Uses of Class
ubic.gemma.core.util.test.BaseTest5

Packages that use BaseTest5

Package	Description
ubic.gemma.apps
ubic.gemma.cli.metrics
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.config
ubic.gemma.core.context
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.geo.singleCell
ubic.gemma.core.loader.expression.simple
ubic.gemma.core.loader.expression.singleCell
ubic.gemma.core.loader.expression.singleCell.transform
ubic.gemma.core.loader.genome.gene
ubic.gemma.core.loader.genome.gene.ncbi
ubic.gemma.core.loader.genome.taxon
ubic.gemma.core.logging.log4j
ubic.gemma.core.mail
ubic.gemma.core.metrics
ubic.gemma.core.ontology
ubic.gemma.core.ontology.providers
ubic.gemma.core.ontology.providers.chebi
ubic.gemma.core.scheduler
ubic.gemma.core.search
ubic.gemma.core.security
ubic.gemma.core.security.audit
ubic.gemma.core.security.authentication
ubic.gemma.core.security.authorization
ubic.gemma.core.security.authorization.acl
ubic.gemma.core.security.concurrent
ubic.gemma.core.security.principal
ubic.gemma.core.util
ubic.gemma.core.util.test
ubic.gemma.core.util.test.fixture
ubic.gemma.core.visualization
ubic.gemma.core.visualization.cellbrowser
ubic.gemma.model.expression.bioAssayData
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
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.analysis.expression.pca
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.common.quantitationtype
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
ubic.gemma.rest
ubic.gemma.rest.serializers
ubic.gemma.rest.servlet
ubic.gemma.rest.util.args

Uses of BaseTest5 in ubic.gemma.apps

Subclasses of BaseTest5 in ubic.gemma.apps

Modifier and Type	Class	Description
class	AclLinterCliTest
class	ArrayDesignMergeCliTest
class	DifferentialExpressionAnalysisCliTest
class	ExpressionExperimentManipulatingCLITest
class	ExternalDatabaseUpdaterCliTest
class	FindObsoleteTermsCliTest
class	GeoSingleCellDataDownloaderCliTest
class	LoadSimpleExpressionDataCliTest
class	NCBIGene2GOAssociationLoaderCLITest
class	ProtocolAdderCliTest
class	ProtocolDeleterCliTest
class	PubMedSearcherIntegrationTest	Tests command line.
class	RNASeqDataAddCliTest
class	UpdateGeoSourceMetadataCliTest	The backfill writes the GEO document and nothing else, and it skips what is already done.
class	VerifyPublicationEvidenceCliTest	The two rules that must not regress: the command refuses to run without being told which half to run, and a curator's assertion is never written over.

Uses of BaseTest5 in ubic.gemma.cli.metrics

Subclasses of BaseTest5 in ubic.gemma.cli.metrics

Modifier and Type	Class	Description
class	MeterRegistryCliConfigurerTest

Uses of BaseTest5 in ubic.gemma.cli.util

Subclasses of BaseTest5 in ubic.gemma.cli.util

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

Uses of BaseTest5 in ubic.gemma.cli.util.test

Subclasses of BaseTest5 in ubic.gemma.cli.util.test

Modifier and Type	Class	Description
class	BaseCliIntegrationTest5	JUnit 5 (Jupiter) counterpart of BaseCliIntegrationTest.
class	BaseCliTest5	JUnit 5 (Jupiter) counterpart of BaseCliTest.

Uses of BaseTest5 in ubic.gemma.core.analysis.expression.diff

Subclasses of BaseTest5 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	EmptySubSetIsSkippedTest	An arm of the subset factor that no analyzed sample carries is skipped, not a fatal condition for the experiment.
class	IncompleteFactorBaselineTest	A factor dropped for missing values must not be left behind in the baseline map.
class	LowVarianceDataTest	Test based on GSE19480, see bug 3177
class	NoSubSetAnalysisIsNotSuccessTest	Producing no analysis at all is a failure of the experiment, not a quiet empty result.
class	SubsettedAnalysis2Test
class	SubsettedAnalysis3Test
class	SubsettedAnalysis4Test	This test covers subset analysis with pre-existing EE subset structure.
class	SubsettedAnalysisFactorConsistencyTest	A subset analysis has to describe itself with the factors it actually modelled.
class	TwoWayAnovaWithInteractionsTest2
class	TwoWayAnovaWithInteractionTest2	Test based on GSE8441

