Uses of Class
ubic.gemma.core.util.test.BaseIntegrationTest5

Packages that use BaseIntegrationTest5

Package	Description
ubic.gemma.apps
ubic.gemma.cli.util
ubic.gemma.cli.util.test
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.report
ubic.gemma.core.analysis.service
ubic.gemma.core.analysis.singleCell.aggregate
ubic.gemma.core.datastructure.matrix.io
ubic.gemma.core.job
ubic.gemma.core.loader.association
ubic.gemma.core.loader.expression
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.expression.cellxgene
ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.expression.geo.service
ubic.gemma.core.loader.expression.simple
ubic.gemma.core.loader.expression.singleCell
ubic.gemma.core.loader.genome.gene
ubic.gemma.core.loader.genome.gene.ncbi
ubic.gemma.core.loader.genome.taxon
ubic.gemma.core.scheduler
ubic.gemma.core.search
ubic.gemma.core.security
ubic.gemma.core.security.authentication
ubic.gemma.core.security.authorization
ubic.gemma.core.security.authorization.acl
ubic.gemma.core.security.principal
ubic.gemma.core.util
ubic.gemma.core.util.test
ubic.gemma.core.util.test.fixture
ubic.gemma.model.genome
ubic.gemma.persistence.hibernate
ubic.gemma.persistence.persister
ubic.gemma.persistence.retry
ubic.gemma.persistence.service
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.blacklist
ubic.gemma.persistence.service.common.auditAndSecurity
ubic.gemma.persistence.service.common.auditAndSecurity.curation
ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.expression.arrayDesign
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.biomaterial
ubic.gemma.persistence.service.expression.designElement
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.service.genome
ubic.gemma.persistence.service.genome.gene
ubic.gemma.persistence.service.genome.sequenceAnalysis
ubic.gemma.persistence.service.maintenance
ubic.gemma.persistence.util

Uses of BaseIntegrationTest5 in ubic.gemma.apps

Subclasses of BaseIntegrationTest5 in ubic.gemma.apps

Modifier and Type	Class	Description
class	PubMedSearcherIntegrationTest	Tests command line.

Uses of BaseIntegrationTest5 in ubic.gemma.cli.util

Subclasses of BaseIntegrationTest5 in ubic.gemma.cli.util

Modifier and Type	Class	Description
class	MarkCLIsAsPrototypesTest	Test various behaviours of CLIs when injected as bean.

Uses of BaseIntegrationTest5 in ubic.gemma.cli.util.test

Subclasses of BaseIntegrationTest5 in ubic.gemma.cli.util.test

Modifier and Type	Class	Description
class	BaseCliIntegrationTest5	JUnit 5 (Jupiter) counterpart of BaseCliIntegrationTest.

Uses of BaseIntegrationTest5 in ubic.gemma.core.analysis.expression.diff

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.analysis.expression.diff

Modifier and Type	Class	Description
class	BaselineDetectionTest
class	ContinuousVariableDiffExTest
class	DifferentialExpressionAnalyzerServiceTest
class	DiffExMetaAnalyzerServiceTest	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.
class	DiffExTest	Tests added to check various cases of differential expression analysis.
class	DiffExWithInvalidInteraction2Test	for bug 3927
class	DiffExWithInvalidInteractionTest
class	LowVarianceDataTest	Test based on GSE19480, see bug 3177
class	SubsettedAnalysis2Test
class	SubsettedAnalysis3Test
class	TwoWayAnovaWithInteractionsTest2
class	TwoWayAnovaWithInteractionTest2	Test based on GSE8441

Uses of BaseIntegrationTest5 in ubic.gemma.core.analysis.preprocess

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.analysis.preprocess

Modifier and Type	Class	Description
class	MeanVarianceServiceTest
class	ProcessedExpressionDataCreateServiceTest
class	SampleCoexpressionAnalysisServiceTest
class	SplitExperimentTest
class	TwoChannelExpressionDataDoubleMatrixTest
class	TwoChannelMissingValuesTest
class	VectorMergingServiceTest	Tests loading, platform switch, vector merge, and complex deletion (in teardown)

Uses of BaseIntegrationTest5 in ubic.gemma.core.analysis.preprocess.batcheffects

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.analysis.preprocess.batcheffects

Modifier and Type	Class	Description
class	BatchInfoPopulationServiceIntegrationTest	Test fetching and loading the batch information from raw files.
class	ExpressionExperimentBatchCorrectionServiceTest
class	RNASeqBatchInfoPopulationTest

Uses of BaseIntegrationTest5 in ubic.gemma.core.analysis.preprocess.svd

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.analysis.preprocess.svd

Modifier and Type	Class	Description
class	SVDServiceImplTest

Uses of BaseIntegrationTest5 in ubic.gemma.core.analysis.report

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.analysis.report

Modifier and Type	Class	Description
class	ArrayDesignReportServiceTest
class	ExpressionExperimentReportServiceTest
class	WhatsNewServiceTest	The report used to be asserted through its on-disk cache — generate, then read the Java-serialized WhatsNew.new / WhatsNew.updated files back and compare.

