Index

A B C D E F G H I J K L M N O P Q R S T U V W Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

a_low_prior_hit_can_still_be_overtaken_on_lucene_rank() - Method in class ubic.gemma.rest.ranking.CommonalityRankingStrategyTest

aBareSampleAnnotationIsListedWithNoPredicate() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObjectStatementTest

And a bare one is listed too, with nothing said about it — one collection, not two kinds of annotation.

aBaselineFactorValueSaysSoOnTheWire() - Method in class ubic.gemma.rest.serializers.FactorValueValueObjectSerializerTest

The baseline designation reaches the wire.

aBinCountBelowOneIsRejectedBeforeAnythingIsLoaded() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServicePvalueDistributionTest

aBlankedColumnStillVotesOnTheReferenceUnlessExcluded() - Method in class ubic.gemma.core.util.math.QuantileReferenceColumnsTest

🛑 The trap this whole change exists for: blanking a column does NOT keep it out of the reference.

aBlankedSampleIsPredictedButDoesNotInfluenceTheFit() - Method in class ubic.gemma.core.util.math.linearmodels.FittedValuesForExcludedSamplesTest

Four samples, two groups, and the fourth blanked.

aboveGigabytePastThreshold_stillRendersAsGigabytes() - Method in class ubic.gemma.core.util.NetUtilsTest

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

AbstractCuratableDaoTest - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation

The rule that decides whether a caller sees troubled entities.

AbstractCuratableDaoTest() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDaoTest

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

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

AbstractFilteringVoEnabledDaoTest - Class in ubic.gemma.persistence.service

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

AbstractFilteringVoEnabledDaoTest.FakeEnum - Enum Class in ubic.gemma.persistence.service

AbstractGeoServiceTest5 - Class in ubic.gemma.core.loader.expression.geo

JUnit 5 parallel of AbstractGeoServiceTest, extending the Jupiter BaseSpringContextTest5 base.

AbstractGeoServiceTest5() - Constructor for class ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest5

AbstractMexSingleCellDataLoaderConfigurerTest - Class in ubic.gemma.core.loader.expression.singleCell

Unit tests for MEX directory resolution in AbstractMexSingleCellDataLoaderConfigurer, in particular the fallback that locates the triplet under a raw 10x Cell Ranger outs/filtered_feature_bc_matrix nesting.

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

AbstractServiceTest - Class in ubic.gemma.persistence.service

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

AbstractServiceTest.ExceptionWithMessage - Exception Class in ubic.gemma.persistence.service

AbstractServiceTest.ExceptionWithoutMessage - Exception Class in ubic.gemma.persistence.service

aCancelledTicketReleasesItsDataset() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentInCurationFilterIT

The half that is easy to get wrong: a ticket that was opened and then cancelled must not keep its dataset on the page forever.

acceptedAndDismissed_reasonStaysOptional() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

acceptedAndRejectedTogetherIsRejected() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationPersistenceIT

acceptedAssertionRoundTrips() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationPersistenceIT

acceptsTheSpellingsOtherProducersEmit() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TriageVerdictTest

accessDecisionManager() - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

accessDecisionManager() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

accessDecisionManager() - Method in class ubic.gemma.rest.TasksWebServiceTest.TasksWebServiceContextConfiguration

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

aclClassIdInitializer(SessionFactory) - Method in class ubic.gemma.core.util.test.BaseDatabaseTest5.BaseDatabaseTestContextConfiguration

Stash the SessionFactory onto AclQueryUtils.sessionFactory so ACL-filtered HQL/SQL queries can resolve acl_class.id during predicate rendering.

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

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

aclDao(SessionFactory, SidRetrievalStrategy) - Method in class ubic.gemma.core.util.test.BaseDatabaseAclConfig

aclDao(SessionFactory, SidRetrievalStrategy) - Method in class ubic.gemma.core.util.test.BaseDatabaseTest5.BaseDatabaseTestContextConfiguration

AclDaoImplParentPersistenceTest - Class in ubic.gemma.core.security.acl.domain

Renovations Phase 2 contract test for AclDaoImpl.update(MutableAcl): verifies that the parent_object_fk column is persisted to the database when an ACL's in-memory parent is wired up via MutableAcl.setParent(...).

AclDaoImplParentPersistenceTest() - Constructor for class ubic.gemma.core.security.acl.domain.AclDaoImplParentPersistenceTest

AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest - Class in ubic.gemma.core.security.acl.afterinvocation

Fast unit tests for AclEntryAfterInvocationByAssociationCollectionFilteringProvider.

AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest() - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest

AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest.Child - Class in ubic.gemma.core.security.acl.afterinvocation

AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest.ChildCollectionToParentByAssociation - Class in ubic.gemma.core.security.acl.afterinvocation

Test-only subclass: maps each Child → its Parent for the ACL check.

AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest.Parent - Class in ubic.gemma.core.security.acl.afterinvocation

AclEntryAfterInvocationByAssociationFilteringProviderTest - Class in ubic.gemma.core.security.acl.afterinvocation

Fast unit tests for AclEntryAfterInvocationByAssociationFilteringProvider: the base delegates the ACL check to a parent/associated Securable returned by getActualDomainObject.

AclEntryAfterInvocationByAssociationFilteringProviderTest() - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProviderTest

AclEntryAfterInvocationByAssociationFilteringProviderTest.Child - Class in ubic.gemma.core.security.acl.afterinvocation

AclEntryAfterInvocationByAssociationFilteringProviderTest.ChildToParentByAssociation - Class in ubic.gemma.core.security.acl.afterinvocation

Test-only concrete subclass that returns Child.parent as the associated Securable.

AclEntryAfterInvocationByAssociationFilteringProviderTest.Parent - Class in ubic.gemma.core.security.acl.afterinvocation

AclEntryAfterInvocationCollectionFilteringProviderTest - Class in ubic.gemma.core.security.acl.afterinvocation

AclEntryAfterInvocationCollectionFilteringProviderTest() - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProviderTest

AclEntryAfterInvocationCollectionFilteringProviderTest.MyModel - Class in ubic.gemma.core.security.acl.afterinvocation

AclEntryAfterInvocationMapFilteringProviderTest - Class in ubic.gemma.core.security.acl.afterinvocation

Fast unit tests for AclEntryAfterInvocationMapFilteringProvider, which filters a Map's key set in place (keys are Securable; values may or may not be Securable — value security isn't checked by this provider, only key security).

AclEntryAfterInvocationMapFilteringProviderTest() - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapFilteringProviderTest

AclEntryAfterInvocationMapFilteringProviderTest.Item - Class in ubic.gemma.core.security.acl.afterinvocation

AclEntryAfterInvocationMapValueFilteringProviderTest - Class in ubic.gemma.core.security.acl.afterinvocation

Fast unit tests for AclEntryAfterInvocationMapValueFilteringProvider: filters a Map's value set (values are Securable; keys are not).

AclEntryAfterInvocationMapValueFilteringProviderTest() - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapValueFilteringProviderTest

AclEntryAfterInvocationMapValueFilteringProviderTest.Item - Class in ubic.gemma.core.security.acl.afterinvocation

AclEntryAfterInvocationOwnedCollectionFilteringProviderTest - Class in ubic.gemma.core.security.acl.afterinvocation

Fast unit tests for AclEntryAfterInvocationOwnedCollectionFilteringProvider.

AclEntryAfterInvocationOwnedCollectionFilteringProviderTest() - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationOwnedCollectionFilteringProviderTest

AclEntryAfterInvocationOwnedCollectionFilteringProviderTest.Item - Class in ubic.gemma.core.security.acl.afterinvocation

AclEntryAfterInvocationPrivateCollectionFilteringProviderTest - Class in ubic.gemma.core.security.acl.afterinvocation

Fast unit tests for AclEntryAfterInvocationPrivateCollectionFilteringProvider.

AclEntryAfterInvocationPrivateCollectionFilteringProviderTest() - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationPrivateCollectionFilteringProviderTest

AclEntryAfterInvocationPrivateCollectionFilteringProviderTest.Item - Class in ubic.gemma.core.security.acl.afterinvocation

AclEntryAfterInvocationProviderTest - Class in ubic.gemma.core.security.acl.afterinvocation

AclEntryAfterInvocationProviderTest() - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationProviderTest

AclEntryAfterInvocationStreamFilteringProviderTest - Class in ubic.gemma.core.security.acl.afterinvocation

Fast unit tests for AclEntryAfterInvocationStreamFilteringProvider, demonstrating the InMemoryAclService fixture in an after-invocation-provider context.

AclEntryAfterInvocationStreamFilteringProviderTest() - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationStreamFilteringProviderTest

AclEntryAfterInvocationStreamFilteringProviderTest.Item - Class in ubic.gemma.core.security.acl.afterinvocation

AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest - Class in ubic.gemma.core.security.acl.afterinvocation

Fast unit tests for AclEntryAfterInvocationValueObjectCollectionFilteringProvider.

AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest() - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest

AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest.ItemVO - Class in ubic.gemma.core.security.acl.afterinvocation

AclEntryAfterInvocationValueObjectMapFilteringProviderTest - Class in ubic.gemma.core.security.acl.afterinvocation

Fast unit tests for AclEntryAfterInvocationValueObjectMapFilteringProvider: Map whose KEYS are SecureValueObjects (values are arbitrary).

AclEntryAfterInvocationValueObjectMapFilteringProviderTest() - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest

AclEntryAfterInvocationValueObjectMapFilteringProviderTest.ItemVO - Class in ubic.gemma.core.security.acl.afterinvocation

AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest - Class in ubic.gemma.core.security.acl.afterinvocation

Fast unit tests for AclEntryAfterInvocationValueObjectMapValueFilteringProvider: Map whose VALUES are SecureValueObjects (keys are arbitrary).

AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest() - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest

AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest.ItemVO - Class in ubic.gemma.core.security.acl.afterinvocation

AclEntryAfterInvocationValueObjectProviderTest - Class in ubic.gemma.core.security.acl.afterinvocation

Fast unit tests for AclEntryAfterInvocationValueObjectProvider: single value-object security check that returns null (instead of throwing) when access is denied AND populates security-status fields on the VO when granted.

AclEntryAfterInvocationValueObjectProviderTest() - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest

AclEntryAfterInvocationValueObjectProviderTest.ItemVO - Class in ubic.gemma.core.security.acl.afterinvocation

Minimal SecureValueObject with mutable security flags so we can assert population.

AclEntryCollectionVoterTest - Class in ubic.gemma.core.security.acl.voter

AclEntryCollectionVoterTest() - Constructor for class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest

AclEntryCollectionVoterTest.Model - Class in ubic.gemma.core.security.acl.voter

AclEntryCollectionVoterTest.MyService - Class in ubic.gemma.core.security.acl.voter

AclEntryMapValueVoterTest - Class in ubic.gemma.core.security.acl.voter

AclEntryMapValueVoterTest() - Constructor for class ubic.gemma.core.security.acl.voter.AclEntryMapValueVoterTest

AclEntryMapVoterTest - Class in ubic.gemma.core.security.acl.voter

AclEntryMapVoterTest() - Constructor for class ubic.gemma.core.security.acl.voter.AclEntryMapVoterTest

AclEntryVoterTest - Class in ubic.gemma.core.security.acl.voter

AclEntryVoterTest() - Constructor for class ubic.gemma.core.security.acl.voter.AclEntryVoterTest

AclEntryVoterTest.Model - Class in ubic.gemma.core.security.acl.voter

AclEventListenerTest - Class in ubic.gemma.core.security.acl

Fast unit tests for AclEventListener.

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

AclEventListenerTest.ChildNoOwner - Class in ubic.gemma.core.security.acl

SecuredChild without a populated getSecurityOwner — the realistic case for BioAssay / FactorValue persisted via ExpressionPersister.

AclEventListenerTest.ChildWithBackRef - Class in ubic.gemma.core.security.acl

SecuredChild with an explicit ManyToOne back-ref to a AclEventListenerTest.ChildNoOwner — exercises the force-flatten reconciliation when the back-ref ACL gets its own parent set late.

AclEventListenerTest.ChildWithOwner - Class in ubic.gemma.core.security.acl

SecuredChild that exposes a populated AclEventListenerTest.ChildWithOwner.getSecurityOwner() — covers the locateParentAcl path (used when entity-author wired the back-ref explicitly).

AclEventListenerTest.NotChildRoot - Class in ubic.gemma.core.security.acl

SecuredNotChild — its own ACL root.

AclEventListenerTest.OneNotChildParent - Class in ubic.gemma.core.security.acl

SecuredChild with only a SecuredNotChild back-ref.

AclEventListenerTest.PersisterBuilder - Class in ubic.gemma.core.security.acl

Fluent builder for a per-entity-class EntityPersister mock.

AclEventListenerTest.Root - Class in ubic.gemma.core.security.acl

Plain top-level Securable.

AclEventListenerTest.SelfRefChild - Class in ubic.gemma.core.security.acl

SecuredChild that references another instance of its own class — covers the cycle guard in the recursive fixup walk.

AclEventListenerTest.StubPersisterRegistry - Class in ubic.gemma.core.security.acl

Mockito-backed substitute for SessionFactoryImplementor → MappingMetamodel → EntityPersister.

AclEventListenerTest.TestAclAdvice - Class in ubic.gemma.core.security.acl

Minimal BaseAclAdvice concrete subclass.

AclEventListenerTest.TwoParentChild - Class in ubic.gemma.core.security.acl

SecuredChild with two ManyToOne back-refs: one to a SecuredNotChild root and one to another SecuredChild.

aclLinterCli() - Method in class ubic.gemma.apps.AclLinterCliTest.AclLinterCliTestContextConfiguration

AclLinterCliTest - Class in ubic.gemma.apps

AclLinterCliTest() - Constructor for class ubic.gemma.apps.AclLinterCliTest

AclLinterCliTest.AclLinterCliTestContextConfiguration - Class in ubic.gemma.apps

AclLinterCliTestContextConfiguration() - Constructor for class ubic.gemma.apps.AclLinterCliTest.AclLinterCliTestContextConfiguration

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

Coverage for the entries_inheriting half of AclLinterServiceImpl.setParentAcl.

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

aclLinterService() - Method in class ubic.gemma.apps.AclLinterCliTest.AclLinterCliTestContextConfiguration

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

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

aclListenerRegistersDespiteLazyByDefault() - Method in class ubic.gemma.core.security.acl.EventListenerRegistrationLazyContextTest

AclObjectIdentityTest - Class in ubic.gemma.core.security.acl.domain

Unit tests for AclObjectIdentity, with particular focus on equals/hashCode behaviour during Hibernate-driven instantiation where fields are populated incrementally by setters.

AclObjectIdentityTest() - Constructor for class ubic.gemma.core.security.acl.domain.AclObjectIdentityTest

AclQueryUtilsTest - Class in ubic.gemma.persistence.util

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

AclSemanticsContractTest - Class in ubic.gemma.persistence.util

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.

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

aclService(AclDao) - Method in class ubic.gemma.core.util.test.BaseDatabaseAclConfig

aclService(AclDao) - Method in class ubic.gemma.core.util.test.BaseDatabaseTest5.BaseDatabaseTestContextConfiguration

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

Methods for checking ACLs.

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

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

Thin unit test for AclVoterAuthorizationManager.

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

aclWithNoMatchingAceIsTreatedAsDeny() - Method in class ubic.gemma.core.search.source.HibernateSearchSourceAclFilterTest

An ACL that exists but carries no ACE matching the caller's sids: Spring's DefaultPermissionGrantingStrategy throws rather than returning false.

aCompoundStatementIsFlattenedIntoTwoStatementsRatherThanExposingTheSecondClauseFields() - Method in class ubic.gemma.rest.serializers.FactorValueValueObjectSerializerTest

A compound statement reaches the wire flattened: two entries in statements sharing one subject, the second clause carrying secondPredicate / secondObject under the generic predicate / object keys.

acquireWithADetachedInvestigation() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockPersistenceIT

The dataset the caller hands in is normally NOT in the session this service runs in — the REST layer resolves it first, and acquire opens its own.

ActingIdentityTest - Class in ubic.gemma.core.security.util

The scoping contract for the acting identity.

ActingIdentityTest() - Constructor for class ubic.gemma.core.security.util.ActingIdentityTest

activeGauge_tracksInFlightTasks() - Method in class ubic.gemma.core.metrics.binder.VirtualThreadExecutorMetricsTest

aCuratorDoesNotSatisfyAnAdminOnlyAce() - Method in class ubic.gemma.core.security.acl.AdminAclEvaluationTest

🛑 And it does NOT run the other way.

aCuratorHasNoAuthorityOverAUserGroup() - Method in class ubic.gemma.core.security.acl.AdminAclEvaluationTest

🛑 A curator has NO ace on a User or UserGroup, so they cannot reach BaseUserService.removeUserFromGroup — whose gate is hasPermission(#group, 'write') or hasPermission(#group, 'administration').

addBlacklistEntry_happyPath_createsBlacklistedExperiment() - Method in class ubic.gemma.rest.AdminWebServiceTest

addBlacklistEntry_happyPath_createsBlacklistedPlatform() - Method in class ubic.gemma.rest.AdminWebServiceTest

addBlacklistEntry_returns400_whenAccessionPrefixUnrecognised() - Method in class ubic.gemma.rest.AdminWebServiceTest

addBlacklistEntry_returns400_whenBodyMissing() - Method in class ubic.gemma.rest.AdminWebServiceTest

addBlacklistEntry_returns400_whenReasonBlank() - Method in class ubic.gemma.rest.AdminWebServiceTest

addBlacklistEntry_returns409_whenAlreadyBlacklisted() - Method in class ubic.gemma.rest.AdminWebServiceTest

addComment_appendsCommentedEvent_withPayload() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

addGroupAuthority(String, GrantedAuthority) - Method in class ubic.gemma.core.security.GroupManagerImpl

addGroupAuthority(UserGroup, String) - Method in class ubic.gemma.core.security.UserServiceImpl

Adding a new endpoint - Section in class ubic.gemma.core.util.test.ExternalUrlReachabilityTest

addTarget_appendsTheTarget_andLogsTargetAdded() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

addTarget_isIdempotentOnADuplicate() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

Idempotent, NOT a conflict.

addTarget_refusesOnACancelledTicket() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

A cancelled ticket is as finished as a resolved one; both refuse target changes.

addTarget_refusesOnAResolvedTicketEvenWithTheFlagOn() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

State wins over the flag: a finished ticket must not quietly grow new work.

addTarget_refusesWhenTheTicketDoesNotAcceptAdditions() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

The flag is the whole gate.

addTestAnalyses(ExpressionExperiment) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

Create test Analysis for the given expression experiment.

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

addUserToGroup(String, String) - Method in class ubic.gemma.core.security.GroupManagerImpl

addUserToGroup(UserGroup, User) - Method in class ubic.gemma.core.security.UserServiceImpl

adHoc() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory

Start building a freshly-created (non-seeded) taxon.

adHoc_defaults_returnsPersistentTaxon() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactoryTest

adHoc_withGenesUsableFalse_appliesOverride() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactoryTest

adHoc_withNcbiId_appliesOverride() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactoryTest

AdminAclEvaluationTest - Class in ubic.gemma.core.security.acl

Reproducer for the long-standing Phase-3 ACL evaluation bug surfaced by UserGroupServiceTest#testUpdateUserGroup: when the admin test user (authority GROUP_ADMIN) calls a method protected by @PreAuthorize("hasPermission(#group, 'administration')") on a UserGroup whose ACL was created by BaseAclAdvice.setupBaseAces(MutableAcl, ObjectIdentity, Sid, boolean) — which inserts a GrantedAuthoritySid("GROUP_ADMIN") ADMINISTRATION granting=true ACE — the evaluation returns false even though by inspection it should return true.

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

AdminAclEvaluationTest.FakeUserGroup - Class in ubic.gemma.core.security.acl

Minimal Securable stand-in — only needs a class name and id for the ObjectIdentityImpl key.

adminHasAdministrationOnUserGroupAcl() - Method in class ubic.gemma.core.security.acl.AdminAclEvaluationTest

The headline reproducer.

adminLacksWriteWhenOnlyAdministrationAceExists() - Method in class ubic.gemma.core.security.acl.AdminAclEvaluationTest

Same setup, but ask for WRITE.

adminUserKeepsEverythingTheyHavePermissionOn_evenIfNotTheOwner() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationOwnedCollectionFilteringProviderTest

AdminWebServiceTest - Class in ubic.gemma.rest

Pure-Mockito tests for AdminWebService: cache list / clear / clear-named, Hibernate stats snapshot.

AdminWebServiceTest() - Constructor for class ubic.gemma.rest.AdminWebServiceTest

advance_allowedTransitionUpdatesStateAndTimestamp() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowServiceTest

advance_disallowedTransitionThrows() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowServiceTest

advance_fullLifecycleSequence() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowServiceTest

Spec §"Acceptance criteria" exercises the full lifecycle: Discovery → Candidate → Preboarded → Loaded → Curate → Audit → Curate → Process → Audit → Public.

advance_idempotentNoOpEmitsNoUpdate() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowServiceTest

advanceDatasetWorkflow_disallowedTransitionReturns409WithAllowedList() - Method in class ubic.gemma.rest.WorkflowWebServiceTest

advanceDatasetWorkflow_idempotentNoOp() - Method in class ubic.gemma.rest.WorkflowWebServiceTest

advanceDatasetWorkflow_missingBodyThrows400() - Method in class ubic.gemma.rest.WorkflowWebServiceTest

advanceDatasetWorkflow_missingTargetStateThrows400() - Method in class ubic.gemma.rest.WorkflowWebServiceTest

advanceDatasetWorkflow_publicToCurateRequiresNonEmptyReason() - Method in class ubic.gemma.rest.WorkflowWebServiceTest

advanceDatasetWorkflow_unknownDatasetThrows404() - Method in class ubic.gemma.rest.WorkflowWebServiceTest

advanceDatasetWorkflow_unknownTargetStateThrows400() - Method in class ubic.gemma.rest.WorkflowWebServiceTest

advanceDatasetWorkflow_validTransitionReturns200() - Method in class ubic.gemma.rest.WorkflowWebServiceTest

aFactorValueCarriesItsOwnEvidenceOnTheWire() - Method in class ubic.gemma.rest.serializers.FactorValueValueObjectSerializerTest

A factor value's OWN evidence reaches the wire, distinct from its statements'.

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.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceTest

afterPropertiesSet() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test

afterPropertiesSet() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

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.rest.OpenApiTest

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

agreesWithTheIndependentlyResolvedPositions() - Method in class ubic.gemma.core.util.SymbolFontPuaTest

alignmentWithoutATargetChromosomeIsRefusedByName() - Method in class ubic.gemma.core.analysis.sequence.BlatResult2PslTest

Guards the ordering bug in the pre-exposure version: the target-chromosome null check sat AFTER the line that dereferenced it, so a chromosome-less alignment produced an NPE from deep inside the formatter rather than a statement of what was wrong.

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

Mark tests that require the Allen Brain Atlas RESTful API.

allowPositionalArguments() - Method in class ubic.gemma.apps.TestCli

anAdministratorSatisfiesACuratorAce() - Method in class ubic.gemma.core.security.acl.AdminAclEvaluationTest

🛑 The rule the whole widening rests on: an ADMINISTRATOR satisfies a GROUP_CURATOR ace through the hierarchy.

anAllZeroStoredHistogramIs204() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServicePvalueDistributionTest

analysisException_causeConstructor_carriesCauseAndConfig() - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisExceptionTest

analysisException_isARuntimeException() - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisExceptionTest

analysisException_messageConstructor_carriesMessageAndConfig() - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisExceptionTest

analysisException_nullConfig_isPermitted_butReadsAsNull() - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisExceptionTest

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

Unit tests for the differential-expression analysis exception family: AnalysisException (base) and its sub-types (MeanVarianceFailureException).

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

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

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).

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

AnalysisResultSetsJerseyTest - Class in ubic.gemma.rest

Integration test for the result sets endpoint.

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

AnalysisResultSetsWebServiceCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to AnalysisResultSetsWebService.getResultSets(DatasetArrayArg, DatabaseEntryArrayArg, FilterArg, OffsetArg, LimitArg, SortArg, CursorArg) for step 1i of CURSOR_PAGINATION_STEP1_PLAN.md.

AnalysisResultSetsWebServiceCursorTest() - Constructor for class ubic.gemma.rest.AnalysisResultSetsWebServiceCursorTest

AnalysisResultSetsWebServicePvalueDistributionTest - Class in ubic.gemma.rest

Unit tests for AnalysisResultSetsWebService.getPvalueDistribution(ExpressionAnalysisResultSetArg, int, String), which serves the stored PVALUE_DISTRIBUTION histogram rather than aggregating DIFFERENTIAL_EXPRESSION_ANALYSIS_RESULT (120.5 GB / ~1.57e9 rows on production) per request.

AnalysisResultSetsWebServicePvalueDistributionTest() - Constructor for class ubic.gemma.rest.AnalysisResultSetsWebServicePvalueDistributionTest

AnalysisResultSetsWebServiceTest - Class in ubic.gemma.rest

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

analyticsProvider() - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

analyticsProvider() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

analyticsProvider() - Method in class ubic.gemma.rest.TasksWebServiceTest.TasksWebServiceContextConfiguration

anAssaysOriginalPlatformIsProjectedToo() - Method in class ubic.gemma.model.expression.bioAssay.BioAssaySamplePayloadShapeTest

The same projection on the switched-from platform, which is the same object with the same bulk.

anAssaysPlatformIsProjectedToTheReferenceShape() - Method in class ubic.gemma.model.expression.bioAssay.BioAssaySamplePayloadShapeTest

The platform is named, not reproduced.

anAuditableWithNoShortNameStillRenders() - Method in class ubic.gemma.core.security.audit.AuditLoggerTest

anEntirelyUnmappedTypeFallsBackToItsClassName() - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObjectTest

Nothing in the hierarchy is mapped for these, so the label restates the class name.

anEventWithNoPerformerIsSummarizedAnyway() - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObjectTest

anExcludedColumnIsStillMappedOntoTheReference() - Method in class ubic.gemma.core.util.math.QuantileReferenceColumnsTest

The excluded column is still placed on the shared scale — it just does not get to define it.

AnnDataSingleCellDataLoaderIntegrationTest - Class in ubic.gemma.core.loader.expression.singleCell

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

AnnDataSingleCellDataLoaderTest - Class in ubic.gemma.core.loader.expression.singleCell

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

AnnDataTest - Class in ubic.gemma.core.loader.util.anndata

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

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

Reads over ANNOTATION_RELATION.

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

AnnotationRelationHarvestTest - Class in ubic.gemma.persistence.service.maintenance

The CURATED harvest: EE2C rows that already carry a predicate and an object become queryable relations.

AnnotationRelationHarvestTest() - Constructor for class ubic.gemma.persistence.service.maintenance.AnnotationRelationHarvestTest

annotationRelationService() - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

Required by AnnotationsWebService since the relation endpoints landed; without it the context fails to build and these cache tests error before asserting anything.

annotationRelationService() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

Required by AnnotationsWebService since the relation endpoints landed; without it every test here fails on context init rather than on anything it asserts.

AnnotationSearchRankingStrategyTest - Class in ubic.gemma.rest

Pure-data tests for the three ranking strategies — no Spring, no Mockito beyond the input fixture.

AnnotationSearchRankingStrategyTest() - Constructor for class ubic.gemma.rest.AnnotationSearchRankingStrategyTest

AnnotationSetDispositionPersistenceIT - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Persistence contract for AnnotationSetDisposition — the row-per-ruling, latest-wins model for a curator's verdict on ONE finding.

AnnotationSetDispositionPersistenceIT() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

AnnotationSetPayloadCountsTest - Class in ubic.gemma.model.common.auditAndSecurity.curation

The counts are a HINT read off a payload whose shape belongs to someone else, so what these pin is mostly the failure behaviour: everything unrecognized has to come back null rather than zero.

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

AnnotationSetPersistenceIT - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Integration test for the V20/V21 ANNOTATION_SET schema migration and the unified AnnotationSet entity + service.

AnnotationSetPersistenceIT() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

AnnotationSetTriagePersistenceIT - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Persistence contract for AnnotationSetTriage — the row-per-judge triage model.

AnnotationSetTriagePersistenceIT() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriagePersistenceIT

AnnotationsRestTest - Class in ubic.gemma.rest

End-to-end checks for AnnotationsWebService.

AnnotationsRestTest() - Constructor for class ubic.gemma.rest.AnnotationsRestTest

AnnotationsUsageCountCacheTest - Class in ubic.gemma.rest

The per-URI corpus usage-count cache behind /annotations/search?rank=composite.

AnnotationsUsageCountCacheTest() - Constructor for class ubic.gemma.rest.AnnotationsUsageCountCacheTest

AnnotationsUsageCountCacheTest.ContextConfig - Class in ubic.gemma.rest

annotationsWebService(OntologyService, SearchService, CharacteristicService, ExpressionExperimentService, DatasetArgService, TaxonArgService, GeneService) - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

annotationsWebService(OntologyService, SearchService, CharacteristicService, ExpressionExperimentService, DatasetArgService, TaxonArgService, GeneService) - Method in class ubic.gemma.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

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

AnnotationsWebServiceTest - Class in ubic.gemma.rest

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

AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration - Class in ubic.gemma.rest

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

Unit tests for AnnotationValueObject's discrimination between plain Characteristic input and the Statement subclass.