Uses of BaseTest5 in ubic.gemma.core.analysis.preprocess

Subclasses of BaseTest5 in ubic.gemma.core.analysis.preprocess

Modifier and Type	Class	Description
class	ExpressionDataSVDTest
class	MeanVarianceServiceTest
class	OutlierDetectionServiceTest	Tests for OutlierDetectionService
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 BaseTest5 in ubic.gemma.core.analysis.preprocess.batcheffects

Subclasses of BaseTest5 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 BaseTest5 in ubic.gemma.core.analysis.preprocess.svd

Subclasses of BaseTest5 in ubic.gemma.core.analysis.preprocess.svd

Modifier and Type	Class	Description
class	SVDServiceImplTest

Uses of BaseTest5 in ubic.gemma.core.analysis.report

Subclasses of BaseTest5 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 BaseTest5 in ubic.gemma.core.analysis.service

Subclasses of BaseTest5 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	ExpressionDataFileServiceTest
class	ExpressionMetadataChangelogFileServiceTest
class	GeneMultifunctionalityPopulationServiceTest

Uses of BaseTest5 in ubic.gemma.core.analysis.singleCell.aggregate

Subclasses of BaseTest5 in ubic.gemma.core.analysis.singleCell.aggregate

Modifier and Type	Class	Description
class	SingleCellExpressionExperimentAggregateServiceTest
class	SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceTest
class	SingleCellExpressionExperimentSubSetServiceTest

Uses of BaseTest5 in ubic.gemma.core.config

Subclasses of BaseTest5 in ubic.gemma.core.config

Modifier and Type	Class	Description
class	SettingsConfigTest

Uses of BaseTest5 in ubic.gemma.core.context

Subclasses of BaseTest5 in ubic.gemma.core.context

Modifier and Type	Class	Description
class	AsyncBeanAutowiringTest
class	AsyncFactoryTest
class	AsyncSingletonFactoryTest

Uses of BaseTest5 in ubic.gemma.core.datastructure.matrix.io

Subclasses of BaseTest5 in ubic.gemma.core.datastructure.matrix.io

Modifier and Type	Class	Description
class	ExperimentalDesignWriterTest

Uses of BaseTest5 in ubic.gemma.core.job

Subclasses of BaseTest5 in ubic.gemma.core.job

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

Uses of BaseTest5 in ubic.gemma.core.loader.association

Subclasses of BaseTest5 in ubic.gemma.core.loader.association

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

Uses of BaseTest5 in ubic.gemma.core.loader.expression

Subclasses of BaseTest5 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 BaseTest5 in ubic.gemma.core.loader.expression.arrayDesign

Subclasses of BaseTest5 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 BaseTest5 in ubic.gemma.core.loader.expression.cellxgene

Subclasses of BaseTest5 in ubic.gemma.core.loader.expression.cellxgene

Modifier and Type	Class	Description
class	CellXGeneConverterTest
class	CellXGeneDataLoaderServiceTest
class	CellXGeneFetcherTest

Uses of BaseTest5 in ubic.gemma.core.loader.expression.geo

Subclasses of BaseTest5 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
class	GeoSingleCellDetectorTest	TODO: Phase 2 — trim and cache per-test download data so the integration-tagged methods can move to fully offline @Test.

Uses of BaseTest5 in ubic.gemma.core.loader.expression.geo.service

Subclasses of BaseTest5 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 BaseTest5 in ubic.gemma.core.loader.expression.geo.singleCell

Subclasses of BaseTest5 in ubic.gemma.core.loader.expression.geo.singleCell

Modifier and Type	Class	Description
class	GeoMexSingleCellDataLoaderConfigurerTest

Uses of BaseTest5 in ubic.gemma.core.loader.expression.simple

Subclasses of BaseTest5 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 BaseTest5 in ubic.gemma.core.loader.expression.singleCell

Subclasses of BaseTest5 in ubic.gemma.core.loader.expression.singleCell

Modifier and Type	Class	Description
class	AnnDataSingleCellDataLoaderIntegrationTest
class	AnnDataSingleCellDataLoaderTest
class	MexSingleCellDataLoaderPersistenceTest	Load and persist single-cell data stored in the MEX format.
class	MexSingleCellDataLoaderTest
class	SingleCellDataLoaderServiceIntegrationTest	Complete integration tests for loading single-cell data.
class	SingleCellDataTransformationsTest