Uses of BaseIntegrationTest5 in ubic.gemma.core.analysis.service

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.analysis.service

Modifier and Type	Class	Description
class	CompositeSequenceGeneMapperServiceFastTest	Fast mock variant of CompositeSequenceGeneMapperServiceTest.
class	CompositeSequenceGeneMapperServiceTest	This test makes use of the ArrayDesignProbeMapperServiceImpl.
class	GeneMultifunctionalityPopulationServiceTest

Uses of BaseIntegrationTest5 in ubic.gemma.core.analysis.singleCell.aggregate

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.analysis.singleCell.aggregate

Modifier and Type	Class	Description
class	SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceTest

Uses of BaseIntegrationTest5 in ubic.gemma.core.datastructure.matrix.io

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.datastructure.matrix.io

Modifier and Type	Class	Description
class	ExperimentalDesignWriterTest

Uses of BaseIntegrationTest5 in ubic.gemma.core.job

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.job

Modifier and Type	Class	Description
class	ExecutingTaskTest
class	SchedulerSecurityTest	Tests security of methods run by Quartz.

Uses of BaseIntegrationTest5 in ubic.gemma.core.loader.association

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.loader.association

Modifier and Type	Class	Description
class	NCBIGene2GOAssociationParserTest	Tests multiple both parsing and loading.

Uses of BaseIntegrationTest5 in ubic.gemma.core.loader.expression

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.loader.expression

Modifier and Type	Class	Description
class	DataUpdaterTest
class	ExonArrayDataAddIntegrationTest	Uses the Affy Power Tools, and full-sized data sets.
class	ExpressionExperimentPlatformSwitchTest	Switching of platforms that have no composite sequences.

Uses of BaseIntegrationTest5 in ubic.gemma.core.loader.expression.arrayDesign

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.loader.expression.arrayDesign

Modifier and Type	Class	Description
class	AbstractArrayDesignProcessingTest	Base test for tests that need persistent array design with sequences.
class	ArrayDesignMergeServiceTest
class	ArrayDesignSequenceAlignmentandMappingTest
class	ArrayDesignSequenceProcessorFastacmdTest	Test exercises the fastacmd - requires executable.
class	ArrayDesignSequenceProcessorTest

Uses of BaseIntegrationTest5 in ubic.gemma.core.loader.expression.cellxgene

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.loader.expression.cellxgene

Modifier and Type	Class	Description
class	CellXGeneDataLoaderServiceTest

Uses of BaseIntegrationTest5 in ubic.gemma.core.loader.expression.geo

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.loader.expression.geo

Modifier and Type	Class	Description
class	AbstractGeoServiceTest5	JUnit 5 parallel of AbstractGeoServiceTest, extending the Jupiter BaseSpringContextTest5 base.
class	GeoConverterTest	Unit test for GeoConversion Added extension BaseIntegrationTest5 as want Taxon Service to be called

Uses of BaseIntegrationTest5 in ubic.gemma.core.loader.expression.geo.service

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.loader.expression.geo.service

Modifier and Type	Class	Description
class	GeoDatasetServiceTest	Test full procedure of loading GEO data, focus on corner cases.
class	GeoPlatformServiceTest	Tests of GeoPlatformService

Uses of BaseIntegrationTest5 in ubic.gemma.core.loader.expression.simple

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.loader.expression.simple

Modifier and Type	Class	Description
class	ExperimentalDesignImportDuplicateValueTest	Test for import that results in multiple factor values for the same factor on a single biomaterial.
class	ExperimentalDesignImporterTest
class	SimpleExpressionDataLoaderServiceTest

Uses of BaseIntegrationTest5 in ubic.gemma.core.loader.expression.singleCell

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.loader.expression.singleCell

Modifier and Type	Class	Description
class	AnnDataSingleCellDataLoaderIntegrationTest
class	SingleCellDataLoaderServiceIntegrationTest	Complete integration tests for loading single-cell data.

