressionDataTestMatrix() - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataTestMatrix

ExpressionExperimentBatchCorrectionServiceTest - Class in ubic.gemma.core.analysis.preprocess.batcheffects

ExpressionExperimentBatchCorrectionServiceTest() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceTest

ExpressionExperimentBibRefFinderTest - Class in ubic.gemma.core.loader.entrez.pubmed

ExpressionExperimentBibRefFinderTest() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest

ExpressionExperimentControllerTest - Class in ubic.gemma.web.controller.expression.experiment

ExpressionExperimentControllerTest() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentControllerTest

ExpressionExperimentDeleteTest - Class in ubic.gemma.model.expression.experiment

ExpressionExperimentDeleteTest() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentDeleteTest

ExpressionExperimentPlatformSwitchTest - Class in ubic.gemma.core.loader.expression

Switching of platforms that have no composite sequences.

ExpressionExperimentPlatformSwitchTest() - Constructor for class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchTest

expressionExperimentService() - Method in class ubic.gemma.core.util.test.BaseCliTest.BaseCliTestContextConfiguration

expressionExperimentService() - Method in class ubic.gemma.web.services.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

ExpressionExperimentServiceImplTest - Class in ubic.gemma.model.expression.experiment

ExpressionExperimentServiceImplTest() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceImplTest

ExpressionExperimentServiceTest - Class in ubic.gemma.model.expression.experiment

ExpressionExperimentServiceTest() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

ExpressionExperimentSetServiceTest - Class in ubic.gemma.model.expression.experiment

Tests for methods that perform operations on or with expressionExperiment sets

ExpressionExperimentSetServiceTest() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentSetServiceTest

ExpressionExperimentSetValueObjectHelperTest - Class in ubic.gemma.model.expression.experiment

Tests for methods that create ExpressionExperimentSetValueObjects from expressionExperiment entities

ExpressionExperimentSetValueObjectHelperTest() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObjectHelperTest

ExpressionExperimentSubSetServiceTest - Class in ubic.gemma.model.expression

ExpressionExperimentSubSetServiceTest() - Constructor for class ubic.gemma.model.expression.ExpressionExperimentSubSetServiceTest

ExternalDatabaseDaoTest - Class in ubic.gemma.persistence.service.common.description

ExternalDatabaseDaoTest() - Constructor for class ubic.gemma.persistence.service.common.description.ExternalDatabaseDaoTest

externalDatabaseService - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest

ExternalDatabaseServiceTest - Class in ubic.gemma.persistence.service.common.description

ExternalDatabaseServiceTest() - Constructor for class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceTest

ExternalDatabaseUpdaterCliTest - Class in ubic.gemma.core.apps

ExternalDatabaseUpdaterCliTest() - Constructor for class ubic.gemma.core.apps.ExternalDatabaseUpdaterCliTest

ExternalFileGeneLoaderServiceTest - Class in ubic.gemma.core.loader.genome.gene

Test that Gemma can load genes from an external gene file with format : #GeneSymbol GeneName Uniprot ZYX ZYXIN Q15942 ZXDC ZXD FAMILY ZINC FINGER C Q8C8V1

ExternalFileGeneLoaderServiceTest() - Constructor for class ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceTest

F

FactorValueServiceTest - Class in ubic.gemma.model.expression.experiment

FactorValueServiceTest() - Constructor for class ubic.gemma.model.expression.experiment.FactorValueServiceTest

FastaParserTest - Class in ubic.gemma.core.loader.genome

FastaParserTest() - Constructor for class ubic.gemma.core.loader.genome.FastaParserTest

FastTests - Class in ubic.gemma.core.util.test.suite

Test suite that excludes all the slow tests (i.e. marked with SlowTest).

FastTests() - Constructor for class ubic.gemma.core.util.test.suite.FastTests

FileUploadUtilTest - Class in ubic.gemma.web.util.upload

FileUploadUtilTest() - Constructor for class ubic.gemma.web.util.upload.FileUploadUtilTest

FilterArgTest - Class in ubic.gemma.web.services.rest.util.args

FilterArgTest() - Constructor for class ubic.gemma.web.services.rest.util.args.FilterArgTest

G

GemmaEndpointTest - Class in ubic.gemma.web.services

GemmaEndpointTest() - Constructor for class ubic.gemma.web.services.GemmaEndpointTest

Gene2GeneCoexpressionServiceTest - Class in ubic.gemma.model.association.coexpression

Gene2GeneCoexpressionServiceTest() - Constructor for class ubic.gemma.model.association.coexpression.Gene2GeneCoexpressionServiceTest

GeneCoexpressionTestedInTest - Class in ubic.gemma.model.analysis.expression.coexpression

GeneCoexpressionTestedInTest() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedInTest

GeneDiffExMetaAnalysisServiceTest - Class in ubic.gemma.model.analysis

GeneDiffExMetaAnalysisServiceTest() - Constructor for class ubic.gemma.model.analysis.GeneDiffExMetaAnalysisServiceTest

GeneMultifunctionalityPopulationServiceTest - Class in ubic.gemma.core.analysis.service

GeneMultifunctionalityPopulationServiceTest() - Constructor for class ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationServiceTest

GeneOntologyServiceTest - Class in ubic.gemma.core.ontology.providers

GeneOntologyServiceTest() - Constructor for class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

GeneOntologyServiceTest2 - Class in ubic.gemma.core.ontology.providers

Additional tests with updated ontology file, fixing problems getting aspects.

GeneOntologyServiceTest2() - Constructor for class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest2

GenericScanFileDateExtractorTest - Class in ubic.gemma.core.analysis.preprocess.batcheffects

GenericScanFileDateExtractorTest() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest

GeneSearchTest - Class in ubic.gemma.model.genome.gene

GeneSearchTest() - Constructor for class ubic.gemma.model.genome.gene.GeneSearchTest

GeneServiceImplTest - Class in ubic.gemma.model.genome.gene

GeneServiceImplTest() - Constructor for class ubic.gemma.model.genome.gene.GeneServiceImplTest

GeneServiceTest - Class in ubic.gemma.model.genome.gene

GeneServiceTest() - Constructor for class ubic.gemma.model.genome.gene.GeneServiceTest

GeneSetServiceTest - Class in ubic.gemma.model.genome.gene

GeneSetServiceTest() - Constructor for class ubic.gemma.model.genome.gene.GeneSetServiceTest

GeneSetValueObjectHelperTest - Class in ubic.gemma.model.genome.gene

GeneSetValueObjectHelperTest() - Constructor for class ubic.gemma.model.genome.gene.GeneSetValueObjectHelperTest

GeneTest - Class in ubic.gemma.model.genome

Tests of 'equals' implementation

GeneTest() - Constructor for class ubic.gemma.model.genome.GeneTest

GeneValueObjectTest - Class in ubic.gemma.model.genome.gene

GeneValueObjectTest() - Constructor for class ubic.gemma.model.genome.gene.GeneValueObjectTest

GenomePersisterTest - Class in ubic.gemma.persistence

GenomePersisterTest() - Constructor for class ubic.gemma.persistence.GenomePersisterTest

GeoBrowserServiceParseTest - Class in ubic.gemma.core.loader.expression.geo.service

GeoBrowserServiceParseTest() - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceParseTest

GeoBrowserServiceTest - Class in ubic.gemma.core.loader.expression.geo.service

GeoBrowserServiceTest() - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceTest

GeoBrowserTest - Class in ubic.gemma.core.loader.expression.geo

GeoBrowserTest() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoBrowserTest

GeoCharacteristicParseTest - Class in ubic.gemma.core.loader.expression.geo

GeoCharacteristicParseTest() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoCharacteristicParseTest

GeoConverterTest - Class in ubic.gemma.core.loader.expression.geo

Unit test for GeoConversion Added extension BaseSpringContextTest as want Taxon Service to be called

GeoConverterTest() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoConverterTest

GeoDatasetServiceTest - Class in ubic.gemma.core.loader.expression.geo.service

Test full procedure of loading GEO data, focus on corner cases.

GeoDatasetServiceTest() - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest

GeoFamilyParserTest - Class in ubic.gemma.core.loader.expression.geo

GeoFamilyParserTest() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest

GeoPlatformServiceTest - Class in ubic.gemma.core.loader.expression.geo.service

Tests of GeoPlatformService

GeoPlatformServiceTest() - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoPlatformServiceTest

GeoPlatformTest - Class in ubic.gemma.core.loader.expression.geo

GeoPlatformTest() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoPlatformTest

geoService - Variable in class ubic.gemma.core.analysis.expression.diff.BaselineDetectionTest

geoService - Variable in class ubic.gemma.model.expression.bioAssayData.DesignElementDataVectorServiceTest

GeoTest - Class in ubic.gemma.core.util.test.category

Test depending on GEO availability.

GeoTest() - Constructor for class ubic.gemma.core.util.test.category.GeoTest

getAcl(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclTestUtils

getAd() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AbstractArrayDesignProcessingTest

getExperimentalDesign(Collection<FactorValue>) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getExperimentalFactors(ExperimentalDesign) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getFactorValues(ExperimentalFactor) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getFactorValues(ExperimentalFactor, Collection<FactorValue>) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getFoo() - Method in class ubic.gemma.persistence.util.EntityUtilsTest.Bar

getId() - Method in class ubic.gemma.persistence.service.AbstractDaoTest.MyEntity

getNewTestPersistentCompleteExpressionExperiment() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTaxon(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestCharacteristic(String, String) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestContainerFactory() - Method in class ubic.gemma.web.services.rest.providers.WebApplicationExceptionMapperTest

getTestContainerFactory() - Method in class ubic.gemma.web.services.rest.util.BaseJerseyTest

getTestElementCollectionSize() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestExpressionExperimentWithAllDependencies() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

Add an expressionExperiment to the database for testing purposes.

getTestExpressionExperimentWithAllDependencies(boolean) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

Add an expressionExperiment to the database for testing purposes.

getTestExpressionExperimentWithAllDependencies(ExpressionExperiment) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestExpressionExperimentWithAnalysisAndResults() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

Create a test EE with analysis results.

getTestFileBasePath() - Method in class ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest

getTestFileBasePath(String) - Method in class ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest

getTestNonPersistentBioSequence(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestNonPersistentBioSequence(Taxon) - Static method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestNonPersistentGeneProduct(Gene) - Static method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestNonPersistentQuantitationType() - Static method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

Note that if you want a 'preferred' qt or other special properties you have to set it yourself.

getTestPersistentArrayDesign(int, boolean) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.

getTestPersistentArrayDesign(int, boolean, boolean) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.

getTestPersistentArrayDesign(int, boolean, boolean, boolean) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.

getTestPersistentArrayDesign(List<String>, Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.

getTestPersistentBasicExpressionExperiment() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentBasicExpressionExperiment() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestPersistentBasicExpressionExperiment(ArrayDesign) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentBasicExpressionExperiment(ArrayDesign) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestPersistentBibliographicReference(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentBibliographicReference(String) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestPersistentBioAssay(ArrayDesign) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.

getTestPersistentBioAssay(ArrayDesign) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestPersistentBioAssay(ArrayDesign, BioMaterial) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.

getTestPersistentBioAssay(ArrayDesign, BioMaterial) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.

getTestPersistentBioMaterial() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentBioMaterial() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestPersistentBioMaterial(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentBioMaterial(Taxon) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestPersistentBioSequence() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentBioSequence() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestPersistentBioSequence(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentBioSequence(Taxon) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestPersistentBioSequence2GeneProducts(BioSequence) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentBioSequence2GeneProducts(BioSequence) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestPersistentBlatResult(BioSequence) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentBlatResult(BioSequence, Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentBlatResult(BioSequence, Taxon) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestPersistentCompleteExpressionExperiment(boolean) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Convenience method to get a (fairly) complete randomly generated persisted expression experiment.

getTestPersistentCompleteExpressionExperimentWithSequences() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Convenience method to get a (fairly) complete randomly generated persisted expression experiment.

getTestPersistentCompleteExpressionExperimentWithSequences(ExpressionExperiment) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentContact() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Convenience method to provide a Contact that can be used to fill non-nullable associations in test objects.

getTestPersistentContact() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

Convenience method to provide a Contact that can be used to fill non-nullable associations in test objects.

getTestPersistentDatabaseEntry() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Get a database entry from a fictitious database.

getTestPersistentDatabaseEntry(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentDatabaseEntry(String, String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentDatabaseEntry(String, String) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestPersistentDatabaseEntry(String, ExternalDatabase) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.

getTestPersistentDatabaseEntry(String, ExternalDatabase) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.

getTestPersistentDatabaseEntry(ExternalDatabase) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.

getTestPersistentDatabaseEntry(ExternalDatabase) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.

getTestPersistentExpressionExperiment() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.

getTestPersistentExpressionExperiment() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.

getTestPersistentExpressionExperiment(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.

getTestPersistentExpressionExperiment(Taxon) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.

getTestPersistentGene() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentGene() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestPersistentGene(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentGene(Taxon) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestPersistentGeneProduct(Gene) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

getTestPersistentGeneProduct(Gene) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

getTestPersistentQuantitationType() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Convenience method to provide a QuantitationType that can be used to fill non-nullable associations in test objects.

getTestPersistentQuantitationType() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

Convenience method to provide a QuantitationType that can be used to fill non-nullable associations in test objects.

getTestPersistentTaxon() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

GoldenPathQueryTest - Class in ubic.gemma.core.externalDb

These tests require a populated Human database.

GoldenPathQueryTest() - Constructor for class ubic.gemma.core.externalDb.GoldenPathQueryTest

GoldenPathTest - Class in ubic.gemma.core.util.test.category

Test depending on GoldenPath database availability.

GoldenPathTest() - Constructor for class ubic.gemma.core.util.test.category.GoldenPathTest

H

HomologeneServiceTest - Class in ubic.gemma.core.loader.genome.gene.ncbi.homology

Tests the homologeneService but only access methods that don't require a DB connection (using the gemma db).