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

aNonDivisorBinCountIsRejectedWithTheAcceptedValues() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServicePvalueDistributionTest

anonymousUser_postInsert_skipsAuditEmission() - Method in class ubic.gemma.persistence.audit.AuditTrailEventListenerTest

anonymousUser_preDelete_skipsAuditEmission() - Method in class ubic.gemma.persistence.audit.AuditTrailEventListenerTest

anUndesignatedFactorValueOmitsTheFlagRatherThanSayingFalse() - Method in class ubic.gemma.rest.serializers.FactorValueValueObjectSerializerTest

Absent, not false, when nothing was designated.

anUnknownColumnIsRejected() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServicePvalueDistributionTest

anUnresolvableTargetStaysNull() - Method in class ubic.gemma.rest.TicketsWebServiceTargetLabelsTest

loadIdentifiers is ACL-filtered, so an id the caller cannot read simply does not come back.

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

aPlainUserDoesNotSatisfyACuratorAce() - Method in class ubic.gemma.core.security.acl.AdminAclEvaluationTest

A plain user is unaffected by the curator ace -- the widening gave nothing to GROUP_USER.

appDataHome - Variable in class ubic.gemma.core.config.SettingsConfigTest

ApplicationContextTest - Class in ubic.gemma.core.security

ApplicationContextTest() - Constructor for class ubic.gemma.core.security.ApplicationContextTest

appliesTo_returnsFalse_whenThresholdIsZero() - Method in class ubic.gemma.core.analysis.preprocess.filter.TooFewDistinctValuesFilterTest

appliesTo_returnsTrue_whenThresholdIsPositive() - Method in class ubic.gemma.core.analysis.preprocess.filter.TooFewDistinctValuesFilterTest

aPredicatedSampleAnnotationKeepsItsPredicateAndObject() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObjectStatementTest

🛑 A predicated sample annotation used to be flattened to its subject on every read: CharacteristicValueObject has no predicate or object, and it was the only shape the sample payload carried.

aPredicatedStatementStillCarriesItsPredicateAndObject() - Method in class ubic.gemma.model.expression.bioAssay.BioAssaySamplePayloadShapeTest

And when something IS said, it is still said.

aRejectedDownloadIsNotReusedByTheSkipCheck(Path) - Method in class ubic.gemma.core.util.NetUtilsTest

A wrong-length file must not survive to be mistaken for a complete download by the skip-if-already-correct check on the next run.

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

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

ArrayDesignDaoTest - Class in ubic.gemma.persistence.service.expression.arrayDesign

ArrayDesignDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest

ArrayDesignFactory - Class in ubic.gemma.core.util.test.fixture

Typed factory for persistent ArrayDesign test fixtures.

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

ArrayDesignFactory.Builder - Class in ubic.gemma.core.util.test.fixture

Fluent builder for an ArrayDesign.

ArrayDesignFactoryTest - Class in ubic.gemma.core.util.test.fixture

Verifies the Phase 3 typed ArrayDesignFactory.

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

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

ArrayDesignMergeCliTest - Class in ubic.gemma.apps

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

ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration - Class in ubic.gemma.apps

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

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

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

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

arrayDesignPersister - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

ArrayDesignServiceTest - Class in ubic.gemma.persistence.service.expression.arrayDesign

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

ArrayUtilsTest - Class in ubic.gemma.core.util

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

aSampleNoLongerCarriesTheDeprecatedFactorsMap() - Method in class ubic.gemma.model.expression.bioAssay.BioAssaySamplePayloadShapeTest

The deprecated factors map — factor id to factor name — is gone.

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.

Assertions - Class in ubic.gemma.cli.util.test

Assertions - Class in ubic.gemma.rest.util

Entrypoint for custom AssertJ assertions.

Assertions() - Constructor for class ubic.gemma.cli.util.test.Assertions

Assertions() - Constructor for class ubic.gemma.rest.util.Assertions

assertThat(Response) - Static method in class ubic.gemma.rest.util.Assertions

assertThat(Errors) - Static method in class ubic.gemma.rest.util.Assertions

assertThat(CLI) - Static method in class ubic.gemma.cli.util.test.Assertions

assign_setsAssignee_andAppendsAssignedEvent() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

assign_withNullAssignee_clearsAssignment_andStillLogsEvent() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

assumeThatExecutableExists(String) - Static method in class ubic.gemma.core.util.test.Assumptions

Check if an executable exists and is executable.

assumeThatFreeMemoryIsGreaterOrEqualTo(long, boolean) - Static method in class ubic.gemma.core.util.test.Assumptions

Assume that a certain amount of memory is available.

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

Reusable assumptions for tests.

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

aStatementCarriesItsEvidenceOnTheWire() - Method in class ubic.gemma.rest.serializers.FactorValueValueObjectSerializerTest

Evidence reaches the wire on the design payload.

aStatementWithNothingSaidAboutItStillAppearsInStatements() - Method in class ubic.gemma.rest.serializers.FactorValueValueObjectSerializerTest

🛑 A grounded value with no predicate is still a statement, and it has to appear in statements.

aStatementWithoutEvidenceOmitsTheKeys() - Method in class ubic.gemma.rest.serializers.FactorValueValueObjectSerializerTest

Absent, not null, when there is no evidence — null reads as "this was cleared" on a payload whose write path treats an empty send as an erasure.

aStoredHistogramWithNoBinsIs204() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServicePvalueDistributionTest

aSubclassAddedLaterInheritsItsNearestMappedAncestor() - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObjectTest

The map covers every event class a dataset's trail can carry today, so the inheritance path is exercised here with a subclass that does not exist yet — which is the case it is for.

aSubjectOnlyStatementOmitsThePredicateAndObjectHalves() - Method in class ubic.gemma.model.expression.bioAssay.BioAssaySamplePayloadShapeTest

A statement with nothing said about it says nothing, rather than saying null seven times.

aSubqueryMustCarryAtLeastOneFilter() - Method in class ubic.gemma.persistence.util.SubqueryConjunctionTest

aSummaryCarriesTheEventsDatePerformerAndTypeName() - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObjectTest

AsyncBeanAutowiringTest - Class in ubic.gemma.core.context

AsyncBeanAutowiringTest() - Constructor for class ubic.gemma.core.context.AsyncBeanAutowiringTest

AsyncBeanAutowiringTest.MyService - Class in ubic.gemma.core.context

AsyncBeanAutowiringTest.MyService2 - Class in ubic.gemma.core.context

AsyncBeanAutowiringTest.MyService2Factory - Class in ubic.gemma.core.context

AsyncBeanAutowiringTest.MyServiceFactory - Class in ubic.gemma.core.context

AsyncFactoryTest - Class in ubic.gemma.core.context

AsyncFactoryTest() - Constructor for class ubic.gemma.core.context.AsyncFactoryTest

AsyncFactoryTest.MyService - Class in ubic.gemma.core.context

AsyncFactoryTest.MyServiceFactory - Class in ubic.gemma.core.context

AsyncSingletonFactoryTest - Class in ubic.gemma.core.context

AsyncSingletonFactoryTest() - Constructor for class ubic.gemma.core.context.AsyncSingletonFactoryTest

AsyncSingletonFactoryTest.MyService - Class in ubic.gemma.core.context

AsyncSingletonFactoryTest.MyServiceFactory - Class in ubic.gemma.core.context

atGigabyteThreshold_rendersAsGigabytes() - Method in class ubic.gemma.core.util.NetUtilsTest

atKilobyteThreshold_rendersAsKilobytes() - Method in class ubic.gemma.core.util.NetUtilsTest

atMegabyteThreshold_rendersAsMegabytes() - Method in class ubic.gemma.core.util.NetUtilsTest

attachAnnotationSet_blankRunIdThrows400() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

attachAnnotationSet_existingRunIdReturns200() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

attachAnnotationSet_newRunIdReturns201() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

attachAnnotationSet_unknownPreboardedThrows404() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

attritionCarriesEveryStageInTheOrderTheFilterAppliesThem() - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCorrelationAttritionMappingTest

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

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.

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

AuditedAspectTest.FakeAuditable - Class in ubic.gemma.core.security.audit

Minimal in-memory Auditable that doesn't require Hibernate or any of the gemma-core entity machinery.

AuditedAspectTest.SamplePayload - Record Class in ubic.gemma.core.security.audit

A locally-defined payload record.

AuditedAspectTest.ValueSpelHelper - Class in ubic.gemma.core.security.audit

Static helper invoked from valueSpel expressions via T(...).pick(#arg).

auditedConditional_brokenWhenSpelSkipsEmission() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C: a broken when SpEL must SKIP emission (safe default — an undecidable predicate is closer to the no-op branch than to the emission branch).

auditedConditional_firesWhenPredicateTrue() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C: AuditedConditional fires only when its when predicate is true.

auditedConditional_predicateCanReferenceArgs() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C: predicate can reference a method parameter by name (same resolution as messageSpel).

auditedConditional_skipsWhenPredicateFalse() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C: when the predicate is false the aspect must skip emission entirely — no service call, no Spring event.

auditedOnError_brokenSpelFallsBackAndStillWritesRow() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C: broken messageSpel on the throwing path must fall back to the literal message() and STILL write the audit row.

auditedOnError_happyPathDoesNotEmit() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C: a method returning normally must NOT trigger @AuditedOnError (the advice is @AfterThrowing-only).

auditedOnError_messageSpelCanReferenceExceptionAndArgs() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C: SpEL on the throwing path can reference both #exception and method parameters by name.

auditedOnError_writesEventAndRethrowsOriginal() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C (AuditedOnError): the aspect must (a) write a Failed* event via the 4-arg Throwable overload (REQUIRES_NEW in production), (b) re-throw the original exception, and (c) publish an AuditedEvent for downstream listeners.

auditedUpdatesStillTriggerAReindexWhenCountsMatch() - Method in class ubic.gemma.core.search.indexer.ScheduledSearchReindexerTest

AuditEventDaoTest - Class in ubic.gemma.persistence.service.common.auditAndSecurity

AuditEventDaoTest() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoTest

auditEventEntity_postInsert_isNotItselfAudited() - Method in class ubic.gemma.persistence.audit.AuditTrailEventListenerTest

auditEventService() - Method in class ubic.gemma.apps.AclLinterCliTest.AclLinterCliTestContextConfiguration

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

AuditEventServiceTest - Class in ubic.gemma.persistence.service.common.auditAndSecurity

AuditEventServiceTest() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceTest

AuditEventTypeTest - Class in ubic.gemma.model.common.auditAndSecurity.eventType

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

auditListenerRegistersDespiteLazyByDefault() - Method in class ubic.gemma.core.security.acl.EventListenerRegistrationLazyContextTest

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

Guards the identifying facts in the AuditLogger line.

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

AuditTrailDaoTest - Class in ubic.gemma.persistence.service.common.auditAndSecurity

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

auditTrailEntity_postInsert_isNotItselfAudited() - Method in class ubic.gemma.persistence.audit.AuditTrailEventListenerTest

AuditTrailEventListenerTest - Class in ubic.gemma.persistence.audit

Fast unit tests for the Phase C-1 additions on AuditTrailEventListener: the PostInsertEventListener and PreDeleteEventListener interfaces.

AuditTrailEventListenerTest() - Constructor for class ubic.gemma.persistence.audit.AuditTrailEventListenerTest

AuditTrailForeignKeyIntegrationTest - Class in ubic.gemma.persistence.hibernate

AUDIT_TRAIL.LAST_EVENT_FK must be ON DELETE SET NULL in a schema Hibernate built.

AuditTrailForeignKeyIntegrationTest() - Constructor for class ubic.gemma.persistence.hibernate.AuditTrailForeignKeyIntegrationTest

auditTrailService() - Method in class ubic.gemma.apps.AclLinterCliTest.AclLinterCliTestContextConfiguration

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

AuditTrailServiceImplCuratableDispatchTest - Class in ubic.gemma.persistence.service.common.auditAndSecurity

Does doAddUpdateEvent recognise a curatable entity when it arrives as a proxy?

AuditTrailServiceImplCuratableDispatchTest() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplCuratableDispatchTest

AuditTrailServiceImplTest - Class in ubic.gemma.persistence.service.common.auditAndSecurity

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

authenticate() - Method in class ubic.gemma.model.expression.bioAssay.BioAssaySamplePayloadShapeTest

ArrayDesignValueObject's constructor asks the security context what to expose, so a bare unit test needs an authentication even though nothing here is about authorization.

authenticate() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObjectTest

ArrayDesignValueObject's constructor asks the security context what to expose, so a bare unit test needs an authentication even though nothing here is about authorization.

authenticateAsOrdinaryUser() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDaoTest

AuthenticatedCliTestConfig - Class in ubic.gemma.cli.util.test

A base class with mocks for testing CLI commands that require authentication.

AuthenticatedCliTestConfig() - Constructor for class ubic.gemma.cli.util.test.AuthenticatedCliTestConfig

authenticatedUser_postInsert_appendsCreateAuditEvent() - Method in class ubic.gemma.persistence.audit.AuditTrailEventListenerTest

authenticatedUser_preDelete_appendsDeleteAuditEvent() - Method in class ubic.gemma.persistence.audit.AuditTrailEventListenerTest

authorityGrantsAreHonored_inAdditionToPrincipalGrants() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationStreamFilteringProviderTest

autowired_fields_must_not_be_impl_typed - Static variable in class ubic.gemma.core.architecture.AutowireImplRuleTest

Intentionally vacuous when no @Autowired Impl-typed fields exist — that is the goal state of the migration.

AutowireImplRuleTest - Class in ubic.gemma.core.architecture

Phase 3 build hygiene: forbid declaring Spring-injected dependencies with an Impl-typed reference in production code.

AutowireImplRuleTest() - Constructor for class ubic.gemma.core.architecture.AutowireImplRuleTest

B

backRefDiscovery_prefersSecuredChildOverSecuredNotChild() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest

backwardDirectionIsInWire() - Method in class ubic.gemma.persistence.util.CursorTest

BAR - Enum constant in enum class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest.FakeEnum

bareBcrypt_matchesWithoutPrefix() - Method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoderTest

BaseCliIntegrationTest5 - Class in ubic.gemma.cli.util.test

JUnit 5 (Jupiter) counterpart of BaseCliIntegrationTest.

BaseCliIntegrationTest5() - Constructor for class ubic.gemma.cli.util.test.BaseCliIntegrationTest5

BaseCliTest5 - Class in ubic.gemma.cli.util.test

JUnit 5 (Jupiter) counterpart of BaseCliTest.

BaseCliTest5() - Constructor for class ubic.gemma.cli.util.test.BaseCliTest5

BaseCodeConfigurerTest - Class in ubic.gemma.core.config

BaseCodeConfigurerTest() - Constructor for class ubic.gemma.core.config.BaseCodeConfigurerTest

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

Configuration for enabling ACLs in a BaseDatabaseTest5.

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

BaseDatabaseTest5 - Class in ubic.gemma.core.util.test

JUnit 5 (Jupiter) counterpart of BaseDatabaseTest.

BaseDatabaseTest5() - Constructor for class ubic.gemma.core.util.test.BaseDatabaseTest5

BaseDatabaseTest5.BaseDatabaseTestContextConfiguration - Class in ubic.gemma.core.util.test

BaseDatabaseTestContextConfiguration() - Constructor for class ubic.gemma.core.util.test.BaseDatabaseTest5.BaseDatabaseTestContextConfiguration

BaseIntegrationTest5 - Class in ubic.gemma.core.util.test

JUnit 5 (Jupiter) base class for integration tests, tagged @Tag("integration") for surefire/failsafe filtering.

BaseIntegrationTest5() - Constructor for class ubic.gemma.core.util.test.BaseIntegrationTest5

BaseJerseyIntegrationTest5 - Class in ubic.gemma.rest.util

JUnit 5 (Jupiter) base class for Jersey integration tests, tagged @Tag("integration") for surefire/failsafe filtering.

BaseJerseyIntegrationTest5() - Constructor for class ubic.gemma.rest.util.BaseJerseyIntegrationTest5

BaseJerseyTest5 - Class in ubic.gemma.rest.util

JUnit 5 (Jupiter) counterpart of BaseJerseyTest.

BaseJerseyTest5() - Constructor for class ubic.gemma.rest.util.BaseJerseyTest5

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

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

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

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

BaselineTest - Class in ubic.gemma.model.analysis.expression.diff

BaselineTest() - Constructor for class ubic.gemma.model.analysis.expression.diff.BaselineTest

BaseSpringContextTest5 - Class in ubic.gemma.core.util.test

Deprecated.

favour the simpler BaseIntegrationTest5 for new tests

BaseSpringContextTest5() - Constructor for class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

Base class for all tests.

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

BaseTest5 - Class in ubic.gemma.core.util.test

JUnit 5 (Jupiter) counterpart of BaseTest.

BaseTest5() - Constructor for class ubic.gemma.core.util.test.BaseTest5

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

Unit tests for BatchConfoundUtils, covering biomaterials that carry no value for a factor.

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

batchedRead_omitsUnruledSets() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

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

BatchInfoRepopulationJobTest - Class in ubic.gemma.core.scheduler

BatchInfoRepopulationJobTest() - Constructor for class ubic.gemma.core.scheduler.BatchInfoRepopulationJobTest

BatchProcessingCliTest - Class in ubic.gemma.apps

BatchProcessingCliTest() - Constructor for class ubic.gemma.apps.BatchProcessingCliTest

bcryptHash_isNotFlaggedForUpgrade() - Method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoderTest

bcryptHash_stillAuthenticatesViaPasswordEncoder() - Method in class ubic.gemma.core.security.authentication.LegacyAwareDaoAuthenticationProviderTest

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

beforeEach(ExtensionContext) - Method in class ubic.gemma.core.util.test.NetworkAvailableExtension

belowGigabyteThreshold_rendersAsMegabytes() - Method in class ubic.gemma.core.util.NetUtilsTest

belowKilobyteThreshold_rendersAsBytes() - Method in class ubic.gemma.core.util.NetUtilsTest

belowMegabyteThreshold_rendersAsKilobytes() - Method in class ubic.gemma.core.util.NetUtilsTest

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

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

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

This class tests the bibliographic reference data access object.

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

BioAssayDimensionCacheStalenessTest - Class in ubic.gemma.persistence.service.expression.bioAssayData

HB6 cascade audit #10 regression guard: BioAssayDimension HBM (Pattern C — mutable="false" class + child list + cache directive).

BioAssayDimensionCacheStalenessTest() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionCacheStalenessTest

BioAssayFactory - Class in ubic.gemma.core.util.test.fixture

Typed factory for persistent BioAssay test fixtures.

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

BioAssayFactory.Builder - Class in ubic.gemma.core.util.test.fixture

Fluent builder for a BioAssay.

BioAssayFactoryTest - Class in ubic.gemma.core.util.test.fixture

Verifies the Phase 3 typed BioAssayFactory.

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

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

What GET /datasets/{dataset}/samples puts on the wire per assay.

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

BioAssayServiceTest - Class in ubic.gemma.persistence.service.expression.bioAssay

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

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

The platform pair on a sample: what it is run on now, and what it was submitted on.

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

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

Tests that biomart fetcher works correctly.

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

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

Class to test BioMartEnsemblNcbiObjectGeneration.

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

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

Tests the parsing of a BioMart file.

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

BioMaterialDaoTest - Class in ubic.gemma.persistence.service.expression.biomaterial

BioMaterialDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoTest

BioMaterialFactory - Class in ubic.gemma.core.util.test.fixture

Typed factory for persistent BioMaterial test fixtures.

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

BioMaterialFactory.Builder - Class in ubic.gemma.core.util.test.fixture

Fluent builder.

BioMaterialFactoryTest - Class in ubic.gemma.core.util.test.fixture

Verifies the Phase 3 typed test-fixture factory for BioMaterial.

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

BioMaterialReadServiceTest - Class in ubic.gemma.persistence.service.expression.biomaterial

Lightweight unit test for BioMaterialReadServiceImpl that verifies each public method delegates to the right BioMaterialDao call without standing up a Spring context.

BioMaterialReadServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceTest

BioMaterialServiceTest - Class in ubic.gemma.persistence.service.expression.biomaterial

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

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

A sample annotation survives the read with whatever was said about it.

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

BioSequencePersistTest - Class in ubic.gemma.persistence.service.genome

BioSequencePersistTest() - Constructor for class ubic.gemma.persistence.service.genome.BioSequencePersistTest

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

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

BlacklistedEntityDaoImplTest - Class in ubic.gemma.persistence.service.blacklist

BlacklistedEntityDaoImplTest() - Constructor for class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImplTest

BlacklistedEntityServiceTest - Class in ubic.gemma.persistence.service.blacklist

BlacklistedEntityServiceTest() - Constructor for class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceTest

BlacklistTest - Class in ubic.gemma.persistence.service.blacklist

BlacklistTest() - Constructor for class ubic.gemma.persistence.service.blacklist.BlacklistTest

blankReason_normalizesToNull() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

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.persistence.service.genome.sequenceAnalysis

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

BlatResult2PslTest - Class in ubic.gemma.core.analysis.sequence

Formatting guards for the UCSC custom track emitted by BlatResult2Psl, which backs GET /platforms/{platform}/elements/{probe}/pslTrack.

BlatResult2PslTest() - Constructor for class ubic.gemma.core.analysis.sequence.BlatResult2PslTest

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

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

BlatResultServiceTest - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis

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

BlatResultTest - Class in ubic.gemma.model.genome

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

body_writesToDescriptionColumn() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

booleanArrayRoundTrip_preservesValues() - Method in class ubic.gemma.persistence.util.ByteArrayUtilsTest

BootstrappedDataSourceFactoryTest - Class in ubic.gemma.persistence.initialization

BootstrappedDataSourceFactoryTest() - Constructor for class ubic.gemma.persistence.initialization.BootstrappedDataSourceFactoryTest

bothConditionsAreRenderedInsideASingleSubquery() - Method in class ubic.gemma.persistence.util.SubqueryConjunctionTest

Both conditions land in ONE subquery, joined by `and`, against one alias.

boundInsideTheScopeAndClearedAfter() - Method in class ubic.gemma.core.security.util.ActingIdentityTest

brainMatcher_hitsOnMeshHeading() - Method in class ubic.gemma.core.geoscrape.MatchersTest

brainMatcher_hitsOnTitle() - Method in class ubic.gemma.core.geoscrape.MatchersTest

brainMatcher_keywordsIncludeCuratedSet() - Method in class ubic.gemma.core.geoscrape.MatchersTest

brainMatcher_missesOnNullRecord() - Method in class ubic.gemma.core.geoscrape.MatchersTest

brainMatcher_missesOnUnrelatedRecord() - Method in class ubic.gemma.core.geoscrape.MatchersTest

brokenSpel_fallsBackToLiteralMessageAndStillWritesAuditRow() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

browserPositionIsClampedAtTheStartOfTheChromosome() - Method in class ubic.gemma.core.analysis.sequence.BlatResult2PslTest

An alignment near the start of a chromosome would otherwise be framed at a negative coordinate, which UCSC rejects.

Bug shape - Section in class ubic.gemma.persistence.service.expression.experiment.ReplaceAllRawDataVectorsQtCollisionTest

build() - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactory.Builder

Build, persist, and return the AD.

build() - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactory.Builder

Build, persist, and return the BA.

build() - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactory

Convenience: build with all defaults.

build() - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactory.Builder

Build, persist, and return the BM.

build() - Method in class ubic.gemma.core.util.test.fixture.CompositeSequenceFactory.Builder

Build, persist, and return the CS.

build() - Method in class ubic.gemma.core.util.test.fixture.ExperimentFactory.Builder

Build, persist, and return the EE.

build() - Method in class ubic.gemma.core.util.test.fixture.GeneFactory.GeneBuilder

Build, persist, and return the gene.

build() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory.AdHocBuilder

build() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory.ResolveBuilder

build_defaults_returnsPersistentBmWithId() - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactoryTest

builder() - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactory

Start building a BioAssay.

builder() - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactory

Start building a BioMaterial with defaults: mouse taxon, no source biomaterial, no external accession, auto-generated name.

builder() - Method in class ubic.gemma.core.util.test.fixture.CompositeSequenceFactory

Start building a CompositeSequence.

builder() - Method in class ubic.gemma.core.util.test.fixture.GeneFactory

Start building a Gene.

buildIdentifyingMetadata_emitsCuratorRelevantFields() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

buildIdentifyingMetadata_nullSafe() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

buildInfo() - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

buildInfo() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

buildInfo() - Method in class ubic.gemma.rest.TasksWebServiceTest.TasksWebServiceContextConfiguration

BuildInfoTest - Class in ubic.gemma.core.util

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

BuildInfoThreadContextPopulatorTest - Class in ubic.gemma.core.logging.log4j

BuildInfoThreadContextPopulatorTest() - Constructor for class ubic.gemma.core.logging.log4j.BuildInfoThreadContextPopulatorTest

buildTicketNote_smallListDoesNotTruncate() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

buildTicketNote_truncatesAt20WithOverflowMarker() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

buildTransient() - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactory.Builder

Build the BA WITHOUT persisting it.

buildTransient_returnsUnpersistedBA_withPersistentBMAndAD() - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactoryTest

BULK_RNA - Enum constant in enum class ubic.gemma.core.util.test.fixture.ExperimentFactory.Modality

BulkDataSlicerUtilsTest - Class in ubic.gemma.core.analysis.preprocess.slice

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

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

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

bulkRna() - Method in class ubic.gemma.core.util.test.fixture.ExperimentFactory

Start building a bulk-RNA expression experiment.

bulkRna_defaults_returnsPersistentEEWithId() - Method in class ubic.gemma.core.util.test.fixture.ExperimentFactoryTest

bulkSummaries_agreeWithFindOpenForTarget() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

bulkSummaries_carryThePerTargetStatus() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

bulkSummaries_carryTheTicketPriority() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

bulkSummaries_emptyIdsIsAnEmptyMap() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

bulkSummaries_groupsByTargetAndExcludesResolved() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

bulkSummaries_quietDatasetIsAbsentNotEmpty() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

bulkSummaries_targetCountIsTheWholeTicket() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

BusinessKeyTest - Class in ubic.gemma.persistence.util

Pure unit tests for the validator portion of BusinessKey added during the Phase 3 persister retirement.

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

byCommonName(String) - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory

Resolve a seeded taxon by its common name.

byCommonName_resolvesSeededTaxon() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactoryTest

byCommonName_unknownThrows() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactoryTest

byNcbiId(Integer) - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory

Resolve a seeded taxon by its NCBI id.

byNcbiId_resolvesSeededTaxon() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactoryTest

byScientificName(String) - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory

Resolve a seeded taxon by its scientific name.

byScientificName_resolvesSeededTaxon() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactoryTest

ByteArrayUtilsTest - Class in ubic.gemma.persistence.util

Round-trip + edge-case unit tests for ByteArrayUtils, the static facade used across the persistence layer to encode/decode primitive arrays into the BLOB columns that store expression-data vectors.

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

byteToCorrel_128_returnsZero() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

byteToCorrel_255_returnsAlmostOne() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

byteToCorrel_zero_returnsNegativeOne() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

C

CachedProcessedExpressionDataVectorServiceTest - Class in ubic.gemma.persistence.service.expression.bioAssayData

CachedProcessedExpressionDataVectorServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.CachedProcessedExpressionDataVectorServiceTest

cacheManager() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test.GeneOntologyService2TestContextConfiguration

cacheManager() - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

carriesListAndMetadata() - Method in class ubic.gemma.persistence.util.CursorPageTest

carriesOptionalTotalElements() - Method in class ubic.gemma.persistence.util.CursorPageTest

CellBrowserMetadataWriterTest - Class in ubic.gemma.core.visualization.cellbrowser

CellBrowserMetadataWriterTest() - Constructor for class ubic.gemma.core.visualization.cellbrowser.CellBrowserMetadataWriterTest

CellBrowserServiceImplTest - Class in ubic.gemma.core.visualization.cellbrowser

CellBrowserServiceImplTest() - Constructor for class ubic.gemma.core.visualization.cellbrowser.CellBrowserServiceImplTest

CellBrowserTabularMatrixWriterTest - Class in ubic.gemma.core.visualization.cellbrowser

CellBrowserTabularMatrixWriterTest() - Constructor for class ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixWriterTest

CellIdOverlapBioAssayMapperTest - Class in ubic.gemma.core.loader.util.mapper

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

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

Exercises the Lucene-9 ontology search index's stemming-with-exclusion behavior against a trimmed CLO fixture (15-term subset of the full Cell Line Ontology, ~5 KB gzipped).

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

CellXGeneAnnDataSingleCellDataLoaderTest - Class in ubic.gemma.core.loader.expression.cellxgene

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

CellXGeneConverterTest - Class in ubic.gemma.core.loader.expression.cellxgene

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

CellXGeneDataLoaderServiceTest - Class in ubic.gemma.core.loader.expression.cellxgene

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

CellXGeneFetcherTest - Class in ubic.gemma.core.loader.expression.cellxgene

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

chainFlatSemantics_grandchildParentsToRootNotImmediateAncestor() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest

changedMind_keepsBothRows() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

changePassword(String, String) - Method in class ubic.gemma.core.security.UserDetailsManagerImpl

changePasswordForUser(String, String, String) - Method in class ubic.gemma.core.security.UserDetailsManagerImpl

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

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).

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

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

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

characteristicService() - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

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

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

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

CharacteristicSortTest - Class in ubic.gemma.core.ontology

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

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

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

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

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

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

Pins the read-time URI canonicaliser — the stand-in for the parked database migration (scripts/sql/term_uri_migration.sql).