Uses of BaseTest5 in ubic.gemma.core.loader.expression.singleCell.transform

Subclasses of BaseTest5 in ubic.gemma.core.loader.expression.singleCell.transform

Modifier and Type	Class	Description
class	SingleCell10xMexFilterTest

Uses of BaseTest5 in ubic.gemma.core.loader.genome.gene

Subclasses of BaseTest5 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 BaseTest5 in ubic.gemma.core.loader.genome.gene.ncbi

Subclasses of BaseTest5 in ubic.gemma.core.loader.genome.gene.ncbi

Modifier and Type	Class	Description
class	NCBIGeneLoadingTest

Uses of BaseTest5 in ubic.gemma.core.loader.genome.taxon

Subclasses of BaseTest5 in ubic.gemma.core.loader.genome.taxon

Modifier and Type	Class	Description
class	TaxonLoaderTest

Uses of BaseTest5 in ubic.gemma.core.logging.log4j

Subclasses of BaseTest5 in ubic.gemma.core.logging.log4j

Modifier and Type	Class	Description
class	BuildInfoThreadContextPopulatorTest
class	TaskExecutorThreadContextInheritPostProcessorTest

Uses of BaseTest5 in ubic.gemma.core.mail

Subclasses of BaseTest5 in ubic.gemma.core.mail

Modifier and Type	Class	Description
class	MailEngineImplTest

Uses of BaseTest5 in ubic.gemma.core.metrics

Subclasses of BaseTest5 in ubic.gemma.core.metrics

Modifier and Type	Class	Description
class	GenericMeterRegistryConfigurerTest

Uses of BaseTest5 in ubic.gemma.core.ontology

Subclasses of BaseTest5 in ubic.gemma.core.ontology

Modifier and Type	Class	Description
class	FactorValueOntologyServiceTest
class	GemmaAndExperimentalFactorOntologyTest	This test covers cases where inference is done across two distinct OntologyService.
class	OntologyServiceTest

Uses of BaseTest5 in ubic.gemma.core.ontology.providers

Subclasses of BaseTest5 in ubic.gemma.core.ontology.providers

Modifier and Type	Class	Description
class	GeneOntologyService2Test	Additional tests with updated ontology file, fixing problems getting aspects.
class	GeneOntologyServiceTest

Uses of BaseTest5 in ubic.gemma.core.ontology.providers.chebi

Subclasses of BaseTest5 in ubic.gemma.core.ontology.providers.chebi

Modifier and Type	Class	Description
class	ChebiSeedResolverSlotsTest	The CHEBI slim is only as good as its seed set, and the seed set used to be built from Characteristic.valueUri alone.

Uses of BaseTest5 in ubic.gemma.core.scheduler

Subclasses of BaseTest5 in ubic.gemma.core.scheduler

Modifier and Type	Class	Description
class	BatchInfoRepopulationJobTest

Uses of BaseTest5 in ubic.gemma.core.search

Subclasses of BaseTest5 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 BaseTest5 in ubic.gemma.core.security

Subclasses of BaseTest5 in ubic.gemma.core.security

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

Uses of BaseTest5 in ubic.gemma.core.security.audit

Subclasses of BaseTest5 in ubic.gemma.core.security.audit

Modifier and Type	Class	Description
class	AuditedAspectTest	Unit-level test for AuditedAspect: the aspect intercepts the Audited annotation, locates the first Auditable argument and optional AuditEventPayload argument, serialises the payload to JSON, delegates to AuditTrailService.addUpdateEventWithPayload(Auditable, Class, String, String), and publishes a Spring AuditedEvent.

Uses of BaseTest5 in ubic.gemma.core.security.authentication

Subclasses of BaseTest5 in ubic.gemma.core.security.authentication

Modifier and Type	Class	Description
class	ManualAuthenticationProcessingTest
class	UserManagerTest
class	UserServiceImplTest

Uses of BaseTest5 in ubic.gemma.core.security.authorization

Subclasses of BaseTest5 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 BaseTest5 in ubic.gemma.core.security.authorization.acl

Subclasses of BaseTest5 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
class	AclClassMetadataTest
class	AclLinterParentInheritanceTest	Coverage for the entries_inheriting half of AclLinterServiceImpl.setParentAcl.
class	AclLinterServiceTest
class	ParentIdentityRetrievalStrategyTest	Phase 3 gsec HQL deprecation: regression coverage for ParentIdentityRetrievalStrategyImpl after its HQL select against AclObjectIdentity was replaced with raw SQL against acl_object_identity JOIN acl_class.