HomologeneServiceTest() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceTest

HttpFetcherTest - Class in ubic.gemma.core.loader.util

HttpFetcherTest() - Constructor for class ubic.gemma.core.loader.util.HttpFetcherTest

I

IlluminaProbeReaderTest - Class in ubic.gemma.core.loader.expression.arrayDesign

IlluminaProbeReaderTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReaderTest

indexAsJson() - Method in class ubic.gemma.web.services.rest.providers.WebApplicationExceptionMapperTest.CustomResource

indexAsString() - Method in class ubic.gemma.web.services.rest.providers.WebApplicationExceptionMapperTest.CustomResource

IntegrationTests - Class in ubic.gemma.core.util.test.suite

IntegrationTests() - Constructor for class ubic.gemma.core.util.test.suite.IntegrationTests

J

jdbcTemplate - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest

The SimpleJdbcTemplate that this base class manages, available to subclasses.

JOB_LENGTH - Static variable in interface ubic.gemma.web.util.MockLongJobController

L

LinkAnalysisServiceTest - Class in ubic.gemma.core.analysis.expression.coexpression.links

LinkAnalysisServiceTest() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisServiceTest

ListUtilsTest - Class in ubic.gemma.persistence.util

Tests for extra utilities for List.

ListUtilsTest() - Constructor for class ubic.gemma.persistence.util.ListUtilsTest

log - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest

LogNcbiError(Log, Exception) - Static method in class ubic.gemma.core.loader.util.TestUtils

Checks whether the given Exception is a known NCBI error and if so, logs the error.

LowVarianceDataTest - Class in ubic.gemma.core.analysis.expression.diff

Test based on GSE19480, see bug 3177

LowVarianceDataTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.LowVarianceDataTest

luceneQueryParser_whenTermIsQuoted_thenPreserveQuoting() - Method in class ubic.gemma.core.search.source.CompassSearchSourceTest

luceneRamIndexTest() - Method in class ubic.gemma.core.search.LuceneTest

Searching uses a ram index to deal with queries using logical operators.

LuceneTest - Class in ubic.gemma.core.search

LuceneTest() - Constructor for class ubic.gemma.core.search.LuceneTest

M

ManualAuthenticationProcessingTest - Class in ubic.gemma.core.security.authentication

ManualAuthenticationProcessingTest() - Constructor for class ubic.gemma.core.security.authentication.ManualAuthenticationProcessingTest

manualAuthenticationService() - Method in class ubic.gemma.core.util.test.BaseCliTest.BaseCliTestContextConfiguration

MatrixConversionTest - Class in ubic.gemma.core.datastructure.matrix

MatrixConversionTest() - Constructor for class ubic.gemma.core.datastructure.matrix.MatrixConversionTest

MeanVarianceServiceTest - Class in ubic.gemma.core.analysis.preprocess

MeanVarianceServiceTest() - Constructor for class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceTest

mockitoRule - Variable in class ubic.gemma.web.services.rest.util.args.FilterArgTest

MockLongJobController - Interface in ubic.gemma.web.util

Note: do not use parameterized collections as parameters for ajax methods in this class!

MockLongJobControllerImpl - Class in ubic.gemma.web.util

Controller that does nothing except wait a while.

MockLongJobControllerImpl() - Constructor for class ubic.gemma.web.util.MockLongJobControllerImpl

mvc - Variable in class ubic.gemma.web.util.BaseSpringWebTest

MyDao(SessionFactory) - Constructor for class ubic.gemma.persistence.service.AbstractDaoTest.MyDao

MyDao(SessionFactory, int) - Constructor for class ubic.gemma.persistence.service.AbstractDaoTest.MyDao

MyEntity() - Constructor for class ubic.gemma.persistence.service.AbstractDaoTest.MyEntity

MyModel() - Constructor for class ubic.gemma.web.services.rest.providers.WebApplicationExceptionMapperTest.CustomResource.MyModel

N

NCBIGene2GOAssociationLoaderCLITest - Class in ubic.gemma.core.apps

NCBIGene2GOAssociationLoaderCLITest() - Constructor for class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLITest

NCBIGene2GOAssociationParserTest - Class in ubic.gemma.core.loader.association

Tests multiple both parsing and loading.

NCBIGene2GOAssociationParserTest() - Constructor for class ubic.gemma.core.loader.association.NCBIGene2GOAssociationParserTest

NCBIGeneHistoryParserTest - Class in ubic.gemma.core.loader.genome.gene.ncbi

TODO Document Me

NCBIGeneHistoryParserTest() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneHistoryParserTest

NCBIGeneLoadingTest - Class in ubic.gemma.core.loader.genome.gene.ncbi

NCBIGeneLoadingTest() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneLoadingTest

NCBIGeneParserTest - Class in ubic.gemma.core.loader.genome.gene.ncbi

NCBIGeneParserTest() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneParserTest

newGet(String) - Method in class ubic.gemma.web.util.BaseSpringWebTest

newPost(String) - Method in class ubic.gemma.web.util.BaseSpringWebTest

Convenience methods to make tests simpler

O

ObjectFilterQueryUtilsTest - Class in ubic.gemma.persistence.util

ObjectFilterQueryUtilsTest() - Constructor for class ubic.gemma.persistence.util.ObjectFilterQueryUtilsTest

ObjectFilterTest - Class in ubic.gemma.persistence.util

ObjectFilterTest() - Constructor for class ubic.gemma.persistence.util.ObjectFilterTest

OneWayAnovaAnalyzerTest - Class in ubic.gemma.core.analysis.expression.diff

Tests the one way anova analyzer.

OneWayAnovaAnalyzerTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.OneWayAnovaAnalyzerTest

onSetUpInTransaction() - Method in class ubic.gemma.model.genome.BioSequencePersistTest

onTearDownInTransaction() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonLoaderTest

onTearDownInTransaction() - Method in class ubic.gemma.model.genome.BioSequencePersistTest

OntologyControllerTest - Class in ubic.gemma.web.controller

OntologyControllerTest() - Constructor for class ubic.gemma.web.controller.OntologyControllerTest

ontologyService() - Method in class ubic.gemma.web.services.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

OntologyServiceTest - Class in ubic.gemma.core.ontology

OntologyServiceTest() - Constructor for class ubic.gemma.core.ontology.OntologyServiceTest

OutlierDetectionServiceTest - Class in ubic.gemma.core.analysis.preprocess

Tests for OutlierDetectionService

OutlierDetectionServiceTest() - Constructor for class ubic.gemma.core.analysis.preprocess.OutlierDetectionServiceTest

P

PersistentDummyObjectHelper - Class in ubic.gemma.core.util.test

Used to generate test data.

PersistentDummyObjectHelper() - Constructor for class ubic.gemma.core.util.test.PersistentDummyObjectHelper

persisterHelper - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest

persisterHelper() - Method in class ubic.gemma.core.util.test.BaseCliTest.BaseCliTestContextConfiguration

PersisterTest - Class in ubic.gemma.persistence

PersisterTest() - Constructor for class ubic.gemma.persistence.PersisterTest

pessimisticOperation() - Method in class ubic.gemma.persistence.retry.RetryTest.TestRetryService

pessimisticOperationWithoutRetry() - Method in class ubic.gemma.persistence.retry.RetryTest.TestRetryService

pessimisticOperationWithTransactionalAnnotation() - Method in class ubic.gemma.persistence.retry.RetryTest.TestRetryService

PhenotypeAssociationTest - Class in ubic.gemma.model.association.phenotype

This test will likely fail if the full disease ontology is configured to load; instead we want to load a small 'fake' one.

PhenotypeAssociationTest() - Constructor for class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

PhenotypeImportingTest - Class in ubic.gemma.core.loader.association.phenotype

Minimal test of PhenotypeProcessingUtil - part of Phenocarta

PhenotypeImportingTest() - Constructor for class ubic.gemma.core.loader.association.phenotype.PhenotypeImportingTest

PlatformsWebServiceTest - Class in ubic.gemma.web.services.rest

PlatformsWebServiceTest() - Constructor for class ubic.gemma.web.services.rest.PlatformsWebServiceTest

PointcutsTest - Class in ubic.gemma.core.security.audit

PointcutsTest() - Constructor for class ubic.gemma.core.security.audit.PointcutsTest

PrincipalTest - Class in ubic.gemma.core.security.principal

Test that we can log users in, etc.

PrincipalTest() - Constructor for class ubic.gemma.core.security.principal.PrincipalTest

ProbeMapperTest - Class in ubic.gemma.core.analysis.sequence

Unaware of the Gemma database but uses the hg19 and mm10 databases (tests will not work with hg38)

ProbeMapperTest() - Constructor for class ubic.gemma.core.analysis.sequence.ProbeMapperTest

ProbeSequenceParserTest - Class in ubic.gemma.core.loader.genome

ProbeSequenceParserTest() - Constructor for class ubic.gemma.core.loader.genome.ProbeSequenceParserTest

ProcessedExpressionDataCreateServiceTest - Class in ubic.gemma.core.analysis.preprocess

ProcessedExpressionDataCreateServiceTest() - Constructor for class ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataCreateServiceTest

processedExpressionDataVectorService - Variable in class ubic.gemma.core.analysis.expression.diff.BaseAnalyzerConfigurationTest

ProcessedExpressionDataVectorServiceTest - Class in ubic.gemma.model.expression.bioAssayData

ProcessedExpressionDataVectorServiceTest() - Constructor for class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVectorServiceTest

ProgressAppenderTest - Class in ubic.gemma.core.util.progress

For this test to work you should have the appender configured in log4j-test.properties.

ProgressAppenderTest() - Constructor for class ubic.gemma.core.util.progress.ProgressAppenderTest

ProgressDataTest - Class in ubic.gemma.core.util.progress

ProgressDataTest() - Constructor for class ubic.gemma.core.util.progress.ProgressDataTest

PubMedQueryControllerTest - Class in ubic.gemma.web.controller.common.description.bibref

PubMedQueryControllerTest() - Constructor for class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerTest

PubMedSearcherIntegrationTest - Class in ubic.gemma.core.loader.entrez.pubmed

Tests command line.

PubMedSearcherIntegrationTest() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcherIntegrationTest

PubMedSearchTest - Class in ubic.gemma.core.loader.entrez.pubmed

PubMedSearchTest() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedSearchTest

PubMedTest - Class in ubic.gemma.core.util.test.category

Test depending on PubMed availability.

PubMedTest() - Constructor for class ubic.gemma.core.util.test.category.PubMedTest

PubMedXMLFetcherTest - Class in ubic.gemma.core.loader.entrez.pubmed

PubMedXMLFetcherTest() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest

PubMedXMLParserTest - Class in ubic.gemma.core.loader.entrez.pubmed

PubMedXMLParserTest() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest

Q

QuantileNormalizerTest - Class in ubic.gemma.core.analysis.preprocess

QuantileNormalizerTest() - Constructor for class ubic.gemma.core.analysis.preprocess.QuantileNormalizerTest

QuantitationTypeDaoTest - Class in ubic.gemma.persistence.service.common.quantitationtype

QuantitationTypeDaoTest() - Constructor for class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoTest

QuantitationTypeParameterGuesserTest - Class in ubic.gemma.core.loader.expression.geo

QuantitationTypeParameterGuesserTest() - Constructor for class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

R

randomName() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Convenience shortcut for RandomStringUtils.randomAlphabetic( 10 ) (or something similar to that)

RawDataFetcherTest - Class in ubic.gemma.core.loader.expression.geo.fetcher

RawDataFetcherTest() - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcherTest

removeGene2CsStatusFileAndDirectory() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilIntegrationTest

RepeatScanTest - Class in ubic.gemma.core.analysis.sequence

RepeatScanTest() - Constructor for class ubic.gemma.core.analysis.sequence.RepeatScanTest

resetTestCollectionSize() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Restore to default.

resetTestElementCollectionSize() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

RestapidocsIndexRewriteFilterTest - Class in ubic.gemma.web.services.rest.servlet

RestapidocsIndexRewriteFilterTest() - Constructor for class ubic.gemma.web.services.rest.servlet.RestapidocsIndexRewriteFilterTest

retryPolicy - Variable in class ubic.gemma.persistence.retry.RetryTest

RetryTest - Class in ubic.gemma.persistence.retry

RetryTest() - Constructor for class ubic.gemma.persistence.retry.RetryTest

RetryTest.TestRetryDao - Interface in ubic.gemma.persistence.retry

RetryTest.TestRetryService - Class in ubic.gemma.persistence.retry

RNASeqBatchInfoPopulationTest - Class in ubic.gemma.core.analysis.preprocess.batcheffects

RNASeqBatchInfoPopulationTest() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

RootWebServiceTest - Class in ubic.gemma.web.services.rest

RootWebServiceTest() - Constructor for class ubic.gemma.web.services.rest.RootWebServiceTest

RssFeedControllerTest - Class in ubic.gemma.web.controller.common.rss

RssFeedControllerTest() - Constructor for class ubic.gemma.web.controller.common.rss.RssFeedControllerTest

rule - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest

This allows the usage of Mock annotation to create mocks.

runAsAdmin() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

runAsAdmin() - Method in interface ubic.gemma.core.util.test.TestAuthenticationUtils

runAsAdmin() - Method in class ubic.gemma.core.util.test.TestAuthenticationUtilsImpl

Elevate to administrative privileges (tests normally run this way, this can be used to set it back if you called runAsUser).

runAsAgent() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

runAsAgent() - Method in interface ubic.gemma.core.util.test.TestAuthenticationUtils

runAsAgent() - Method in class ubic.gemma.core.util.test.TestAuthenticationUtilsImpl

runAsAnonymous() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

runAsAnonymous() - Method in interface ubic.gemma.core.util.test.TestAuthenticationUtils

runAsAnonymous() - Method in class ubic.gemma.core.util.test.TestAuthenticationUtilsImpl

runAsUser(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

runAsUser(String) - Method in interface ubic.gemma.core.util.test.TestAuthenticationUtils

runAsUser(String) - Method in class ubic.gemma.core.util.test.TestAuthenticationUtilsImpl

Run as a regular user.

runJob(TaskCommand) - Method in interface ubic.gemma.web.util.MockLongJobController

runJob(TaskCommand) - Method in class ubic.gemma.web.util.MockLongJobControllerImpl

runSecuredMethodOnSchedule() - Method in class ubic.gemma.web.scheduler.SchedulerSecurityTest

runSecuredMethodOnScheduleMultiGroup() - Method in class ubic.gemma.web.scheduler.SchedulerSecurityTest

runUnauthorizedMethodOnSchedule() - Method in class ubic.gemma.web.scheduler.SchedulerSecurityTest

S

SampleCoexpressionAnalysisServiceTest - Class in ubic.gemma.core.analysis.preprocess

SampleCoexpressionAnalysisServiceTest() - Constructor for class ubic.gemma.core.analysis.preprocess.SampleCoexpressionAnalysisServiceTest

SchedulerSecurityTest - Class in ubic.gemma.web.scheduler

Tests security of methods run by Quartz.