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

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

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

charArrayRoundTrip_preservesValues() - Method in class ubic.gemma.persistence.util.ByteArrayUtilsTest

ChebiSeedResolverSlotsTest - Class in ubic.gemma.core.ontology.providers.chebi

The CHEBI slim is only as good as its seed set, and the seed set used to be built from Characteristic.valueUri alone.

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

checkAptIsAvailable() - Static method in class ubic.gemma.core.loader.expression.ExonArrayDataAddIntegrationTest

checkDeletedAcl(Securable) - 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

checkFastaCmdExecutableExists() - Static method in class ubic.gemma.core.loader.genome.SimpleFastaCmdTest

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

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

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

checkKeyBioAssayDimension_emptyRejected() - Method in class ubic.gemma.persistence.util.BusinessKeyTest

checkKeyBioAssayDimension_happyPath() - Method in class ubic.gemma.persistence.util.BusinessKeyTest

checkKeyBioAssayDimension_transientBioAssayRejected() - Method in class ubic.gemma.persistence.util.BusinessKeyTest

checkKeyQuantitationType_blankNameRejected() - Method in class ubic.gemma.persistence.util.BusinessKeyTest

checkKeyQuantitationType_happyPath() - Method in class ubic.gemma.persistence.util.BusinessKeyTest

checkKeyQuantitationType_nullRejected() - Method in class ubic.gemma.persistence.util.BusinessKeyTest

checkLacksAces(Securable) - 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

checkValidKeyChromosome_blankNameRejected() - Method in class ubic.gemma.persistence.util.BusinessKeyTest

checkValidKeyChromosome_happyPath() - Method in class ubic.gemma.persistence.util.BusinessKeyTest

Child(Long, AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest.Parent) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest.Child

Child(Long, AclEntryAfterInvocationByAssociationFilteringProviderTest.Parent) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProviderTest.Child

ChildCollectionToParentByAssociation(AclService, String, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest.ChildCollectionToParentByAssociation

ChildToParentByAssociation(AclService, String, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProviderTest.ChildToParentByAssociation

classes_are_actually_imported(JavaClasses) - Static method in class ubic.gemma.core.architecture.AutowireImplRuleTest

🛑 The guard against a guard that checks nothing.

classes_are_actually_imported(JavaClasses) - Static method in class ubic.gemma.core.architecture.ReadServiceTransactionalRuleTest

🛑 The guard against a guard that checks nothing.

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

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

cleanUp() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceTest

cleanUp() - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactoryTest

cleanUp() - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactoryTest

cleanUp() - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactoryTest

cleanUp() - Method in class ubic.gemma.core.util.test.fixture.CompositeSequenceFactoryTest

cleanUp() - Method in class ubic.gemma.core.util.test.fixture.ExperimentFactoryTest

cleanUp() - Method in class ubic.gemma.core.util.test.fixture.GeneFactoryTest

cleanUp() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactoryTest

clearAllCachesIteratesEveryCache() - Method in class ubic.gemma.rest.AdminWebServiceTest

clearAllCachesTolleratesMissingCache() - Method in class ubic.gemma.rest.AdminWebServiceTest

clearAllowDevFallbackSystemProperty() - Method in class ubic.gemma.core.context.SpringContextUtilsTest

clearAuthentication() - Method in class ubic.gemma.model.expression.bioAssay.BioAssaySamplePayloadShapeTest

clearAuthentication() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObjectTest

clearCache() - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest

clearContext() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDaoTest

clearDispositions_erasesEveryRulingAndCounts() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

clearDispositions_onAnUnruledSet_isZero() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

clearedWhenTheBodyThrows() - Method in class ubic.gemma.core.security.util.ActingIdentityTest

It is cleared even when the body throws — an exception must not leave the name bound.

clearMissingCacheThrows404() - Method in class ubic.gemma.rest.AdminWebServiceTest

clearNamedCacheReturns204() - Method in class ubic.gemma.rest.AdminWebServiceTest

clearSecurityContext() - Method in class ubic.gemma.rest.AdminWebServiceTest

CliAssert - Class in ubic.gemma.cli.util.test

CliAssert(CLI) - Constructor for class ubic.gemma.cli.util.test.CliAssert

cliAuthenticationManager() - Method in class ubic.gemma.cli.util.test.AuthenticatedCliTestConfig

closeEnough(double[], double[], double) - Static method in class ubic.gemma.core.util.RegressionTesting

closeEnough(Object[], Object[]) - Static method in class ubic.gemma.core.util.RegressionTesting

Test whether two object arrays are the same (element-wise, ordered).

closeEnough(DoubleMatrix, DoubleMatrix, double) - Static method in class ubic.gemma.core.util.RegressionTesting

Test whether two DoubleMatrixes are 'close enough' to call equal.

collapsedSuffixIsStrippedFromTheVisibleQueryName() - Method in class ubic.gemma.core.analysis.sequence.BlatResult2PslTest

Gemma names the collapsed Affymetrix BioSequence <probe>_collapsed and UCSC renders the PSL query name as the track's visible item label, so the suffix reached the visitor: UIB measured the label reading "1007_s_at_collapsed" in the browser.

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

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

commitCuration_advancesAndResolvesTheLinkedCurationTicket() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

commitCuration_echoingIsBaselineFalseOnANullFlagIsNotAnEdit() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

Echoing isBaseline: false on a value whose stored flag is null is NOT an edit.

commitCuration_leavesATargetTheCuratorAlreadyFinished() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

A second commit does not drag a target backwards.

commitCuration_withoutAdvanceFlag_leavesTheTicketOpen() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

CommonalityRankingStrategyTest - Class in ubic.gemma.rest.ranking

Pure-data tests for ?rank=commonality.

CommonalityRankingStrategyTest() - Constructor for class ubic.gemma.rest.ranking.CommonalityRankingStrategyTest

CommonQueriesTest - Class in ubic.gemma.persistence.util

Native-SQL coverage gap from NATIVE_SQL_COVERAGE_AUDIT_2026_05_25.md Tier 1.

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

compassDir - Variable in class ubic.gemma.core.config.SettingsConfigTest

CompletionGeneratorTest - Class in ubic.gemma.cli.util

CompletionGeneratorTest() - Constructor for class ubic.gemma.cli.util.CompletionGeneratorTest

CompletionsWebServiceTest - Class in ubic.gemma.rest

Pure Mockito unit tests for CompletionsWebService.

CompletionsWebServiceTest() - Constructor for class ubic.gemma.rest.CompletionsWebServiceTest

composite_differsFromBothComponentsOnMixedSignal() - Method in class ubic.gemma.rest.AnnotationSearchRankingStrategyTest

composite_handlesEmptyQuery() - Method in class ubic.gemma.rest.AnnotationSearchRankingStrategyTest

composite_handlesEmptyUsageMap() - Method in class ubic.gemma.rest.AnnotationSearchRankingStrategyTest

composite_pullsHighCoveragePlusHighUsageToTop() - Method in class ubic.gemma.rest.AnnotationSearchRankingStrategyTest

composite_scoresCoverageAgainstTheMatchedSynonymNotJustTheLabel() - Method in class ubic.gemma.rest.AnnotationSearchRankingStrategyTest

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

Pins the identifier-match short-circuit in CompositeSearchSource: once any source returns a result tagged SearchResult.isExactIdentifierMatch(), subsequent sources are not consulted.

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

CompositeSequenceArgTest - Class in ubic.gemma.rest.util.args

CompositeSequenceArgTest() - Constructor for class ubic.gemma.rest.util.args.CompositeSequenceArgTest

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

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

CompositeSequenceFactory - Class in ubic.gemma.core.util.test.fixture

Typed factory for persistent CompositeSequence (probe) test fixtures.

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

CompositeSequenceFactory.Builder - Class in ubic.gemma.core.util.test.fixture

Fluent builder for a CompositeSequence.

CompositeSequenceFactoryTest - Class in ubic.gemma.core.util.test.fixture

Verifies the Phase 3 typed CompositeSequenceFactory.

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

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

Fast mock variant of CompositeSequenceGeneMapperServiceTest.

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

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

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

Lightweight unit test for CompositeSequenceReadServiceImpl that verifies each public method delegates to the right CompositeSequenceDao call without standing up a Spring context.

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

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

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

CompRowMatrixUtilsTest - Class in ubic.gemma.core.datastructure.sparse

CompRowMatrixUtilsTest() - Constructor for class ubic.gemma.core.datastructure.sparse.CompRowMatrixUtilsTest

Config() - Constructor for class ubic.gemma.core.loader.expression.singleCell.SingleCellDataTransformationsTest.Config

configurationsWithSideEffectsMustOptOutOfLazyByDefault() - Method in class ubic.gemma.core.context.SideEffectConfigurationEagerTest

configurationTravelsWithTheCounts() - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCorrelationAttritionMappingTest

The configuration travels with the counts: the sample-correlation filter is not the one the "filtered" data download runs, so the numbers are not interpretable on their own.

configure() - Method in class ubic.gemma.rest.OpenApiWebServiceTest

configure() - Method in class ubic.gemma.rest.providers.OntologyTermValidationExceptionMapperTest

configure() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterDisabledTest

configure() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest

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

configure() - Method in class ubic.gemma.rest.TicketsWebServiceScratchpadRoutingTest

configure() - Method in class ubic.gemma.rest.util.BaseJerseyTest5

configureClient(ClientConfig) - Method in class ubic.gemma.rest.util.BaseJerseyTest5

ConfigUtilsTest - Class in ubic.gemma.core.config

Covers the *_FILE indirection in ConfigUtils.resolveEnvVar(String, java.util.function.Function).

ConfigUtilsTest() - Constructor for class ubic.gemma.core.config.ConfigUtilsTest

conflictMessage_fallsBackToTheIdWhenThereIsNoShortName() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationServiceImplTest

An investigation that is not an experiment, or one with no short name yet, still has to produce a usable message rather than blowing up.

conflictMessage_namesTheExperimentByShortName() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationServiceImplTest

conflictMessage_namesTheExperimentByShortName_evenThroughALazyProxy() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationServiceImplTest

constantTimeHexEquals_caseInsensitive() - Method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoderTest

constructor_acceptsOneThreshold() - Method in class ubic.gemma.core.analysis.preprocess.filter.TooFewDistinctValuesFilterTest

constructor_acceptsZeroThreshold() - Method in class ubic.gemma.core.analysis.preprocess.filter.TooFewDistinctValuesFilterTest

constructor_parameters_must_not_be_impl_typed - Static variable in class ubic.gemma.core.architecture.AutowireImplRuleTest

Intentionally vacuous when no constructor-injected Impl-typed parameters exist — that is the goal state, subject to the same caveat as above: see AutowireImplRuleTest.classes_are_actually_imported(JavaClasses).

constructor_rejectsNegativeThreshold() - Method in class ubic.gemma.core.analysis.preprocess.filter.TooFewDistinctValuesFilterTest

constructor_rejectsThresholdAboveOne() - Method in class ubic.gemma.core.analysis.preprocess.filter.TooFewDistinctValuesFilterTest

containsSame(double[], double[]) - Static method in class ubic.gemma.core.util.RegressionTesting

Test whether two double arrays contain the same items in any order (tolerance is ZERO).

containsSame(Object[], Object[]) - Static method in class ubic.gemma.core.util.RegressionTesting

Test whether two object arrays contain the same items in any order.

containsSame(Collection, Collection) - Static method in class ubic.gemma.core.util.RegressionTesting

Test whether two collections contain the same items.

ContextConfig() - Constructor for class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

continuousFactorWithAMissingValueExcludesThatSample() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfoundUtilsTest

A batch factor confounded with a continuous factor, where one sample has no value for that factor.

continuousFactorWithTooFewUsableSamplesIsSkipped() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfoundUtilsTest

Once samples with no value are excluded, too few may be left to rank.

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

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

ContrastTest - Class in ubic.gemma.model.analysis.expression.diff

ContrastTest() - Constructor for class ubic.gemma.model.analysis.expression.diff.ContrastTest

cookies() - Method in class ubic.gemma.rest.util.ResponseAssert

copiesFieldsFromCursorPage() - Method in class ubic.gemma.rest.util.CursorPaginatedResponseDataObjectTest

correctedIsRejectedRatherThanSilentlyServedTheRawDistribution() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServicePvalueDistributionTest

correlAsByte_atNegativeOne_maps0() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

correlAsByte_atOne_maps255() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

correlAsByte_byteToCorrel_roundTrip_isLossyButBounded() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

correlAsByte_zero_isOneBelowHalfRange() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

correlationOfStandardized_array_identicalVectors_isOne() - Method in class ubic.gemma.core.util.math.DistanceTest

correlationOfStandardized_array_oppositeVectors_isNegativeOne() - Method in class ubic.gemma.core.util.math.DistanceTest

correlationOfStandardized_list_allNaN_returnsSentinel() - Method in class ubic.gemma.core.util.math.DistanceTest

correlationOfStandardized_list_mismatchedSizes_throws() - Method in class ubic.gemma.core.util.math.DistanceTest

correlationOfStandardized_list_skipsNaNs() - Method in class ubic.gemma.core.util.math.DistanceTest

CorrelationStatsTest - Class in ubic.gemma.core.util.math

Unit tests for CorrelationStats — the static stats facade used across coexpression, batch-confound detection, and PCA-correlate analyses.

CorrelationStatsTest() - Constructor for class ubic.gemma.core.util.math.CorrelationStatsTest

correlationTstat_atZero_isZero() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

correlationTstat_sign_matchesCorrelationSign() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

CorsFilterTest - Class in ubic.gemma.rest.servlet

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

countByRole() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

countRowsInTable(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

Count the rows in the given table.

counts_areDerivedAndStayInStepWithThePayload() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

countTicketsExtended_passesAllFiltersThroughToDao() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

Extended countTickets mirrors findTickets in dispatch — each filter argument lands on the DAO without massaging.

Coverage scope - Section in class ubic.gemma.persistence.service.expression.experiment.ReplaceAllRawDataVectorsQtCollisionTest

create(User) - Method in class ubic.gemma.core.security.UserServiceImpl

create(UserGroup) - Method in class ubic.gemma.core.security.UserServiceImpl

createAcl(ObjectIdentity) - Method in class ubic.gemma.core.security.acl.InMemoryAclService

createElementsMappingFromResourceFile(String) - Static method in class ubic.gemma.core.loader.expression.singleCell.MexTestUtils

Read the content of a MEX features file into an elements mapping.

createFactorWithMeasurementThatDiffersFromValue() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoTest

createFixtures() - Method in class ubic.gemma.rest.GeneWebServiceTest

createFixtures() - Method in class ubic.gemma.rest.TaxaWebServiceTest

createGroup(String, List) - Method in class ubic.gemma.core.security.GroupManagerImpl

createLoaderForResourceDir(String) - Static method in class ubic.gemma.core.loader.expression.singleCell.MexTestUtils

createObject() - Method in class ubic.gemma.core.context.AsyncBeanAutowiringTest.MyService2Factory

createObject() - Method in class ubic.gemma.core.context.AsyncBeanAutowiringTest.MyServiceFactory

createObject() - Method in class ubic.gemma.core.context.AsyncFactoryTest.MyServiceFactory

createObject() - Method in class ubic.gemma.core.context.AsyncSingletonFactoryTest.MyServiceFactory

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

createPreboarded_blankAccessionThrows() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceTest

createPreboarded_defaultsSourceWhenNull() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceTest

createPreboarded_existingAccessionReturns409WithIdAndType() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

createPreboarded_existingEEAccessionReturns409WithEEType() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

createPreboarded_existingExpressionExperimentThrows409() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceTest

createPreboarded_existingPreboardedThrows409() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceTest

createPreboarded_freshAccessionPersistsAndEmitsEvent() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceTest

createPreboarded_freshAccessionReturns201() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

createPreboarded_missingBodyThrows400() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

createUser(UserDetails) - Method in class ubic.gemma.core.security.UserDetailsManagerImpl

createUser_addsToAdminGroup_whenIsAdminTrue() - Method in class ubic.gemma.rest.AdminWebServiceTest

createUser_returns409_whenEmailTaken() - Method in class ubic.gemma.rest.AdminWebServiceTest

createUser_returns409_whenUsernameTaken() - Method in class ubic.gemma.rest.AdminWebServiceTest

createUser_returnsTempPassword_andCallsManager() - Method in class ubic.gemma.rest.AdminWebServiceTest

ctx - Variable in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataTransformationsTest

cumulativeProbability(int) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.NegativeBinomialDistribution

CuratableDaoTest - Class in ubic.gemma.persistence.service.common.auditAndSecurity

CuratableDaoTest() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.CuratableDaoTest

curatableOverload_rejectsTransientCuratable() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

curatableOverload_routesArrayDesignToADType() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

curatableOverload_routesExpressionExperimentToEEType() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

CuratableValueObjectTest - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation

CuratableValueObjectTest() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableValueObjectTest

CurationDecisionPersistenceIT - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Persistence contract for CurationDecision -- the record of a change a curator ruled must NOT be made.

CurationDecisionPersistenceIT() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionPersistenceIT

CurationDetailsServiceImplTest - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Lightweight Mockito unit tests for CurationDetailsServiceImpl, the compatibility shim that exposes the legacy CurationDetails read API over the Phase B-1 ticket layer (see AUDIT_AS_WORKFLOW_RECCE.md Decision 1).

CurationDetailsServiceImplTest() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

curationDetailsValueObjectBuiltAfterAThawCarriesTheEvents() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.DetachedCuratableValueObjectTest

curationDetailsValueObjectBuiltWithoutAThawDropsTheEventsRatherThanThrowing() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.DetachedCuratableValueObjectTest

CurationDraftDispositionsTest - Class in ubic.gemma.model.common.auditAndSecurity.curation

Pure unit tests for CurationDraftDispositions.

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

CurationLockPersistenceIT - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Contract for the advisory curation lock.

CurationLockPersistenceIT() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockPersistenceIT

curatorHasAdministrationOnAnObjectFromSetupBaseAces() - Method in class ubic.gemma.core.security.acl.AdminAclEvaluationTest

A curator holds ADMINISTRATION through the ace setupBaseAces now grants GROUP_CURATOR, which is what lets every ACL_SECURABLE_EDIT check pass for them.

curatorOverridesAnEarlierRejection() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationPersistenceIT

currentUserIsAdmin() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.TestAclAdvice

currentUserIsAnonymous() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.TestAclAdvice

currentUserIsRunningAsAdmin() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.TestAclAdvice

CursorArgTest - Class in ubic.gemma.rest.util.args

CursorArgTest() - Constructor for class ubic.gemma.rest.util.args.CursorArgTest

cursorModeBackwardWalkReversesOrderAndYieldsAscendingPage() - Method in class ubic.gemma.rest.DatasetsWebServiceExpressionLevelsForGeneCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.DatasetsWebServiceBlacklistedCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.DatasetsWebServiceByIdsCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.DatasetsWebServiceSamplesCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.DatasetsWebServiceSubSetSamplesCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.GeneWebServiceProbesCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.PlatformsWebServiceBlacklistedCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.PlatformsWebServiceByIdsCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.PlatformsWebServiceCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.PlatformsWebServiceDatasetsCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.PlatformsWebServiceElementCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.PlatformsWebServiceElementGenesCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.PlatformsWebServiceElementsCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.TaxaWebServiceCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.TaxaWebServiceGeneProbesCursorTest

cursorModeDecodesCursorAndForwardsToArgService() - Method in class ubic.gemma.rest.TaxaWebServiceGenesCursorTest

cursorModeDecodesCursorAndForwardsToService() - Method in class ubic.gemma.rest.DatasetsWebServiceAuditEventsCursorTest

cursorModeDecodesCursorAndForwardsToService() - Method in class ubic.gemma.rest.DatasetsWebServiceTicketsCursorTest

cursorModeDecodesCursorAndForwardsToService() - Method in class ubic.gemma.rest.PlatformsWebServiceTicketsCursorTest

cursorModeDecodesCursorAndForwardsToService() - Method in class ubic.gemma.rest.TicketsWebServiceCursorTest

cursorModeDecodesCursorAndForwardsToService() - Method in class ubic.gemma.rest.TicketsWebServiceEventsCursorTest

cursorModeEmptyDatasetIdsRoundTripsEmptyPage() - Method in class ubic.gemma.rest.DatasetsWebServiceExpressionLevelsForGeneCursorTest

cursorModeEmptyPageProducesEmptyResponseWithNoCursors() - Method in class ubic.gemma.rest.DatasetsWebServiceAuditEventsCursorTest

cursorModeEmptyPageProducesEmptyResponseWithNoCursors() - Method in class ubic.gemma.rest.DatasetsWebServiceTicketsCursorTest

cursorModeEmptyPageProducesEmptyResponseWithNoCursors() - Method in class ubic.gemma.rest.PlatformsWebServiceTicketsCursorTest

cursorModeEmptyPageProducesEmptyResponseWithNoCursors() - Method in class ubic.gemma.rest.TicketsWebServiceCursorTest

cursorModeEmptyPageProducesEmptyResponseWithNoCursors() - Method in class ubic.gemma.rest.TicketsWebServiceEventsCursorTest

cursorModeEmptyPageProducesEmptyResponseWithNoNextCursor() - Method in class ubic.gemma.rest.GeneWebServiceProbesCursorTest

cursorModeEmptyPageProducesEmptyResponseWithNoNextCursor() - Method in class ubic.gemma.rest.PlatformsWebServiceElementGenesCursorTest

cursorModeEmptyPageProducesEmptyResponseWithNoNextCursor() - Method in class ubic.gemma.rest.TaxaWebServiceGeneProbesCursorTest

cursorModeEmptyPageRoundTripsWithoutSynthesizedTokens() - Method in class ubic.gemma.rest.DatasetsWebServiceBlacklistedCursorTest

cursorModeEmptyPageRoundTripsWithoutSynthesizedTokens() - Method in class ubic.gemma.rest.DatasetsWebServiceByIdsCursorTest

cursorModeFirstPageReturnsAscendingIdsAndEmitsNextCursorWhenMore() - Method in class ubic.gemma.rest.DatasetsWebServiceExpressionLevelsForGeneCursorTest

cursorModeForwardsBothPlatformArgAndProbeArg() - Method in class ubic.gemma.rest.PlatformsWebServiceElementGenesCursorTest

cursorModeForwardsBothPlatformArgAndProbesArg() - Method in class ubic.gemma.rest.PlatformsWebServiceElementCursorTest

cursorModeForwardsComposedFiltersIncludingPathDatasetArg() - Method in class ubic.gemma.rest.DatasetsWebServiceByIdsCursorTest

cursorModeForwardsFiltersBuiltByArgService() - Method in class ubic.gemma.rest.DatasetsWebServiceBlacklistedCursorTest

cursorModeForwardsFilterTripleUnchanged() - Method in class ubic.gemma.rest.TicketsWebServiceCursorTest

cursorModeForwardsGeneArgUnchanged() - Method in class ubic.gemma.rest.GeneWebServiceProbesCursorTest

cursorModeForwardsGeneEntityResolution() - Method in class ubic.gemma.rest.DatasetsWebServiceExpressionLevelsForGeneCursorTest

cursorModeForwardsPlatformArg() - Method in class ubic.gemma.rest.PlatformsWebServiceDatasetsCursorTest

cursorModeForwardsPlatformArg() - Method in class ubic.gemma.rest.PlatformsWebServiceElementsCursorTest

cursorModeForwardsResolvedTaxon() - Method in class ubic.gemma.rest.TaxaWebServiceGenesCursorTest

cursorModeForwardsResolvedTaxonAndGeneArgUnchanged() - Method in class ubic.gemma.rest.TaxaWebServiceGeneProbesCursorTest

cursorModeInferredTermsEchoedInResponse() - Method in class ubic.gemma.rest.DatasetsWebServiceBlacklistedCursorTest

cursorModeInferredTermsEchoedInResponse() - Method in class ubic.gemma.rest.DatasetsWebServiceByIdsCursorTest

cursorModeInferredTermsEchoedInResponse() - Method in class ubic.gemma.rest.DatasetsWebServiceExpressionLevelsForGeneCursorTest

cursorModeLastPageOmitsNextCursor() - Method in class ubic.gemma.rest.DatasetsWebServiceExpressionLevelsForGeneCursorTest

cursorModeMapsGeneEntitiesToValueObjects() - Method in class ubic.gemma.rest.PlatformsWebServiceElementGenesCursorTest

cursorModePassesNullCursorThrough() - Method in class ubic.gemma.rest.GeneWebServiceCursorTest

cursorModePreservesAscendingIdOrderFromDao() - Method in class ubic.gemma.rest.GeneWebServiceProbesCursorTest

cursorModePreservesAscendingIdOrderFromDao() - Method in class ubic.gemma.rest.TaxaWebServiceGeneProbesCursorTest

cursorModePreservesAscendingIdOrderFromService() - Method in class ubic.gemma.rest.DatasetsWebServiceAuditEventsCursorTest

cursorModePreservesAscendingIdOrderFromService() - Method in class ubic.gemma.rest.DatasetsWebServiceTicketsCursorTest

cursorModePreservesAscendingIdOrderFromService() - Method in class ubic.gemma.rest.PlatformsWebServiceTicketsCursorTest

cursorModePreservesAscendingIdOrderFromService() - Method in class ubic.gemma.rest.TicketsWebServiceCursorTest

cursorModePreservesAscendingIdOrderFromService() - Method in class ubic.gemma.rest.TicketsWebServiceEventsCursorTest

cursorModePreservesDatasetScope() - Method in class ubic.gemma.rest.DatasetsWebServiceAuditEventsCursorTest

cursorModePreservesDatasetScope() - Method in class ubic.gemma.rest.DatasetsWebServiceTicketsCursorTest

cursorModePreservesPathIdSetPredicate() - Method in class ubic.gemma.rest.PlatformsWebServiceByIdsCursorTest

cursorModePreservesPlatformScope() - Method in class ubic.gemma.rest.PlatformsWebServiceTicketsCursorTest

cursorModePreservesTicketScope() - Method in class ubic.gemma.rest.TicketsWebServiceEventsCursorTest

cursorModeRejectsMismatchedSortSpec() - Method in class ubic.gemma.rest.DatasetsWebServiceExpressionLevelsForGeneCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorPaginatedResponse() - Method in class ubic.gemma.rest.DatasetsWebServiceAuditEventsCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorPaginatedResponse() - Method in class ubic.gemma.rest.DatasetsWebServiceSamplesCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorPaginatedResponse() - Method in class ubic.gemma.rest.DatasetsWebServiceSubSetSamplesCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorPaginatedResponse() - Method in class ubic.gemma.rest.DatasetsWebServiceTicketsCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorPaginatedResponse() - Method in class ubic.gemma.rest.PlatformsWebServiceTicketsCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorPaginatedResponse() - Method in class ubic.gemma.rest.TicketsWebServiceEventsCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorResponse() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorResponse() - Method in class ubic.gemma.rest.DatasetsWebServiceBlacklistedCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorResponse() - Method in class ubic.gemma.rest.DatasetsWebServiceByIdsCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorResponse() - Method in class ubic.gemma.rest.GeneWebServiceCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorResponse() - Method in class ubic.gemma.rest.GeneWebServiceProbesCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorResponse() - Method in class ubic.gemma.rest.PlatformsWebServiceBlacklistedCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorResponse() - Method in class ubic.gemma.rest.PlatformsWebServiceByIdsCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorResponse() - Method in class ubic.gemma.rest.PlatformsWebServiceCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorResponse() - Method in class ubic.gemma.rest.PlatformsWebServiceDatasetsCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorResponse() - Method in class ubic.gemma.rest.PlatformsWebServiceElementsCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorResponse() - Method in class ubic.gemma.rest.TaxaWebServiceCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorResponse() - Method in class ubic.gemma.rest.TaxaWebServiceGeneProbesCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorResponse() - Method in class ubic.gemma.rest.TaxaWebServiceGenesCursorTest

cursorModeRoutesToCursorHelperAndReturnsCursorResponse() - Method in class ubic.gemma.rest.TicketsWebServiceCursorTest

cursorModeRoutesToCursorHelperAndReturnsFilteredCursorResponse() - Method in class ubic.gemma.rest.PlatformsWebServiceElementCursorTest

cursorModeRoutesToCursorHelperAndReturnsFilteredCursorResponse() - Method in class ubic.gemma.rest.PlatformsWebServiceElementGenesCursorTest

cursorModeSkipsUserSortArg() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceCursorTest

cursorModeSkipsUserSortArg() - Method in class ubic.gemma.rest.DatasetsWebServiceBlacklistedCursorTest

cursorModeSkipsUserSortArg() - Method in class ubic.gemma.rest.DatasetsWebServiceByIdsCursorTest

cursorModeSkipsUserSortArg() - Method in class ubic.gemma.rest.PlatformsWebServiceBlacklistedCursorTest

cursorModeSkipsUserSortArg() - Method in class ubic.gemma.rest.PlatformsWebServiceByIdsCursorTest

cursorModeSkipsUserSortArg() - Method in class ubic.gemma.rest.PlatformsWebServiceCursorTest

cursorModeSkipsUserSortArg() - Method in class ubic.gemma.rest.TaxaWebServiceCursorTest

cursorModeWithEmptyPageRoundTripsThroughWrapper() - Method in class ubic.gemma.rest.DatasetsWebServiceSubSetSamplesCursorTest

cursorModeWithoutLimitUsesTheDefaultPageSize() - Method in class ubic.gemma.rest.DatasetsWebServiceAuditEventsCursorTest

cursorModeWithoutLimitUsesTheDefaultPageSize() - Method in class ubic.gemma.rest.DatasetsWebServiceSamplesCursorTest

Cursor mode still has a page size when the caller sends none — dropping @DefaultValue("20") from the parameter moved that default into the method, and it has to still be there.

cursorModeWithoutLimitUsesTheDefaultPageSize() - Method in class ubic.gemma.rest.DatasetsWebServiceSubSetSamplesCursorTest

Cursor mode still has a page size when the caller sends none — dropping @DefaultValue("20") from the parameter moved that default into the method, and it has to still be there.