Uses of BaseTest5 in ubic.gemma.core.security.concurrent

Subclasses of BaseTest5 in ubic.gemma.core.security.concurrent

Modifier and Type	Class	Description
class	DelegatingSecurityContextTaskExecutorTest

Uses of BaseTest5 in ubic.gemma.core.security.principal

Subclasses of BaseTest5 in ubic.gemma.core.security.principal

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

Uses of BaseTest5 in ubic.gemma.core.util

Subclasses of BaseTest5 in ubic.gemma.core.util

Modifier and Type	Class	Description
class	BuildInfoTest
class	MailServiceTest
class	MissingBuildInfoTest
class	StrictBeanDefinitionValidatorTest

Uses of BaseTest5 in ubic.gemma.core.util.test

Subclasses of BaseTest5 in ubic.gemma.core.util.test

Modifier and Type	Class	Description
class	BaseDatabaseTest5	JUnit 5 (Jupiter) counterpart of BaseDatabaseTest.
class	BaseIntegrationTest5	JUnit 5 (Jupiter) base class for integration tests, tagged @Tag("integration") for surefire/failsafe filtering.
class	BaseSpringContextTest5	Deprecated. favour the simpler BaseIntegrationTest5 for new tests

Uses of BaseTest5 in ubic.gemma.core.util.test.fixture

Subclasses of BaseTest5 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 BaseTest5 in ubic.gemma.core.visualization

Subclasses of BaseTest5 in ubic.gemma.core.visualization

Modifier and Type	Class	Description
class	ExperimentalDesignVisualizationServiceTest

Uses of BaseTest5 in ubic.gemma.core.visualization.cellbrowser

Subclasses of BaseTest5 in ubic.gemma.core.visualization.cellbrowser

Modifier and Type	Class	Description
class	CellBrowserServiceImplTest

Uses of BaseTest5 in ubic.gemma.model.expression.bioAssayData

Subclasses of BaseTest5 in ubic.gemma.model.expression.bioAssayData

Modifier and Type	Class	Description
class	RawExpressionDataVectorTest

Uses of BaseTest5 in ubic.gemma.model.genome

Subclasses of BaseTest5 in ubic.gemma.model.genome

Modifier and Type	Class	Description
class	GeneSetValueObjectHelperTest

Uses of BaseTest5 in ubic.gemma.persistence.hibernate

Subclasses of BaseTest5 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 BaseTest5 in ubic.gemma.persistence.persister

Subclasses of BaseTest5 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 BaseTest5 in ubic.gemma.persistence.retry

Subclasses of BaseTest5 in ubic.gemma.persistence.retry

Modifier and Type	Class	Description
class	RetryTest

Uses of BaseTest5 in ubic.gemma.persistence.service

Subclasses of BaseTest5 in ubic.gemma.persistence.service

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

Uses of BaseTest5 in ubic.gemma.persistence.service.analysis.expression

Subclasses of BaseTest5 in ubic.gemma.persistence.service.analysis.expression

Modifier and Type	Class	Description
class	ExpressionExperimentSetDaoTest

Uses of BaseTest5 in ubic.gemma.persistence.service.analysis.expression.diff

Subclasses of BaseTest5 in ubic.gemma.persistence.service.analysis.expression.diff

Modifier and Type	Class	Description
class	AnalysisResultSetCacheStalenessTest	Regression guard for the Hibernate-6 cache-staleness shape flagged as HB6 cascade audit finding #6 (HIBERNATE6_CASCADE_AUDIT.md): the AnalysisResultSet + DifferentialExpressionAnalysisResult HBM mapping has the same mutable="false" parent + child collection + <cache usage="read-only"/> shape that caused the AuditTrail / AuditEvent stale-empty-bag bug (fixed in ab8b4c443c).
class	DifferentialExpressionAnalysisDaoTest
class	DifferentialExpressionAnalysisServiceTest
class	DifferentialExpressionResultDaoTest
class	DifferentialExpressionResultServiceTest
class	ExpressionAnalysisResultSetDaoTest
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 BaseTest5 in ubic.gemma.persistence.service.analysis.expression.pca