SchedulerSecurityTest() - Constructor for class ubic.gemma.web.scheduler.SchedulerSecurityTest

SDRFFetcherTest - Class in ubic.gemma.core.loader.expression.arrayExpress

SDRFFetcherTest() - Constructor for class ubic.gemma.core.loader.expression.arrayExpress.SDRFFetcherTest

search(StringArrayArg) - Method in class ubic.gemma.web.services.rest.args.StringArrayArgTest.Api

searchExpressionExperiment_whenQueryHasMultipleClauses_thenParseAccordingly() - Method in class ubic.gemma.core.search.SearchServiceTest

SearchResultTest - Class in ubic.gemma.core.search

Tests for SearchResult.

SearchResultTest() - Constructor for class ubic.gemma.core.search.SearchResultTest

searchService() - Method in class ubic.gemma.web.services.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

searchService() - Method in class ubic.gemma.web.services.rest.SearchWebServiceTest.SearchWebServiceTestContextConfiguration

SearchServiceIntegrationTest - Class in ubic.gemma.core.search

SearchServiceIntegrationTest() - Constructor for class ubic.gemma.core.search.SearchServiceIntegrationTest

SearchServiceTest - Class in ubic.gemma.core.search

SearchServiceTest() - Constructor for class ubic.gemma.core.search.SearchServiceTest

SearchServiceVoConversionTest - Class in ubic.gemma.core.search

SearchServiceVoConversionTest() - Constructor for class ubic.gemma.core.search.SearchServiceVoConversionTest

SearchSettingsTest - Class in ubic.gemma.model.common.search

SearchSettingsTest() - Constructor for class ubic.gemma.model.common.search.SearchSettingsTest

searchWebService() - Method in class ubic.gemma.web.services.rest.SearchWebServiceTest.SearchWebServiceTestContextConfiguration

SearchWebServiceTest - Class in ubic.gemma.web.services.rest

SearchWebServiceTest() - Constructor for class ubic.gemma.web.services.rest.SearchWebServiceTest

SearchWebServiceTest.SearchWebServiceTestContextConfiguration - Class in ubic.gemma.web.services.rest

SearchWebServiceTestContextConfiguration() - Constructor for class ubic.gemma.web.services.rest.SearchWebServiceTest.SearchWebServiceTestContextConfiguration

SecureValueObjectAuthorizationTest - Class in ubic.gemma.core.security.authorization

SecureValueObjectAuthorizationTest() - Constructor for class ubic.gemma.core.security.authorization.SecureValueObjectAuthorizationTest

SecurityControllerTest - Class in ubic.gemma.web.controller.security

SecurityControllerTest() - Constructor for class ubic.gemma.web.controller.security.SecurityControllerTest

SecurityServiceTest - Class in ubic.gemma.core.security.authorization

Tests the SecurityService: making objects public or private and testing the permissions.

SecurityServiceTest() - Constructor for class ubic.gemma.core.security.authorization.SecurityServiceTest

SequenceBinUtilsTest - Class in ubic.gemma.core.analysis.sequence

Test values are from hg18 all_est.

SequenceBinUtilsTest() - Constructor for class ubic.gemma.core.analysis.sequence.SequenceBinUtilsTest

SequenceManipulationTest - Class in ubic.gemma.core.analysis.sequence

SequenceManipulationTest() - Constructor for class ubic.gemma.core.analysis.sequence.SequenceManipulationTest

ServletUtilsTest - Class in ubic.gemma.web.services.rest.util

ServletUtilsTest() - Constructor for class ubic.gemma.web.services.rest.util.ServletUtilsTest

setId(long) - Method in class ubic.gemma.persistence.service.AbstractDaoTest.MyEntity

setPersisterHelper(PersisterHelper) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

setTaxonService(TaxonService) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

setTestCollectionSize(int) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Change the number of elements created in collections (basically controls the size of test data sets).

setTestElementCollectionSize(int) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper

Override the number of elements made in collections.

setTestRetryDao(RetryTest.TestRetryDao) - Method in class ubic.gemma.persistence.retry.RetryTest.TestRetryService

setup() - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationParserTest

setup() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneLoadingTest

setup() - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmdTest

setUp() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisServiceTest

setUp() - Method in class ubic.gemma.core.analysis.expression.diff.BaseAnalyzerConfigurationTest

setUp() - Method in class ubic.gemma.core.analysis.expression.diff.BaselineDetectionTest

setUp() - Method in class ubic.gemma.core.analysis.expression.diff.ContinuousVariableDiffExTest

setUp() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExWithInvalidInteraction2Test

setUp() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExWithInvalidInteractionTest

setUp() - Method in class ubic.gemma.core.analysis.expression.diff.LowVarianceDataTest

setUp() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysis2Test

setUp() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysis3Test

setUp() - Method in class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionsTest2

setUp() - Method in class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionTest2

setUp() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceTest

setUp() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

setUp() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest

setUp() - Method in class ubic.gemma.core.analysis.preprocess.QuantileNormalizerTest

setUp() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceTest

setUp() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest

setUp() - Method in class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperServiceTest

setUp() - Method in class ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationServiceTest

setUp() - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImplTest

setUp() - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceTest

setUp() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCliTest

setUp() - Method in class ubic.gemma.core.datastructure.matrix.ExperimentalDesignWriterTest

setUp() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixTest

setUp() - Method in class ubic.gemma.core.externalDb.GoldenPathQueryTest

setUp() - Method in class ubic.gemma.core.job.ExecutingTaskTest

setUp() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest

setUp() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest

setUp() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReaderTest

setUp() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorTest

setUp() - Method in class ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParserTest

setUp() - Method in class ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReaderTest

setUp() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest

setUp() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

setUp() - Method in class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImportDuplicateValueTest

setUp() - Method in class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterTest

setUp() - Method in class ubic.gemma.core.loader.genome.FastaParserTest

setUp() - Method in class ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceTest

setUp() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceTest

setUp() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonLoaderTest

setUp() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonParserTest

setUp() - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

setUp() - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest2

setUp() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest

setUp() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest

setUp() - Method in class ubic.gemma.core.security.authentication.UserServiceImplTest

setUp() - Method in class ubic.gemma.core.security.authorization.acl.AclAuthorizationTest

setUp() - Method in class ubic.gemma.core.security.authorization.acl.AclCollectionBeforeTest

setUp() - Method in class ubic.gemma.core.security.authorization.SecureValueObjectAuthorizationTest

setUp() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest

setUp() - Method in class ubic.gemma.core.security.UserGroupServiceTest

setUp() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiFetcherTest

setUp() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiObjectGeneratorTest

setUp() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiParserTest

setUp() - Method in class ubic.gemma.core.util.progress.ProgressAppenderTest

setUp() - Method in class ubic.gemma.core.util.progress.ProgressDataTest

setUp() - Method in class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest

setUp() - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpressionServiceTest

setUp() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

setUp() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventDaoImplTest

setUp() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailDaoTest

setUp() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest

setUp() - Method in class ubic.gemma.model.common.description.CharacteristicServiceTest

setUp() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

setUp() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayServiceTest

setUp() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialServiceTest

setUp() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceImplTest

setUp() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

setUp() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetServiceTest

setUp() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObjectHelperTest

setUp() - Method in class ubic.gemma.model.genome.BlatResultTest

setUp() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest

setUp() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest

setUp() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObjectHelperTest

setUp() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest

setUp() - Method in class ubic.gemma.model.genome.GeneTest

setUp() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociationServiceTest

setUp() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultServiceTest

setUp() - Method in class ubic.gemma.persistence.service.AbstractDaoTest

setUp() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest

setUp() - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceTest

setUp() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceTest

setUp() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilTest

setUp() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupControllerTest

setUp() - Method in class ubic.gemma.web.controller.common.description.bibref.BibRefControllerTest

setUp() - Method in class ubic.gemma.web.controller.common.rss.RssFeedControllerTest

setUp() - Method in class ubic.gemma.web.controller.expression.CuratableValueObjectTest

setUp() - Method in class ubic.gemma.web.controller.security.SecurityControllerTest

setUp() - Method in class ubic.gemma.web.logging.SlackAppenderTest

setUp() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsJerseyTest

setUp() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

setUp() - Method in class ubic.gemma.web.services.rest.AnnotationsWebServiceTest

setUp() - Method in class ubic.gemma.web.services.rest.DatasetsRestTest

setUp() - Method in class ubic.gemma.web.services.rest.DatasetsWebServiceTest

setUp() - Method in class ubic.gemma.web.services.rest.PlatformsWebServiceTest

setUp() - Method in class ubic.gemma.web.services.rest.SearchWebServiceTest

setUp() - Method in class ubic.gemma.web.services.rest.TaxaWebServiceTest

setUp() - Method in class ubic.gemma.web.services.rest.util.args.FilterArgTest

SetUp() - Method in class ubic.gemma.core.image.aba.AllenBrainAtlasServiceTest

setupArrayDesign() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AbstractArrayDesignProcessingTest

setUpAuthentication() - Method in class ubic.gemma.core.util.test.BaseCliTest

setUpAuthentication() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Setup the authentication for the test.

setUpAuthentication() - Method in class ubic.gemma.web.services.rest.util.BaseJerseyIntegrationTest

setUpMockMvc() - Method in class ubic.gemma.web.util.BaseSpringWebTest

setUpSecurityContextHolderStrategy() - Static method in class ubic.gemma.core.util.test.BaseSpringContextTest

setUpSecurityContextHolderStrategy() - Static method in class ubic.gemma.web.services.rest.util.BaseJerseyIntegrationTest

SignupControllerTest - Class in ubic.gemma.web.controller.common.auditAndSecurity

Tortures the signup system by starting many threads and signing up many users, while at the same time creating a lot of expression experiments.

SignupControllerTest() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SignupControllerTest

SimpleExpressionDataLoaderServiceTest - Class in ubic.gemma.core.loader.expression.simple

SimpleExpressionDataLoaderServiceTest() - Constructor for class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceTest

SimpleFastaCmdTest - Class in ubic.gemma.core.loader.genome

SimpleFastaCmdTest() - Constructor for class ubic.gemma.core.loader.genome.SimpleFastaCmdTest

SlackAppenderTest - Class in ubic.gemma.web.logging

SlackAppenderTest() - Constructor for class ubic.gemma.web.logging.SlackAppenderTest

SlowTest - Class in ubic.gemma.core.util.test.category

Used to mark slow tests.

SlowTest() - Constructor for class ubic.gemma.core.util.test.category.SlowTest

SortArgTest - Class in ubic.gemma.web.services.rest.util.args

SortArgTest() - Constructor for class ubic.gemma.web.services.rest.util.args.SortArgTest

SortValueObjectTest - Class in ubic.gemma.web.services.rest.util

SortValueObjectTest() - Constructor for class ubic.gemma.web.services.rest.util.SortValueObjectTest

SpearmanMetricsTest - Class in ubic.gemma.core.analysis.expression.coexpression.links

SpearmanMetricsTest() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetricsTest

SplitExperimentTest - Class in ubic.gemma.core.analysis.preprocess

SplitExperimentTest() - Constructor for class ubic.gemma.core.analysis.preprocess.SplitExperimentTest

SpringContextTest - Interface in ubic.gemma.core.util.test.category

Mark tests requiring a full Spring context to run.

startup() - Method in class ubic.gemma.core.loader.expression.ExonArrayDataAddIntegrationTest

StopWatchUtilsTest - Class in ubic.gemma.core.util

StopWatchUtilsTest() - Constructor for class ubic.gemma.core.util.StopWatchUtilsTest

StringArrayArgTest - Class in ubic.gemma.web.services.rest.args

StringArrayArgTest() - Constructor for class ubic.gemma.web.services.rest.args.StringArrayArgTest

StringArrayArgTest.Api - Class in ubic.gemma.web.services.rest.args

SubsettedAnalysis2Test - Class in ubic.gemma.core.analysis.expression.diff

SubsettedAnalysis2Test() - Constructor for class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysis2Test

SubsettedAnalysis3Test - Class in ubic.gemma.core.analysis.expression.diff

SubsettedAnalysis3Test() - Constructor for class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysis3Test

SubsettedAnalysisTest - Class in ubic.gemma.core.analysis.expression.diff

SubsettedAnalysisTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysisTest

SupportDetailsTest - Class in ubic.gemma.model.analysis.expression.coexpression

SupportDetailsTest() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.SupportDetailsTest

SVDServiceImplTest - Class in ubic.gemma.core.analysis.preprocess.svd

SVDServiceImplTest() - Constructor for class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImplTest

SwissProtParserTest - Class in ubic.gemma.core.loader.genome.gene

SwissProtParserTest() - Constructor for class ubic.gemma.core.loader.genome.gene.SwissProtParserTest

T

TableMaintenanceUtilIntegrationTest - Class in ubic.gemma.persistence.service

TableMaintenanceUtilIntegrationTest() - Constructor for class ubic.gemma.persistence.service.TableMaintenanceUtilIntegrationTest

TableMaintenanceUtilTest - Class in ubic.gemma.persistence.service

TableMaintenanceUtilTest() - Constructor for class ubic.gemma.persistence.service.TableMaintenanceUtilTest

TaskRunningTest - Class in ubic.gemma.web.controller

Test of long job control.