CursorPageTest - Class in ubic.gemma.persistence.util

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

CursorPaginatedResponseDataObjectTest - Class in ubic.gemma.rest.util

CursorPaginatedResponseDataObjectTest() - Constructor for class ubic.gemma.rest.util.CursorPaginatedResponseDataObjectTest

CursorTest - Class in ubic.gemma.persistence.util

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

cursorWithQuantitationTypeIsRejectedAs400() - Method in class ubic.gemma.rest.DatasetsWebServiceSamplesCursorTest

cursorWithUseProcessedQuantitationTypeIsRejectedAs400() - Method in class ubic.gemma.rest.DatasetsWebServiceSamplesCursorTest

CustomResource() - Constructor for class ubic.gemma.rest.providers.OntologyTermValidationExceptionMapperTest.CustomResource

CustomResource() - Constructor for class ubic.gemma.rest.providers.UnknownQueryParameterFilterDisabledTest.CustomResource

CustomResource() - Constructor for class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest.CustomResource

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

cycleGuard_handlesSelfReferentialBackRef() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest

D

DatabaseEntryArgTest - Class in ubic.gemma.rest.util.args

DatabaseEntryArgTest() - Constructor for class ubic.gemma.rest.util.args.DatabaseEntryArgTest

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

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

datasetArgService(ExpressionExperimentService, SearchService) - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

DatasetArgTest - Class in ubic.gemma.rest.util.args

DatasetArgTest() - Constructor for class ubic.gemma.rest.util.args.DatasetArgTest

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

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

datasetRestService(ExpressionExperimentService, SearchService) - Method in class ubic.gemma.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

DatasetsCurationCommitRestTest - Class in ubic.gemma.rest

End-to-end regression harness for the composite curation commit (PUT /datasets/{id}/curation) against a real (gemdtest) database — the persistence half the mocked DatasetsWebServiceTest can't reach.

DatasetsCurationCommitRestTest() - Constructor for class ubic.gemma.rest.DatasetsCurationCommitRestTest

DatasetsDiagnosticsRestTest - Class in ubic.gemma.rest

Integration tests for the diagnostics endpoints (mean-variance, sample-correlation, svd) on DatasetsWebService.

DatasetsDiagnosticsRestTest() - Constructor for class ubic.gemma.rest.DatasetsDiagnosticsRestTest

DatasetsPlatformsRestTest - Class in ubic.gemma.rest

Integration tests for GET /datasets/{dataset}/platforms, in both modes, against a real (gemdtest) database.

DatasetsPlatformsRestTest() - Constructor for class ubic.gemma.rest.DatasetsPlatformsRestTest

DatasetsRestTest - Class in ubic.gemma.rest

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

DatasetsWebServiceAuditEventsCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to DatasetsWebService.getDatasetAuditEvents(DatasetArg, CursorArg, LimitArg, boolean, boolean) as step 1q of CURSOR_PAGINATION_STEP1_PLAN.md.

DatasetsWebServiceAuditEventsCursorTest() - Constructor for class ubic.gemma.rest.DatasetsWebServiceAuditEventsCursorTest

DatasetsWebServiceBlacklistedCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to DatasetsWebService.getBlacklistedDatasets(FilterArg, SortArg, OffsetArg, LimitArg, CursorArg) as step 1t of CURSOR_PAGINATION_STEP1_PLAN.md (the EE-targeted twin of step 1h's /platforms/blacklisted).

DatasetsWebServiceBlacklistedCursorTest() - Constructor for class ubic.gemma.rest.DatasetsWebServiceBlacklistedCursorTest

DatasetsWebServiceByIdsCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to DatasetsWebService.getDatasetsByIds(DatasetArrayArg, FilterArg, OffsetArg, LimitArg, SortArg, CursorArg) as step 1w of CURSOR_PAGINATION_STEP1_PLAN.md.

DatasetsWebServiceByIdsCursorTest() - Constructor for class ubic.gemma.rest.DatasetsWebServiceByIdsCursorTest

DatasetsWebServiceExpressionLevelsForGeneCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to DatasetsWebService.getDatasetsExpressionLevelsForGene(GeneArg, ubic.gemma.rest.util.args.QueryArg, FilterArg, OffsetArg, LimitArg, Boolean, ubic.gemma.rest.util.args.ExpLevelConsolidationArg, CursorArg, Boolean) and its taxon-scoped sibling, as step 1v of CURSOR_PAGINATION_STEP1_PLAN.md.

DatasetsWebServiceExpressionLevelsForGeneCursorTest() - Constructor for class ubic.gemma.rest.DatasetsWebServiceExpressionLevelsForGeneCursorTest

DatasetsWebServiceSamplesCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to DatasetsWebService.getDatasetSamples(DatasetArg, QuantitationTypeArg, boolean, CursorArg, LimitArg, ExcludeArg, boolean) as step 1k of CURSOR_PAGINATION_STEP1_PLAN.md.

DatasetsWebServiceSamplesCursorTest() - Constructor for class ubic.gemma.rest.DatasetsWebServiceSamplesCursorTest

DatasetsWebServiceSubSetSamplesCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to DatasetsWebService#getDatasetSubSetSamples(DatasetArg, Long, CursorArg, LimitArg) as step 1u of CURSOR_PAGINATION_STEP1_PLAN.md.

DatasetsWebServiceSubSetSamplesCursorTest() - Constructor for class ubic.gemma.rest.DatasetsWebServiceSubSetSamplesCursorTest

DatasetsWebServiceTest - Class in ubic.gemma.rest

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

DatasetsWebServiceTicketsBulkTest - Class in ubic.gemma.rest

Unit tests for DatasetsWebService.getDatasetTicketsBulk(DatasetsWebService.DatasetTicketsBulkRequest) — the bulk read behind the experiment list's "on a ticket" glyph.

DatasetsWebServiceTicketsBulkTest() - Constructor for class ubic.gemma.rest.DatasetsWebServiceTicketsBulkTest

DatasetsWebServiceTicketsCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to DatasetsWebService.getDatasetTickets(DatasetArg, CursorArg, LimitArg) as step 1p of CURSOR_PAGINATION_STEP1_PLAN.md.

DatasetsWebServiceTicketsCursorTest() - Constructor for class ubic.gemma.rest.DatasetsWebServiceTicketsCursorTest

DatasetUpdateSummaryValueObjectTest - Class in ubic.gemma.rest

Pure-data tests for the lastUpdate label vocabulary — no Spring, no database.

DatasetUpdateSummaryValueObjectTest() - Constructor for class ubic.gemma.rest.DatasetUpdateSummaryValueObjectTest

DatasetVisualizationWebServiceTest - Class in ubic.gemma.rest

Unit tests for HeatmapDataService (the assembler that backs DatasetVisualizationWebService).

DatasetVisualizationWebServiceTest() - Constructor for class ubic.gemma.rest.DatasetVisualizationWebServiceTest

dataSource() - Method in class ubic.gemma.core.util.test.BaseDatabaseTest5.BaseDatabaseTestContextConfiguration

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

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

DataVectorDescriptiveTest - Class in ubic.gemma.core.analysis.stats

DataVectorDescriptiveTest() - Constructor for class ubic.gemma.core.analysis.stats.DataVectorDescriptiveTest

DateStorageTest - Class in ubic.gemma.persistence.util

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

decodeRejectsEmpty() - Method in class ubic.gemma.persistence.util.CursorTest

decodeRejectsEmptyKeyTupleInPayload() - Method in class ubic.gemma.persistence.util.CursorTest

decodeRejectsInvalidDirection() - Method in class ubic.gemma.persistence.util.CursorTest

decodeRejectsMissingFields() - Method in class ubic.gemma.persistence.util.CursorTest

decodeRejectsNonBase64() - Method in class ubic.gemma.persistence.util.CursorTest

decodeRejectsNonJson() - Method in class ubic.gemma.persistence.util.CursorTest

decodeRejectsNull() - Method in class ubic.gemma.persistence.util.CursorTest

decodeRejectsUnsupportedVersion() - Method in class ubic.gemma.persistence.util.CursorTest

decodesValidCursor() - Method in class ubic.gemma.rest.util.args.CursorArgTest

defaults_returnPersistentBA_withAutoCreatedBMAndAD() - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactoryTest

defaults_returnPersistentCS_withAutoCreatedADAndBioSequence() - Method in class ubic.gemma.core.util.test.fixture.CompositeSequenceFactoryTest

defaults_returnPersistentMouseGene_withSyntheticNcbiId() - Method in class ubic.gemma.core.util.test.fixture.GeneFactoryTest

defaults_roundTrip() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

degradedPathStillEnforcesRead() - Method in class ubic.gemma.core.search.source.HibernateSearchSourceAclFilterTest

Per-hit READ decisions still apply on the degraded path — it re-reads the ACLs, it doesn't wave them through.

DelegatingSecurityContextSchedulingTaskExecutorTest - Class in ubic.gemma.core.security.concurrent

Guards the shutdown-event round-trip for the scheduling wrapper.

DelegatingSecurityContextSchedulingTaskExecutorTest() - Constructor for class ubic.gemma.core.security.concurrent.DelegatingSecurityContextSchedulingTaskExecutorTest

DelegatingSecurityContextTaskExecutorTest - Class in ubic.gemma.core.security.concurrent

DelegatingSecurityContextTaskExecutorTest() - Constructor for class ubic.gemma.core.security.concurrent.DelegatingSecurityContextTaskExecutorTest

delete(User) - Method in class ubic.gemma.core.security.UserServiceImpl

delete(UserGroup) - Method in class ubic.gemma.core.security.UserServiceImpl

deleteAcl(ObjectIdentity, boolean) - Method in class ubic.gemma.core.security.acl.InMemoryAclService

deleteBlacklistEntry_happyPath_returns204() - Method in class ubic.gemma.rest.AdminWebServiceTest

deleteBlacklistEntry_returns404_whenAccessionNotFound() - Method in class ubic.gemma.rest.AdminWebServiceTest

deleteFromTables(String...) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

Convenience method for deleting all rows from the specified tables.

deleteGroup(String) - Method in class ubic.gemma.core.security.GroupManagerImpl

deleteLineNamesTheExperimentNotJustItsId() - Method in class ubic.gemma.core.security.audit.AuditLoggerTest

deleteSid(Sid) - Method in class ubic.gemma.core.security.acl.InMemoryAclService

deleteUser(String) - Method in class ubic.gemma.core.security.UserDetailsManagerImpl

deleteUser_callsSoftDelete_andReturns204() - Method in class ubic.gemma.rest.AdminWebServiceTest

deleteUser_returns404_whenUserNotFound() - Method in class ubic.gemma.rest.AdminWebServiceTest

deleteUser_returns409_whenSelfDelete() - Method in class ubic.gemma.rest.AdminWebServiceTest

denies_when_voter_denies() - Method in class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManagerTest

derivedLabelsKeepAcronymsAndDropTheEventSuffix() - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObjectTest

DescribableUtilsTest - Class in ubic.gemma.model.common

DescribableUtilsTest() - Constructor for class ubic.gemma.model.common.DescribableUtilsTest

designation_penalty_does_not_fire_on_ordinary_names() - Method in class ubic.gemma.rest.ranking.CommonalityRankingStrategyTest

DetachedCuratableValueObjectTest - Class in ubic.gemma.model.common.auditAndSecurity.curation

Pins the contract between thawing a curatable and building its value object once the entity has left the session it was loaded in.

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

detachedEntitySkipsEntityPathEntirely() - Method in class ubic.gemma.core.search.SearchServiceImplTest

A DETACHED entity must go straight to the id-path, without attempting the entity path at all: the entity-path converter walks lazy associations, so on a detached entity it can only fail — and before the up-front check, every anonymous /search result did exactly that (sub-transaction, LazyInitException, one retry by the generic retry advice, a WARN, and then the id-path anyway; 6/6 requests in the 2026-08-19 perf baseline).

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

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

DifferentialExpressionAnalysisCliTest - Class in ubic.gemma.apps

DifferentialExpressionAnalysisCliTest() - Constructor for class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

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

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

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

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

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

Lightweight unit test for DifferentialExpressionAnalysisReadServiceImpl that verifies each public method delegates to the right DAO call without standing up a Spring context.

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

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

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

DifferentialExpressionAnalysisTaskImplTest - Class in ubic.gemma.core.tasks.analysis.diffex

Removing an analysis has to take its on-disk artifacts with it, whichever route asks for the removal.

DifferentialExpressionAnalysisTaskImplTest() - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskImplTest

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

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

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

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

DifferentialExpressionResultPrecisionTest - Class in ubic.gemma.model.analysis.expression.diff

Wire-form guards for the differential-expression statistics, which serialize on every route that carries these value objects — /resultSets/{id} and the /datasets/analyses/differential/results family among them.

DifferentialExpressionResultPrecisionTest() - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionResultPrecisionTest

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

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

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

Unit tests for the R-friendly name helpers in DiffExAnalyzerUtils + the interaction-term formatter.

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

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

Samples marked DE_Exclude and samples whose assays are flagged as outliers must leave the analysis before anything is decided from the sample set.

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

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

Pure-mock unit test for DiffExGeneWarmupService.

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

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

DistanceTest - Class in ubic.gemma.core.util.math

Unit tests for Distance: alternative distance + similarity helpers used by the coexpression and sample-clustering paths.

DistanceTest() - Constructor for class ubic.gemma.core.util.math.DistanceTest

DOE - Enum constant in enum class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest.FakeEnum

doesNotCutInsideALegend() - Method in class ubic.gemma.core.loader.expression.geo.GeoColonSplitTest

doesNotCutInsideAParenthesisedValue() - Method in class ubic.gemma.core.loader.expression.geo.GeoColonSplitTest

doesNotHaveEncoding(String) - Method in class ubic.gemma.rest.util.ResponseAssert

doesNotHaveHeader(String) - Method in class ubic.gemma.rest.util.ResponseAssert

Asserts that the response does not have the given header.

doesNotHaveHeaderWithValue(String, String) - Method in class ubic.gemma.rest.util.ResponseAssert

Asserts that the response does not have the given header with a particular value.

doesNotHavePath(String) - Method in class ubic.gemma.rest.util.JsonAssert

Ensure that a given path does not exist.

doesNotShatterASinglePairOnItsValuesCommas() - Method in class ubic.gemma.core.loader.expression.geo.GeoColonSplitTest

doesNotTouchRealGreek() - Method in class ubic.gemma.core.util.SymbolFontPuaTest

doubleArrayRoundTrip_preservesValuesInOrder() - Method in class ubic.gemma.persistence.util.ByteArrayUtilsTest

doubleMatrixRoundTrip_preservesShape() - Method in class ubic.gemma.persistence.util.ByteArrayUtilsTest

downBinningMergesWholeStoredBinsAndPreservesTheTotal() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServicePvalueDistributionTest

downloadMatchingTheRemoteSize_succeedsAndKeepsTheFile(Path) - Method in class ubic.gemma.core.util.NetUtilsTest

downloadPath - Variable in class ubic.gemma.core.config.SettingsConfigTest

downloadServesAnAttachmentNamedForTheProbe() - Method in class ubic.gemma.rest.PlatformsWebServicePslTrackTest

draft_parentLineageRoundTrip() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

draft_upsertReplacesInPlace() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

draftWithNoParent_reportsOnlyParked() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositionsTest

A draft with no parent has no diff baseline: every element reads as new, so nothing but parked keys can be reported.

dropsItemsCurrentUserOwnsButLacksRequiredPermissionOn() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationOwnedCollectionFilteringProviderTest

dropsPrivateItemsTheUserCannotRead() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationPrivateCollectionFilteringProviderTest

dryRun_cleanScanReportsNoIncompleteRecords() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

dryRun_emitsWhyEachCriterionFired() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

dryRun_namesRecordsGeoServedUnusableMinimlFor() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

dryRun_reportsAnAbsoluteNextOffset() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

dryRun_reportsTheLastRecordScannedNotJustTheLastMatched() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

dryRun_skipResumesAtRecordLevelNotAtTheStartOfTheDay() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

dualAnnotated_failurePath_firesOnlyAuditedOnError() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C: dual-annotated method on the failure path — only the @AuditedOnError path fires; the @Audited @AfterReturning advice does not.

dualAnnotated_successPath_firesOnlyAuditedNotOnError() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C: a method may carry BOTH Audited AND AuditedOnError — the two advice paths are disjoint.

E

edited_whenProposalAndDraftDiffer() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositionsTest

EeWriteServiceImplQtDedupTest - Class in ubic.gemma.persistence.persister

Pins the behaviourally load-bearing QuantitationType dedup semantic that was lifted out of CommonPersister.persistQuantitationType into a per-EE local map in EeWriteServiceImpl.

EeWriteServiceImplQtDedupTest() - Constructor for class ubic.gemma.persistence.persister.EeWriteServiceImplQtDedupTest

effectiveForIds_omitsUnruledSets() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriagePersistenceIT

effectiveIsMostRecent_notCuratorByRank() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriagePersistenceIT

emitsSnakeCase() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TriageVerdictTest

emptyAD_hasNoProbes_withSequencesIsNoOp() - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactoryTest

emptyAlignmentSetIsRefused() - Method in class ubic.gemma.core.analysis.sequence.BlatResult2PslTest

emptyArraysAreZero() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetPayloadCountsTest

emptyBothSides_stillSurfacesParkedKeys() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositionsTest

emptyCollection_passesThrough() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest

emptyCollection_passesThrough() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationOwnedCollectionFilteringProviderTest

emptyCollection_passesThrough() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationPrivateCollectionFilteringProviderTest

emptyCollection_passesThrough() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest

emptyDoubleArray_roundTrips() - Method in class ubic.gemma.persistence.util.ByteArrayUtilsTest

emptyFactorList_yieldsEmptyMap() - Method in class ubic.gemma.core.util.math.linearmodels.LinearModelSummaryUtilsTest

emptyFirstSourceFallsThroughToSecond() - Method in class ubic.gemma.core.search.source.CompositeSearchSourceTest

emptyGeneMappingSummariesSerializeAsEmptyArray() - Method in class ubic.gemma.rest.PlatformsWebServiceMappingSummaryTest

A probe with no alignments must serialize as an EMPTY array, not an absent key — UIB cannot otherwise distinguish "this probe has no mappings" from "the feature is missing".

emptyMap_passesThroughEmpty() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapFilteringProviderTest

emptyMap_passesThroughEmpty() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapValueFilteringProviderTest

emptyMap_passesThroughEmpty() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest

emptyMap_passesThroughEmpty() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest

emptyPageWorks() - Method in class ubic.gemma.persistence.util.CursorPageTest

emptyRejectedStillClearsStandingRejections() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationPersistenceIT

emptyResultsShortCircuitWithoutTouchingTheAclService() - Method in class ubic.gemma.core.search.source.HibernateSearchSourceAclFilterTest

emptyStream_passesThroughEmpty() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationStreamFilteringProviderTest

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

An arm of the subset factor that no analyzed sample carries is skipped, not a fatal condition for the experiment.

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

encode_isNotDeterministic() - Method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoderTest

encode_producesBcryptPrefixed_andMatchesBack() - Method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoderTest

encodedTokenIsBase64UrlSafe() - Method in class ubic.gemma.persistence.util.CursorTest

encodingHeaderWithoutAWrappedStreamStillUsesSendfile() - Method in class ubic.gemma.rest.providers.SendfileProviderTest

A Content-Encoding header alone must NOT disable sendfile: that is exactly the situation of the endpoints declaring @GZIP(alreadyCompressed = true), whose header is appended after the encoder has already declined to wrap the stream.

EnsemblIdDesignElementMapperTest - Class in ubic.gemma.core.loader.util.mapper

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

ensureAcl(Securable) - Method in class ubic.gemma.core.security.acl.InMemoryAclService

Create-or-get the ACL for entity without granting anything — useful when a test needs the entity to be ACL-known but with no permissions for the test principal.

entity() - Method in class ubic.gemma.rest.util.ResponseAssert

EntityArrayArgsTest - Class in ubic.gemma.rest.util.args

Focused tests for the AbstractEntityArrayArg-backed comma-delimited arg parsers.

EntityArrayArgsTest() - Constructor for class ubic.gemma.rest.util.args.EntityArrayArgsTest

entityAs(Class) - Method in class ubic.gemma.rest.util.ResponseAssert

entityAsStream() - Method in class ubic.gemma.rest.util.ResponseAssert

entityAsString() - Method in class ubic.gemma.rest.util.ResponseAssert

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

entityPathFailurePromotesToIdPath() - Method in class ubic.gemma.core.search.SearchServiceImplTest

Behavioural fallback: when the entity-path converter throws ConversionFailedException (the wrap around LazyInitializationException), SearchServiceImpl.loadValueObjects(Collection) must catch it and fall through to the id-path rather than propagating.

entityPathFallsBackToInlineWhenNoTxManager() - Method in class ubic.gemma.core.search.SearchServiceImplTest

When no PlatformTransactionManager is wired (existing unit-test contexts), the entity path falls back to an inline convert.

entityPathTxTemplateUsesRequiresNewAndReadOnly() - Method in class ubic.gemma.core.search.SearchServiceImplTest

Pins the sub-transaction template configuration: REQUIRES_NEW + readOnly.

EntityUrlBuilderTest - Class in ubic.gemma.persistence.util

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

EntityUtilsTest - Class in ubic.gemma.persistence.util

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

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

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

EnumConverterTest - Class in ubic.gemma.cli.util

EnumConverterTest() - Constructor for class ubic.gemma.cli.util.EnumConverterTest

equals(Object) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest.ItemVO

equals(Object) - Method in class ubic.gemma.core.security.audit.AuditedAspectTest.FakeAuditable

equals(Object) - Method in record class ubic.gemma.core.security.audit.AuditedAspectTest.SamplePayload

Indicates whether some other object is "equal to" this one.

equalsAndHashCode() - Method in class ubic.gemma.persistence.util.CursorTest

equalsByTypeAndIdentifierWhenPopulated() - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentityTest

equalsHandlesUninitializedTypeAndIdentifier() - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentityTest

ErrorsAssert - Class in ubic.gemma.rest.util

ErrorsAssert(Errors) - Constructor for class ubic.gemma.rest.util.ErrorsAssert

euclDistance_identicalVectors_isZero() - Method in class ubic.gemma.core.util.math.DistanceTest

euclDistance_mismatchedSizes_throws() - Method in class ubic.gemma.core.util.math.DistanceTest

euclDistance_simpleCase_pythagorean() - Method in class ubic.gemma.core.util.math.DistanceTest

euclDistance_skipsNaNs() - Method in class ubic.gemma.core.util.math.DistanceTest

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

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

EventListenerRegistrationLazyContextTest - Class in ubic.gemma.core.security.acl

Regression guard for the CLI-only failure in which the Hibernate event listeners were never registered.

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

events_listOrderedByOccurredAt() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

everyAlignmentOfTheProbeLandsInTheOneTrack() - Method in class ubic.gemma.rest.PlatformsWebServicePslTrackTest

The whole point of keying on the probe rather than on a BLAT result id: every alignment of the probe belongs in one track, so the user sees them together.

everyColumnExcludedIsRejectedRatherThanProducingNaN() - Method in class ubic.gemma.core.util.math.QuantileReferenceColumnsTest

everyDivisorOf100IsAcceptedIncludingTheDefault20() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServicePvalueDistributionTest

everyRenderedParameterIsBound() - Method in class ubic.gemma.persistence.util.SubqueryConjunctionTest

Rendering and binding derive parameter names independently; if they drift, the query builds and then dies at bind time.

everyRepresentationOfTheRepeatedShapeGetsExactlyOneDecorator() - Method in class ubic.gemma.rest.providers.GzipHeaderDecoratorTest

Neither decorator may leave a representation both unlabelled and uncompressed — that is the silent-regression shape, and it is what a dropped container annotation looks like from the outside.

everyTargetAcrossEveryTicketResolvesInOneCall() - Method in class ubic.gemma.rest.TicketsWebServiceTargetLabelsTest

🛑 The point of the fix.

everyValueRoundTrips() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TriageVerdictTest

exactIdentifierHitShortCircuitsLaterSources() - Method in class ubic.gemma.core.search.source.CompositeSearchSourceTest

ExceptionWithMessage(String) - Constructor for exception class ubic.gemma.persistence.service.AbstractServiceTest.ExceptionWithMessage

ExceptionWithoutMessage() - Constructor for exception class ubic.gemma.persistence.service.AbstractServiceTest.ExceptionWithoutMessage

ExcludeArgTest - Class in ubic.gemma.rest.util.args

ExcludeArgTest() - Constructor for class ubic.gemma.rest.util.args.ExcludeArgTest

excludedWordsFromStemming() - Method in class ubic.gemma.core.ontology.TestOntologyConfig

excludingAnExtremeColumnLeavesTheOthersToNormalizeAmongThemselves() - Method in class ubic.gemma.core.util.math.QuantileReferenceColumnsTest

An extreme column left in the reference drags it; excluded, the remaining columns normalize among themselves.

executeAs(JobExecutionContext) - Method in class ubic.gemma.core.job.SchedulerSecurityTest.TestSecureJob

executeCommand(CLIContext) - Method in class ubic.gemma.apps.TestCli

executeRunnableThatThrows_incrementsFailed() - Method in class ubic.gemma.core.metrics.binder.VirtualThreadExecutorMetricsTest

ExecutingTaskTest - Class in ubic.gemma.core.job

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

ExecutorsTest - Class in ubic.gemma.core.util.concurrent

Unit tests for Executors: the in-tree factory that wraps every executor produced for the project with Spring-Security's DelegatingSecurityContextExecutorService plus the log4j ThreadContext propagator.

ExecutorsTest() - Constructor for class ubic.gemma.core.util.concurrent.ExecutorsTest

existingNonEmptyTrail_postInsert_doesNotAppendDuplicateCreate() - Method in class ubic.gemma.persistence.audit.AuditTrailEventListenerTest

exitCause() - Method in class ubic.gemma.cli.util.test.CliAssert

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

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

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

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

ExperimentalDesignVisualizationServiceTest - Class in ubic.gemma.core.visualization

ExperimentalDesignVisualizationServiceTest() - Constructor for class ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceTest

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

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

experimentalFactorOntologyService(TaskExecutor) - Method in class ubic.gemma.core.ontology.TestOntologyConfig

ExperimentalFactorServiceTest - Class in ubic.gemma.persistence.service.expression.experiment

ExperimentalFactorServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorServiceTest

experimentBehindAnInvestigationProxy_stillUpdatesCurationDetails() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplCuratableDispatchTest

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

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

ExperimentFactory - Class in ubic.gemma.core.util.test.fixture

Typed factory for persistent ExpressionExperiment test fixtures.

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

ExperimentFactory.Builder - Class in ubic.gemma.core.util.test.fixture

Fluent builder for an ExpressionExperiment.

ExperimentFactory.Modality - Enum Class in ubic.gemma.core.util.test.fixture

Modality of the experiment being built.

ExperimentFactoryTest - Class in ubic.gemma.core.util.test.fixture

Verifies the Phase 3 typed test-fixture factory.

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

ExperimentSetsWebServiceTest - Class in ubic.gemma.rest

Pure Mockito tests for ExperimentSetsWebService: the resource → service wiring, and the guards that decide what reaches the service at all.

ExperimentSetsWebServiceTest() - Constructor for class ubic.gemma.rest.ExperimentSetsWebServiceTest

expiredLockReadsAsFree() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockPersistenceIT

ExpLevelConsolidationArgTest - Class in ubic.gemma.rest.util.args

ExpLevelConsolidationArgTest() - Constructor for class ubic.gemma.rest.util.args.ExpLevelConsolidationArgTest

explicitFields_roundTrip() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

exposes_configured_attribute() - Method in class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManagerTest

ExpressionAnalysisResultSetArgTest - Class in ubic.gemma.rest.util.args

ExpressionAnalysisResultSetArgTest() - Constructor for class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArgTest

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

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

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 org.hibernate.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

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

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

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

Unit tests for ExpressionDataFileUtils.getDiffExArchiveFileName(DifferentialExpressionAnalysis), which resolves an analysis' experimentAnalyzed down to a short name.

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

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

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

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

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

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

Unit tests for ExpressionExperimentBatchCorrectionServiceImpl that need no Spring context: the comBat(ee, matrix) path only reads the experiment's in-memory design, so the impl can be constructed directly.

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

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

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

ExpressionExperimentBatchInformationServiceTest - Class in ubic.gemma.persistence.service.expression.experiment

ExpressionExperimentBatchInformationServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentBatchInformationServiceTest

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

The over-the-wire half of ExpressionExperimentBibRefFinderTest, which stubs GeoBrowser and never leaves the JVM.

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

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

Resolution is exercised against a stubbed GeoBrowser rather than live Entrez.

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

ExpressionExperimentDaoCursorTest - Class in ubic.gemma.persistence.service.expression.experiment

Integration tests for the keyset (cursor) pagination DAO mechanism on ExpressionExperimentDao.

ExpressionExperimentDaoCursorTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoCursorTest

ExpressionExperimentDaoTest - Class in ubic.gemma.persistence.service.expression.experiment

ExpressionExperimentDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

ExpressionExperimentDataVectorServiceTest - Class in ubic.gemma.persistence.service.expression.experiment

Lightweight unit test for ExpressionExperimentDataVectorServiceImpl that verifies delegation to the ExpressionExperimentDao and the create-if-needed orchestration of BioAssayDimensionService and QuantitationTypeService.

ExpressionExperimentDataVectorServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceTest

ExpressionExperimentDeleteTest - Class in ubic.gemma.persistence.service.expression.experiment

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

ExpressionExperimentFilterRewriteHelperServiceTest - Class in ubic.gemma.persistence.service.expression.experiment

ExpressionExperimentFilterRewriteHelperServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentFilterRewriteHelperServiceTest

ExpressionExperimentFilterTest - Class in ubic.gemma.core.analysis.preprocess.filter

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

ExpressionExperimentInCurationFilterIT - Class in ubic.gemma.persistence.service.expression.experiment

The inCuration filter behind the curation UI's "Experiments staged for curation" page.

ExpressionExperimentInCurationFilterIT() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentInCurationFilterIT

ExpressionExperimentManipulatingCLITest - Class in ubic.gemma.apps

ExpressionExperimentManipulatingCLITest() - Constructor for class ubic.gemma.apps.ExpressionExperimentManipulatingCLITest

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

ExpressionExperimentReadServiceAnnotationsTest - Class in ubic.gemma.persistence.service.expression.experiment

De-duplication contract of ExpressionExperimentReadServiceImpl.getAnnotations(ExpressionExperiment, boolean).

ExpressionExperimentReadServiceAnnotationsTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceAnnotationsTest

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

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

expressionExperimentService() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest.VoConverterTestContextConfiguration

expressionExperimentService() - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

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

ExpressionExperimentServiceDetachedEntityTest - Class in ubic.gemma.persistence.service.expression.experiment

ExpressionExperimentService.isSingleCell(ExpressionExperiment) must not require its argument to be attached to a session.

ExpressionExperimentServiceDetachedEntityTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceDetachedEntityTest

ExpressionExperimentServiceImplTest - Class in ubic.gemma.persistence.service.expression.experiment

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

ExpressionExperimentServiceIntegrationTest - Class in ubic.gemma.persistence.service.expression.experiment

ExpressionExperimentServiceIntegrationTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

ExpressionExperimentServiceTest - Class in ubic.gemma.persistence.service.expression.experiment

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

ExpressionExperimentSetDaoTest - Class in ubic.gemma.persistence.service.analysis.expression

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

ExpressionExperimentSetServiceTest - Class in ubic.gemma.persistence.service.expression.experiment

Tests for methods that perform operations on or with expressionExperiment sets

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

ExpressionExperimentSetValueObjectHelperImplTest - Class in ubic.gemma.persistence.service.expression.experiment

Unit tests for the taxon rule ExpressionExperimentSetValueObjectHelperImpl.updateMembers(Long, Collection) applies when replacing a set's membership.

ExpressionExperimentSetValueObjectHelperImplTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperImplTest

ExpressionExperimentSetValueObjectHelperTest - Class in ubic.gemma.persistence.service.expression.experiment

Tests for methods that create ExpressionExperimentSetValueObjects from expressionExperiment entities

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

ExpressionExperimentSubSetDaoTest - Class in ubic.gemma.persistence.service.expression.experiment

ExpressionExperimentSubSetDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoTest

ExpressionExperimentSubSetReadServiceTest - Class in ubic.gemma.persistence.service.expression.experiment

Lightweight unit test for ExpressionExperimentSubSetReadServiceImpl that verifies each public method delegates to the right ExpressionExperimentDao call without standing up a Spring context.

ExpressionExperimentSubSetReadServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceTest

ExpressionExperimentSubSetServiceTest - Class in ubic.gemma.persistence.service.expression.experiment

ExpressionExperimentSubSetServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceTest

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

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

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

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

ExtendedRuntimeTest - Class in ubic.gemma.core.util.runtime

ExtendedRuntimeTest() - Constructor for class ubic.gemma.core.util.runtime.ExtendedRuntimeTest

externalDatabaseService - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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.apps

ExternalDatabaseUpdaterCliTest() - Constructor for class ubic.gemma.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

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

Out-of-band reachability probe for every external URL Gemma talks to.

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

F

facSortedDatasets() - Static method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest2

These datasets were pulled from Gemma database on January 14th, 2026.

factorCategoryWithNoValueIsTolerated() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfoundUtilsTest

A factor whose category carries no value.

FactorValueArgTest - Class in ubic.gemma.rest.util.args

FactorValueArgTest() - Constructor for class ubic.gemma.rest.util.args.FactorValueArgTest

FactorValueDaoTest - Class in ubic.gemma.persistence.service.expression.experiment

FactorValueDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoTest

FactorValueNeedsAttentionServiceTest - Class in ubic.gemma.persistence.service.expression.experiment

Tests the Ticket-layer migration of FactorValueNeedsAttentionService (see CURATION_DETAILS_RETIREMENT.md).

FactorValueNeedsAttentionServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionServiceTest

FactorValueOntologyServiceTest - Class in ubic.gemma.core.ontology

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

FactorValueOntologyUtilsTest - Class in ubic.gemma.core.ontology

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

FactorValueReadServiceTest - Class in ubic.gemma.persistence.service.expression.experiment

Lightweight unit test for FactorValueReadServiceImpl that verifies each public method delegates to the right FactorValueDao call without standing up a Spring context.

FactorValueReadServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

FactorValueServiceIntegrationTest - Class in ubic.gemma.persistence.service.expression.experiment

FactorValueServiceIntegrationTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceIntegrationTest

FactorValueServiceTest - Class in ubic.gemma.persistence.service.expression.experiment

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

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

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

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

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

FactorValueValueObjectSerializerTest - Class in ubic.gemma.rest.serializers

FactorValueValueObjectSerializerTest() - Constructor for class ubic.gemma.rest.serializers.FactorValueValueObjectSerializerTest

factorWithNoCoefficients_yieldsEmptyCollection() - Method in class ubic.gemma.core.util.math.linearmodels.LinearModelSummaryUtilsTest

failedAnalysisEventsNameTheAnalysisRatherThanTheAttentionFlagTheySet() - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObjectTest

🛑 The regression this file exists for.

fails() - Method in class ubic.gemma.cli.util.test.CliAssert

Assert that the command fails.

failsWith(int) - Method in class ubic.gemma.cli.util.test.CliAssert

Assert that the command fails with the given exit status.

Failure behaviour - Section in class ubic.gemma.core.util.test.ExternalUrlReachabilityTest

FakeAuditable(long) - Constructor for class ubic.gemma.core.security.audit.AuditedAspectTest.FakeAuditable

FakeUserGroup(Long) - Constructor for class ubic.gemma.core.security.acl.AdminAclEvaluationTest.FakeUserGroup

falseIsTheComplement() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentInCurationFilterIT

The two halves partition the fixtures: nothing is in both, nothing is in neither.

FASTA_CMD_CONFIG_NAME - Static variable in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorFastacmdTest

FASTA_CMD_CONFIG_NAME - Static variable in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorTest

FASTA_CMD_CONFIG_NAME - Static variable in class ubic.gemma.core.loader.genome.SimpleFastaCmdTest

FASTA_CMD_EXE - Static variable in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorFastacmdTest

FASTA_CMD_EXE - Static variable in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorTest

FASTA_CMD_EXE - Static variable in class ubic.gemma.core.loader.genome.SimpleFastaCmdTest

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

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

fetch_withoutSetLocalBasePath_throwsIllegalState() - Method in class ubic.gemma.core.loader.util.HttpFetcherTest

Regression guard for the Settings-retirement refactor (commit f31cba192d): HttpFetcher.fetch(String) no longer reads gemma.download.path from Settings; the caller must call AbstractFetcher.setLocalBasePath(String) first.

FileLockManagerTest - Class in ubic.gemma.core.util.locking

FileLockManagerTest() - Constructor for class ubic.gemma.core.util.locking.FileLockManagerTest

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

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

FilteringVoEnabledServiceIntegrationTest - Class in ubic.gemma.persistence.service

Test all possible filterable properties for filtering and sorting results.

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

FilterQueryUtilsTest - Class in ubic.gemma.persistence.util

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

filtersChildrenByParentPermission() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest

filtersMapKeys_keepingOnlyGrantedSecurables() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapFilteringProviderTest

filtersMapValues_keepingOnlyGrantedEntries() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapValueFilteringProviderTest

FiltersTest - Class in ubic.gemma.persistence.util

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

FilterTest - Class in ubic.gemma.persistence.util

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

finalize_reopen() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

finalizedSet_refusesRuling() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

findAllGroups() - Method in class ubic.gemma.core.security.GroupManagerImpl

findAllSubBioMaterials() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoTest

findAllUsers() - Method in class ubic.gemma.core.security.UserDetailsManagerImpl

findByBioAssayIn_delegatesToSubSetDao() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceTest

findByEmail(String) - Method in class ubic.gemma.core.security.UserServiceImpl

findByExperimentAnalyzed() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoTest

findByUserName(String) - Method in class ubic.gemma.core.security.UserServiceImpl

findChildren(ObjectIdentity) - Method in class ubic.gemma.core.security.acl.InMemoryAclService

findGroupAuthorities(String) - Method in class ubic.gemma.core.security.GroupManagerImpl

findGroupByName(String) - Method in class ubic.gemma.core.security.UserServiceImpl

findGroupsForUser(String) - Method in class ubic.gemma.core.security.GroupManagerImpl

findGroupsForUser(User) - Method in class ubic.gemma.core.security.UserServiceImpl

findingKeyedAndTargetKeyed_areSeparateBuckets() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

FindObsoleteTermsCliTest - Class in ubic.gemma.apps

FindObsoleteTermsCliTest() - Constructor for class ubic.gemma.apps.FindObsoleteTermsCliTest

findsTheSeparatorAfterAParenthesisedAside() - Method in class ubic.gemma.core.loader.expression.geo.GeoColonSplitTest

findTicketsByCursorExtended_passesAllFiltersThroughToDao() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

Cursor-mode dispatch parity: extended cursor signature forwards each of the four new filter arguments verbatim to the DAO.

findTicketsExtended_passesAllFiltersThroughToDao() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

Extended findTickets dispatches each of the four new filter arguments (type / state / targetType / updatedSince) through to the DAO unchanged, preserving the state value (it doesn't get coerced into the legacy openOnly path).

findUsersInGroup(String) - Method in class ubic.gemma.core.security.GroupManagerImpl

fisherTransform_atHalf_isClassicValue() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

fisherTransform_atNegativeOne_returnsPositiveInfinity() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

fisherTransform_atOne_returnsPositiveInfinity() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

fisherTransform_atZero_returnsZero() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

fisherTransform_list_appliesPerElement() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

fisherTransform_outOfRange_throws() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

FittedValuesForExcludedSamplesTest - Class in ubic.gemma.core.util.math.linearmodels

Predicting a sample that did not contribute to the fit.

FittedValuesForExcludedSamplesTest() - Constructor for class ubic.gemma.core.util.math.linearmodels.FittedValuesForExcludedSamplesTest

fixedSaltHash_authenticatesViaGooblyfoobly() - Method in class ubic.gemma.core.security.authentication.LegacyAwareDaoAuthenticationProviderTest

fixedSaltHash_wrongPassword_rejected() - Method in class ubic.gemma.core.security.authentication.LegacyAwareDaoAuthenticationProviderTest

floatArrayRoundTrip_preservesValuesAndSize() - Method in class ubic.gemma.persistence.util.ByteArrayUtilsTest

flushAndClearSession() - Method in class ubic.gemma.core.util.test.BaseDatabaseTest5

Flush and clear the session after each test.

fly() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory

Resolve the seeded fly taxon (NCBI 7227).

flyway(DataSource) - Method in class ubic.gemma.core.util.test.BaseDatabaseTest5.BaseDatabaseTestContextConfiguration

FOO - Enum constant in enum class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest.FakeEnum

forceFlatten_reconcilesChildThatWasParentedToIntermediate() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest

forceOverridesTheSkip(Path) - Method in class ubic.gemma.core.util.NetUtilsTest

forceReleaseClearsAnyHolder() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockPersistenceIT

formatInteraction_joinsFactorNamesByColon_sortedDeterministic() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsRNameTest

formatInteraction_singleFactor_returnsBareFactorName() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsRNameTest

forwardDirectionIsOmittedFromWire() - Method in class ubic.gemma.persistence.util.CursorTest

fractionalBytes_preservesTwoDecimals() - Method in class ubic.gemma.core.util.NetUtilsTest

fractionalKilobytes_preservesTwoDecimals() - Method in class ubic.gemma.core.util.NetUtilsTest

fromRow_projectsTheColumnsInTheOrderTheQuerySelectsThem() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketSearchQueryTest

fromRow_readsAZeroTargetTicketAsZeroNotNull() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketSearchQueryTest

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

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

G

GeeqCormatMaskingTest - Class in ubic.gemma.persistence.service.expression.experiment

The stored sample-correlation matrix keeps the outlier samples' values, so a curator can review the call against them.

GeeqCormatMaskingTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.GeeqCormatMaskingTest

GemmaAndExperimentalFactorOntologyTest - Class in ubic.gemma.core.ontology

This test covers cases where inference is done across two distinct OntologyService.

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

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

Verifies GemmaLegacyAwarePasswordEncoder against fixtures lifted from gemma-core/src/main/resources/sql/init-data.sql — these are the actual hashes shipped with Gemma so any production user row with the legacy SHA-1 format must still be recognized as legacy (and trigger upgradeEncoding).

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

gemmaOntologyService(TaskExecutor) - Method in class ubic.gemma.core.ontology.TestOntologyConfig

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

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

gemmaRestApiClient() - Method in class ubic.gemma.apps.AclLinterCliTest.AclLinterCliTestContextConfiguration

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

GemmaRestApiClientTest - Class in ubic.gemma.core.util

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

gene2GOAssociationReadService() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test.GeneOntologyService2TestContextConfiguration

GeneArgServiceTest - Class in ubic.gemma.rest.util.args

GeneArgServiceTest() - Constructor for class ubic.gemma.rest.util.args.GeneArgServiceTest

GeneArgTest - Class in ubic.gemma.rest.util.args

GeneArgTest() - Constructor for class ubic.gemma.rest.util.args.GeneArgTest

geneChip() - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactory

Start building a "GENE_CHIP" (Affymetrix-style) array design.

geneChip_setsTechnologyType() - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactoryTest

GeneDaoTest - Class in ubic.gemma.persistence.service.genome

GeneDaoTest() - Constructor for class ubic.gemma.persistence.service.genome.GeneDaoTest

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

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

GeneFactory - Class in ubic.gemma.core.util.test.fixture

Typed factory for persistent Gene test fixtures.

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

GeneFactory.GeneBuilder - Class in ubic.gemma.core.util.test.fixture

Fluent builder for a Gene.

GeneFactoryTest - Class in ubic.gemma.core.util.test.fixture

Verifies the Phase 3 typed GeneFactory.

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

geneMappingSummariesSurviveSerialization() - Method in class ubic.gemma.rest.PlatformsWebServiceMappingSummaryTest

The regression guard that matters: the field must survive SERIALIZATION.

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

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

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

Guards GeneOntologyServiceImpl.requireAllTerms(String), the rewrite that makes the GO fallback require every token instead of the parser's default OR.

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

geneOntologyService() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test.GeneOntologyService2TestContextConfiguration

GeneOntologyService2Test - Class in ubic.gemma.core.ontology.providers

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

GeneOntologyService2Test() - Constructor for class ubic.gemma.core.ontology.providers.GeneOntologyService2Test

GeneOntologyService2Test.GeneOntologyService2TestContextConfiguration - Class in ubic.gemma.core.ontology.providers

GeneOntologyService2TestContextConfiguration() - Constructor for class ubic.gemma.core.ontology.providers.GeneOntologyService2Test.GeneOntologyService2TestContextConfiguration

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

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

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

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

generateAnnotationFile_whenATermIsNotInTheLoadedOntology_writesTheRemainingTerms() - Method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImplTest

A GO association whose URI is not in the loaded ontology makes GeneOntologyService.getTerm(String) return null.

generateSignupToken(String) - Method in class ubic.gemma.core.security.UserDetailsManagerImpl

GeneReadServiceTest - Class in ubic.gemma.persistence.service.genome.gene

Lightweight unit test for GeneReadServiceImpl that verifies each public method delegates to the right GeneDao call without standing up a Spring context.

GeneReadServiceTest() - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

GenericMetadataSingleCellDataLoaderTest - Class in ubic.gemma.core.loader.expression.singleCell

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

GenericMeterRegistryConfigurerTest - Class in ubic.gemma.core.metrics

GenericMeterRegistryConfigurerTest() - Constructor for class ubic.gemma.core.metrics.GenericMeterRegistryConfigurerTest

GenericMeterRegistryConfigurerTest.MyService - Class in ubic.gemma.core.metrics

GenericMeterRegistryConfigurerTest.MyService2 - Interface in ubic.gemma.core.metrics

GenericMeterRegistryConfigurerTest.MyService2Impl - Class in ubic.gemma.core.metrics

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.persistence.service.genome.gene

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

geneService() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test.GeneOntologyService2TestContextConfiguration

geneService() - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

geneService() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

GeneServiceImplTest - Class in ubic.gemma.persistence.service.genome.gene

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

GeneServiceTest - Class in ubic.gemma.persistence.service.genome.gene

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

GeneSetServiceTest - Class in ubic.gemma.persistence.service.genome.gene

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

GeneSetValueObjectHelperTest - Class in ubic.gemma.model.genome

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

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

GeneWebServiceCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to GeneWebService.getGenes(OffsetArg, LimitArg, CursorArg) as proof-of-concept for step 1b of CURSOR_PAGINATION_STEP1_PLAN.md.

GeneWebServiceCursorTest() - Constructor for class ubic.gemma.rest.GeneWebServiceCursorTest

GeneWebServiceOverviewTest - Class in ubic.gemma.rest

Pure-Mockito tests for the two gene-page additions on GeneWebService: GET /genes/{gene}/overview (the fully-populated VO replacing the legacy loadGeneDetails DWR) and GET /genes/{gene}/homologues.

GeneWebServiceOverviewTest() - Constructor for class ubic.gemma.rest.GeneWebServiceOverviewTest

GeneWebServiceProbesCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to GeneWebService.getGeneProbes(GeneArg, OffsetArg, LimitArg, CursorArg, boolean) as step 1m of CURSOR_PAGINATION_STEP1_PLAN.md.

GeneWebServiceProbesCursorTest() - Constructor for class ubic.gemma.rest.GeneWebServiceProbesCursorTest

GeneWebServiceTest - Class in ubic.gemma.rest

GeneWebServiceTest() - Constructor for class ubic.gemma.rest.GeneWebServiceTest

GeneWriteServiceTest - Class in ubic.gemma.persistence.service.genome.gene

Quirk-pinning tests for GeneWriteService.

GeneWriteServiceTest() - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceTest

GenomePersisterTest - Class in ubic.gemma.persistence.persister

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

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

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

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

Pins what GeoConverterImpl.parseGEOSampleCharacteristicString(String, BioMaterial) makes of a submitter's sample descriptor string.

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

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

The real strings frinkbro measured in production on 2026-09-11, and the ordinary cases that must keep splitting as they always did.

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

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

Which channel's molecule describes the SAMPLE.

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

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

Unit test for GeoConversion Added extension BaseIntegrationTest5 as want Taxon Service to be called

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

GeoConverterTest2 - Class in ubic.gemma.core.loader.expression.geo

GeoConverterTest2() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoConverterTest2

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

GeoFetcherTest - Class in ubic.gemma.core.loader.expression.geo.fetcher2

GeoFetcherTest() - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher2.GeoFetcherTest

GeoGrabberCliTest - Class in ubic.gemma.apps

GeoGrabberCliTest() - Constructor for class ubic.gemma.apps.GeoGrabberCliTest

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

The library-strategy vocabulary, and the one case where GEO's declared value is not believed.

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

GeoMexSingleCellDataLoaderConfigurerTest - Class in ubic.gemma.core.loader.expression.geo.singleCell

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

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

GeoScrapeServiceImplTest - Class in ubic.gemma.core.geoscrape

Pure-Mockito tests for the GeoScrapeServiceImpl watermark-loop + enrichment + ticket-emission paths.

GeoScrapeServiceImplTest() - Constructor for class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

geoScrapeWatermarkTarget_persists() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

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

geoService - Variable in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceGeoTest

GeoSingleCellDataDownloaderCliTest - Class in ubic.gemma.apps

GeoSingleCellDataDownloaderCliTest() - Constructor for class ubic.gemma.apps.GeoSingleCellDataDownloaderCliTest

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

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

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

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

Test replacements for GEO terms.

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

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

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

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

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

getActualDomainObject(Object) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest.ChildCollectionToParentByAssociation

getActualDomainObject(Object) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProviderTest.ChildToParentByAssociation

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

getAnnotations_defaultsToIncludingUngroundedTags() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceAnnotationsTest

🛑 Paul, 2026-08-31: "annotations should ALWAYS show ALL the annotations, including ungrounded EEtags." The old default hid tags with no ontology mapping, and a caller cannot tell an incomplete list from a complete one by inspecting it — it cost a curator an hour hunting a strain tag that was there all along, and silently truncated a corpus snapshot taken through this route.

getAnnotations_plainTag_valueIsTheTermAndStatementFieldsAreNull() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceAnnotationsTest

A plain tag has no statement, so the predicate/object fields stay null and the value is the term.

getAnnotations_reversedPredicateStatement_valueIsStillTheTerm() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceAnnotationsTest

The second composition shape, and the one that hid the term worst: a reversed predicate (RO_0002200 has phenotype) put the object in front of the subject and dropped the predicate altogether, so "headache" was reported as "acute headache".

getAnnotations_sameTagAtExperimentAndSampleLevel_collapses() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceAnnotationsTest

The same tag reaching the aggregate from two different levels still collapses to one entry — objectClass is not part of the de-duplication key.

getAnnotations_sameTermAndCategoryDifferingStatement_returnsBoth() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceAnnotationsTest

Regression guard for the negative control measured on experiment 27103: two factor-value statements that share a term URI and a category, differing only in their predicate/object, both come back.

getAnnotations_sameTermUnderSameCategory_collapses() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceAnnotationsTest

Exact duplicates — same category and same term — still collapse.

getAnnotations_sameTermUnderTwoCategories_returnsBoth() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceAnnotationsTest

Two experiment tags on the same term under different categories are two distinct curation claims, and both must be returned.

getAnnotations_statementRow_valueIsTheTermNotASentence() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceAnnotationsTest

🛑 On a factor-value statement row value is the subject's label and nothing else.

getArguments() - Method in class ubic.gemma.cli.util.TestCLIContext

getArrayDesignsUsed_delegatesToSubSetDao() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceTest

getCommandAliases() - Method in class ubic.gemma.apps.TestCli

getCommandGroup() - Method in class ubic.gemma.apps.TestCli

getCommandName() - Method in class ubic.gemma.apps.TestCli

getCommandNameOrAliasUsed() - Method in class ubic.gemma.cli.util.TestCLIContext

getConsole() - Method in class ubic.gemma.cli.util.TestCLIContext

getCurationStatusEmptyTablesReturnsZeroes() - Method in class ubic.gemma.rest.AdminWebServiceTest

getCurationStatusSnapshotComposesAnnotationSetAndTicketAggregates() - Method in class ubic.gemma.rest.AdminWebServiceTest

getCurrentState_returnsField() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowServiceTest

getCurrentState_returnsLoadedForNullField() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowServiceTest

getCurrentUser_isCalledWithManualFlushMode_andPreviousModeRestored() - Method in class ubic.gemma.persistence.audit.AuditTrailEventListenerTest

getCurrentUsername() - Method in class ubic.gemma.core.security.UserDetailsManagerImpl

getDatasetSvd_returns200_andExperimentAnalyzedSurfacesUnderlyingEntity() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

Regression guard for dd63676978.

getDatasetSvd_returns404_whenNoSvd() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

Negative case: an EE without a PCA → 404.

getDatasetSvdLoadings_returns200_forValidPcAndTop() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

Companion: /svd/loadings on a valid PCA should return 200 with at most top rows and the requested PC.

getDatasetSvdLoadings_returns404_whenNoSvd() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

Negative case: /svd/loadings on an EE without a PCA → 404.

getDatasetWorkflow_returnsCurrentStateAndEmptyHistory() - Method in class ubic.gemma.rest.WorkflowWebServiceTest

getDatasetWorkflow_unknownIdThrows404() - Method in class ubic.gemma.rest.WorkflowWebServiceTest

getEnvironment() - Method in class ubic.gemma.cli.util.TestCLIContext

getErrorStream() - Method in class ubic.gemma.cli.util.TestCLIContext

getExitCause() - Method in class ubic.gemma.cli.util.TestCLIContext

getExitStatus() - Method in class ubic.gemma.cli.util.TestCLIContext

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

getFactorValuesUsed_entityAndFactor_delegatesToSubSetDao() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceTest

getFactorValuesUsedAsVO_emptyResult_returnsEmptyCollection() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceTest

getFilterRefusesToSpeakForAConjunction() - Method in class ubic.gemma.persistence.util.SubqueryConjunctionTest

getFilter() is only meaningful for a single filter; a conjunction must be read via getFilters().

getId() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.ChildNoOwner

getId() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.ChildWithBackRef

getId() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.ChildWithOwner

getId() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.NotChildRoot

getId() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.OneNotChildParent

getId() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.Root

getId() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.SelfRefChild

getId() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.TwoParentChild

getId() - Method in class ubic.gemma.core.security.acl.AdminAclEvaluationTest.FakeUserGroup

getId() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest.Child

getId() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest.Parent

getId() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProviderTest.Child

getId() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProviderTest.Parent

getId() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProviderTest.MyModel

getId() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapFilteringProviderTest.Item

getId() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapValueFilteringProviderTest.Item

getId() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationOwnedCollectionFilteringProviderTest.Item

getId() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationPrivateCollectionFilteringProviderTest.Item

getId() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationStreamFilteringProviderTest.Item

getId() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest.ItemVO

getId() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest.ItemVO

getId() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest.ItemVO

getId() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest.ItemVO

getId() - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest.Model

getId() - Method in class ubic.gemma.core.security.acl.voter.AclEntryVoterTest.Model

getId() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest.FakeAuditable

getInputStream() - Method in class ubic.gemma.cli.util.TestCLIContext

getIsPublic() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest.ItemVO

getIsPublic() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest.ItemVO

getIsPublic() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest.ItemVO

getIsPublic() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest.ItemVO

getIsShared() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest.ItemVO

getIsShared() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest.ItemVO

getIsShared() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest.ItemVO

getIsShared() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest.ItemVO

getJdbcTemplate() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

getJobsAggregatesStatusCountsAndSortsNewestFirst() - Method in class ubic.gemma.rest.AdminWebServiceTest

getJobsReturnsEmptyListWhenNoTasks() - Method in class ubic.gemma.rest.AdminWebServiceTest

getLastGeoScrape_happyPath_returnsValueObject() - Method in class ubic.gemma.rest.AdminWebServiceTest

getLastGeoScrape_returns404_whenNoWatermark() - Method in class ubic.gemma.rest.AdminWebServiceTest

getMyQueue_returns401_whenAnonymous() - Method in class ubic.gemma.rest.TicketsWebServiceTest

getMyQueue_returnsOpenAndRecentlyResolved_forCallingUser() - Method in class ubic.gemma.rest.TicketsWebServiceTest

getMyQueueSummary_returnsCountsAndOldestOpen() - Method in class ubic.gemma.rest.TicketsWebServiceTest

getNewTestPersistentCompleteExpressionExperiment() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

getNumericalMean() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.NegativeBinomialDistribution

getNumericalVariance() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.NegativeBinomialDistribution

getOpenTicketSummary_holdsScratchpadsOutOfTotalOpen_butStillReportsThem() - Method in class ubic.gemma.rest.TicketsWebServiceTest

A scratchpad is never resolved, so counting one as open work would put every curator permanently behind.

getOptions() - Method in class ubic.gemma.apps.TestCli

getOrCreateScratchpad_createsOneOnFirstCall() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

First call mints it.

getOrCreateScratchpad_isScopedToTheCurator() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

The lookup is scoped by curator, not global.

getOrCreateScratchpad_rejectsANullCurator() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

getOrCreateScratchpad_returnsTheExistingOne_withoutCreating() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

An existing scratchpad is handed back untouched — no second row, no second OPENED event.

getOrCreateScratchpad_secondCallReturnsTheSameTicket_andCreatesOnlyOnce() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

The duplicate guard as a caller experiences it: call twice, get one ticket.

getOrCreateScratchpad_titlesItByUsername_whenTheContactNameIsMissing() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

The title names the owner, and a curator whose Contact name was never filled in is named by their username rather than losing their identity to a bare "Scratchpad" (uib, 2026-09-02).

getOutputStream() - Method in class ubic.gemma.cli.util.TestCLIContext

getPlatformsOriginal_excludesANoopSwitch() - Method in class ubic.gemma.rest.DatasetsPlatformsRestTest

A no-op switch — the original recorded as the platform already in use — is excluded, so a non-empty answer always names something that actually changed.

getPlatformsOriginal_isEmptyWhenNeverSwitched() - Method in class ubic.gemma.rest.DatasetsPlatformsRestTest

Never switched: an empty list, NOT the platform the dataset is on.

getPlatformsOriginal_isTwoHundredOverHttp() - Method in class ubic.gemma.rest.DatasetsPlatformsRestTest

The wire check, and the reason this class exists: the route answers 200 with the submitted platform in the body.

getPlatformsOriginal_namesTheSubmittedPlatform() - Method in class ubic.gemma.rest.DatasetsPlatformsRestTest

A real switch: ?original=true names the submitted platform, and the default mode still names the one in use.

getPreboarded_carriesTheSchemaVersionAlongsideThePayload() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

The payload is opaque to Gemma, so the only way a consumer can tell which document shape it holds is the schema version.

getPreboarded_returnsLatestAnnotationSetAndCount() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

getPreboarded_schemaVersionIsNullWhenTheWriterSetNone() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

Null is a real answer — the scrape path leaves it unset, and "unset" is what distinguishes those rows.

getPreboarded_unknownIdThrows404() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

getScratchpad_provisionsAndReturnsTheCallersOwn() - Method in class ubic.gemma.rest.TicketsWebServiceTest

The route provisions through the service and hands back the projection.

getScratchpad_requiresAuthentication() - Method in class ubic.gemma.rest.TicketsWebServiceTest

getScratchpad_returns401_whenAnonymous() - Method in class ubic.gemma.rest.TicketsWebServiceTest

getSecurableClass() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest.ItemVO

getSecurableClass() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest.ItemVO

getSecurableClass() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest.ItemVO

getSecurableClass() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest.ItemVO

getSecurityOwner() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.ChildNoOwner

getSecurityOwner() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.ChildWithBackRef

getSecurityOwner() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.ChildWithOwner

getSecurityOwner() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.OneNotChildParent

getSecurityOwner() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.SelfRefChild

getSecurityOwner() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.TwoParentChild

getSessionsAggregatesUserDetailsAndStringPrincipals() - Method in class ubic.gemma.rest.AdminWebServiceTest

getSessionsReturnsEmptyWhenNoPrincipals() - Method in class ubic.gemma.rest.AdminWebServiceTest

getSessionsSkipsPrincipalsWithNoActiveSessions() - Method in class ubic.gemma.rest.AdminWebServiceTest

getShortDesc() - Method in class ubic.gemma.apps.TestCli

getSubSetByIdWithCharacteristics_nonNullResult_initializesCharacteristics() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceTest

getSubSetByIdWithCharacteristics_nullResult_passesThroughWithoutInit() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceTest

getSubSets_byDimension_delegatesToDao() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceTest

getSubSetsByDimension_delegatesToDao() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceTest

getSubSetsByFactorValue_emptySubSets_returnsEmptyMap() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceTest

getSubSetsWithBioAssays_batch_delegatesToDaoGetSubSetsByExpressionExperiments() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceTest

getSubSetsWithBioAssays_singleEE_delegatesToDaoGetSubSets() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceTest

getSupportLowerBound() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.NegativeBinomialDistribution

getSupportUpperBound() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.NegativeBinomialDistribution

getSystemReturnsHeapNonHeapThreadsAndOsBlocks() - Method in class ubic.gemma.rest.AdminWebServiceTest

getTaxon(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

Obtain a taxon by its common name.