Subclasses of BaseTest5 in ubic.gemma.persistence.service.analysis.expression.pca

Modifier and Type	Class	Description
class	PrincipalComponentAnalysisDaoImplTest

Uses of BaseTest5 in ubic.gemma.persistence.service.blacklist

Subclasses of BaseTest5 in ubic.gemma.persistence.service.blacklist

Modifier and Type	Class	Description
class	BlacklistedEntityDaoImplTest
class	BlacklistedEntityServiceTest
class	BlacklistTest

Uses of BaseTest5 in ubic.gemma.persistence.service.common.auditAndSecurity

Subclasses of BaseTest5 in ubic.gemma.persistence.service.common.auditAndSecurity

Modifier and Type	Class	Description
class	AuditEventDaoTest
class	AuditEventServiceTest
class	AuditTrailDaoTest
class	AuditTrailServiceImplTest
class	CuratableDaoTest
class	UserDaoTest

Uses of BaseTest5 in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Subclasses of BaseTest5 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 BaseTest5 in ubic.gemma.persistence.service.common.description

Subclasses of BaseTest5 in ubic.gemma.persistence.service.common.description

Modifier and Type	Class	Description
class	AnnotationRelationDaoTest	Reads over ANNOTATION_RELATION.
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	CharacteristicDaoTest
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 BaseTest5 in ubic.gemma.persistence.service.common.quantitationtype

Subclasses of BaseTest5 in ubic.gemma.persistence.service.common.quantitationtype

Modifier and Type	Class	Description
class	QuantitationTypeDaoTest

Uses of BaseTest5 in ubic.gemma.persistence.service.expression.arrayDesign

Subclasses of BaseTest5 in ubic.gemma.persistence.service.expression.arrayDesign

Modifier and Type	Class	Description
class	ArrayDesignDaoTest
class	ArrayDesignServiceTest

Uses of BaseTest5 in ubic.gemma.persistence.service.expression.bioAssay

Subclasses of BaseTest5 in ubic.gemma.persistence.service.expression.bioAssay

Modifier and Type	Class	Description
class	BioAssayServiceTest

Uses of BaseTest5 in ubic.gemma.persistence.service.expression.bioAssayData

Subclasses of BaseTest5 in ubic.gemma.persistence.service.expression.bioAssayData

Modifier and Type	Class	Description
class	BioAssayDimensionCacheStalenessTest	HB6 cascade audit #10 regression guard: BioAssayDimension HBM (Pattern C — mutable="false" class + child list + cache directive).
class	CachedProcessedExpressionDataVectorServiceTest
class	ProcessedExpressionDataVectorCreationHelperServiceTest
class	ProcessedExpressionDataVectorDaoTest
class	ProcessedExpressionDataVectorServiceTest
class	RawAndProcessedExpressionDataVectorDaoTest
class	RawAndProcessedExpressionDataVectorServiceGeoTest
class	RawAndProcessedExpressionDataVectorServiceTest
class	RawExpressionDataVectorDaoTest
class	SingleCellDimensionCacheStalenessTest	HB6 cascade audit #9 regression guard: SingleCellDimension family (Pattern C — mutable="false" class + child collection + cache directive).

Uses of BaseTest5 in ubic.gemma.persistence.service.expression.biomaterial

Subclasses of BaseTest5 in ubic.gemma.persistence.service.expression.biomaterial

Modifier and Type	Class	Description
class	BioMaterialDaoTest
class	BioMaterialServiceTest

Uses of BaseTest5 in ubic.gemma.persistence.service.expression.designElement

Subclasses of BaseTest5 in ubic.gemma.persistence.service.expression.designElement

Modifier and Type	Class	Description
class	CompositeSequenceDaoTest
class	CompositeSequenceServiceTest