TaskRunningTest() - Constructor for class ubic.gemma.web.controller.TaskRunningTest

TaskUtilsTest - Class in ubic.gemma.core.job

TaskUtilsTest() - Constructor for class ubic.gemma.core.job.TaskUtilsTest

TaxaWebServiceTest - Class in ubic.gemma.web.services.rest

TaxaWebServiceTest() - Constructor for class ubic.gemma.web.services.rest.TaxaWebServiceTest

TaxonLoaderTest - Class in ubic.gemma.core.loader.genome.taxon

TaxonLoaderTest() - Constructor for class ubic.gemma.core.loader.genome.taxon.TaxonLoaderTest

TaxonParserTest - Class in ubic.gemma.core.loader.genome.taxon

TaxonParserTest() - Constructor for class ubic.gemma.core.loader.genome.taxon.TaxonParserTest

taxonService - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest

taxonService() - Method in class ubic.gemma.web.services.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

taxonService() - Method in class ubic.gemma.web.services.rest.SearchWebServiceTest.SearchWebServiceTestContextConfiguration

TaxonServiceImplTest - Class in ubic.gemma.model.genome

TaxonServiceImplTest() - Constructor for class ubic.gemma.model.genome.TaxonServiceImplTest

TaxonUtilityTest - Class in ubic.gemma.core.util

TaxonUtilityTest() - Constructor for class ubic.gemma.core.util.TaxonUtilityTest

teardown() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceTest

teardown() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysis2Test

teardown() - Method in class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionsTest2

teardown() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceTest

teardown() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

teardown() - Method in class ubic.gemma.core.analysis.preprocess.SplitExperimentTest

tearDown() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisServiceTest

tearDown() - Method in class ubic.gemma.core.analysis.expression.diff.BaseAnalyzerConfigurationTest

tearDown() - Method in class ubic.gemma.core.analysis.expression.diff.BaselineDetectionTest

tearDown() - Method in class ubic.gemma.core.analysis.expression.diff.ContinuousVariableDiffExTest

tearDown() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest

tearDown() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExTest

tearDown() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExWithInvalidInteraction2Test

tearDown() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExWithInvalidInteractionTest

tearDown() - Method in class ubic.gemma.core.analysis.preprocess.QuantileNormalizerTest

tearDown() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImplTest

tearDown() - Method in class ubic.gemma.core.analysis.preprocess.VectorMergingServiceTest

tearDown() - Method in class ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationServiceTest

tearDown() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCliTest

tearDown() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCliTest

tearDown() - Method in class ubic.gemma.core.datastructure.matrix.ExperimentalDesignWriterTest

tearDown() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixTest

tearDown() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest

tearDown() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest

tearDown() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AbstractArrayDesignProcessingTest

tearDown() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReaderTest

tearDown() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentandMappingTest

tearDown() - Method in class ubic.gemma.core.loader.expression.DataUpdaterTest

tearDown() - Method in class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchTest

tearDown() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest

tearDown() - Method in class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterTest

tearDown() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneLoadingTest

tearDown() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonParserTest

tearDown() - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcherTest

tearDown() - Method in class ubic.gemma.core.loader.util.HttpFetcherTest

tearDown() - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

tearDown() - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest2

tearDown() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest

tearDown() - Method in class ubic.gemma.core.search.SearchServiceTest

tearDown() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest

tearDown() - Method in class ubic.gemma.core.search.source.CompassSearchSourceTest

tearDown() - Method in class ubic.gemma.core.search.source.DatabaseSearchSourceTest

tearDown() - Method in class ubic.gemma.core.security.audit.PointcutsTest

tearDown() - Method in class ubic.gemma.core.util.progress.ProgressDataTest

tearDown() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

tearDown() - Method in class ubic.gemma.model.expression.bioAssayData.DesignElementDataVectorServiceTest

tearDown() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceImplTest

tearDown() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetServiceTest

tearDown() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObjectHelperTest

tearDown() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest

tearDown() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest

tearDown() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest

tearDown() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociationServiceTest

tearDown() - Method in class ubic.gemma.persistence.retry.RetryTest

tearDown() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest

tearDown() - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseDaoTest

tearDown() - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceTest

tearDown() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilTest

tearDown() - Method in class ubic.gemma.web.controller.expression.CuratableValueObjectTest

tearDown() - Method in class ubic.gemma.web.logging.SlackAppenderTest

tearDown() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsJerseyTest

tearDown() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

tearDown() - Method in class ubic.gemma.web.services.rest.AnnotationsWebServiceTest

tearDown() - Method in class ubic.gemma.web.services.rest.DatasetsRestTest

tearDown() - Method in class ubic.gemma.web.services.rest.DatasetsWebServiceTest

tearDown() - Method in class ubic.gemma.web.services.rest.PlatformsWebServiceTest

tearDown() - Method in class ubic.gemma.web.services.rest.SearchWebServiceTest

tearDown() - Method in class ubic.gemma.web.services.rest.TaxaWebServiceTest

tearDownSecurityContext() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest

Clear the SecurityContextHolder so that subsequent tests don't inherit authentication.

tearDownSecurityContext() - Method in class ubic.gemma.web.services.rest.util.BaseJerseyIntegrationTest

Clear the SecurityContextHolder so that subsequent tests don't inherit authentication.

test() - Method in class ubic.gemma.core.analysis.expression.diff.ContinuousVariableDiffExTest

test() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExWithInvalidInteraction2Test

test() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExWithInvalidInteractionTest

This should automatically drop the interaction.

test() - Method in class ubic.gemma.core.analysis.expression.diff.LowVarianceDataTest

test() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysis2Test

test() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysis3Test

test() - Method in class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionsTest2

test() - Method in class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionTest2

test() - Method in class ubic.gemma.core.analysis.preprocess.SampleCoexpressionAnalysisServiceTest

test() - Method in class ubic.gemma.core.analysis.preprocess.VectorMergingServiceTest

test() - Method in class ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationServiceTest

test() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCliTest

test() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCliTest

test() - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLITest

test() - Method in class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchTest

for bug 3451

test() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

test() - Method in class ubic.gemma.core.search.source.CompassSearchSourceTest

test() - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedInTest

test() - Method in class ubic.gemma.model.analysis.expression.coexpression.SupportDetailsTest

test() - Method in class ubic.gemma.model.analysis.GeneDiffExMetaAnalysisServiceTest

test() - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceTest

test() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilTest

test() - Method in class ubic.gemma.persistence.util.AclCriteriaUtilsTest

test() - Method in class ubic.gemma.web.logging.SlackAppenderTest

test() - Method in class ubic.gemma.web.services.rest.RootWebServiceTest

test() - Method in class ubic.gemma.web.services.rest.servlet.RestapidocsIndexRewriteFilterTest

test() - Method in class ubic.gemma.web.services.rest.util.SortValueObjectTest

test_multipleQuotedTerms() - Method in class ubic.gemma.core.search.source.CompassSearchSourceTest

test_multipleQuotedTermsWithOr() - Method in class ubic.gemma.core.search.source.CompassSearchSourceTest

test_quotedTerm() - Method in class ubic.gemma.core.search.source.CompassSearchSourceTest

test_quotedTerms() - Method in class ubic.gemma.core.search.source.DatabaseSearchSourceTest

test_whenQueryContainsAsterisk_thenSubstituteForPercent() - Method in class ubic.gemma.core.search.source.DatabaseSearchSourceTest

test_whenQueryContainsLikePatterns_thenEscape() - Method in class ubic.gemma.core.search.source.DatabaseSearchSourceTest

test_whenQueryContainsQuote_thenStripThem() - Method in class ubic.gemma.core.search.source.DatabaseSearchSourceTest

test_whenQueryIsEmpty_thenReturnNothing() - Method in class ubic.gemma.core.search.source.CompassSearchSourceTest

test_whenQueryOnlyContainsAWildCard_thenReturnNothing() - Method in class ubic.gemma.core.search.source.CompassSearchSourceTest

test_whenQueryOnlyContainsNonWordCharacters_thenReturnNothing() - Method in class ubic.gemma.core.search.source.CompassSearchSourceTest

test_whenTaxonIsNameIsUsedInQuery_thenAddTaxonToSearchSettings() - Method in class ubic.gemma.core.search.SearchServiceTest

test1() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBatTest

test2WithMissingValues() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBatTest

test3() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBatTest

Based on GSE13712

test3NoCovariate() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBatTest

test4() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBatTest

test5C() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

test5NonParametric() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBatTest

testa() - Method in class ubic.gemma.model.analysis.expression.coexpression.CoexpressionNodeDegreeValueObjectTest

testAbsCall() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testAclCollectionEntryVoter() - Method in class ubic.gemma.core.security.authorization.acl.AclCollectionBeforeTest

testAclCollectionEntryVoterOK() - Method in class ubic.gemma.core.security.authorization.acl.AclCollectionBeforeTest

testAddAclJoinParameters() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

testAddAffyExonArrayDataExpressionExperiment() - Method in class ubic.gemma.core.loader.expression.ExonArrayDataAddIntegrationTest

testAddAffyExonHuman() - Method in class ubic.gemma.core.loader.expression.ExonArrayDataAddIntegrationTest

testAddAffyExonRat() - Method in class ubic.gemma.core.loader.expression.ExonArrayDataAddIntegrationTest

testAddCharacteristicToFactorValue() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest

testAddData() - Method in class ubic.gemma.core.loader.expression.DataUpdaterTest

testAddDoesNotNeedsAttentionEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest

testAddingExperimentOfWrongTaxonUpdate() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetServiceTest

testAddingExperimentOfWrongTaxonUpdateDatabaseEntityMembers() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetServiceTest

testAddNeedsAttentionEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest

testAddOKEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest

testAddTroubleEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest

testAddUpdateEvent() - Method in class ubic.gemma.web.remote.AuditControllerTest

testAddUpdateEventAuditableAuditEventTypeString() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest

testAddUpdateEventAuditableString() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest

testAll() - Method in class ubic.gemma.web.services.rest.DatasetsRestTest

testAll() - Method in class ubic.gemma.web.services.rest.PlatformsWebServiceTest

testAllFilterById() - Method in class ubic.gemma.web.services.rest.DatasetsRestTest

testAllFilterByIdIn() - Method in class ubic.gemma.web.services.rest.DatasetsRestTest

testAllFilterByIdInOrShortNameIn() - Method in class ubic.gemma.web.services.rest.DatasetsRestTest

testAllFilterByShortName() - Method in class ubic.gemma.web.services.rest.DatasetsRestTest

testAllFilterByShortNameIn() - Method in class ubic.gemma.web.services.rest.DatasetsRestTest

testAllParents() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testAllParents() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest2

testAllParents2() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testAllWithTooLargeLimit() - Method in class ubic.gemma.web.services.rest.DatasetsRestTest

testAnalysisAcl() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

testAnalyze() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceTest

testAnalyzeAndDelete() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest

testAnalyzeAndDeleteSpecificAnalysis() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest

Test for bug 2026, not a subsetted analysis.

testAnalyzeAndDeleteSpecificAnalysisWithSubset() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest

Tests running with a subset factor, then deleting.

testAnalyzeWithSubsetWhenOneIsNotUsableAndWithInteractionInTheOther() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest

Test inspired by bug 2605

testAncovaContinuousCovariate() - Method in class ubic.gemma.core.analysis.expression.diff.AncovaTest

testAncovaCovariate() - Method in class ubic.gemma.core.analysis.expression.diff.AncovaTest

testAncovaTriLevel() - Method in class ubic.gemma.core.analysis.expression.diff.AncovaTest

testAncovaTwoway() - Method in class ubic.gemma.core.analysis.expression.diff.AncovaTest

testAncovaWithInteraction() - Method in class ubic.gemma.core.analysis.expression.diff.AncovaTest

testareaCall() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testArrayDesignAcls() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

testArrayDesignAclsUser() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

testAsAdmin() - Method in class ubic.gemma.persistence.util.AclCriteriaUtilsTest

testAsRegularGoId() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testAssignSequencesToDesignElements() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorTest

testAssignSequencesToDesignElementsMissingSequence() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorTest

testAttemptAuthentication() - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationProcessingTest

testAttemptAuthenticationNonexistentUser() - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationProcessingTest

testAttemptAuthenticationWrongPassword() - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationProcessingTest

testAttributesToRetrieveFromBioMart() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiFetcherTest

testAuditCreateAndDeleteExpressionExperiment() - Method in class ubic.gemma.core.security.audit.AuditAdviceTest

testAuditFindOrCreateConcurrentTorture() - Method in class ubic.gemma.core.security.audit.AuditAdviceTest

testAuthenticationUtils() - Method in class ubic.gemma.core.util.test.BaseCliTest.BaseCliTestContextConfiguration

TestAuthenticationUtils - Interface in ubic.gemma.core.util.test

TestAuthenticationUtilsImpl - Class in ubic.gemma.core.util.test

Utilities for manipulating the SecurityContextHolder in a test envirnoment.