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

getTestContainerFactory() - Method in class ubic.gemma.rest.OpenApiWebServiceTest

getTestContainerFactory() - Method in class ubic.gemma.rest.providers.OntologyTermValidationExceptionMapperTest

getTestContainerFactory() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterDisabledTest

getTestContainerFactory() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest

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

getTestContainerFactory() - Method in class ubic.gemma.rest.TicketsWebServiceScratchpadRoutingTest

getTestContainerFactory() - Method in class ubic.gemma.rest.util.BaseJerseyTest5

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.AbstractGeoServiceTest5

getTestFileBasePath(String) - Method in class ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest5

getTestNonPersistentBioSequence(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

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

getTestNonPersistentQuantitationType() - 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.BaseSpringContextTest5

Deprecated.

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.BaseSpringContextTest5

Deprecated.

getTestPersistentArrayDesign(List, Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

getTestPersistentBasicExpressionExperiment() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

getTestPersistentBasicExpressionExperiment(ArrayDesign) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

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

getTestPersistentBibliographicReference(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

getTestPersistentBioAssay(ArrayDesign) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

getTestPersistentBioAssay(ArrayDesign, BioMaterial) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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.BaseSpringContextTest5

Deprecated.

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

getTestPersistentBioMaterial(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

getTestPersistentBioSequence() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

getTestPersistentBioSequence(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

getTestPersistentBioSequence2GeneProducts(BioSequence) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

getTestPersistentBlatResult(BioSequence) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

getTestPersistentBlatResult(BioSequence, Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

getTestPersistentCompleteExpressionExperiment(boolean) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

getTestPersistentCompleteExpressionExperimentWithSequences() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

getTestPersistentCompleteExpressionExperimentWithSequences(ExpressionExperiment) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

getTestPersistentContact() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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.BaseSpringContextTest5

Deprecated.

getTestPersistentDatabaseEntry(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

getTestPersistentDatabaseEntry(String, String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

getTestPersistentDatabaseEntry(String, ExternalDatabase) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

getTestPersistentDatabaseEntry(ExternalDatabase) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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.BaseSpringContextTest5

Deprecated.

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.BaseSpringContextTest5

Deprecated.

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.BaseSpringContextTest5

Deprecated.

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

getTestPersistentGene(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

getTestPersistentGeneProduct(Gene) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

getTestPersistentQuantitationType() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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.

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

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

Provide the shared "elephant" taxon that fills non-nullable taxon associations throughout the fixture, caching it for the life of this (context-scoped singleton) bean.

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

getTickets_passesNewFilterArgs_through() - Method in class ubic.gemma.rest.TicketsWebServiceTest

getUserCanWrite() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest.ItemVO

getUserCanWrite() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest.ItemVO

getUserCanWrite() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest.ItemVO

getUserCanWrite() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest.ItemVO

getUserGroupGrantedAuthority(Securable) - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.TestAclAdvice

getUserName(Securable) - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.TestAclAdvice

getUserOwned() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest.ItemVO

getUserOwned() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest.ItemVO

getUserOwned() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest.ItemVO

getUserOwned() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest.ItemVO

getUsers_excludesSoftDeleted_byDefault() - Method in class ubic.gemma.rest.AdminWebServiceTest

getUsers_includesSoftDeleted_whenFlagTrue() - Method in class ubic.gemma.rest.AdminWebServiceTest

getUsers_marksAdminFlag_whenAdministratorsGroupPresent() - Method in class ubic.gemma.rest.AdminWebServiceTest

getWorkflowQueue_missingStateThrows400() - Method in class ubic.gemma.rest.WorkflowWebServiceTest

getWorkflowQueue_unknownStateThrows400() - Method in class ubic.gemma.rest.WorkflowWebServiceTest

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

One-shot capture utility that records every GoldenPathSequenceAnalysis.findAssociations(String, Long, Long, String, String, String, ThreePrimeDistanceMethod, ProbeMapperConfig) response for the gpl96.blatresults.psl.gz fixture against a live hg19 GoldenPath database, and writes a JSON fixture used by the fast mock variant of CompositeSequenceGeneMapperServiceTest.

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

GoldenPathQueryTest - Class in ubic.gemma.core.goldenpath

These tests require a populated Human database.

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

GoogleAnalytics4ProviderTest - Class in ubic.gemma.rest.analytics.ga4

GoogleAnalytics4ProviderTest() - Constructor for class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4ProviderTest

grabGeoRecords_returns400_whenAccessionsEmpty() - Method in class ubic.gemma.rest.AdminWebServiceTest

grabGeoRecords_returns502_whenGeoBrowserThrowsIOException() - Method in class ubic.gemma.rest.AdminWebServiceTest

grabGeoRecords_returnsMappedValueObjects() - Method in class ubic.gemma.rest.AdminWebServiceTest

grantedItems_passThroughAndDeniedItemsAreFiltered() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationStreamFilteringProviderTest

grantedKeyVoPassesThrough_andSecurityStatusPopulated() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest

grantedValueVoPassesThrough_andSecurityStatusPopulated() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest

grantedVo_returnsTheVo_andPopulatesSecurityStatus() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest

grantedVoPassesThrough_andSecurityStatusPopulated() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest

grants_when_voter_grants() - Method in class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManagerTest

grantToAuthority(Securable, String, Permission) - Method in class ubic.gemma.core.security.acl.InMemoryAclService

Same as InMemoryAclService.grantToPrincipal(Securable, String, Permission) but grants to a granted-authority Sid (group / role).

grantToPrincipal(Securable, String, Permission) - Method in class ubic.gemma.core.security.acl.InMemoryAclService

Create-or-get the ACL for entity and grant permission to a principal Sid (the kind you get from a logged-in user).

groupExists(String) - Method in class ubic.gemma.core.security.GroupManagerImpl

groupExists(String) - Method in class ubic.gemma.core.security.UserServiceImpl

GroupManagerImpl - Class in ubic.gemma.core.security

GroupManagerImpl() - Constructor for class ubic.gemma.core.security.GroupManagerImpl

GroupsWebServiceTest - Class in ubic.gemma.rest

Pure Mockito unit tests for GroupsWebService.

GroupsWebServiceTest() - Constructor for class ubic.gemma.rest.GroupsWebServiceTest

GzipHeaderDecoratorTest - Class in ubic.gemma.rest.providers

Pins which of the two Content-Encoding decorators fires, for each shape of the GZIP annotation.

GzipHeaderDecoratorTest() - Constructor for class ubic.gemma.rest.providers.GzipHeaderDecoratorTest

H

H5FileTest - Class in ubic.gemma.core.loader.util.hdf5

H5FileTest() - Constructor for class ubic.gemma.core.loader.util.hdf5.H5FileTest

H5UtilsTest - Class in ubic.gemma.core.loader.util.hdf5

H5UtilsTest() - Constructor for class ubic.gemma.core.loader.util.hdf5.H5UtilsTest

handlesAColonInsideTheKeysOwnParentheses() - Method in class ubic.gemma.core.loader.expression.geo.GeoColonSplitTest

handleTestExecutionException(ExtensionContext, Throwable) - Method in class ubic.gemma.core.util.test.NetworkAvailableExtension

hasEncoding(String) - Method in class ubic.gemma.rest.util.ResponseAssert

Asserts that the response has the given 'Content-Encoding' header.

hasFieldError(String, String, String) - Method in class ubic.gemma.rest.util.ErrorsAssert

Asserts that the errors object has a field error.

hasFieldError(String, String, String, Object) - Method in class ubic.gemma.rest.util.ErrorsAssert

Asserts that the errors object has a field error with a given rejected value.

hasGlobalError(String, String) - Method in class ubic.gemma.rest.util.ErrorsAssert

Asserts that the errors object has a global error.

hashCode() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProviderTest.MyModel

hashCode() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest.ItemVO

hashCode() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest.FakeAuditable

hashCode() - Method in record class ubic.gemma.core.security.audit.AuditedAspectTest.SamplePayload

Returns a hash code value for this object.

hasHeader(String) - Method in class ubic.gemma.rest.util.ResponseAssert

Asserts that the response has the given header.

hasHeaderSatisfying(String, Consumer) - Method in class ubic.gemma.rest.util.ResponseAssert

hasHeaderWithValue(String, String) - Method in class ubic.gemma.rest.util.ResponseAssert

Asserts that the response has the given header with a particular value.

hasLanguage(Locale) - Method in class ubic.gemma.rest.util.ResponseAssert

hasLength() - Method in class ubic.gemma.rest.util.ResponseAssert

Asserts that the response has a 'Content-Length' header.

hasLength(int) - Method in class ubic.gemma.rest.util.ResponseAssert

Asserts that the response has a 'Content-Length' header with the given length.

hasMediaType(MediaType) - Method in class ubic.gemma.rest.util.ResponseAssert

Asserts that the response has the given media type.

hasMediaTypeCompatibleWith(MediaType) - Method in class ubic.gemma.rest.util.ResponseAssert

Asserts that the response has a media type compatible with the given media type.

hasPath(String) - Method in class ubic.gemma.rest.util.JsonAssert

Ensure that a given path exists.

hasPathWithValue(String, Object) - Method in class ubic.gemma.rest.util.JsonAssert

Ensure that a JSON path has the given value.

hasStatus(Response.Status) - Method in class ubic.gemma.rest.util.ResponseAssert

Asserts that the response has the given status code and reason phrase.

hasStatusFamily(Response.Status.Family) - Method in class ubic.gemma.rest.util.ResponseAssert

Asserts that that response status is within the given status family.

headers() - Method in class ubic.gemma.rest.util.ResponseAssert

HeatmapTest - Class in ubic.gemma.core.visualization

HeatmapTest() - Constructor for class ubic.gemma.core.visualization.HeatmapTest

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

Pins the ACL post-filter in HibernateSearchSource against unresolvable ACL identities.

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

HibernateSqmFragileShapesIT - Class in ubic.gemma.persistence.util

HB6 SQM-translator regression guard.

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

hibernateStatsSnapshotMirrorsStatisticsFields() - Method in class ubic.gemma.rest.AdminWebServiceTest

hitWithNoAclRowIsDroppedRatherThanFailingTheSearch() - Method in class ubic.gemma.core.search.source.HibernateSearchSourceAclFilterTest

The reported failure: EE 91719 was in the Lucene index but gone from the database, so its ACL row was gone too and the batch read aborted the entire search with a 500.

Holder() - Constructor for class ubic.gemma.core.util.RoundingUtilsTest.Holder

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

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

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

Factory for HomologeneService.

homologuesRaceWithDeleteThrows404() - Method in class ubic.gemma.rest.GeneWebServiceOverviewTest

homologuesReturnsEmptyListWhenNoneRegistered() - Method in class ubic.gemma.rest.GeneWebServiceOverviewTest

homologuesReturnsListFromFullyPopulatedVo() - Method in class ubic.gemma.rest.GeneWebServiceOverviewTest

How to run - Section in class ubic.gemma.core.util.test.ExternalUrlReachabilityTest

HqlSmokeIT - Class in ubic.gemma.persistence.util

Mass parse-only smoke test for every statically-extractable HQL string in gemma-core/src/main/java.

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

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

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

human() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory

Resolve the seeded human taxon (NCBI 9606).

human_returnsSeededTaxonWithNcbi9606() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactoryTest

humanPhenotypeOntologyServiceOntologyService(TaskExecutor) - Method in class ubic.gemma.core.ontology.TestOntologyConfig

I

idOnAnotherPlatformWithNoNameMatchStillRaises() - Method in class ubic.gemma.rest.util.args.CompositeSequenceArgTest

The pre-existing 400 is preserved where it was actually right: the id names a real probe on another platform and nothing on this platform carries that name.

idOnTheRequestedPlatformWinsWithoutANameLookup() - Method in class ubic.gemma.rest.util.args.CompositeSequenceArgTest

The id keeps precedence, and costs no extra query: a numeric argument that resolves to a probe on the requested platform must not also trigger a name lookup.

idQuery_hasNoOrderBy() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketSearchQueryTest

The id lookup returns at most one row, and the service puts it first.

idQuery_matchesTheIdColumnVerbatim() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketSearchQueryTest

ignoresTheReplacementCharacter() - Method in class ubic.gemma.core.util.SymbolFontPuaTest

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

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

importGeoBatch_happyPath_submitsOneTaskPerAccession() - Method in class ubic.gemma.rest.AdminWebServiceTest

importGeoBatch_returns400_whenAccessionsEmpty() - Method in class ubic.gemma.rest.AdminWebServiceTest

importGeoBatch_returns400_whenAllAccessionsBlank() - Method in class ubic.gemma.rest.AdminWebServiceTest

importGeoBatch_returns400_whenBatchExceedsCap() - Method in class ubic.gemma.rest.AdminWebServiceTest

importGeoBatch_returns400_whenBodyMissing() - Method in class ubic.gemma.rest.AdminWebServiceTest

importGeoBatch_skipsBlankEntries_butSubmitsTheRest() - Method in class ubic.gemma.rest.AdminWebServiceTest

includeRawDataQt(boolean) - Method in class ubic.gemma.core.util.test.fixture.ExperimentFactory.Builder

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

A factor dropped for missing values must not be left behind in the baseline map.

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

inCurationIsTheUnionOfBothHalves() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentInCurationFilterIT

index() - Method in class ubic.gemma.rest.providers.OntologyTermValidationExceptionMapperTest.CustomResource

index(String) - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterDisabledTest.CustomResource

index(String, String) - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest.CustomResource

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

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

initializedExperiment_isItsOwnSecurityOwner() - Method in class ubic.gemma.model.analysis.SingleExperimentAnalysisTest

initializedExperiment_resolvesToItsShortName() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtilsTest

initializedSubset_isOwnedByItsSourceExperiment() - Method in class ubic.gemma.model.analysis.SingleExperimentAnalysisTest

initializedSubset_resolvesToItsSourceExperimentShortName() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtilsTest

InMemoryAclService - Class in ubic.gemma.core.security.acl

Test-only AclService that stores ACLs in an in-memory Map using real Spring Security AclImpl instances.

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

intArrayRoundTrip_preservesValuesAndSize() - Method in class ubic.gemma.persistence.util.ByteArrayUtilsTest

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

Mark a test as an integration test.

interactionRow_matchesInteractionFactorAfterFvStripping() - Method in class ubic.gemma.core.util.math.linearmodels.LinearModelSummaryUtilsTest

interceptRow_isSkipped() - Method in class ubic.gemma.core.util.math.linearmodels.LinearModelSummaryUtilsTest

isBareBcrypt_acceptsKnownVariants() - Method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoderTest

isLegacySha1Hex_rejectsBcryptAndOther() - Method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoderTest

isSingleton() - Method in class ubic.gemma.core.context.AsyncBeanAutowiringTest.MyService2Factory

isSingleton() - Method in class ubic.gemma.core.context.AsyncBeanAutowiringTest.MyServiceFactory

isSingleton() - Method in class ubic.gemma.core.context.AsyncFactoryTest.MyServiceFactory

isSingleton() - Method in class ubic.gemma.core.context.AsyncSingletonFactoryTest.MyServiceFactory

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

isSupportConnected() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.NegativeBinomialDistribution

isTermId() - Method in class ubic.gemma.core.ontology.OntologyUtilsTest

isValidPearsonCorrelation_acceptsInRangeValues() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

isValidPearsonCorrelation_acceptsTinyRoundoffOutsideRange() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

isValidPearsonCorrelation_rejectsOutOfRangeValues() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

it_is_a_frequency_comparison_not_a_preference_for_synonyms() - Method in class ubic.gemma.rest.ranking.CommonalityRankingStrategyTest

Item(Long) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapFilteringProviderTest.Item

Item(Long) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapValueFilteringProviderTest.Item

Item(Long) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationOwnedCollectionFilteringProviderTest.Item

Item(Long) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationPrivateCollectionFilteringProviderTest.Item

itemsOfNonDomainClassAreFiltered() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationStreamFilteringProviderTest

itemsWithoutAclAreFiltered() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationStreamFilteringProviderTest

ItemVO(Long) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest.ItemVO

ItemVO(Long) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest.ItemVO

ItemVO(Long) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest.ItemVO

ItemVO(Long) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest.ItemVO

J

JOHN - Enum constant in enum class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest.FakeEnum

json() - Static method in class ubic.gemma.rest.util.JsonAssert

JsonAssert - Class in ubic.gemma.rest.util

Assertions for JSON based on JsonPath.

JsonAssert(String) - Constructor for class ubic.gemma.rest.util.JsonAssert

K

keepsItemsOwnedByCurrentUser_dropsItemsOwnedByOthers() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationOwnedCollectionFilteringProviderTest

keepsItemsWhereUserHasOnlyAdministrationButNotRead() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationPrivateCollectionFilteringProviderTest

keepsPrivateItemsTheUserCanRead_dropsPubliclyReadableItems() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationPrivateCollectionFilteringProviderTest

keyOrderDoesNotMakeAnEdit() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositionsTest

Key order must not decide the verdict — the payloads are objects, and two objects with the same members are the same content.

keyTupleIsDefensivelyCopied() - Method in class ubic.gemma.persistence.util.CursorTest

L

labelsADifferentialExpressionAnalysis() - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObjectTest

labelsTheEventTypeThatDominatesRecentUpdates() - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObjectTest

lastUpdated_noOpenTickets_isNull() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

lastUpdated_returnsMaxOccurredAtAcrossOpenTickets() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

LazyInitByDefaultPostProcessorTest - Class in ubic.gemma.core.context

LazyInitByDefaultPostProcessorTest() - Constructor for class ubic.gemma.core.context.LazyInitByDefaultPostProcessorTest

lazyProxiedExperiment_resolvesRatherThanReturningNull() - Method in class ubic.gemma.model.analysis.SingleExperimentAnalysisTest

lazyProxiedExperiment_resolvesRatherThanThrowing() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtilsTest

lazyProxiedSubset_isOwnedByItsSourceExperiment() - Method in class ubic.gemma.model.analysis.SingleExperimentAnalysisTest

lazyProxiedSubset_resolvesToItsSourceExperimentShortName() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtilsTest

leavesCleanTextAlone() - Method in class ubic.gemma.core.util.SymbolFontPuaTest

leavesItWholeWhenNothingQualifies() - Method in class ubic.gemma.core.loader.expression.geo.GeoColonSplitTest

legacyAttachOverload_leavesRunProvenanceNull() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

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

Verifies LegacyAwareDaoAuthenticationProvider can authenticate legacy SHA-1+username-salt hashes without any ThreadLocal state, and triggers the Spring Security 6 password-upgrade hook (UserDetailsPasswordService) on success.

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

legacyHash_isFlaggedForUpgrade() - Method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoderTest

legacyHash_isRecognizedAsLegacyFormat() - Method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoderTest

legacyHash_matchesIsFailClosed() - Method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoderTest

legacyHash_successfulLogin_triggersBcryptUpgrade() - Method in class ubic.gemma.core.security.authentication.LegacyAwareDaoAuthenticationProviderTest

legacyHash_wrongPassword_rejected() - Method in class ubic.gemma.core.security.authentication.LegacyAwareDaoAuthenticationProviderTest

legacyModeLimitAppliesAfterCompact() - Method in class ubic.gemma.rest.DatasetsWebServiceAuditEventsCursorTest

legacyModeLimitAppliesAfterExcludeEmpty() - Method in class ubic.gemma.rest.DatasetsWebServiceAuditEventsCursorTest

legacyModeLimitReturnsTheMostRecentEntries() - Method in class ubic.gemma.rest.DatasetsWebServiceAuditEventsCursorTest

legacyModeWithoutCursorReturnsUnpaginatedResponseDataObject() - Method in class ubic.gemma.rest.DatasetsWebServiceAuditEventsCursorTest

legacyModeWithoutCursorReturnsUnpaginatedResponseDataObject() - Method in class ubic.gemma.rest.DatasetsWebServiceSamplesCursorTest

legacyModeWithoutCursorReturnsUnpaginatedResponseDataObject() - Method in class ubic.gemma.rest.DatasetsWebServiceSubSetSamplesCursorTest

legacyModeWithoutCursorReturnsUnpaginatedResponseDataObject() - Method in class ubic.gemma.rest.DatasetsWebServiceTicketsCursorTest

legacyModeWithoutCursorReturnsUnpaginatedResponseDataObject() - Method in class ubic.gemma.rest.PlatformsWebServiceTicketsCursorTest

legacyModeWithoutCursorReturnsUnpaginatedResponseDataObject() - Method in class ubic.gemma.rest.TicketsWebServiceEventsCursorTest

legacyModeWithoutLimitReturnsTheWholeTrail() - Method in class ubic.gemma.rest.DatasetsWebServiceAuditEventsCursorTest

lifecycle_open_inProgress_resolved() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

liftingARefusal_keepsTheOriginal() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionPersistenceIT

likePattern_escapesTheCallersOwnWildcards() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketSearchQueryTest

A curator's own wildcards are data, not syntax: 50% looks for a title containing "50%", and TNF_alpha does not match "TNFXalpha".

likePattern_isASubstringMatchAgainstLowercasedText() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketSearchQueryTest

LimitArgTest - Class in ubic.gemma.rest.util.args

LimitArgTest() - Constructor for class ubic.gemma.rest.util.args.LimitArgTest

limitWithoutCursorIsRejectedAs400() - Method in class ubic.gemma.rest.DatasetsWebServiceSamplesCursorTest

🛑 The route bound limit and then never used it outside cursor mode.

limitWithoutCursorIsRejectedAs400() - Method in class ubic.gemma.rest.DatasetsWebServiceSubSetSamplesCursorTest

Same rule as the parent /datasets/{id}/samples listing: this route is unpaginated without a cursor and has no field in which to declare a truncation, so a limit it cannot honour is refused rather than dropped.

limitWithQuantitationTypeAndNoCursorIsRejectedAs400() - Method in class ubic.gemma.rest.DatasetsWebServiceSamplesCursorTest

The QT-narrowed listings are legacy-mode too, so they refuse a limit on the same grounds — the rejection is a property of "not paginating", not of the plain branch.

LinearModelSummaryUtilsTest - Class in ubic.gemma.core.util.math.linearmodels

Unit tests for LinearModelSummaryUtils.createTerm2CoefficientNames(List, DoubleMatrix): the helper that maps factor names to the set of R-side coefficient-row names belonging to that factor.

LinearModelSummaryUtilsTest() - Constructor for class ubic.gemma.core.util.math.linearmodels.LinearModelSummaryUtilsTest

lineStillCarriesClassIdActionAndPerformer() - Method in class ubic.gemma.core.security.audit.AuditLoggerTest

listAvailableGroups() - Method in class ubic.gemma.core.security.UserServiceImpl

listBlacklistEntries_capsLimitAtMaxPageSize() - Method in class ubic.gemma.rest.AdminWebServiceTest

listBlacklistEntries_paginatesAndSortsByAccession() - Method in class ubic.gemma.rest.AdminWebServiceTest

listBlacklistEntries_returns400_whenLimitNegative() - Method in class ubic.gemma.rest.AdminWebServiceTest

listCachesReturnsAlphabeticallySortedNames() - Method in class ubic.gemma.rest.AdminWebServiceTest

listener_implements_postInsert_preDelete_and_persist() - Method in class ubic.gemma.persistence.audit.AuditTrailEventListenerTest

listOrResolvePreboarded_byAccessionReturnsPreboarded() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

listOrResolvePreboarded_byAccessionUnknownThrows404() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

listOrResolvePreboarded_byStateReturns501PointerToWorkflowQueue() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

listOrResolvePreboarded_neitherParamThrows400() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

listSummaries_filtersByKindAndStatus() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

listSummaries_leftJoinKeepsNonExperimentRows() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

listSummaries_sortsByRanAt() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

ListUtilsTest - Class in ubic.gemma.core.util

Tests for extra utilities for List.

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

load(Long) - Method in class ubic.gemma.core.security.UserServiceImpl

loadAll() - Method in class ubic.gemma.core.security.UserServiceImpl

loadAllIdentifiersStillRuns() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentInCurationFilterIT

The unscoped sibling has to keep working — both share one query string.

loadDetachedInFreshSession(SessionFactory, Class, Long) - Static method in class ubic.gemma.core.util.test.ThawTestUtils

Load an entity in a fresh Session, then close that session, returning a detached instance whose lazy associations are unrealised.

loadFixture() - Static method in class ubic.gemma.rest.AnnotationSearchRankingStrategyTest

loadGroupAuthorities(User) - Method in class ubic.gemma.core.security.UserServiceImpl

loadIdentifiersEmptyIsEmpty() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentInCurationFilterIT

loadIdentifiersReturnsTheRequestedExperiments() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentInCurationFilterIT

🛑 This runs the HQL.