Uses of BaseTest5 in ubic.gemma.persistence.service.expression.experiment

Subclasses of BaseTest5 in ubic.gemma.persistence.service.expression.experiment

Modifier and Type	Class	Description
class	ExperimentalFactorServiceTest
class	ExpressionExperimentBatchInformationServiceTest
class	ExpressionExperimentDaoCursorTest	Integration tests for the keyset (cursor) pagination DAO mechanism on ExpressionExperimentDao.
class	ExpressionExperimentDaoTest
class	ExpressionExperimentDeleteTest
class	ExpressionExperimentInCurationFilterIT	The inCuration filter behind the curation UI's "Experiments staged for curation" page.
class	ExpressionExperimentServiceDetachedEntityTest	ExpressionExperimentService.isSingleCell(ExpressionExperiment) must not require its argument to be attached to a session.
class	ExpressionExperimentServiceImplTest
class	ExpressionExperimentServiceIntegrationTest
class	ExpressionExperimentServiceTest
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	ExpressionExperimentSubSetDaoTest
class	ExpressionExperimentSubSetServiceTest
class	FactorValueDaoTest
class	FactorValueNeedsAttentionServiceTest	Tests the Ticket-layer migration of FactorValueNeedsAttentionService (see CURATION_DETAILS_RETIREMENT.md).
class	FactorValueServiceIntegrationTest
class	FactorValueServiceTest
class	PreboardedExperimentMappingTest	Regression guard for the PreboardedExperiment discriminator mapping added in commit 44bf890061.
class	ReplaceAllRawDataVectorsQtCollisionTest	Fast H2-backed regression guard for the QT entity-identity collision that DataUpdater.addCountData re-run path tripped (commit ef838e08fc).
class	SingleCellExpressionExperimentServiceTest	Tests covering integration of single-cell.
class	SingleCellIntegrationTest
class	SingleCellStreamingAddTest	Tests for the streaming overload of SingleCellExpressionExperimentService.addSingleCellDataVectors(ExpressionExperiment, QuantitationType, SingleCellDimension, Stream, String, boolean, boolean).
class	StatementTagPersistenceTest	A statement-shaped experiment tag must survive the round trip as a Statement.

Uses of BaseTest5 in ubic.gemma.persistence.service.genome

Subclasses of BaseTest5 in ubic.gemma.persistence.service.genome

Modifier and Type	Class	Description
class	BioSequencePersistTest
class	GeneDaoTest
class	TaxonServiceImplTest
class	TaxonUtilsTest

Uses of BaseTest5 in ubic.gemma.persistence.service.genome.gene

Subclasses of BaseTest5 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 BaseTest5 in ubic.gemma.persistence.service.genome.sequenceAnalysis

Subclasses of BaseTest5 in ubic.gemma.persistence.service.genome.sequenceAnalysis

Modifier and Type	Class	Description
class	BlatAssociationServiceTest
class	BlatResultServiceTest

Uses of BaseTest5 in ubic.gemma.persistence.service.maintenance

Subclasses of BaseTest5 in ubic.gemma.persistence.service.maintenance

Modifier and Type	Class	Description
class	AnnotationRelationHarvestTest	The CURATED harvest: EE2C rows that already carry a predicate and an object become queryable relations.
class	TableMaintenanceUtilIntegrationTest
class	TableMaintenanceUtilTest

Uses of BaseTest5 in ubic.gemma.persistence.util

Subclasses of BaseTest5 in ubic.gemma.persistence.util

Modifier and Type	Class	Description
class	AclQueryUtilsTest
class	AclSemanticsContractTest	Contract harness for the planned rewrite of AclQueryUtils.formAclRestrictionClause(String) (and its sibling formNativeAclRestrictionClause) from the current row-multiplying JOIN strategy to a correlated EXISTS subquery.
class	DateStorageTest
class	HibernateSqmFragileShapesIT	HB6 SQM-translator regression guard.
class	HqlSmokeIT	Mass parse-only smoke test for every statically-extractable HQL string in gemma-core/src/main/java.
class	PointcutsTest
class	ServiceBasedValueObjectConverterTest

Uses of BaseTest5 in ubic.gemma.rest

Subclasses of BaseTest5 in ubic.gemma.rest

Modifier and Type	Class	Description
class	OpenApiTest

Uses of BaseTest5 in ubic.gemma.rest.serializers

Subclasses of BaseTest5 in ubic.gemma.rest.serializers

Modifier and Type	Class	Description
class	FactorValueValueObjectSerializerTest

Uses of BaseTest5 in ubic.gemma.rest.servlet

Subclasses of BaseTest5 in ubic.gemma.rest.servlet

Modifier and Type	Class	Description
class	CorsFilterTest

Uses of BaseTest5 in ubic.gemma.rest.util.args

Subclasses of BaseTest5 in ubic.gemma.rest.util.args

Modifier and Type	Class	Description
class	GeneArgServiceTest
class	TaxonArgServiceTest