TestAuthenticationUtilsImpl() - Constructor for class ubic.gemma.core.util.test.TestAuthenticationUtilsImpl

testbackground() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testbackgroundB() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testBadRatio() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testBatchA() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchB() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchC() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchD() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchDX() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchE() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchF() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchG() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchH() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchI() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchingNotAdvisableWhenFlushModeIsManual() - Method in class ubic.gemma.persistence.service.AbstractDaoTest

testBatchJ() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchK() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchL() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchM() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchMixedHeaders() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

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

testBatchMixedHeadersSinglePlatform() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchMixedHeadersSinglePlatformSingleton() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchO() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchP() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchQ() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testBatchSizeFlushRightAway() - Method in class ubic.gemma.persistence.service.AbstractDaoTest

testBatchSizeSmall() - Method in class ubic.gemma.persistence.service.AbstractDaoTest

testBatchSizeUnlimited() - Method in class ubic.gemma.persistence.service.AbstractDaoTest

testBinFromRangeA() - Method in class ubic.gemma.core.analysis.sequence.SequenceBinUtilsTest

testBinFromRangeB() - Method in class ubic.gemma.core.analysis.sequence.SequenceBinUtilsTest

testBinFromRangeC() - Method in class ubic.gemma.core.analysis.sequence.SequenceBinUtilsTest

testBinFromRangeD() - Method in class ubic.gemma.core.analysis.sequence.SequenceBinUtilsTest

testbkdst() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testBlacklist() - Method in class ubic.gemma.model.expression.BlacklistTest

testBulkAdd() - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedInTest

testCancelledRun() - Method in class ubic.gemma.web.controller.TaskRunningTest

testCascadeCreateCompositeSequences() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testCascadingCreateOnUpdate() - Method in class ubic.gemma.core.security.audit.AuditAdviceTest

testCascadingCreateWithAssociatedAuditable() - Method in class ubic.gemma.core.security.audit.AuditAdviceTest

testCELnameregex() - Method in class ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarizeTest

testChangePassword() - Method in class ubic.gemma.core.security.principal.PrincipalTest

testCheckBiologicalReplicates() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperServiceTest

testColumnMapping() - Method in class ubic.gemma.core.datastructure.matrix.MatrixConversionTest

testComBatOnEE() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceTest

testCompareToCategory() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest

testCompareToNull() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest

testCompareToOrdering() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest

testCompareToTaxon() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest

testCompareToValue() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest

testCompareToValueUri() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest

testComplexClause() - Method in class ubic.gemma.persistence.util.ObjectFilterQueryUtilsTest

testCompositeSequenceWithoutBioSequences() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testCompositeSequenceWithoutBlatResults() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testCompositeSequenceWithoutGenes() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testComputeDevRankForExpressionExperimentB() - Method in class ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataCreateServiceTest

testComputeDevRankForExpressionExperimentMultiArrayWithGaps() - Method in class ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataCreateServiceTest

Three platforms, one sample was not run on GPL81.

testComputeSpecificityA() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest

testComputeSpecificityB() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest

testComputeSpecificityC() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest

testComputeSpecificityD() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest

testConfigurationCookieA() - Method in class ubic.gemma.web.util.ConfigurationCookieTest

testConfigurationCookieB() - Method in class ubic.gemma.web.util.ConfigurationCookieTest

testConfigurationCookieC() - Method in class ubic.gemma.web.util.ConfigurationCookieTest

testConfigurationCookieD() - Method in class ubic.gemma.web.util.ConfigurationCookieTest

testConfigurationCookieE() - Method in class ubic.gemma.web.util.ConfigurationCookieTest

testConjunction() - Method in class ubic.gemma.web.services.rest.util.args.FilterArgTest

testConjunctionOfDisjunctions() - Method in class ubic.gemma.web.services.rest.util.args.FilterArgTest

testConstructExpressionDataDoubleMatrix() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixTest

Tests the construction of an ExpressionDataDoubleMatrix

testConstructExpressionDataDoubleMatrixWithGeoValues() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixTest

This is a self-contained test.

testConvertArrayDesign() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest

testConvertDataDoubles() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertDataIntegers() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertExpressionExperiment() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest

testConvertGenePix() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertGeneSet() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest

testConvertGSE106() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertGSE18Stress() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertGSE2122SAGE() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertGSE29014() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertGSE2982() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertGSE360() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertGSE3791() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertGSE404() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertGSE4229IMAGE() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertGse59() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertGSE60() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertGSE8134() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertMultiSeriesPerSample() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertMultiTaxonDatasetGSE7540() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertPhenotypeAssociation() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest

testConvertToEntity() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObjectHelperTest

testConvertToLightValueObject() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObjectHelperTest

Tests loading 'light' value objects - VOs without EEIds

testConvertToLightValueObject() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObjectHelperTest

testConvertToValueObject() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObjectHelperTest

Tests loading value objects with EEIds.

testConvertToValueObject() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObjectHelperTest

testConvertWithLotsOfPlatforms() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testCopyUploadedFileStreamClosed() - Method in class ubic.gemma.web.util.upload.FileUploadUtilTest

testCorrel() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetricsTest

Value from R; this has ties.

testCorrelB() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetricsTest

This tests the same values as testCorrelWithMissing, different method than testCorrelC

testCorrelC() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetricsTest

Without missing values, fast method (same data as testCorrelB)

testCorrelFromRanks() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetricsTest

testCorrelWithMissing() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetricsTest

See testCorrelB for the same numbers tested a different way (with no missing values)

testCountAll() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testCountByValueLike() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest

testCountByValueUriIn() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest

testCountData() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExTest

Test differential expression analysis on RNA-seq data.

testCreate() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailDaoTest

testCreateDatabaseEntry() - Method in class ubic.gemma.model.common.description.DatabaseEntryDaoImplTest

testCreateEnsureThatAuditTrailIsCreatedByAop() - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseDaoTest

testCreateExperimentalFactor() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest

testCreateLoadAndRemove() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest

Test of cascade create

testCreateUserGroup() - Method in class ubic.gemma.core.security.UserGroupServiceTest

Tests creating a UserGroup

testCrud() - Method in class ubic.gemma.core.security.audit.PointcutsTest

testCrudDelete() - Method in class ubic.gemma.core.security.audit.PointcutsTest

testCrudRead() - Method in class ubic.gemma.core.security.audit.PointcutsTest

testCtd() - Method in class ubic.gemma.core.loader.association.phenotype.PhenotypeImportingTest

testCuratableValueObjectCreation() - Method in class ubic.gemma.web.controller.expression.CuratableValueObjectTest

testCuratableValueObjectInteraction() - Method in class ubic.gemma.web.controller.expression.CuratableValueObjectTest

testDatesToBatchA() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceTest

testDatesToBatchB() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceTest

testDatesToBatchC() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceTest

testDatesToBatchD() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceTest

testDelete() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testDelete() - Method in class ubic.gemma.model.expression.experiment.FactorValueServiceTest

testDelete() - Method in class ubic.gemma.web.controller.common.description.bibref.BibRefControllerTest

testDeleteOfNonExistingEntry() - Method in class ubic.gemma.web.controller.common.description.bibref.BibRefControllerTest

testDeleteUserGroup() - Method in class ubic.gemma.core.security.UserGroupServiceTest

Test for deleting a user group

testDetermineAnalysisA() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerTest

testDetermineAnalysisB() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerTest

testDirectionParsing() - Method in class ubic.gemma.web.services.rest.util.args.SortArgTest

testDisjunction() - Method in class ubic.gemma.web.services.rest.util.args.FilterArgTest

testDisplayForm() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerTest

testDuplicateAcesNotAddedOnPrivateExpressionExperiment() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest

testEditArrayDesignDisallowed() - Method in class ubic.gemma.core.security.authorization.acl.AclAuthorizationTest

testEigenvalues() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest

testEmptyFilter() - Method in class ubic.gemma.web.services.rest.util.args.FilterArgTest

testEmptySortArg() - Method in class ubic.gemma.web.services.rest.util.args.SortArgTest

testEnglishAnalyzer() - Method in class ubic.gemma.core.search.LuceneTest

testEqualsA() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest

testEqualsA() - Method in class ubic.gemma.model.genome.GeneTest

testEqualsB() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest

testEqualsB() - Method in class ubic.gemma.model.genome.GeneTest

testEqualsC() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest

testEqualsC() - Method in class ubic.gemma.model.genome.GeneTest

testEqualsD() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest

testEqualsD() - Method in class ubic.gemma.model.genome.GeneTest

testEqualsE() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest

testEqualsE() - Method in class ubic.gemma.model.genome.GeneTest

testEqualsF() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest

testEqualsG() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest

testEqualsID() - Method in class ubic.gemma.model.genome.biosequence.BioSequenceTest

testEqualsName() - Method in class ubic.gemma.model.genome.biosequence.BioSequenceTest

testEqualsSeq() - Method in class ubic.gemma.model.genome.biosequence.BioSequenceTest

testEqualsTaxon() - Method in class ubic.gemma.model.genome.biosequence.BioSequenceTest

testExceptionTranslation() - Method in class ubic.gemma.persistence.service.AbstractDaoIntegrationTest

testExonArrayInfo() - Method in class ubic.gemma.core.loader.expression.geo.GeoPlatformTest

testExpressionExperimentAcls() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

testExpressionExperimentFindAll() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceImplTest

testExtractAgilent() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractorTest

testExtractAgilent2() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractorTest

testExtractGenePix() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest

testExtractGenePixB() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest

testExtractGeneSpring() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest

testExtractGpr() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest

testExtractGPR() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractorTest

testExtractImagene() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest

testExtractInputStreamGCOS() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractorTest

testExtractInputStreamGCOS() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractorTest

testExtractInputStreamV3() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractorTest

testExtractInputStreamV3() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractorTest

testExtractInputStreamV4() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractorTest

testExtractInputStreamV4() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractorTest

testExtractInputStreamVx() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractorTest

testExtractInputStreamVx() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractorTest

testExtractLongDate() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest

testFailedRun() - Method in class ubic.gemma.web.controller.TaskRunningTest

testFetch() - Method in class ubic.gemma.core.loader.entrez.EutilFetchTest

testFetch() - Method in class ubic.gemma.core.loader.expression.arrayExpress.SDRFFetcherTest

testFetch() - Method in class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcherTest

Test method for 'ubic.gemma.core.loader.expression.geo.RawDataFetcher.fetch(String)'.

testFetch() - Method in class ubic.gemma.core.loader.util.HttpFetcherTest

testFetchAndLoadGPL101Short() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoPlatformServiceTest

testFetchAndLoadGSE1133() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest

testFetchAndLoadGSE12135EXON() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest

testFetchAndLoadGSE13657() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest

testFetchAndLoadGSE16035() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest

testFetchAndLoadGSE18162() - Method in class ubic.gemma.core.analysis.expression.diff.BaselineDetectionTest

testFetchAndLoadGSE18707() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest

testFetchAndLoadGSE37646RNASEQ() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest

testFetchAndLoadGSE5949() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest

testFetchAndLoadGSE8294() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testFetchAndLoadGSE9048() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest

testFetchAndLoadMultiChipPerSeriesShort() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest

testFetchAndLoadWithIdentifiers() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorTest

testFetchAndLoadWithSequences() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorTest

testFetchNothingThere() - Method in class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcherTest

testFileIncorrectFormatIllegalArgumentExceptionException() - Method in class ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceTest

testFilterByGeeqPublicationScore() - Method in class ubic.gemma.web.services.rest.DatasetsRestTest

testfind() - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceTest

testFind() - Method in class ubic.gemma.model.expression.ExpressionExperimentSubSetServiceTest

testFindAll() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest

testFindAllWhenDatabaseEntryDoesNotExistThenRaise404NotFound() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

testFindAllWhenDatasetDoesNotExistThenRaise404NotFound() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

testFindAllWhenNoDatasetsAreProvidedThenReturnLatestAnalysisResults() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

testFindAllWithDatabaseEntriesThenReturnLatestAnalysisResults() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

testFindAllWithDatasetIdsThenReturnLatestAnalysisResults() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

testFindAllWithFilters() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

testFindAllWithFiltersAndCollections() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

testFindAllWithInvalidFilters() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

testFindBibliographicReference() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

testFindBioAssayDimensionsLong() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayServiceTest

Tests HQL

testFindBioMaterial() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialServiceTest

Test method for BioMaterialDaoImpl.find(ubic.gemma.model.expression.biomaterial.BioMaterial) .

testFindBioMaterialByAccessionOnly() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialServiceTest

testFindBioMaterialByNameOnly() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialServiceTest

testFindBioSequence() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociationServiceTest

testFindBlatResultByBioSequence() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultServiceTest

testFindByAccession() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayServiceTest

testFindByAccession() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

testFindByAccessionNcbi() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest

testFindByAccessionNcbiWithSource() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest

testFindByAccessionNoSource() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest

testFindByAccessionOther() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest

testFindByExternalId() - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImplTest

testFindByExternalIdentString() - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceTest

testFindByFactor() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

testFindByFactorValue() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

testFindByFactorValueId() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

testFindByGene() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest

testFindByGoId() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest

testFindByIdThenReturn200Success() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

testFindByIdToTsv() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

testFindByIdWhenExcludeResultsThenReturn200Success() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

testFindByIdWhenInvalidIdentifierThenThrowMalformedArgException() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

testFindByIdWhenResultSetDoesNotExistsThenReturn404NotFoundError() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsWebServiceTest

testFindByInvestigation() - Method in class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest

testFindByInvestigations() - Method in class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest

testFindByName() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest

testFindByNameExact() - Method in class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest

testFindByNameRecent() - Method in class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest

testFindByNcbiId() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest

testFindByNcbiId() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest

testFindByOfficialName() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest

testFindByOfficialSymbol() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest

testFindByOfficialSymbolInexact() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest

testFindByQt() - Method in class ubic.gemma.model.expression.bioAssayData.DesignElementDataVectorServiceTest

testFindCandidateGenes() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

testFindCoexpressionRelationships() - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpressionServiceTest

testFindDatabaseEntry() - Method in class ubic.gemma.model.common.description.DatabaseEntryDaoImplTest

testFindEvenThoughHaveSameSymbol() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest

testFindEvidenceByFilters() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

testFindEvidenceByGeneId() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

testFindGDSGrouping() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testFindGene() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociationServiceTest

testFindGenesWithEvidence() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

testFindGenesWithPhenotype() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

testFindGSE13() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testFindGSE267() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testFindGSE3193() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testFindGSE469() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testFindGSE493() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testFindGSE611() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testFindGSE88() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testFindGSE91() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testFindGSECorrespondence() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testFindOrCreate() - Method in class ubic.gemma.model.genome.TaxonServiceImplTest

Test method for TaxonService.findOrCreate(Taxon) )}.

testFindPhenotypesForBibliographicReference() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

testFindWithExternalReference() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testFindWithExternalReferenceNotFound() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testFormAclJoinClauseAsAdmin() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

testFormAclJoinClauseAsNonAdminIncludesAoiEntriesInnerJointure() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

testFormParamName() - Method in class ubic.gemma.persistence.util.ObjectFilterQueryUtilsTest

testFormRestrictionAndGroupByAndOrderByClauses() - Method in class ubic.gemma.persistence.util.ObjectFilterQueryUtilsTest

testFraction() - Method in class ubic.gemma.core.analysis.sequence.RepeatScanTest

testgcrma() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testGDS186() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testGeneLoader() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneLoadingTest

testGeneralSearch4Brain() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest

Tests that general search terms are resolved to their proper ontology terms and objects tagged with those terms are found, -- requires LARQ index.

testGenerate() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiObjectGeneratorTest

Tests that given a taxon biomart file a BioMartEnsembleNcbi can be returned and that the genes are correctly mapped.

testGenerateArrayDesignGeneMappingEvent() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceTest

testGenerateArrayDesignSequenceAnalysisEvent() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceTest

testGenerateArrayDesignSequenceUpdateEvent() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceTest

testGenerateTaskId() - Method in class ubic.gemma.core.job.TaskUtilsTest

Test method for TaskUtils.generateTaskId().

testGeneUriSearch() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest

Tests that gene uris get handled correctly

testGeneValueObjectWithoutTaxon() - Method in class ubic.gemma.model.genome.gene.GeneValueObjectTest

testGeqWithNullRequiredValue() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testGetAllChildren() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testGetAspect() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testGetAspect() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest2

testGetAspect2() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest2

testGetBatches() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

Test of creating batch factor.

testGetBioMartFieldsPerRow() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiParserTest

testGetBioMartTaxonName() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiFetcherTest

testGetByGeneAlias() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest

testGetByTaxon() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

testGetChildren() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testGetChildrenPartOf() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testGetCompositeSequencesByGeneId() - Method in class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperServiceTest

Tests finding the composite sequences for a given gene id.

testGetCompositeSequencesForArrayDesign() - Method in class ubic.gemma.core.security.authorization.acl.AclAuthorizationTest

testGetCount() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayServiceTest

testGetDatasetProcessedExpression() - Method in class ubic.gemma.web.services.rest.DatasetsWebServiceTest

testGetDatasetProcessedExpressionByQuantitationType() - Method in class ubic.gemma.web.services.rest.DatasetsWebServiceTest

testGetDatasetQuantitationTypes() - Method in class ubic.gemma.web.services.rest.DatasetsWebServiceTest

testGetDatasetRawExpression() - Method in class ubic.gemma.web.services.rest.DatasetsRestTest

testGetDatasetRawExpression() - Method in class ubic.gemma.web.services.rest.DatasetsWebServiceTest

testGetDatasetRawExpressionByQuantitationType() - Method in class ubic.gemma.web.services.rest.DatasetsWebServiceTest

testGetDatasets() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsJerseyTest

testGetDesignElementDataVectorsByQt() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

testGetDetails() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceTest

testGetEnsemblNcibidata() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiFetcherTest

testGetEntitiesWithEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest

testGetExperimentalFactors() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest

testGetExperimentalFactorValues() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest

testGetExpressionExperimentsById() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testGetGene() - Method in class ubic.gemma.core.image.aba.AllenBrainAtlasServiceTest

testGetGenesForCompositeSequence() - Method in class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperServiceTest

Tests finding all genes for a given composite sequence.

testGetGeoRecordGSE93825() - Method in class ubic.gemma.core.loader.expression.geo.GeoBrowserTest

testGetGeoRecords() - Method in class ubic.gemma.core.loader.expression.geo.GeoBrowserTest

Exercises getting details

testGetGeoRecordsB() - Method in class ubic.gemma.core.loader.expression.geo.GeoBrowserTest

testGetGeoRecordsBySearchTerm() - Method in class ubic.gemma.core.loader.expression.geo.GeoBrowserTest

testGetHomologues() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceTest

testGetHomologues2() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceTest

testGetIdMap() - Method in class ubic.gemma.persistence.util.EntityUtilsTest

testGetInfo() - Method in class ubic.gemma.web.controller.security.SecurityControllerTest

Experiment has to be public.

testGetLatestExperiments() - Method in class ubic.gemma.web.controller.common.rss.RssFeedControllerTest

testGetMicroRnaByTaxon() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest

testGetMultiple() - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmdTest

testGetMultipleAcc() - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmdTest

testGetMultipleAccSomeNotFound() - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmdTest

testGetNestedPropertyMap() - Method in class ubic.gemma.persistence.util.EntityUtilsTest

testGetObjectFilter() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

EE service has a few extensions for supporting various filtering strategies in the frontend, so we need to test them here.

testGetObo() - Method in class ubic.gemma.web.controller.OntologyControllerTest

testGetParents() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testGetParents() - Method in class ubic.gemma.model.common.description.CharacteristicServiceTest

testGetParentsPartOf() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testGetParentsWithClazzConstraint() - Method in class ubic.gemma.model.common.description.CharacteristicServiceTest

testGetPerTaxonCount() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

testGetPlatforms() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsJerseyTest

testGetProcessedDataMatrices() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVectorServiceTest

Test method for ProcessedExpressionDataVectorDaoImpl.getProcessedDataArrays(java.util.Collection, java.util.Collection) .

testGetProperty() - Method in class ubic.gemma.persistence.util.EntityUtilsTest

testGetPropertyMap() - Method in class ubic.gemma.persistence.util.EntityUtilsTest

testGetQuantitationTypes() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

testGetQuantitationTypesForArrayDesign() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

testGetRawExpressionDataVectors() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

testGetRecentGeoRecords() - Method in class ubic.gemma.core.loader.expression.geo.GeoBrowserTest

testGetRecentRecords() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceTest

testGetResultSets() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsJerseyTest

testGetS() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest

testGetSingle() - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmdTest

testGetSingleAcc() - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmdTest

testGetSingleAccNotFound() - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmdTest

testGetSort() - Method in class ubic.gemma.web.services.rest.util.args.SortArgTest

testGetSortWhenFieldDoesNotExistThenRaiseMalformedArgumentException() - Method in class ubic.gemma.web.services.rest.util.args.SortArgTest

testGetTaxaMultipleTaxonForArray() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

Test retrieving multiple taxa for an arraydesign where hibernate query is not restricted to return just 1 taxon.

testGetTaxaOneTaxonForArray() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testGetTaxon() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testGetTermForId() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testGetU() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest

testGPL6096ExonArray() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testGSE14285OneBatch() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testGSE156689NoBatchinfo() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testGSE35930() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExTest

Test where probes have constant values.

testGSE44903() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testGSE465() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testGSE8872() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testGuessQuantitationTypeParameters() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testHandleAddEventAuditableAuditEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailDaoTest

testHandleGetNewSinceDate() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventDaoImplTest

testHandleGetUpdatedSinceDate() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventDaoImplTest

testHandleGetUser() - Method in class ubic.gemma.core.security.authentication.UserServiceImplTest

testHandleRemoveUser() - Method in class ubic.gemma.core.security.authentication.UserServiceImplTest

testHandleSaveUser() - Method in class ubic.gemma.core.security.authentication.UserServiceImplTest

testHelper - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest

testIdentifyOutliers() - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetectionServiceTest

testIllegalArgumentExceptionChannel1Channel2taxonDifferent() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testIllegalArgumentExceptionMultipleTaxaOnArrayWithNoOrganismColumn() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testImageClones() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testIndexOfCaseInsensitiveStringElements() - Method in class ubic.gemma.persistence.util.ListUtilsTest

testIndexOfElements() - Method in class ubic.gemma.persistence.util.ListUtilsTest

testIntronIssues() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest

testInvalidCollectionTypeConversion() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testInvalidFilter() - Method in class ubic.gemma.web.services.rest.util.args.FilterArgTest

testInvalidSubsetFactor() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysisTest

testIsAutomaticallyGenerated() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetServiceTest

testIsBaselineA() - Method in class ubic.gemma.core.datastructure.matrix.DetectFactorBaselineTest

testIsBaselineB() - Method in class ubic.gemma.core.datastructure.matrix.DetectFactorBaselineTest

testIsHuman() - Method in class ubic.gemma.core.util.TaxonUtilityTest

testIsMouse() - Method in class ubic.gemma.core.util.TaxonUtilityTest

testIsNotBaselineA() - Method in class ubic.gemma.core.datastructure.matrix.DetectFactorBaselineTest

testIsRat() - Method in class ubic.gemma.core.util.TaxonUtilityTest

testJsonRepresentation() - Method in class ubic.gemma.web.services.rest.providers.WebApplicationExceptionMapperTest

testLike() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testLikeWithInvalidPropertyType() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testLikeWithInvalidRequiredValue() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testLoad() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceIntegrationTest

testLoad() - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceTest

testLoad() - Method in class ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceTest

testloadAllNeurocartaPhenotypes() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

testLoadAllPhenotypeUris() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

testLoadAllValueObjects() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testLoadAllValueObjects() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

testLoadAllValueObjectsOneTaxon() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

Test to ensure that if one taxon is present on an array only 1 string is returned with taxon name

testLoadAnalyzeSaveAndCoexpSearch() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisServiceTest

testLoadB() - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceTest

testLoadByCollection() - Method in class ubic.gemma.persistence.service.AbstractDaoTest

testLoadCommandConsoleFormat() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceIntegrationTest

testLoadCompositeSequences() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testLoadDuplicatedRow() - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceTest

testLoadEvidenceWithExternalDatabaseName() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

testLoadGeneFileNotFoundIOException() - Method in class ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceTest

testLoadGenes() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest

testLoadGSE28383ExonArray() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest

testLoadGSE30521ExonArray() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest

testLoadInputStream() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonLoaderTest

testLoadMPSNames() - Method in class ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarizeTest

testLoadRNASeqData() - Method in class ubic.gemma.core.loader.expression.DataUpdaterTest

testLoadRNASeqDataWithMissingSamples() - Method in class ubic.gemma.core.loader.expression.DataUpdaterTest

testLoadStatistics() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

testLoadStatusSummariesLimit() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentControllerTest

testLoadTree() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

testLoadUpdateDeleteEvidence() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

testLoadValueObject() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest

testLoadValueObject() - Method in class ubic.gemma.model.genome.TaxonServiceImplTest

testLoadValueObjects() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

testLoadValueObjectsPreFilter() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceTest

testLoadValueObjectsPreFilter() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoTest

testLoadValueObjectsPreFilterByBioAssay() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

testLoadValueObjectsPreFilterByCharacteristic() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest

testLoadValueObjectsPreFilterWithPagination() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceTest

testLoadValueObjetsPreFilterByArrayDesign() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceTest

testLoadWithEmptyCollection() - Method in class ubic.gemma.model.common.description.DatabaseEntryDaoImplTest

testLocateGene() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest

testLocateGeneOnWrongStrand() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest

testLocatePrimaryReference() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest

testLocatePrimaryReferenceInvalidGSE() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest

testLoggingInProgressUpdateCallbackDoesNotResultInLoggingRecursion() - Method in class ubic.gemma.core.util.progress.ProgressAppenderTest

testLogin() - Method in class ubic.gemma.core.security.principal.PrincipalTest

testLoginNonexistentUser() - Method in class ubic.gemma.core.security.principal.PrincipalTest

testLoginWrongPassword() - Method in class ubic.gemma.core.security.principal.PrincipalTest

testMain() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcherIntegrationTest

Test method for AbstractCLI.executeCommand(String[]).

testMakeEEGroupReadWrite() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest

testMakeExpressionExperimentPrivate() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest

testMakePrivateWithoutPermission() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest

testMakeTitle() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testMas5() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testMas6() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testMaskPwd() - Method in class ubic.gemma.core.apps.CliTest

testMatrixConversion() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixTest

testMatrixReconstruct() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest

testMatrixReconstructB() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest

testMeasuredRegion() - Method in class ubic.gemma.core.util.StopWatchUtilsTest

testMeasuredRegionWhhenStopWatchIsAlreadyStarted() - Method in class ubic.gemma.core.util.StopWatchUtilsTest

testMeasuredRegionWhhenStopWatchIsStopped() - Method in class ubic.gemma.core.util.StopWatchUtilsTest

testMeasuredRegionWithInnerRegion() - Method in class ubic.gemma.core.util.StopWatchUtilsTest

testMerge() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeServiceTest

testMINiMLParse() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceParseTest

testMissingValue() - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesTest

testMissingValueGSE11017() - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesTest

Was giving all missing values.

testMissingValueGSE523() - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesTest

testMissingValueGSE56() - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesTest

GSE56 is corrupt: there is no Channel 1 signal value in the data file.

testMkdirAlreadyExists() - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcherTest

testMkdirMakeSubdirs() - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcherTest

testMkdirMakeTemp() - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcherTest

testNormalize() - Method in class ubic.gemma.core.analysis.preprocess.QuantileNormalizerTest

testNotEqualsID() - Method in class ubic.gemma.model.genome.biosequence.BioSequenceTest

testNullFilter() - Method in class ubic.gemma.web.services.rest.util.args.FilterArgTest

testNumBioSequencesById() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testNumBlatResultsById() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testNumCompositeSequencesArrayDesign() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testNumExperiments() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

testNumGenesById() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testOneSampleTtest() - Method in class ubic.gemma.core.analysis.expression.diff.TTestAnalyzerTest

testOneWayAnova() - Method in class ubic.gemma.core.analysis.expression.diff.OneWayAnovaAnalyzerTest

Tests the OneWayAnova method.