Uses of BaseIntegrationTest5 in ubic.gemma.core.loader.genome.gene

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.loader.genome.gene

Modifier and Type	Class	Description
class	ExternalFileGeneLoaderServiceTest	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

Uses of BaseIntegrationTest5 in ubic.gemma.core.loader.genome.gene.ncbi

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.loader.genome.gene.ncbi

Modifier and Type	Class	Description
class	NCBIGeneLoadingTest

Uses of BaseIntegrationTest5 in ubic.gemma.core.loader.genome.taxon

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.loader.genome.taxon

Modifier and Type	Class	Description
class	TaxonLoaderTest

Uses of BaseIntegrationTest5 in ubic.gemma.core.scheduler

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.scheduler

Modifier and Type	Class	Description
class	BatchInfoRepopulationJobTest

Uses of BaseIntegrationTest5 in ubic.gemma.core.search

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.search

Modifier and Type	Class	Description
class	MassIndexerSmokeIntegrationTest	End-to-end smoke test for the Hibernate Search 7 mass-indexer + search service round-trip (SEARCH_RECCE.md Step 6).

Uses of BaseIntegrationTest5 in ubic.gemma.core.security

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.security

Modifier and Type	Class	Description
class	UserGroupServiceTest	Tests the Group facilities of the UserManager..

Uses of BaseIntegrationTest5 in ubic.gemma.core.security.authentication

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.security.authentication

Modifier and Type	Class	Description
class	ManualAuthenticationProcessingTest

Uses of BaseIntegrationTest5 in ubic.gemma.core.security.authorization

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.security.authorization

Modifier and Type	Class	Description
class	SecureValueObjectAuthorizationTest
class	SecurityServiceTest	Tests the SecurityService: making objects public or private and testing the permissions.

Uses of BaseIntegrationTest5 in ubic.gemma.core.security.authorization.acl

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.security.authorization.acl

Modifier and Type	Class	Description
class	AclAdviceTest	Tests of ACL management: adding and removing from objects during CRUD operations.
class	AclAuthorizationTest

Uses of BaseIntegrationTest5 in ubic.gemma.core.security.principal

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.security.principal

Modifier and Type	Class	Description
class	PrincipalTest	Test that we can log users in, etc.

Uses of BaseIntegrationTest5 in ubic.gemma.core.util

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.util

Modifier and Type	Class	Description
class	StrictBeanDefinitionValidatorTest

Uses of BaseIntegrationTest5 in ubic.gemma.core.util.test

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.util.test

Modifier and Type	Class	Description
class	BaseSpringContextTest5	Deprecated. favour the simpler BaseIntegrationTest5 for new tests

Uses of BaseIntegrationTest5 in ubic.gemma.core.util.test.fixture

Subclasses of BaseIntegrationTest5 in ubic.gemma.core.util.test.fixture

Modifier and Type	Class	Description
class	ArrayDesignFactoryTest	Verifies the Phase 3 typed ArrayDesignFactory.
class	BioAssayFactoryTest	Verifies the Phase 3 typed BioAssayFactory.
class	BioMaterialFactoryTest	Verifies the Phase 3 typed test-fixture factory for BioMaterial.
class	CompositeSequenceFactoryTest	Verifies the Phase 3 typed CompositeSequenceFactory.
class	ExperimentFactoryTest	Verifies the Phase 3 typed test-fixture factory.
class	GeneFactoryTest	Verifies the Phase 3 typed GeneFactory.
class	TaxonFactoryTest	Verifies the Phase 3 typed TaxonFactory.

Uses of BaseIntegrationTest5 in ubic.gemma.model.genome

Subclasses of BaseIntegrationTest5 in ubic.gemma.model.genome

Modifier and Type	Class	Description
class	GeneSetValueObjectHelperTest

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.hibernate

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.hibernate

Modifier and Type	Class	Description
class	AuditTrailForeignKeyIntegrationTest	AUDIT_TRAIL.LAST_EVENT_FK must be ON DELETE SET NULL in a schema Hibernate built.

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.persister

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.persister

Modifier and Type	Class	Description
class	EeWriteServiceImplQtDedupTest	Pins the behaviourally load-bearing QuantitationType dedup semantic that was lifted out of CommonPersister.persistQuantitationType into a per-EE local map in EeWriteServiceImpl.
class	GenomePersisterTest
class	PersisterTest

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.retry

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.retry

Modifier and Type	Class	Description
class	RetryTest

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service

Modifier and Type	Class	Description
class	FilteringVoEnabledServiceIntegrationTest	Test all possible filterable properties for filtering and sorting results.