LoadSimpleExpressionDataCliTest - Class in ubic.gemma.apps

LoadSimpleExpressionDataCliTest() - Constructor for class ubic.gemma.apps.LoadSimpleExpressionDataCliTest

loadSubSet_delegatesToSubSetDaoLoad() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceTest

loadSubSetWithBioAssays_delegatesToSubSetDao() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceTest

loadTroubledIds() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

loadUserByUsername(String) - Method in class ubic.gemma.core.security.UserDetailsManagerImpl

loadValueObjectOfEmptyResultListIsEmpty() - Method in class ubic.gemma.core.search.SearchServiceImplTest

localFileAlreadyMatchingTheRemoteSize_skipsTheDownload(Path) - Method in class ubic.gemma.core.util.NetUtilsTest

The skip path pre-staging relies on: a local file already matching the remote size is used as-is and no transfer happens.

log - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

loggedIn() - Method in class ubic.gemma.core.security.UserDetailsManagerImpl

LoggingTest - Class in ubic.gemma.core.logging

LoggingTest() - Constructor for class ubic.gemma.core.logging.LoggingTest

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.

longArrayRoundTrip_preservesValuesAndSize() - Method in class ubic.gemma.persistence.util.ByteArrayUtilsTest

longestEnumValue_roundTrips() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

lowerAuthorityDoesNotRestateEvidence() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationPersistenceIT

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

LowVarianceFilterTest - Class in ubic.gemma.core.analysis.preprocess.filter

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

luceneOrder_keepsRawOrder() - Method in class ubic.gemma.rest.AnnotationSearchRankingStrategyTest

M

MailEngineImplTest - Class in ubic.gemma.core.mail

MailEngineImplTest() - Constructor for class ubic.gemma.core.mail.MailEngineImplTest

MailServiceTest - Class in ubic.gemma.core.util

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

main(String[]) - Static method in class ubic.gemma.core.loader.expression.singleCell.SampleMexDataset

main(String[]) - Static method in class ubic.gemma.core.util.locking.ReadWriteFileLockTestScript

main(String[]) - Static method in class ubic.gemma.core.util.test.MysqlSchemaBaselineDumper

main(String[]) - Static method in class ubic.gemma.core.util.test.SchemaBaselineDumper

mainEffect_doesNotLeakAcrossFactors() - Method in class ubic.gemma.core.util.math.linearmodels.LinearModelSummaryUtilsTest

mainEffectCoefficient_isAttachedToMatchingFactor() - Method in class ubic.gemma.core.util.math.linearmodels.LinearModelSummaryUtilsTest

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

The date a dataset FIRST became public has to come from somewhere, and until now nothing recorded it: only two REST endpoints emitted MakePublicEvent, so anything made public by the CLI or a bulk job left no trace.

malformedJsonIsTreatedAsAbsent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositionsTest

Unparseable JSON degrades to "no baseline" rather than throwing: a corrupt payload must not take down the read of every other element.

malformedOrAbsentIsUnknown() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetPayloadCountsTest

mammalianPhenotypeOntologyServiceOntologyService(TaskExecutor) - Method in class ubic.gemma.core.ontology.TestOntologyConfig

manhattanDistance_identicalVectors_isZero() - Method in class ubic.gemma.core.util.math.DistanceTest

manhattanDistance_mismatchedSizes_throws() - Method in class ubic.gemma.core.util.math.DistanceTest

manhattanDistance_simpleCase() - Method in class ubic.gemma.core.util.math.DistanceTest

manhattanDistance_skipsNaNs() - Method in class ubic.gemma.core.util.math.DistanceTest

Manifest - Section in class ubic.gemma.persistence.util.HqlSmokeIT

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

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

manualAuthenticationService() - Method in class ubic.gemma.apps.AclLinterCliTest.AclLinterCliTestContextConfiguration

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

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

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

map(K, V, Object...) - Static method in class ubic.gemma.core.util.test.Maps

mappingSummaryReturnsVoWithGeneMappingSummariesPopulated() - Method in class ubic.gemma.rest.PlatformsWebServiceMappingSummaryTest

mappingSummaryThrows404WhenServiceReturnsNull() - Method in class ubic.gemma.rest.PlatformsWebServiceMappingSummaryTest

mapPreservesMetadata() - Method in class ubic.gemma.persistence.util.CursorPageTest

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

Extensions for AssertJ's Maps.

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

MarkCLIsAsPrototypesTest - Class in ubic.gemma.cli.util

Test various behaviours of CLIs when injected as bean.

MarkCLIsAsPrototypesTest() - Constructor for class ubic.gemma.cli.util.MarkCLIsAsPrototypesTest

MarkdownUtilsTest - Class in ubic.gemma.core.util

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

markerHoldsAParseableInstant() - Method in class ubic.gemma.core.search.indexer.ScheduledSearchReindexerTest

The audit cutoff comes from the marker, so a rebuild has to leave a parseable timestamp behind — an unparseable one silently degrades every later run to a full-history scan.

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

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

massIndexerRebuildMakesFixturesSearchable() - Method in class ubic.gemma.core.search.MassIndexerSmokeIntegrationTest

MassIndexerSmokeIntegrationTest - Class in ubic.gemma.core.search

End-to-end smoke test for the Hibernate Search 7 mass-indexer + search service round-trip (SEARCH_RECCE.md Step 6).

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

matchersHaveStableNames() - Method in class ubic.gemma.core.geoscrape.MatchersTest

MatchersTest - Class in ubic.gemma.core.geoscrape

Pure-Mockito-less tests for the v1 GEO scrape matchers.

MatchersTest() - Constructor for class ubic.gemma.core.geoscrape.MatchersTest

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

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

meanVarianceFailureException_carriesCauseAndConfig() - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisExceptionTest

meanVarianceFailureException_extendsAnalysisException() - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisExceptionTest

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

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

mediaTypeRestrictionIsHonoured() - Method in class ubic.gemma.rest.providers.GzipHeaderDecoratorTest

messageSpel_canReferenceReturnValueWithHashResult() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

MeterRegistryCliConfigurerTest - Class in ubic.gemma.cli.metrics

MeterRegistryCliConfigurerTest() - Constructor for class ubic.gemma.cli.metrics.MeterRegistryCliConfigurerTest

MetricsConfigTest - Class in ubic.gemma.core.config

Smoke test for the metrics Spring profile.

MetricsConfigTest() - Constructor for class ubic.gemma.core.config.MetricsConfigTest

metricsProfileBeansInstantiateCleanly() - Method in class ubic.gemma.core.config.MetricsConfigTest

metricsProfileInactiveByDefault() - Method in class ubic.gemma.core.config.MetricsConfigTest

MexMatrixBundlerTest - Class in ubic.gemma.core.datastructure.matrix.io

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

MexMatrixWriterTest - Class in ubic.gemma.core.datastructure.matrix.io

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

MexSingleCellDataLoaderPersistenceTest - Class in ubic.gemma.core.loader.expression.singleCell

Load and persist single-cell data stored in the MEX format.

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

MexSingleCellDataLoaderTest - Class in ubic.gemma.core.loader.expression.singleCell

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

MexTestUtils - Class in ubic.gemma.core.loader.expression.singleCell

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

MinimumCellsFilterTest - Class in ubic.gemma.core.analysis.preprocess.filter

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

minPresentCount_exceedingColumnCount_throws() - Method in class ubic.gemma.core.util.matrix.datafilter.RowMissingFilterTest

minPresentCount_keepsOnlyRowsMeetingThreshold() - Method in class ubic.gemma.core.util.matrix.datafilter.RowMissingFilterTest

minPresentCount_oneAdmitsRowsWithAnyPresentValue() - Method in class ubic.gemma.core.util.matrix.datafilter.RowMissingFilterTest

minPresentCount_threeRequiresAllValues() - Method in class ubic.gemma.core.util.matrix.datafilter.RowMissingFilterTest

minPresentFraction_isConvertedToCount() - Method in class ubic.gemma.core.util.matrix.datafilter.RowMissingFilterTest

MissingBuildInfoTest - Class in ubic.gemma.core.util

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

missingOrEmptyBodyIsRefused() - Method in class ubic.gemma.rest.DatasetsWebServiceTicketsBulkTest

modeAndStatus_persistAsEnumNameStrings() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

Model() - Constructor for class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest.Model

Model(Long) - Constructor for class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest.Model

ModelUtilsTest - Class in ubic.gemma.model.util

ModelUtilsTest() - Constructor for class ubic.gemma.model.util.ModelUtilsTest

mondoOntologyServiceOntologyService(TaskExecutor) - Method in class ubic.gemma.core.ontology.TestOntologyConfig

mouse() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory

Resolve the seeded mouse taxon (NCBI 10090).

mouse_returnsSeededTaxonWithNcbi10090() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactoryTest

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

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

multipleAlignmentsShareOneTrackFramedOnTheBestScoring() - Method in class ubic.gemma.core.analysis.sequence.BlatResult2PslTest

A probe usually has several alignments and they are only useful side by side, so they share one track.

multipleIdentifiers_lintEachOne() - Method in class ubic.gemma.apps.AclLinterCliTest

multiTarget_mixedTypes() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

multiTarget_perTargetStatusIndependent() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

MyModel() - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProviderTest.MyModel

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

MyService() - Constructor for class ubic.gemma.core.context.AsyncBeanAutowiringTest.MyService

MyService() - Constructor for class ubic.gemma.core.context.AsyncFactoryTest.MyService

MyService() - Constructor for class ubic.gemma.core.context.AsyncSingletonFactoryTest.MyService

MyService() - Constructor for class ubic.gemma.core.metrics.GenericMeterRegistryConfigurerTest.MyService

MyService() - Constructor for class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest.MyService

MyService2() - Constructor for class ubic.gemma.core.context.AsyncBeanAutowiringTest.MyService2

MyService2Factory() - Constructor for class ubic.gemma.core.context.AsyncBeanAutowiringTest.MyService2Factory

MyService2Impl() - Constructor for class ubic.gemma.core.metrics.GenericMeterRegistryConfigurerTest.MyService2Impl

MyServiceFactory() - Constructor for class ubic.gemma.core.context.AsyncBeanAutowiringTest.MyServiceFactory

MyServiceFactory() - Constructor for class ubic.gemma.core.context.AsyncFactoryTest.MyServiceFactory

MyServiceFactory() - Constructor for class ubic.gemma.core.context.AsyncSingletonFactoryTest.MyServiceFactory

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

One-off Flyway baseline generator for the MySQL/InnoDB path.

N

nameFallbackPreservesLeadingZeroes() - Method in class ubic.gemma.rest.util.args.CompositeSequenceArgTest

The fallback looks up the spelling as written, not a re-rendering of the parsed long -- a probe named "007" is not a probe named "7".

nameForR_bioMaterial_prependsBiomatPrefix() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsRNameTest

nameForR_bioMaterial_withNullId_throws() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsRNameTest

nameForR_compositeSequence_returnsStringifiedId() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsRNameTest

nameForR_compositeSequence_withNullId_throws() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsRNameTest

nameForR_experimentalFactor_prependsFactPrefix() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsRNameTest

nameForR_experimentalFactor_withNullId_throws() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsRNameTest

nameForR_factorValue_categoricalBaseline_appendsBaselineSuffix() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsRNameTest

nameForR_factorValue_categoricalNonBaseline_prependsFvPrefix() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsRNameTest

nameForR_factorValue_continuousMarkedAsBaseline_throws() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsRNameTest

nameForR_factorValue_continuousNotBaseline_works() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsRNameTest

nameForR_factorValue_withNullId_throws() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsRNameTest

namingNoCheck_runsThemAll() - Method in class ubic.gemma.apps.AclLinterCliTest

Naming no check keeps the previous behaviour: all five run.

namingOneCheck_runsOnlyThatCheck() - Method in class ubic.gemma.apps.AclLinterCliTest

Naming one check must run only that one.

NCBIGene2GOAssociationLoaderCLITest - Class in ubic.gemma.apps

NCBIGene2GOAssociationLoaderCLITest() - Constructor for class ubic.gemma.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

needsAttention_noOpenTickets_isFalse() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

needsAttention_openBatchInfoTicket_isTrue() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

needsAttention_openGenericTicket_isTrue() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

needsAttention_openQualityReviewTicket_isTrue() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

needsAttention_openRealignmentTicket_isFalse() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

needsMoreInfoWithoutReason_isRefused() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

NegativeBinomialDistribution - Class in ubic.gemma.persistence.service.expression.bioAssayData

NegativeBinomialDistribution(int, double) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.NegativeBinomialDistribution

neitherIdNorNameYieldsNull() - Method in class ubic.gemma.rest.util.args.CompositeSequenceArgTest

Neither an id nor a name match yields null, which the arg service turns into a 404.

nestedScopeRestoresTheOuterName() - Method in class ubic.gemma.core.security.util.ActingIdentityTest

A nested scope RESTORES the outer name rather than clearing it.

NetUtilsTest - Class in ubic.gemma.core.util

Unit tests for NetUtils.

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

NetworkAvailable - Annotation Interface in ubic.gemma.core.util.test

Test annotation to indicate that a test requires network access or access to a specific resource.

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

Enables the NetworkAvailable annotation on JUnit 5 tests.

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

neverReplacesOnePrivateUseCharacterWithAnother() - Method in class ubic.gemma.core.util.SymbolFontPuaTest

newCachedThreadPool_returnsSecurityContextWrappedExecutor() - Method in class ubic.gemma.core.util.concurrent.ExecutorsTest

newFixedThreadPool_returnsSecurityContextWrappedExecutor() - Method in class ubic.gemma.core.util.concurrent.ExecutorsTest

newFixedThreadPool_withThreadFactory_returnsWrappedExecutor() - Method in class ubic.gemma.core.util.concurrent.ExecutorsTest

newInDraftOnly_isOmittedFromDispositionMap() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositionsTest

newSingleThreadExecutor_returnsSecurityContextWrappedExecutor() - Method in class ubic.gemma.core.util.concurrent.ExecutorsTest

newSingleThreadExecutor_withThreadFactory_consultsTheFactory() - Method in class ubic.gemma.core.util.concurrent.ExecutorsTest

newSingleThreadScheduledExecutor_returnsSecurityContextWrappedExecutor() - Method in class ubic.gemma.core.util.concurrent.ExecutorsTest

newVirtualThreadPerTaskExecutorIfAvailable_returnsWrappedExecutor() - Method in class ubic.gemma.core.util.concurrent.ExecutorsTest

noArgConstructor_postInsert_doesNotTouchUserManagerOrTrail() - Method in class ubic.gemma.persistence.audit.AuditTrailEventListenerTest

noArgConstructor_preDelete_doesNotTouchUserManagerOrTrail() - Method in class ubic.gemma.persistence.audit.AuditTrailEventListenerTest

noAuditableArg_logsWarnAndDoesNotCallService() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

noBreakSpacesAreNormalizedToo() - Method in class ubic.gemma.model.common.description.CharacteristicTest

The no-break spaces are the ones a normalizer quietly misses.

noDatasetTargetsAsksNothing() - Method in class ubic.gemma.rest.TicketsWebServiceTargetLabelsTest

No EE targets at all must not cost a query.

noExperimentAnalyzed_hasNoSecurityOwner() - Method in class ubic.gemma.model.analysis.SingleExperimentAnalysisTest

noMinPresentSet_returnsInputUnchanged() - Method in class ubic.gemma.core.util.matrix.datafilter.RowMissingFilterTest

nonAuditable_postInsert_isIgnored() - Method in class ubic.gemma.persistence.audit.AuditTrailEventListenerTest

nonCuratableInvestigation_doesNotUpdateCurationDetails() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplCuratableDispatchTest

none() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest.CustomResource

nonIdentifierHitDoesNotShortCircuit() - Method in class ubic.gemma.core.search.source.CompositeSearchSourceTest

nonMapReturnObject_throwsAuthorizationServiceException() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapFilteringProviderTest

nonMapReturnObject_throwsAuthorizationServiceException() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapValueFilteringProviderTest

nonMapReturnObject_throwsAuthorizationServiceException() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest

nonMapReturnObject_throwsAuthorizationServiceException() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest

nonSecurableEntity_isIgnored() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest

nonStreamReturnObject_throwsAuthorizationServiceException() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationStreamFilteringProviderTest

nonVoSecurable_isPassedThroughIfPermissionGranted() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest

noPermissionOnParent_throwsAccessDenied() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProviderTest

noReadableDatasetsShortCircuits() - Method in class ubic.gemma.rest.DatasetsWebServiceTicketsBulkTest

Nothing readable is an empty map, and no reason to run the ticket query at all.

noReason_leavesTheNoteUntouched() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

🛑 And no reason must leave the note exactly as it was.

noStoredHistogramIs404NotAnEmpty200Or204() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServicePvalueDistributionTest

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

Producing no analysis at all is a failure of the experiment, not a quiet empty result.

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

notVisibleFromAnotherThread() - Method in class ubic.gemma.core.security.util.ActingIdentityTest

Not inherited by another thread: work handed to an executor is attributed to whoever ran it.

nullAndBlankAreRejectedRatherThanDefaulted() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TriageVerdictTest

nullAndBlankBindNothing() - Method in class ubic.gemma.core.security.util.ActingIdentityTest

A null or blank name binds nothing, so callers do not have to branch before opening a scope.

nullDraft_returnsEmptyMap() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositionsTest

nullReferenceKeepsTheHistoricalBehaviour() - Method in class ubic.gemma.core.util.math.QuantileReferenceColumnsTest

Null means every column votes, which is what every caller outside the processed-vector pipeline still does.

nullRejectedLeavesStandingRejectionsAlone() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationPersistenceIT

nullTermTextStaysNull() - Method in class ubic.gemma.model.common.description.CharacteristicTest

Null must survive as null: "no value" stays distinct from "blank".

numericIdStillRoutesToTheSingleTicketHandler() - Method in class ubic.gemma.rest.TicketsWebServiceScratchpadRoutingTest

The numeric-id route is still live, so the 200 above is a contest won, not a template gone.

numericNameIsFoundWhenNoSuchIdExistsAtAll() - Method in class ubic.gemma.rest.util.args.CompositeSequenceArgTest

numericNameIsFoundWhenTheIdBelongsToAnotherPlatform() - Method in class ubic.gemma.rest.util.args.CompositeSequenceArgTest

A probe NAME can be entirely numeric -- Agilent feature-number arrays name every probe with a bare integer -- and the numeric branch of CompositeSequenceArg.valueOf(String) reads it as an id.

O

obiService(TaskExecutor) - Method in class ubic.gemma.core.ontology.TestOntologyConfig

objectIdentityRetrievalStrategy() - Method in class ubic.gemma.core.util.test.BaseDatabaseAclConfig

objectIdentityRetrievalStrategy() - Method in class ubic.gemma.core.util.test.BaseDatabaseTest5.BaseDatabaseTestContextConfiguration

ObjectIdentityRetrievalStrategyImplTest - Class in ubic.gemma.core.security.acl

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

objectIsUser(Securable) - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.TestAclAdvice

objectIsUserGroup(Securable) - Method in class ubic.gemma.core.security.acl.AclEventListenerTest.TestAclAdvice

ObsoleteTermCorrectionServiceTest - Class in ubic.gemma.core.ontology

The correction path writes to production annotations, so what is pinned here is mostly what it must NOT do: not touch a term a curator has to decide, not sweep up a deferred term, not write anything on a dry run, and not lose a curator's existing supportingEvidence.

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

OffsetArgTest - Class in ubic.gemma.rest.util.args

OffsetArgTest() - Constructor for class ubic.gemma.rest.util.args.OffsetArgTest

offsetModeRoutesToLegacyHelperAndReturnsFilteredInferredPaginatedResponse() - Method in class ubic.gemma.rest.DatasetsWebServiceBlacklistedCursorTest

offsetModeRoutesToLegacyHelperAndReturnsFilteredInferredPaginatedResponse() - Method in class ubic.gemma.rest.DatasetsWebServiceByIdsCursorTest

offsetModeRoutesToLegacyHelperAndReturnsFilteredPaginatedResponse() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceCursorTest

offsetModeRoutesToLegacyHelperAndReturnsFilteredPaginatedResponse() - Method in class ubic.gemma.rest.PlatformsWebServiceBlacklistedCursorTest

offsetModeRoutesToLegacyHelperAndReturnsFilteredPaginatedResponse() - Method in class ubic.gemma.rest.PlatformsWebServiceByIdsCursorTest

offsetModeRoutesToLegacyHelperAndReturnsFilteredPaginatedResponse() - Method in class ubic.gemma.rest.PlatformsWebServiceCursorTest

offsetModeRoutesToLegacyHelperAndReturnsFilteredPaginatedResponse() - Method in class ubic.gemma.rest.PlatformsWebServiceElementCursorTest

offsetModeRoutesToLegacyHelperAndReturnsFilteredPaginatedResponse() - Method in class ubic.gemma.rest.PlatformsWebServiceElementGenesCursorTest

offsetModeRoutesToLegacyHelperAndReturnsFilteredPaginatedResponse() - Method in class ubic.gemma.rest.TaxaWebServiceCursorTest

offsetModeRoutesToLegacyHelperAndReturnsPaginatedResponse() - Method in class ubic.gemma.rest.GeneWebServiceCursorTest

offsetModeRoutesToLegacyHelperAndReturnsPaginatedResponse() - Method in class ubic.gemma.rest.GeneWebServiceProbesCursorTest

offsetModeRoutesToLegacyHelperAndReturnsPaginatedResponse() - Method in class ubic.gemma.rest.PlatformsWebServiceDatasetsCursorTest

offsetModeRoutesToLegacyHelperAndReturnsPaginatedResponse() - Method in class ubic.gemma.rest.PlatformsWebServiceElementsCursorTest

offsetModeRoutesToLegacyHelperAndReturnsPaginatedResponse() - Method in class ubic.gemma.rest.TaxaWebServiceGeneProbesCursorTest

offsetModeRoutesToLegacyHelperAndReturnsPaginatedResponse() - Method in class ubic.gemma.rest.TaxaWebServiceGenesCursorTest

offsetModeRoutesToLegacyHelperAndReturnsPaginatedResponse() - Method in class ubic.gemma.rest.TicketsWebServiceCursorTest

offsetModeRoutesToLegacyHelperAndReturnsQueriedFilteredInferredPaginatedResponse() - Method in class ubic.gemma.rest.DatasetsWebServiceExpressionLevelsForGeneCursorTest

OlsTermResolverImplTest - Class in ubic.gemma.core.ontology.ols

Offline tests for the OLS response parser.

OlsTermResolverImplTest() - Constructor for class ubic.gemma.core.ontology.ols.OlsTermResolverImplTest

OlsTermResolverIntegrationTest - Class in ubic.gemma.core.ontology.ols

Live probe against the real EBI OLS service.

OlsTermResolverIntegrationTest() - Constructor for class ubic.gemma.core.ontology.ols.OlsTermResolverIntegrationTest

oneColor() - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactory

Start building a one-color (single-channel) array design.

oneColor_defaults_returnsPersistentEmptyAD() - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactoryTest

oneUnresolvableHitDoesNotDenyTheWholePage() - Method in class ubic.gemma.core.search.source.HibernateSearchSourceAclFilterTest

The over-correction guard: one unresolvable identity must not deny its readable neighbours, which is what catching NotFoundException into an empty map would do.

onlyOneTrailingCollapsedSuffixIsStripped() - Method in class ubic.gemma.core.analysis.sequence.BlatResult2PslTest

Only one trailing occurrence goes, so a probe genuinely carrying the suffix in its own name is not truncated past it.

onlyTheOutlierStageReportsAColumnCount() - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCorrelationAttritionMappingTest

Only the outlier stage can drop samples, and the correlation-matrix run deliberately does not mask them -- so a reader has to be able to see that the columns never moved.

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

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

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

OntologyCacheTest - Class in ubic.gemma.core.ontology

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

OntologyExternalLinksTest - Class in ubic.gemma.core.ontology

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

OntologyLoadingTest - Class in ubic.gemma.core.ontology

This test does not use the test profile as it aims to verify that all the ontologies we use in production are working properly.

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

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

The opt-in widening of a search into inferred relations.

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

ontologyService() - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

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

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

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

OntologyServiceTest - Class in ubic.gemma.core.ontology

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

ontologyTaskExecutor() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test.GeneOntologyService2TestContextConfiguration

ontologyTaskExecutor() - Method in class ubic.gemma.core.ontology.TestOntologyConfig

Executor used for loading ontologies in background.

OntologyTermValidationExceptionMapperTest - Class in ubic.gemma.rest.providers

OntologyTermValidationExceptionMapperTest() - Constructor for class ubic.gemma.rest.providers.OntologyTermValidationExceptionMapperTest

OntologyTermValidationExceptionMapperTest.CustomResource - Class in ubic.gemma.rest.providers

OntologyTermValidatorImplTest - Class in ubic.gemma.core.ontology

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

OntologyUtilsTest - Class in ubic.gemma.core.ontology

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

openApi() - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

openApi() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

openApi() - Method in class ubic.gemma.rest.TasksWebServiceTest.TasksWebServiceContextConfiguration

OpenApiTest - Class in ubic.gemma.rest

OpenApiTest() - Constructor for class ubic.gemma.rest.OpenApiTest

OpenApiWebServiceTest - Class in ubic.gemma.rest

Pin the invariant that /openapi.{json,yaml} serves the very OpenAPI instance held by the openApi bean — the instance OpenApiFactory decorates with the servers list, the FilterArg/SortArg examples and placeholder resolution.

OpenApiWebServiceTest() - Constructor for class ubic.gemma.rest.OpenApiWebServiceTest

openOnly_restrictsToTheOpenStates() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketSearchQueryTest

openOnlyFalse_leavesTheStatePredicateOut() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketSearchQueryTest

openSession() - Method in class ubic.gemma.core.security.acl.InMemoryAclService

openTicket_rejectsBlankTitle() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

openTicket_rejectsEmptyTargets() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

openTicket_secondScratchpadIsRefusedWithTheExistingId() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

POST /tickets {"type":"SCRATCHPAD"} answered 500 with the schema in the body — Duplicate entry '1' for key 'TICKET_ONE_SCRATCHPAD_PER_CURATOR' (cab, 2026-09-01, on gemma2).

openTicket_seedsOpenedEvent_andDelegatesToCreate() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

optionalReason_isAppendedToTheServersOwnNote() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

A supplied reason joins the server's mechanical description rather than replacing it — cab's ask was explicitly "appended to the server's own note", so the description survives.

OptionsUtilsTest - Class in ubic.gemma.cli.util

OptionsUtilsTest() - Constructor for class ubic.gemma.cli.util.OptionsUtilsTest

ordering_is_stable_when_nothing_separates_the_hits() - Method in class ubic.gemma.rest.ranking.CommonalityRankingStrategyTest

other - Variable in class ubic.gemma.core.util.RoundingUtilsTest.Holder

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

Tests for OutlierDetectionService

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

Output - Section in class ubic.gemma.core.util.test.ExternalUrlReachabilityTest

overlongDownload_isRejectedAndTheFileRemoved(Path) - Method in class ubic.gemma.core.util.NetUtilsTest

The fault actually observed against NCBI: the transfer replays a run of bytes and the local file ends up bigger than the remote.

overlongNoteIsTruncated() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriagePersistenceIT

overTheCapIsRefusedRatherThanTruncated() - Method in class ubic.gemma.rest.DatasetsWebServiceTicketsBulkTest

Over the cap is a 400 that names the cap, not a request that quietly truncates the page.

overviewPayloadCarriesTheFieldsItAdvertises() - Method in class ubic.gemma.rest.GeneWebServiceOverviewTest

overviewRaceWithDeleteThrows404() - Method in class ubic.gemma.rest.GeneWebServiceOverviewTest

overviewReturnsFullyPopulatedVoWithGoTermCount() - Method in class ubic.gemma.rest.GeneWebServiceOverviewTest

P

parent - Variable in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest.Child

parent - Variable in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProviderTest.Child

Parent(Long) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest.Parent

Parent(Long) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProviderTest.Parent

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

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.

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

parentStash_isPopulatedByParentInsert_andConsumedByChildInsert() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest

parked_overridesDiff() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositionsTest

parkedElementAbsentFromBothSides_isStillListed() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositionsTest

passes_configured_attribute_to_voter() - Method in class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManagerTest

passthrough() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest.CustomResource

Stands in for the 302 pass-through aliases, which forward every parameter they are given.

patchUser_addsToAdminGroup_whenIsAdminTrueAndNotAlready() - Method in class ubic.gemma.rest.AdminWebServiceTest

patchUser_removesFromAdminGroup_whenIsAdminFalseAndCurrentlyAdmin() - Method in class ubic.gemma.rest.AdminWebServiceTest

patchUser_returns400_whenBodyEmpty() - Method in class ubic.gemma.rest.AdminWebServiceTest

patchUser_returns404_whenUserNotFound() - Method in class ubic.gemma.rest.AdminWebServiceTest

patchUser_togglesEnabled() - Method in class ubic.gemma.rest.AdminWebServiceTest

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

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

payload_survivesUpdateMetadata() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

payloadRoundTripsThroughTheAuditEventPayloadType() - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCorrelationAttritionMappingTest

The aspect writes the payload through the polymorphic AuditEventPayload type, so the stored JSON carries a @type discriminator and a reader has to register the subtype to resolve it.

peek(ObjectIdentity) - Method in class ubic.gemma.core.security.acl.InMemoryAclService

Direct map-style access to the stored ACL by entity OID, bypassing the NotFoundException contract — useful in assertions that want a nullable view.

pendingIsNotAVerdict() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TriageVerdictTest

There is no pending verdict — an un-triaged set has no row — so a caller sending one is told rather than quietly given a verdict nobody chose.

permissionOnAssociatedParent_lettsThroughChild() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProviderTest

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.BaseSpringContextTest5

Deprecated.

Persister-shrink S4b: retained for subclasses that still inject directly via the inherited field (migrated alongside their own persisterHelper sites in the junit5 batch agents).

PersisterTest - Class in ubic.gemma.persistence.persister

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

pick(String) - Static method in class ubic.gemma.core.security.audit.AuditedAspectTest.ValueSpelHelper

placeholderConfigurer() - Static method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

placeholderConfigurer() - Static method in class ubic.gemma.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

placeholderConfigurer() - Static method in class ubic.gemma.rest.TasksWebServiceTest.TasksWebServiceContextConfiguration

plainCharacteristic_leavesStatementFieldsNull() - Method in class ubic.gemma.model.common.description.AnnotationValueObjectTest

plainExperiment_updatesCurationDetails() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplCuratableDispatchTest

plainGeneValueObjectOmitsTheOverviewOnlyFields() - Method in class ubic.gemma.rest.GeneWebServiceOverviewTest

plainStreamTakesTheSendfilePath() - Method in class ubic.gemma.rest.providers.SendfileProviderTest

PlatformArgTest - Class in ubic.gemma.rest.util.args

PlatformArgTest() - Constructor for class ubic.gemma.rest.util.args.PlatformArgTest

PlatformsWebServiceBlacklistedCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to PlatformsWebService.getBlacklistedPlatforms(FilterArg, SortArg, OffsetArg, LimitArg, CursorArg) as step 1h of CURSOR_PAGINATION_STEP1_PLAN.md.