testOnewayAnovaB() - Method in class ubic.gemma.core.analysis.expression.diff.OneWayAnovaAnalyzerTest

testOnSubmit() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerTest

testOnSubmitAlreadyExists() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerTest

testOnSubmitInvalidValue() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerTest

testOnSubmitNotFound() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerTest

testOpenApiEndpoint() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsJerseyTest

testOrderByExperimentalDesignB() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSortTest

testOrderOfExecutionFailure() - Method in class ubic.gemma.core.job.ExecutingTaskTest

testOrderOfExecutionSuccess() - Method in class ubic.gemma.core.job.ExecutingTaskTest

testParametersAnnotatedWithExplode() - Method in class ubic.gemma.web.services.rest.args.StringArrayArgTest

testParents() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest2

testParse() - Method in class ubic.gemma.core.analysis.service.AbstractTsvFileServiceTest

testParse() - Method in class ubic.gemma.core.loader.entrez.pubmed.ESearchXMLParserTest

testParse() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest

testParse() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceParseTest

testParse() - Method in class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImportDuplicateValueTest

testParse() - Method in class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterTest

testParse() - Method in class ubic.gemma.core.loader.genome.gene.SwissProtParserTest

testParse2() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceParseTest

testParse3() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceParseTest

testParseA() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneHistoryParserTest

testParseAndLoad() - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationParserTest

testParseB() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneHistoryParserTest

testParseBigA() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest

testParseBigBPlatformOnly() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest

testParseBook() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest

testParseBookArticle() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest

testParseBoolean() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testParsecodelink() - Method in class ubic.gemma.core.loader.genome.FastaParserTest

testParseCollection() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testParseCollectionOfDates() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testParseCollectionOfDateTimes() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testParseDataset() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest

testParseDate() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testParseDateTime() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testParseDateTimeWithoutZuluSuffix() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testParseDouble() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testParseDoubleHeader() - Method in class ubic.gemma.core.loader.genome.FastaParserTest

testParseDryRun() - Method in class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterTest

testParseFailedDryRun() - Method in class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterTest

testParseGene2Accession() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneParserTest

testParseGeneInfo() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneParserTest

testParseGenePix() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest

testParseGEOSampleCharacteristic() - Method in class ubic.gemma.core.loader.expression.geo.GeoCharacteristicParseTest

testParseGSE18707() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testParseGSE29014() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest

testParseGse432() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest

testParseGSE44625() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testParseHeaders() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testParseInputStream() - Method in class ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParserTest

testParseInputStream() - Method in class ubic.gemma.core.loader.genome.FastaParserTest

testParseInputStream() - Method in class ubic.gemma.core.loader.genome.ProbeSequenceParserTest

testParseInputStream() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonParserTest

testParseInputStreamAffyTarget() - Method in class ubic.gemma.core.loader.genome.FastaParserTest

testParseInputStreamNoheader() - Method in class ubic.gemma.core.loader.genome.BlatResultParserTest

testParseInputStreamWheader() - Method in class ubic.gemma.core.loader.genome.BlatResultParserTest

testParseInteger() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testParseInvalidCollection() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testParseInvalidOperator() - Method in class ubic.gemma.web.services.rest.util.args.FilterArgTest

testParseMasked() - Method in class ubic.gemma.core.loader.genome.FastaParserTest

testParseMesh() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest

testParseMixtureOfDateAndDateTime() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testParseMulti() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest

testParseMultipartAbstract() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest

testParseNIA() - Method in class ubic.gemma.core.loader.genome.FastaParserTest

testParseOneValidLineHuman() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiParserTest

testParseOneValidLineNonHuman() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiParserTest

testParseRetracted() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest

testParseSAGE() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest

testParseStandardDate() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest

testParseStandardDateWithGap() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest

testParseString() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testParseUnsupportedType() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testParseValidFileHuman() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiParserTest

testParseValidFileMouse() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiParserTest

testParseWhereExtraValue() - Method in class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterTest

testPercent() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testPersistBioSequence() - Method in class ubic.gemma.model.genome.BioSequencePersistTest

testPersistGene() - Method in class ubic.gemma.persistence.GenomePersisterTest

testPersistGeneProduct() - Method in class ubic.gemma.persistence.GenomePersisterTest

testPersistNewArrayDesign() - Method in class ubic.gemma.persistence.PersisterTest

testPixels() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testPlatformDatasets() - Method in class ubic.gemma.web.services.rest.PlatformsWebServiceTest

testPlatformElements() - Method in class ubic.gemma.web.services.rest.PlatformsWebServiceTest

testPreflightRequest() - Method in class ubic.gemma.web.services.rest.servlet.CorsFilterTest

testPrimitiveType() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testPrimitiveTypeDoubleWrong() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testPrimitiveTypeInteger() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testPrimitiveTypeIntegerWrong() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testPrimitiveTypeToWrapperConversion() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testProcessArrayDesign() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentandMappingTest

testProcessArrayDesignWithFastaCmdFetch() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorFastacmdTest

testProcessBlatResults() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest

testProgressData() - Method in class ubic.gemma.core.util.progress.ProgressDataTest

testProgressLogging() - Method in class ubic.gemma.core.util.progress.ProgressAppenderTest

testQueryEst() - Method in class ubic.gemma.core.externalDb.GoldenPathQueryTest

testQueryMrna() - Method in class ubic.gemma.core.externalDb.GoldenPathQueryTest

testQueryNoResult() - Method in class ubic.gemma.core.externalDb.GoldenPathQueryTest

testRatio() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testReadInputStream() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReaderTest

testReadInputStream() - Method in class ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReaderTest

Class under test for Map read(InputStream)

testReadInputStreamNew() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReaderTest

testReadReport() - Method in class ubic.gemma.web.services.GemmaEndpointTest

testRedirection() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsJerseyTest

testReflectionOnFactory() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest

testRemove() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDeleteTest

testRemoveMultipleAcesFromPrivateExpressionExperiment() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest

testRemoveUsersFromGroupDisallowed() - Method in class ubic.gemma.web.controller.security.SecurityControllerTest

testReorder() - Method in class ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataCreateServiceTest

testRepeatedMeasuredRegion() - Method in class ubic.gemma.core.util.StopWatchUtilsTest

testRequestWithOrigin() - Method in class ubic.gemma.web.services.rest.servlet.CorsFilterTest

testRequestWithoutOrigin() - Method in class ubic.gemma.web.services.rest.servlet.CorsFilterTest

testRestrictionClauseWithCollection() - Method in class ubic.gemma.persistence.util.ObjectFilterQueryUtilsTest

testRestrictionClauseWithNullObjectAlias() - Method in class ubic.gemma.persistence.util.ObjectFilterQueryUtilsTest

testRestrictionClauseWithNullRequiredValue() - Method in class ubic.gemma.persistence.util.ObjectFilterQueryUtilsTest

testResultObject() - Method in class ubic.gemma.core.search.SearchResultTest

testResultObjectWithNullId() - Method in class ubic.gemma.core.search.SearchResultTest

testRetrieveByHTTP() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest

testRetrieveByHTTP2() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest

testRetrieveByHTTPBookshelf() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest

testRetrieveByHTTPNotFound() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest

testRetry() - Method in class ubic.gemma.persistence.retry.RetryTest

testRetryableMethod() - Method in class ubic.gemma.core.security.audit.PointcutsTest

testRetryNonTransactionalOperation() - Method in class ubic.gemma.persistence.retry.RetryTest

TestRetryService() - Constructor for class ubic.gemma.persistence.retry.RetryTest.TestRetryService

testRetryTransactionalOperation() - Method in class ubic.gemma.persistence.retry.RetryTest

testRetryWhenNoExceptionIsRaised() - Method in class ubic.gemma.persistence.retry.RetryTest

testRetryWithNonRetryableException() - Method in class ubic.gemma.persistence.retry.RetryTest

testRetryWithRetryableExceptionInCause() - Method in class ubic.gemma.persistence.retry.RetryTest

testrma() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testSampleMINiMLParse() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceParseTest

testScore() - Method in class ubic.gemma.model.genome.BlatResultTest

testScoreResults() - Method in class ubic.gemma.core.analysis.sequence.BlatAssociationScorerTest

testScorewr() - Method in class ubic.gemma.model.genome.BlatResultTest

testSearchAndRetrieveByHTTP() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearchTest

testSearchAndRetrieveByHTTPInChunks() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearchTest

testSearchAndRetrieveIdByHTTPBookshelf() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearchTest

testSearchAndRetrieveIdsByHTTP() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearchTest

testSearchByArrayDesign() - Method in class ubic.gemma.web.services.rest.SearchWebServiceTest

testSearchByBibRefIdProblems() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest

testSearchByBibRefIdProblemsB() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest

testSearchByTaxon() - Method in class ubic.gemma.web.services.rest.SearchWebServiceTest

testSearchEverything() - Method in class ubic.gemma.web.services.rest.SearchWebServiceTest

testSearchGenes() - Method in class ubic.gemma.model.genome.gene.GeneSearchTest

testSearchOntologyForPhenotypes() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest

testSearchTaxonDatasets() - Method in class ubic.gemma.web.services.rest.AnnotationsWebServiceTest

testSearchWhenQueryIsEmpty() - Method in class ubic.gemma.web.services.rest.SearchWebServiceTest

testSearchWhenQueryIsMissing() - Method in class ubic.gemma.web.services.rest.SearchWebServiceTest

testSearchWhenUnknownPlatformIsProvided() - Method in class ubic.gemma.web.services.rest.SearchWebServiceTest

testSearchWhenUnknownTaxonIsProvided() - Method in class ubic.gemma.web.services.rest.SearchWebServiceTest

testSearchWhenUnsupportedResultTypeIsProvided() - Method in class ubic.gemma.web.services.rest.SearchWebServiceTest

testSecurableEntitiesNamesAreUnchanged() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

Since ACL relies on the class name, and these class names are stored in the database, we must ensure that they are never changed.

testSecuredExpressionExperimentValueObject() - Method in class ubic.gemma.core.security.authorization.SecureValueObjectAuthorizationTest

testSecuredNotChild() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

testSecurityContextManagement() - Method in class ubic.gemma.core.job.ExecutingTaskTest

testSerializeEWAHCompressedBitmap() - Method in class ubic.gemma.model.analysis.expression.coexpression.SupportDetailsTest

testServiceCreateCountData() - Method in class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceTest

testServiceCreateExistingEe() - Method in class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceTest

testServiceCreateOneColor() - Method in class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceTest

testServiceCreateTwoColor() - Method in class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceTest

testSetDescription() - Method in class ubic.gemma.core.util.progress.ProgressDataTest

testSetDone() - Method in class ubic.gemma.core.util.progress.ProgressDataTest

testSetOwner() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest

testSetPercent() - Method in class ubic.gemma.core.util.progress.ProgressDataTest

testSetPrincipalSID() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest

testSetQueryWhenQueryContainsBlankThenTrimAccordingly() - Method in class ubic.gemma.model.common.search.SearchSettingsTest

testSetQueryWhenQueryIsATermUri() - Method in class ubic.gemma.model.common.search.SearchSettingsTest

testSetQueryWhenQueryIsATermUriWithTrailingBlanks() - Method in class ubic.gemma.model.common.search.SearchSettingsTest

testSetQueryWhenQueryIsNull() - Method in class ubic.gemma.model.common.search.SearchSettingsTest

testSetResultObject() - Method in class ubic.gemma.core.search.SearchResultTest

testSetResultObjectWithDifferentId() - Method in class ubic.gemma.core.search.SearchResultTest

testSetResultObjectWithNullId() - Method in class ubic.gemma.core.search.SearchResultTest

testSetTermUriWhenUriIsBlank() - Method in class ubic.gemma.model.common.search.SearchSettingsTest

testSetTermUriWhenUriIsNull() - Method in class ubic.gemma.model.common.search.SearchSettingsTest

testShow() - Method in class ubic.gemma.web.controller.common.description.bibref.BibRefControllerTest

testShowAllArrayDesigns() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerTest

testShowAllForExperiments() - Method in class ubic.gemma.web.controller.common.description.bibref.BibRefControllerTest

testShowExperimentalDesign() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest

testSignup() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

testSignup() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupControllerTest

testSimpleAuditFindOrCreate() - Method in class ubic.gemma.core.security.audit.AuditAdviceTest

testSimpleEquality() - Method in class ubic.gemma.web.services.rest.util.args.FilterArgTest

testSingleTaxonOnArrayWithNoOrganismColumn() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testSome() - Method in class ubic.gemma.web.services.rest.DatasetsRestTest

testSomeById() - Method in class ubic.gemma.web.services.rest.DatasetsRestTest

testSortArgWithoutField() - Method in class ubic.gemma.web.services.rest.util.args.SortArgTest

testSortCharacteristics() - Method in class ubic.gemma.core.ontology.CharacteristicSortTest

testSpeedA() - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedInTest

testSpeedB() - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedInTest

testSplitByPlatform() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testSplitGSE123753ByCollectionOfMaterial() - Method in class ubic.gemma.core.analysis.preprocess.SplitExperimentTest

testSplitGSE17183ByOrganismPart() - Method in class ubic.gemma.core.analysis.preprocess.SplitExperimentTest

testStringCannotContainSpace() - Method in class ubic.gemma.web.services.rest.util.args.FilterArgTest

testStripPolyA() - Method in class ubic.gemma.core.analysis.sequence.SequenceManipulationTest

testStripPolyAtooShort() - Method in class ubic.gemma.core.analysis.sequence.SequenceManipulationTest

testStripPolyT() - Method in class ubic.gemma.core.analysis.sequence.SequenceManipulationTest

testSuccessfulRun() - Method in class ubic.gemma.web.controller.TaskRunningTest

testSummarizeRequest() - Method in class ubic.gemma.web.services.rest.util.ServletUtilsTest

testSummarizeRequestWithPrincipal() - Method in class ubic.gemma.web.services.rest.util.ServletUtilsTest

testSummarizeRequestWithQueryString() - Method in class ubic.gemma.web.services.rest.util.ServletUtilsTest

testsvd() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImplTest

testsvdGapped() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImplTest

testTaxonByCommonName() - Method in class ubic.gemma.web.services.rest.TaxaWebServiceTest

testTaxonById() - Method in class ubic.gemma.web.services.rest.TaxaWebServiceTest

testTaxonByNcbiId() - Method in class ubic.gemma.web.services.rest.TaxaWebServiceTest

testTaxonByScientificName() - Method in class ubic.gemma.web.services.rest.TaxaWebServiceTest

testTaxonDatasetsByNcbiId() - Method in class ubic.gemma.web.services.rest.TaxaWebServiceTest

testTaxonNotFoundIllegalArgumentExceptionException() - Method in class ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceTest

testTextRepresentation() - Method in class ubic.gemma.web.services.rest.providers.WebApplicationExceptionMapperTest

testThaw() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testToggleUsability() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceTest

testTortureQuantitationTypes() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testTransactionalService() - Method in class ubic.gemma.core.security.audit.PointcutsTest

testTTestWithExpressionExperiment() - Method in class ubic.gemma.core.analysis.expression.diff.TTestAnalyzerTest