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service.analysis.expression.diff

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service.analysis.expression.diff

Modifier and Type	Class	Description
class	DifferentialExpressionAnalysisServiceTest
class	DifferentialExpressionResultServiceTest
class	ExpressionAnalysisResultSetServiceTest	This implementation is using the Hibernate Criteria API, so we want to minimally test the logic of translating Filters and Sort into proper org.hibernate.Criteria queries.
class	GeneDiffExMetaAnalysisServiceTest

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service.blacklist

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service.blacklist

Modifier and Type	Class	Description
class	BlacklistedEntityServiceTest
class	BlacklistTest

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service.common.auditAndSecurity

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service.common.auditAndSecurity

Modifier and Type	Class	Description
class	AuditEventServiceTest
class	AuditTrailDaoTest
class	AuditTrailServiceImplTest

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Modifier and Type	Class	Description
class	AnnotationSetDispositionPersistenceIT	Persistence contract for AnnotationSetDisposition — the row-per-ruling, latest-wins model for a curator's verdict on ONE finding.
class	AnnotationSetPersistenceIT	Integration test for the V20/V21 ANNOTATION_SET schema migration and the unified AnnotationSet entity + service.
class	AnnotationSetTriagePersistenceIT	Persistence contract for AnnotationSetTriage — the row-per-judge triage model.
class	CuratableValueObjectTest
class	CurationDecisionPersistenceIT	Persistence contract for CurationDecision -- the record of a change a curator ruled must NOT be made.
class	CurationLockPersistenceIT	Contract for the advisory curation lock.
class	TicketPersistenceIT	Integration test for the V19 migration (TICKET.MODE + TICKET_TARGET.STATUS) and the corresponding Ticket/TicketTarget entity mappings.

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service.common.description

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service.common.description

Modifier and Type	Class	Description
class	BibliographicReferenceServiceImplTest
class	BibliographicReferenceServiceTest	This class tests the bibliographic reference data access object.
class	CharacteristicDaoMySqlIntegrationTest	Real-MySQL counterpart of the H2-backed CharacteristicDaoTest, pinning the native-query methods of CharacteristicDaoImpl against the production Spring context (real MySQL gemdtest via BaseIntegrationTest5).
class	CharacteristicServiceTest
class	DatabaseEntryDaoImplTest
class	ExternalDatabaseServiceTest
class	PublicationAssociationPersistenceIT	Integration test for the PUBLICATION_ASSOCIATION schema migration (MySQL V25 / H2 V26) and the PublicationAssociation entity + service, against the real MySQL gemdtest.

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service.expression.arrayDesign

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service.expression.arrayDesign

Modifier and Type	Class	Description
class	ArrayDesignServiceTest

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service.expression.bioAssay

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service.expression.bioAssay

Modifier and Type	Class	Description
class	BioAssayServiceTest

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service.expression.bioAssayData

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service.expression.bioAssayData

Modifier and Type	Class	Description
class	ProcessedExpressionDataVectorCreationHelperServiceTest
class	ProcessedExpressionDataVectorServiceTest
class	RawAndProcessedExpressionDataVectorServiceGeoTest

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service.expression.biomaterial

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service.expression.biomaterial

Modifier and Type	Class	Description
class	BioMaterialServiceTest

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service.expression.designElement

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service.expression.designElement

Modifier and Type	Class	Description
class	CompositeSequenceServiceTest

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service.expression.experiment

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service.expression.experiment

Modifier and Type	Class	Description
class	ExpressionExperimentDeleteTest
class	ExpressionExperimentInCurationFilterIT	The inCuration filter behind the curation UI's "Experiments staged for curation" page.
class	ExpressionExperimentServiceIntegrationTest
class	ExpressionExperimentSetServiceTest	Tests for methods that perform operations on or with expressionExperiment sets
class	ExpressionExperimentSetValueObjectHelperTest	Tests for methods that create ExpressionExperimentSetValueObjects from expressionExperiment entities
class	ExpressionExperimentSubSetServiceTest
class	FactorValueServiceIntegrationTest
class	SingleCellIntegrationTest

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service.genome

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service.genome

Modifier and Type	Class	Description
class	BioSequencePersistTest
class	TaxonServiceImplTest
class	TaxonUtilsTest

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service.genome.gene

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service.genome.gene

Modifier and Type	Class	Description
class	GeneSearchTest
class	GeneServiceTest
class	GeneSetServiceTest
class	GeneWriteServiceTest	Quirk-pinning tests for GeneWriteService.

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service.genome.sequenceAnalysis

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service.genome.sequenceAnalysis

Modifier and Type	Class	Description
class	BlatAssociationServiceTest
class	BlatResultServiceTest

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.service.maintenance

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.service.maintenance

Modifier and Type	Class	Description
class	TableMaintenanceUtilIntegrationTest

Uses of BaseIntegrationTest5 in ubic.gemma.persistence.util

Subclasses of BaseIntegrationTest5 in ubic.gemma.persistence.util

Modifier and Type	Class	Description
class	AclQueryUtilsTest