Tests the t-test with an ExpressionExperiment.

testTwoWayAnova() - Method in class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionsAnalyzerTest

testTwoWayAnova() - Method in class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithoutInteractionsAnalyzerTest

Tests the TwoWayAnova method.

testUMatrixAsExpressionData() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest

testUMatrixAsExpressionDataUnnormalized() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest

testUnmappedRoute() - Method in class ubic.gemma.web.services.rest.AnalysisResultSetsJerseyTest

testUnsupportedResultTypeRaisesIllegalArgumentException() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest

testUpdate() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetServiceTest

testUpdate() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest

Test adding a new member via a cascade.

testUpdateAcl() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

testUpdateBioSequence() - Method in class ubic.gemma.persistence.GenomePersisterTest

testUpdatePermissions() - Method in class ubic.gemma.web.controller.security.SecurityControllerTest

testUpdateSubsumingStatus() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testUpdateSubsumingStatusTrue() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest

testUpdateUserGroup() - Method in class ubic.gemma.core.security.UserGroupServiceTest

Tests updating the UserGroup

testUpdateWhenTableIsFresh() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilTest

testURIChildSearch() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest

Test we find EE tagged with a child term that matches the given uri.

testURISearch() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest

Does the search engine correctly match the spinal cord URI and find objects directly tagged with that URI

testUserAddSelvesToAdmin() - Method in class ubic.gemma.core.security.UserGroupServiceTest

testUserCanEdit() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest

testUserCanRead() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest

TestUtils - Class in ubic.gemma.core.loader.util

TestUtils() - Constructor for class ubic.gemma.core.loader.util.TestUtils

testValueOf() - Method in class ubic.gemma.web.services.rest.util.args.SortArgTest

testVarianceFractions() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest

testWarnLogsShouldNotBeAppended() - Method in class ubic.gemma.web.logging.SlackAppenderTest

testWhenUserIsAgent() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilIntegrationTest

testWhenUserIsAnonymous() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilIntegrationTest

testWinnow() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest

testWithDifferentPath() - Method in class ubic.gemma.web.services.rest.servlet.RestapidocsIndexRewriteFilterTest

testWithImageNoGenbank() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testWithImages() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testWithoutTrailingSlash() - Method in class ubic.gemma.web.services.rest.servlet.RestapidocsIndexRewriteFilterTest

testWithQuery() - Method in class ubic.gemma.web.services.rest.servlet.RestapidocsIndexRewriteFilterTest

testWithSubset() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysisTest

testWrapperToPrimitiveConversion() - Method in class ubic.gemma.persistence.util.ObjectFilterTest

testWrite() - Method in class ubic.gemma.core.datastructure.matrix.ExperimentalDesignWriterTest

testWritePValuesHistogram() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest

TTestAnalyzerTest - Class in ubic.gemma.core.analysis.expression.diff

See test/data/stat-tests/README.txt for R code.

TTestAnalyzerTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.TTestAnalyzerTest

TwoChannelMissingValuesTest - Class in ubic.gemma.core.analysis.preprocess

TwoChannelMissingValuesTest() - Constructor for class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesTest

TwoWayAnovaWithInteractionsAnalyzerTest - Class in ubic.gemma.core.analysis.expression.diff

Tests the two way anova analyzer with interactions.

TwoWayAnovaWithInteractionsAnalyzerTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionsAnalyzerTest

TwoWayAnovaWithInteractionsTest2 - Class in ubic.gemma.core.analysis.expression.diff

TwoWayAnovaWithInteractionsTest2() - Constructor for class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionsTest2

TwoWayAnovaWithInteractionTest2 - Class in ubic.gemma.core.analysis.expression.diff

Test based on GSE8441

TwoWayAnovaWithInteractionTest2() - Constructor for class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionTest2

TwoWayAnovaWithoutInteractionsAnalyzerTest - Class in ubic.gemma.core.analysis.expression.diff

Tests the two way anova analyzer.

TwoWayAnovaWithoutInteractionsAnalyzerTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithoutInteractionsAnalyzerTest

U

ubic.gemma.core.analysis.expression.coexpression.links - package ubic.gemma.core.analysis.expression.coexpression.links

ubic.gemma.core.analysis.expression.diff - package ubic.gemma.core.analysis.expression.diff

ubic.gemma.core.analysis.preprocess - package ubic.gemma.core.analysis.preprocess

ubic.gemma.core.analysis.preprocess.batcheffects - package ubic.gemma.core.analysis.preprocess.batcheffects

ubic.gemma.core.analysis.preprocess.svd - package ubic.gemma.core.analysis.preprocess.svd

ubic.gemma.core.analysis.report - package ubic.gemma.core.analysis.report

ubic.gemma.core.analysis.sequence - package ubic.gemma.core.analysis.sequence

ubic.gemma.core.analysis.service - package ubic.gemma.core.analysis.service

ubic.gemma.core.annotation.reference - package ubic.gemma.core.annotation.reference

ubic.gemma.core.apps - package ubic.gemma.core.apps

ubic.gemma.core.datastructure.matrix - package ubic.gemma.core.datastructure.matrix

ubic.gemma.core.externalDb - package ubic.gemma.core.externalDb

ubic.gemma.core.image.aba - package ubic.gemma.core.image.aba

ubic.gemma.core.job - package ubic.gemma.core.job

ubic.gemma.core.loader.association - package ubic.gemma.core.loader.association

ubic.gemma.core.loader.association.phenotype - package ubic.gemma.core.loader.association.phenotype

ubic.gemma.core.loader.entrez - package ubic.gemma.core.loader.entrez

ubic.gemma.core.loader.entrez.pubmed - package ubic.gemma.core.loader.entrez.pubmed

ubic.gemma.core.loader.expression - package ubic.gemma.core.loader.expression

ubic.gemma.core.loader.expression.arrayDesign - package ubic.gemma.core.loader.expression.arrayDesign

ubic.gemma.core.loader.expression.arrayExpress - package ubic.gemma.core.loader.expression.arrayExpress

ubic.gemma.core.loader.expression.geo - package ubic.gemma.core.loader.expression.geo

ubic.gemma.core.loader.expression.geo.fetcher - package ubic.gemma.core.loader.expression.geo.fetcher

ubic.gemma.core.loader.expression.geo.service - package ubic.gemma.core.loader.expression.geo.service

ubic.gemma.core.loader.expression.simple - package ubic.gemma.core.loader.expression.simple

ubic.gemma.core.loader.genome - package ubic.gemma.core.loader.genome

ubic.gemma.core.loader.genome.gene - package ubic.gemma.core.loader.genome.gene

ubic.gemma.core.loader.genome.gene.ncbi - package ubic.gemma.core.loader.genome.gene.ncbi

ubic.gemma.core.loader.genome.gene.ncbi.homology - package ubic.gemma.core.loader.genome.gene.ncbi.homology

ubic.gemma.core.loader.genome.taxon - package ubic.gemma.core.loader.genome.taxon

ubic.gemma.core.loader.util - package ubic.gemma.core.loader.util

ubic.gemma.core.loader.util.fetcher - package ubic.gemma.core.loader.util.fetcher

ubic.gemma.core.ontology - package ubic.gemma.core.ontology

ubic.gemma.core.ontology.providers - package ubic.gemma.core.ontology.providers

ubic.gemma.core.search - package ubic.gemma.core.search

ubic.gemma.core.search.source - package ubic.gemma.core.search.source

ubic.gemma.core.security - package ubic.gemma.core.security

ubic.gemma.core.security.audit - package ubic.gemma.core.security.audit

ubic.gemma.core.security.authentication - package ubic.gemma.core.security.authentication

ubic.gemma.core.security.authorization - package ubic.gemma.core.security.authorization

ubic.gemma.core.security.authorization.acl - package ubic.gemma.core.security.authorization.acl

ubic.gemma.core.security.principal - package ubic.gemma.core.security.principal

ubic.gemma.core.util - package ubic.gemma.core.util

ubic.gemma.core.util.biomart - package ubic.gemma.core.util.biomart

ubic.gemma.core.util.progress - package ubic.gemma.core.util.progress

ubic.gemma.core.util.test - package ubic.gemma.core.util.test

ubic.gemma.core.util.test.category - package ubic.gemma.core.util.test.category

ubic.gemma.core.util.test.suite - package ubic.gemma.core.util.test.suite

ubic.gemma.model.analysis - package ubic.gemma.model.analysis

ubic.gemma.model.analysis.expression.coexpression - package ubic.gemma.model.analysis.expression.coexpression

ubic.gemma.model.association.coexpression - package ubic.gemma.model.association.coexpression

ubic.gemma.model.association.phenotype - package ubic.gemma.model.association.phenotype

ubic.gemma.model.common.auditAndSecurity - package ubic.gemma.model.common.auditAndSecurity

ubic.gemma.model.common.description - package ubic.gemma.model.common.description

ubic.gemma.model.common.search - package ubic.gemma.model.common.search

ubic.gemma.model.expression - package ubic.gemma.model.expression

ubic.gemma.model.expression.arrayDesign - package ubic.gemma.model.expression.arrayDesign

ubic.gemma.model.expression.bioAssay - package ubic.gemma.model.expression.bioAssay

ubic.gemma.model.expression.bioAssayData - package ubic.gemma.model.expression.bioAssayData

ubic.gemma.model.expression.biomaterial - package ubic.gemma.model.expression.biomaterial

ubic.gemma.model.expression.experiment - package ubic.gemma.model.expression.experiment

ubic.gemma.model.genome - package ubic.gemma.model.genome

ubic.gemma.model.genome.biosequence - package ubic.gemma.model.genome.biosequence

ubic.gemma.model.genome.gene - package ubic.gemma.model.genome.gene

ubic.gemma.model.genome.gene.phenotype.valueObject - package ubic.gemma.model.genome.gene.phenotype.valueObject

ubic.gemma.model.genome.sequenceAnalysis - package ubic.gemma.model.genome.sequenceAnalysis

ubic.gemma.persistence - package ubic.gemma.persistence

ubic.gemma.persistence.retry - package ubic.gemma.persistence.retry

ubic.gemma.persistence.service - package ubic.gemma.persistence.service

ubic.gemma.persistence.service.analysis.expression.diff - package ubic.gemma.persistence.service.analysis.expression.diff

ubic.gemma.persistence.service.common.description - package ubic.gemma.persistence.service.common.description

ubic.gemma.persistence.service.common.quantitationtype - package ubic.gemma.persistence.service.common.quantitationtype

ubic.gemma.persistence.service.expression.designElement - package ubic.gemma.persistence.service.expression.designElement

ubic.gemma.persistence.util - package ubic.gemma.persistence.util

ubic.gemma.web.controller - package ubic.gemma.web.controller

ubic.gemma.web.controller.common.auditAndSecurity - package ubic.gemma.web.controller.common.auditAndSecurity

ubic.gemma.web.controller.common.description.bibref - package ubic.gemma.web.controller.common.description.bibref

ubic.gemma.web.controller.common.rss - package ubic.gemma.web.controller.common.rss

ubic.gemma.web.controller.expression - package ubic.gemma.web.controller.expression

ubic.gemma.web.controller.expression.arrayDesign - package ubic.gemma.web.controller.expression.arrayDesign

ubic.gemma.web.controller.expression.experiment - package ubic.gemma.web.controller.expression.experiment

ubic.gemma.web.controller.security - package ubic.gemma.web.controller.security

ubic.gemma.web.logging - package ubic.gemma.web.logging

ubic.gemma.web.remote - package ubic.gemma.web.remote

ubic.gemma.web.scheduler - package ubic.gemma.web.scheduler

ubic.gemma.web.services - package ubic.gemma.web.services

ubic.gemma.web.services.rest - package ubic.gemma.web.services.rest

ubic.gemma.web.services.rest.args - package ubic.gemma.web.services.rest.args

ubic.gemma.web.services.rest.providers - package ubic.gemma.web.services.rest.providers

ubic.gemma.web.services.rest.servlet - package ubic.gemma.web.services.rest.servlet

ubic.gemma.web.services.rest.util - package ubic.gemma.web.services.rest.util

ubic.gemma.web.services.rest.util.args - package ubic.gemma.web.services.rest.util.args

ubic.gemma.web.util - package ubic.gemma.web.util

ubic.gemma.web.util.upload - package ubic.gemma.web.util.upload

UnitTests - Class in ubic.gemma.core.util.test.suite

UnitTests() - Constructor for class ubic.gemma.core.util.test.suite.UnitTests

update(MutableAcl) - Method in class ubic.gemma.core.security.authorization.acl.AclTestUtils

UserGroupServiceTest - Class in ubic.gemma.core.security

Tests the Group facilities of the UserManager..

UserGroupServiceTest() - Constructor for class ubic.gemma.core.security.UserGroupServiceTest

userManager() - Method in class ubic.gemma.core.util.test.BaseCliTest.BaseCliTestContextConfiguration

UserServiceImplTest - Class in ubic.gemma.core.security.authentication

UserServiceImplTest() - Constructor for class ubic.gemma.core.security.authentication.UserServiceImplTest

V

VectorMergingServiceTest - Class in ubic.gemma.core.analysis.preprocess

Tests loading, platform switch, vector merge, and complex deletion (in teardown)

VectorMergingServiceTest() - Constructor for class ubic.gemma.core.analysis.preprocess.VectorMergingServiceTest

W

WebApplicationExceptionMapperTest - Class in ubic.gemma.web.services.rest.providers

WebApplicationExceptionMapperTest() - Constructor for class ubic.gemma.web.services.rest.providers.WebApplicationExceptionMapperTest

WebApplicationExceptionMapperTest.CustomResource - Class in ubic.gemma.web.services.rest.providers

This is a very simplisitc example that produces two representation for the same resource.

WebApplicationExceptionMapperTest.CustomResource.MyModel - Class in ubic.gemma.web.services.rest.providers

work() - Method in interface ubic.gemma.persistence.retry.RetryTest.TestRetryDao

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