PlatformsWebServiceBlacklistedCursorTest() - Constructor for class ubic.gemma.rest.PlatformsWebServiceBlacklistedCursorTest

PlatformsWebServiceByIdsCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to PlatformsWebService#getPlatformsByIds(PlatformArrayArg, FilterArg, OffsetArg, LimitArg, SortArg, CursorArg) — the GET /platforms/{platform} variant (step 1x).

PlatformsWebServiceByIdsCursorTest() - Constructor for class ubic.gemma.rest.PlatformsWebServiceByIdsCursorTest

PlatformsWebServiceCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to PlatformsWebService#getPlatforms(FilterArg, OffsetArg, LimitArg, SortArg, CursorArg) as proof-of-concept for step 1c of CURSOR_PAGINATION_STEP1_PLAN.md.

PlatformsWebServiceCursorTest() - Constructor for class ubic.gemma.rest.PlatformsWebServiceCursorTest

PlatformsWebServiceDatasetsCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to PlatformsWebService.getPlatformDatasets(PlatformArg, OffsetArg, LimitArg, CursorArg) as step 1f of CURSOR_PAGINATION_STEP1_PLAN.md.

PlatformsWebServiceDatasetsCursorTest() - Constructor for class ubic.gemma.rest.PlatformsWebServiceDatasetsCursorTest

PlatformsWebServiceElementCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to PlatformsWebService.getPlatformElement(PlatformArg, CompositeSequenceArrayArg, OffsetArg, LimitArg, CursorArg, boolean, boolean) as step 1j of CURSOR_PAGINATION_STEP1_PLAN.md.

PlatformsWebServiceElementCursorTest() - Constructor for class ubic.gemma.rest.PlatformsWebServiceElementCursorTest

PlatformsWebServiceElementGenesCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to PlatformsWebService.getPlatformElementGenes(PlatformArg, CompositeSequenceArg, OffsetArg, LimitArg, CursorArg) as step 1l of CURSOR_PAGINATION_STEP1_PLAN.md.

PlatformsWebServiceElementGenesCursorTest() - Constructor for class ubic.gemma.rest.PlatformsWebServiceElementGenesCursorTest

PlatformsWebServiceElementsCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to PlatformsWebService.getPlatformElements(PlatformArg, OffsetArg, LimitArg, CursorArg, boolean, boolean, QueryArg, FilterArg) as step 1e of CURSOR_PAGINATION_STEP1_PLAN.md.

PlatformsWebServiceElementsCursorTest() - Constructor for class ubic.gemma.rest.PlatformsWebServiceElementsCursorTest

PlatformsWebServiceMappingSummaryTest - Class in ubic.gemma.rest

Pure-Mockito test for the GET /platforms/{platform}/elements/{probe}/mappingSummary endpoint added to PlatformsWebService.

PlatformsWebServiceMappingSummaryTest() - Constructor for class ubic.gemma.rest.PlatformsWebServiceMappingSummaryTest

PlatformsWebServicePslTrackTest - Class in ubic.gemma.rest

Pure-Mockito test for GET /platforms/{platform}/elements/{probe}/pslTrack, which replaces the retired gemma-web BlatResultTrackController (blatTrack.html?id=).

PlatformsWebServicePslTrackTest() - Constructor for class ubic.gemma.rest.PlatformsWebServicePslTrackTest

PlatformsWebServiceTest - Class in ubic.gemma.rest

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

PlatformsWebServiceTicketsCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to PlatformsWebService.getPlatformTickets(PlatformArg, CursorArg, LimitArg) as step 1s of CURSOR_PAGINATION_STEP1_PLAN.md.

PlatformsWebServiceTicketsCursorTest() - Constructor for class ubic.gemma.rest.PlatformsWebServiceTicketsCursorTest

PointcutsTest - Class in ubic.gemma.persistence.util

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

postDelete_cascadesToChildAcls() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest

postDelete_removesAcl() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest

PreboardedExperimentMappingTest - Class in ubic.gemma.persistence.service.expression.experiment

Regression guard for the PreboardedExperiment discriminator mapping added in commit 44bf890061.

PreboardedExperimentMappingTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentMappingTest

PreboardedExperimentServiceTest - Class in ubic.gemma.persistence.service.expression.experiment

Pure-Mockito unit tests for PreboardedExperimentServiceImpl: the 409-on-existing logic in createPreboarded, the promotion FK-rebind + workflow-state advance.

PreboardedExperimentServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceTest

preboardedRoundTripsThroughHibernate() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentMappingTest

preboardedTargetsAreLabelledByAccession() - Method in class ubic.gemma.rest.TicketsWebServiceTargetLabelsTest

A preboarded target is labelled by its accession — the batch triage ticket carries every candidate from a scrape, and a curator opening it should see GSE numbers rather than bare ids.

PreboardedWebServiceTest - Class in ubic.gemma.rest

Pure-Mockito unit tests for PreboardedWebService.

PreboardedWebServiceTest() - Constructor for class ubic.gemma.rest.PreboardedWebServiceTest

preCompressedGzipIsHandledAfterTheEncoder() - Method in class ubic.gemma.rest.providers.GzipHeaderDecoratorTest

prefersTheAuthoritativeAdobeMapping() - Method in class ubic.gemma.core.util.SymbolFontPuaTest

PrincipalComponentAnalysisDaoImplTest - Class in ubic.gemma.persistence.service.analysis.expression.pca

PrincipalComponentAnalysisDaoImplTest() - Constructor for class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDaoImplTest

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

prior_is_scored_against_the_best_candidate_in_the_same_result_set() - Method in class ubic.gemma.rest.ranking.CommonalityRankingStrategyTest

prior_separates_two_legitimate_hits_that_usage_cannot() - Method in class ubic.gemma.rest.ranking.CommonalityRankingStrategyTest

probability(int) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.NegativeBinomialDistribution

probe_groupByEntityOverChainedCollectionJoins() - Method in class ubic.gemma.persistence.util.HibernateSqmFragileShapesIT

Shape 3: multi-association entity projection with group by on an entity reference.

probe_implicitPolymorphismOnUnmappedBase() - Method in class ubic.gemma.persistence.util.HibernateSqmFragileShapesIT

Shape 2 (P7): implicit polymorphism over the unmapped BulkExpressionDataVector base class.

probe_subqueryOverCollectionJoin() - Method in class ubic.gemma.persistence.util.HibernateSqmFragileShapesIT

Shape 1 (B2): multi-collection join with a correlated subquery driving from BioAssayDimension.

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

probeWithNoAlignmentsIsA404() - Method in class ubic.gemma.rest.PlatformsWebServicePslTrackTest

probeWithNoBiologicalCharacteristicIsA404() - Method in class ubic.gemma.rest.PlatformsWebServicePslTrackTest

probeWithOnlyUnplaceableAlignmentsIsA404() - Method in class ubic.gemma.rest.PlatformsWebServicePslTrackTest

Only unplaceable alignments is a 404 too -- there is nothing to show in the browser, and an empty track would read as "aligned nowhere" rather than "cannot be placed".

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

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

ProcessedExpressionDataVectorCreationHelperServiceTest - Class in ubic.gemma.persistence.service.expression.bioAssayData

ProcessedExpressionDataVectorCreationHelperServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorCreationHelperServiceTest

ProcessedExpressionDataVectorDaoTest - Class in ubic.gemma.persistence.service.expression.bioAssayData

ProcessedExpressionDataVectorDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoTest

ProcessedExpressionDataVectorServiceTest - Class in ubic.gemma.persistence.service.expression.bioAssayData

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

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

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

ProgressUpdateAppenderTest - Class in ubic.gemma.core.logging.log4j

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

ProgressUpdateAppenderTest() - Constructor for class ubic.gemma.core.logging.log4j.ProgressUpdateAppenderTest

promote_alreadyPromotedThrows() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceTest

promote_carriesTheSourceMetadataForward() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceTest

Promotion used to drop the preboarded's harvested payload, so whatever the scrape found was lost the moment the data landed.

promote_doesNotOverwriteASourceMetadataDocumentTheImportAlreadyWrote() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceTest

The import writes the schema-v1 document from the parsed series; a preboarded carries only the smaller scrape payload.

promote_doesNotRegressEeAlreadyCurated() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceTest

promote_rebindsProposalsAndAdvancesState() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceTest

promotePreboarded_alreadyPromotedReturns409() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

promotePreboarded_missingEeIdThrows400() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

promotePreboarded_unknownEeThrows404() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

promotePreboarded_validReturns200WithCounts() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

proposal_attachAndIdempotency() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

proposalScoped_namesTheSet() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionPersistenceIT

ProtocolAdderCliTest - Class in ubic.gemma.apps

ProtocolAdderCliTest() - Constructor for class ubic.gemma.apps.ProtocolAdderCliTest

ProtocolDeleterCliTest - Class in ubic.gemma.apps

ProtocolDeleterCliTest() - Constructor for class ubic.gemma.apps.ProtocolDeleterCliTest

pslTrackIsServedAsPlainTextNamedAfterTheProbe() - Method in class ubic.gemma.rest.PlatformsWebServicePslTrackTest

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

Integration test for the PUBLICATION_ASSOCIATION schema migration (MySQL V25 / H2 V26) and the PublicationAssociation entity + service, against the real MySQL gemdtest.

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

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

Unit tests for the refusal message PublicationAssociationServiceImpl raises when a standing rejection blocks an acceptance.

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

publicationIsFetchJoined() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationPersistenceIT

publicVoIsKept_andIsPublicFlagPopulated() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest

PubMedSearcherIntegrationTest - Class in ubic.gemma.apps

Tests command line.

PubMedSearcherIntegrationTest() - Constructor for class ubic.gemma.apps.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

pvalue_atPerfectCorrelation_isZero() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

pvalue_atZeroCorrelation_isOne() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

pvalue_insufficientDof_isOne() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

Q

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

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

QuantileReferenceColumnsTest - Class in ubic.gemma.core.util.math

Which columns define the quantile reference distribution.

QuantileReferenceColumnsTest() - Constructor for class ubic.gemma.core.util.math.QuantileReferenceColumnsTest

QuantitationTypeArgTest - Class in ubic.gemma.rest.util.args

QuantitationTypeArgTest() - Constructor for class ubic.gemma.rest.util.args.QuantitationTypeArgTest

QuantitationTypeConversionUtilsTest - Class in ubic.gemma.core.analysis.preprocess.convert

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

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

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

QuantitationTypeDetectionUtilsTest - Class in ubic.gemma.core.analysis.preprocess.detect

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

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

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

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

Lightweight unit test for QuantitationTypeReadServiceImpl that verifies each public method delegates to the right QuantitationTypeDao call without standing up a Spring context.

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

QuantitationTypeUtilsTest - Class in ubic.gemma.model.common.quantitationtype

QuantitationTypeUtilsTest() - Constructor for class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtilsTest

QueryArgTest - Class in ubic.gemma.rest.util.args

QueryArgTest() - Constructor for class ubic.gemma.rest.util.args.QueryArgTest

queryDetachedInFreshSession(SessionFactory, Function) - Static method in class ubic.gemma.core.util.test.ThawTestUtils

Run a query inside a fresh Session and return its result detached.

queryNameIsNotQuoted() - Method in class ubic.gemma.core.analysis.sequence.BlatResult2PslTest

The query name went out wrapped in literal double quotes from 2007 until 2026-08-22.

queryTokens_dropStopWordsThatCoverageWouldOtherwiseMatchAsSubstrings() - Method in class ubic.gemma.rest.AnnotationSearchRankingStrategyTest

QueryUtilsTest - Class in ubic.gemma.persistence.util

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

quietNightWithMatchingCountsDoesNotReindex() - Method in class ubic.gemma.core.search.indexer.ScheduledSearchReindexerTest

R

RandomBulkDataUtils - Class in ubic.gemma.persistence.service.expression.bioAssayData

Utilities for generating random bulk vectors.

RandomBulkDataUtils() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.RandomBulkDataUtils

randomBulkVectors(ExpressionExperiment, Collection, ArrayDesign, QuantitationType, Class) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomBulkDataUtils

Generate bulk vectors for a collection of subsets.

randomBulkVectors(ExpressionExperiment, ArrayDesign, QuantitationType, Class) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomBulkDataUtils

randomBulkVectors(ExpressionExperiment, BioAssayDimension, ArrayDesign, QuantitationType, Class) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomBulkDataUtils

randomCategoricalFactor(ExperimentalDesign, Collection, String, int) - Static method in class ubic.gemma.persistence.service.expression.experiment.RandomExperimentalDesignUtils

Create and assign a categorical factor.

randomCategoricalFactor(ExpressionExperiment, String, int) - Static method in class ubic.gemma.persistence.service.expression.experiment.RandomExperimentalDesignUtils

Create and assign a categorical factor to all the samples of an experiment.

randomCellTypeAssignment(SingleCellDimension) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomSingleCellDataUtils

Generate a random cell type assignment with 10 cell types and 10% sparsity.

randomCellTypeAssignment(SingleCellDimension, int, double) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomSingleCellDataUtils

randomContinuousFactor(ExperimentalDesign, Collection, String) - Static method in class ubic.gemma.persistence.service.expression.experiment.RandomExperimentalDesignUtils

Create and assign a continuous factor.

randomContinuousFactor(ExpressionExperiment, String) - Static method in class ubic.gemma.persistence.service.expression.experiment.RandomExperimentalDesignUtils

Create and assign a continuous factor to all the samples of an experiment.

randomCountMatrix(ExpressionExperiment) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils

Generate a count matrix.

randomCountMatrix(ExpressionExperiment, ScaleType) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils

Generate a "transformed" count matrix.

randomExperimentalDesign(Collection, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.RandomExperimentalDesignUtils

Create a random experimental design with the given number of categorical and continuous factors.

randomExperimentalDesign(Collection, int, int, int, double) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignUtilsTest

randomExperimentalDesign(ExpressionExperiment, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.RandomExperimentalDesignUtils

Create and assign a random experimental design to the given experiment.

RandomExperimentalDesignUtils - Class in ubic.gemma.persistence.service.expression.experiment

Generate random experimental design for a given experiment.

RandomExperimentalDesignUtils() - Constructor for class ubic.gemma.persistence.service.expression.experiment.RandomExperimentalDesignUtils

RandomExpressionDataMatrixUtils - Class in ubic.gemma.persistence.service.expression.bioAssayData

Utilities for generating random ExpressionDataDoubleMatrix following various random distributions.

RandomExpressionDataMatrixUtils() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils

randomExpressionExperiment(Taxon, int, ArrayDesign) - Static method in class ubic.gemma.persistence.service.expression.experiment.RandomExpressionExperimentUtils

Create a random ExpressionExperiment with a desired number of assays.

RandomExpressionExperimentUtils - Class in ubic.gemma.persistence.service.expression.experiment

RandomExpressionExperimentUtils() - Constructor for class ubic.gemma.persistence.service.expression.experiment.RandomExpressionExperimentUtils

randomExpressionMatrix(int, int, IntegerDistribution) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils

Generate a random raw expression matrix following the given discrete distribution.

randomExpressionMatrix(int, int, RealDistribution) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils

Generate a random raw expression matrix following the given continuous distribution.

randomExpressionMatrix(ExpressionExperiment, QuantitationType, List, List, RealDistribution) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils

randomExpressionMatrix(ExpressionExperiment, QuantitationType, RealDistribution) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils

randomLinearMatrix(ExpressionExperiment) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils

randomLog2cpmMatrix(ExpressionExperiment) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils

randomLog2Matrix(ExpressionExperiment) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils

randomLog2Matrix(ExpressionExperiment, BioAssayDimension) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils

Create a random matrix with a specific sample structure.

randomLog2RatiometricMatrix(ExpressionExperiment) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils

randomName() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

RandomSingleCellDataUtils - Class in ubic.gemma.persistence.service.expression.bioAssayData

Utilities for generating random single-cell data.

RandomSingleCellDataUtils() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.RandomSingleCellDataUtils

randomSingleCellVector(ExpressionExperiment, CompositeSequence, QuantitationType, int, double) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomSingleCellDataUtils

randomSingleCellVector(ExpressionExperiment, CompositeSequence, QuantitationType, SingleCellDimension, double) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomSingleCellDataUtils

Generate a single random single-cell vector.

randomSingleCellVectors() - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomSingleCellDataUtils

randomSingleCellVectors(int, int, int, double, QuantitationType) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomSingleCellDataUtils

randomSingleCellVectors(int, int, int, double, ScaleType) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomSingleCellDataUtils

randomSingleCellVectors(QuantitationType) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomSingleCellDataUtils

randomSingleCellVectors(ExpressionExperiment, ArrayDesign, QuantitationType) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomSingleCellDataUtils

Generate random single-cell vectors with 1000 cells/sample and 90% sparsity.

randomSingleCellVectors(ExpressionExperiment, ArrayDesign, QuantitationType, int, double) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomSingleCellDataUtils

Generate random single-cell vectors.

rat() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory

Resolve the seeded rat taxon (NCBI 10116).

RawAndProcessedExpressionDataVectorDaoTest - Class in ubic.gemma.persistence.service.expression.bioAssayData

RawAndProcessedExpressionDataVectorDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoTest

RawAndProcessedExpressionDataVectorServiceGeoTest - Class in ubic.gemma.persistence.service.expression.bioAssayData

RawAndProcessedExpressionDataVectorServiceGeoTest() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceGeoTest

RawAndProcessedExpressionDataVectorServiceTest - Class in ubic.gemma.persistence.service.expression.bioAssayData

RawAndProcessedExpressionDataVectorServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceTest

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

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

RawExpressionDataVectorDaoTest - Class in ubic.gemma.persistence.service.expression.bioAssayData

RawExpressionDataVectorDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoTest

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

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

read_service_methods_reaching_a_dao_must_be_transactional - Static variable in class ubic.gemma.core.architecture.ReadServiceTransactionalRuleTest

allowEmptyShould stays false deliberately — see ReadServiceTransactionalRuleTest.classes_are_actually_imported(JavaClasses).

readableHitsSurviveAndUnreadableOnesAreDropped() - Method in class ubic.gemma.core.search.source.HibernateSearchSourceAclFilterTest

readAclById(ObjectIdentity) - Method in class ubic.gemma.core.security.acl.InMemoryAclService

readAclById(ObjectIdentity, List) - Method in class ubic.gemma.core.security.acl.InMemoryAclService

readAclById(ObjectIdentity, Session) - Method in class ubic.gemma.core.security.acl.InMemoryAclService

readAclsById(List) - Method in class ubic.gemma.core.security.acl.InMemoryAclService

readAclsById(List, List) - Method in class ubic.gemma.core.security.acl.InMemoryAclService

ReadServiceTransactionalRuleTest - Class in ubic.gemma.core.architecture

A service method that reaches a DAO must declare its own transaction.

ReadServiceTransactionalRuleTest() - Constructor for class ubic.gemma.core.architecture.ReadServiceTransactionalRuleTest

readsFactorsAndTags() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetPayloadCountsTest

readsUriInfo(UriInfo) - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest.CustomResource

Holds the raw UriInfo, so it can read any parameter and none can be shown to be ignored.

ReadWriteFileLockTest - Class in ubic.gemma.core.util.locking

ReadWriteFileLockTest() - Constructor for class ubic.gemma.core.util.locking.ReadWriteFileLockTest

ReadWriteFileLockTestScript - Class in ubic.gemma.core.util.locking

Test script to validate locking behaviors for ReadWriteFileLockTest.

ReadWriteFileLockTestScript() - Constructor for class ubic.gemma.core.util.locking.ReadWriteFileLockTestScript

reason() - Method in record class ubic.gemma.core.security.audit.AuditedAspectTest.SamplePayload

Returns the value of the reason record component.

reasonIsRequired() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionPersistenceIT

reasonSurvivesReload() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionPersistenceIT

reauthenticate(String, String) - Method in class ubic.gemma.core.security.UserDetailsManagerImpl

rebindDoesNotViolateTheUniqueKey() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationPersistenceIT

rebindMovesAssertionsToTheCanonicalReference() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationPersistenceIT

reconcileRetractsDroppedPublications() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationPersistenceIT

recordFixture() - Method in class ubic.gemma.core.analysis.service.GoldenPathFixtureRecorder

refreshExtendsTheHoldersLease() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockPersistenceIT

refreshIsNotAnAcquire() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockPersistenceIT

The rule that keeps autosave from being a weapon.

refusal_standsOnItsOwn() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionPersistenceIT

Re-generating the fixture - Section in class ubic.gemma.core.ontology.providers.CellLineOntologyTest

RegressionTesting - Class in ubic.gemma.core.util

Tools to help make regression testing easier — comparing matrices, arrays, and collections within a tolerance.

rejected_whenProposalHadKeyAndDraftDoesNot() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositionsTest

rejectionOutranksALaterAgent() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationPersistenceIT

rejectionsAreQueryable() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationPersistenceIT

rejects_unsupported_attribute_at_construction() - Method in class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManagerTest

rejectsEmptyAsMalformed() - Method in class ubic.gemma.rest.util.args.CursorArgTest

rejectsEmptyKeyTupleInConstructor() - Method in class ubic.gemma.persistence.util.CursorTest

rejectsGarbageAsMalformed() - Method in class ubic.gemma.rest.util.args.CursorArgTest

rejectsNullArgumentsInConstructor() - Method in class ubic.gemma.persistence.util.CursorTest

rejectsNullAsMalformed() - Method in class ubic.gemma.rest.util.args.CursorArgTest

rejectsNullTargetId() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

rejectsNullTargetType() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

releaseRequiresTheHolder() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockPersistenceIT

reloadByNcbiId_findsTheSameGene() - Method in class ubic.gemma.core.util.test.fixture.GeneFactoryTest

removed() - Method in record class ubic.gemma.core.security.audit.AuditedAspectTest.SamplePayload

Returns the value of the removed record component.

removeExperiment() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

removeFixtures() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderServiceIntegrationTest

removeFixtures() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

removeFixtures() - Method in class ubic.gemma.rest.AnalysisResultSetsJerseyTest

removeFixtures() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

removeFixtures() - Method in class ubic.gemma.rest.GeneWebServiceTest

removeFixtures() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

removeFixtures() - Method in class ubic.gemma.rest.TaxaWebServiceTest

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

removeGroupAuthority(String, GrantedAuthority) - Method in class ubic.gemma.core.security.GroupManagerImpl

removeGroupAuthority(UserGroup, String) - Method in class ubic.gemma.core.security.UserServiceImpl

removeTarget_allowsRemovingCompletedWork_butReportsIt() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

A completed target may be removed — a scratchpad's rows are all NOT_DONE and refusing would make the common case pay for the rare one.

removeTarget_isIdempotentWhenAbsent() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

Removing something that is not there has already reached the asked-for state.

removeTarget_removesMembership_andLogsTargetRemoved() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

On a scratchpad, removing IS finishing (Paul, 2026-08-31) — the ticket stays open and the dataset leaves it — so this is the counterpart of addTarget, not an afterthought.

removeUserFromGroup(String, String) - Method in class ubic.gemma.core.security.GroupManagerImpl

removeUserFromGroup(User, UserGroup) - Method in class ubic.gemma.core.security.UserServiceImpl

removeWithBioAssayDimension() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

removeWithPayload_serialisesJsonAndIncludesTypeDiscriminator() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

removeWithUninitializedSingleCellDataVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

Removing an experiment whose single-cell vectors were never loaded must go through the projection-query branch of removeAllSingleCellDataVectors rather than walking the lazy collection.

renameGroup(String, String) - Method in class ubic.gemma.core.security.GroupManagerImpl

repairsTheCorpusCases() - Method in class ubic.gemma.core.util.SymbolFontPuaTest

repeatable_defaultClassFallback_firesForUnmatchedType() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C (repeatable): a default-class declaration acts as a fallback when no more-specific declaration matches.

repeatable_dispatchesToCorrectEventType_iae() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C (repeatable): two repeated declarations dispatch to different event types.

repeatable_dispatchesToCorrectEventType_ise() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C (repeatable): two repeated declarations dispatch to different event types.

repeatable_mostSpecificMatchWins() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C (repeatable): most-specific match wins.

repeatable_noMatch_emitsNothing() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C (repeatable): when no declaration matches the throwable, nothing is recorded — like a Java multi-catch where the thrown type isn't in the catch list.

repeatedGzipCompressesJsonThroughTheEncoder() - Method in class ubic.gemma.rest.providers.GzipHeaderDecoratorTest

The repeated-annotation case.

repeatedGzipLabelsTsvWithoutInvokingTheEncoder() - Method in class ubic.gemma.rest.providers.GzipHeaderDecoratorTest

repeatedIdsAreDeduplicated() - Method in class ubic.gemma.rest.DatasetsWebServiceTicketsBulkTest

A repeated id must not become a repeated key or a doubled ticket list; the other two bulk dataset reads deduplicate the same way.

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

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

RepetitiveValuesFilterTest - Class in ubic.gemma.core.analysis.preprocess.filter

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

ReplaceAllRawDataVectorsQtCollisionTest - Class in ubic.gemma.persistence.service.expression.experiment

Fast H2-backed regression guard for the QT entity-identity collision that DataUpdater.addCountData re-run path tripped (commit ef838e08fc).

ReplaceAllRawDataVectorsQtCollisionTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ReplaceAllRawDataVectorsQtCollisionTest

replaceAllRawDataVectorsWithDetachedExistingQtDoesNotCollide() - Method in class ubic.gemma.persistence.service.expression.experiment.ReplaceAllRawDataVectorsQtCollisionTest

Reproduce the NonUniqueObjectException bug from commit ef838e08fc.

reportsRatherThanGuesses() - Method in class ubic.gemma.core.util.SymbolFontPuaTest

RepresentationConversionUtilsTest - Class in ubic.gemma.core.analysis.preprocess.convert

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

requiresPostCommitHandling_isFalse_soAclOpsRunInTx() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest

requiresPostCommitHandling_isFalse_soAuditWritesRunInTx() - Method in class ubic.gemma.persistence.audit.AuditTrailEventListenerTest

reseedRandomGenerator(long) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.NegativeBinomialDistribution

resetBaseCodeConfiguration() - Method in class ubic.gemma.core.config.BaseCodeConfigurerTest

resetHibernateStatsClearsStatistics() - Method in class ubic.gemma.rest.AdminWebServiceTest

resetMocks() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCliTest

resetMocks() - Method in class ubic.gemma.apps.ProtocolAdderCliTest

resetMocks() - Method in class ubic.gemma.apps.UpdateGeoSourceMetadataCliTest

resetMocks() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceTest

resetMocks() - Method in class ubic.gemma.core.ontology.OntologyCacheTest

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

resetMocks() - Method in class ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceTest

resetMocks() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentBatchInformationServiceTest

resetMocks() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

resetMocks() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

resetMocks() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellStreamingAddTest

resetMocks() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

resetMocks() - Method in class ubic.gemma.rest.DatasetsRestTest

resetMocks() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

resetMocks() - Method in class ubic.gemma.rest.TasksWebServiceTest

resetMocks() - Method in class ubic.gemma.rest.util.args.GeneArgServiceTest

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

Reset the seed to the default value.

resetTestCollectionSize() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

Restore to default.

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

resetTimeZone() - Static method in class ubic.gemma.cli.util.OptionsUtilsTest

resetUserPassword_returns404_whenUserNotFound() - Method in class ubic.gemma.rest.AdminWebServiceTest

resetUserPassword_returns409_whenUserSoftDeleted() - Method in class ubic.gemma.rest.AdminWebServiceTest

resetUserPassword_returnsTempPassword_andCallsManager() - Method in class ubic.gemma.rest.AdminWebServiceTest

residualDriftAfterARebuildStillAdvancesTheMarker() - Method in class ubic.gemma.core.search.indexer.ScheduledSearchReindexerTest

resolvedDriftIsRecheckedOnceAfterTheRebuild() - Method in class ubic.gemma.core.search.indexer.ScheduledSearchReindexerTest

A drift-triggered rebuild re-checks afterwards.

resolveSecurityContextProxy() - Method in class ubic.gemma.core.job.SchedulerSecurityTest

resolvesTheExtenderTheFontKnowsAbout() - Method in class ubic.gemma.core.util.SymbolFontPuaTest

ResourceUtilsTest - Class in ubic.gemma.core.util

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

ResponseAssert - Class in ubic.gemma.rest.util

Assertions for jax-rs Response.

ResponseAssert(Response) - Constructor for class ubic.gemma.rest.util.ResponseAssert

RestapidocsIndexRewriteFilterTest - Class in ubic.gemma.rest.servlet

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

resultSetsListingIsCompressedThroughTheEncoder() - Method in class ubic.gemma.rest.providers.GzipHeaderDecoratorTest

The GET /resultSets list route, driven off its real annotations rather than a fixture.

retained_whenProposalAndDraftEqual() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositionsTest

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

returns_null_when_voter_abstains() - Method in class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManagerTest

reviewedByHuman_onlyWhenACuratorRuled() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriagePersistenceIT

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

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

RNASeqDataAddCliTest - Class in ubic.gemma.apps

RNASeqDataAddCliTest() - Constructor for class ubic.gemma.apps.RNASeqDataAddCliTest

rootSecurable_insertCreatesAclWithoutParent() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest

RootWebServiceTest - Class in ubic.gemma.rest

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

RoundingUtilsTest - Class in ubic.gemma.core.util

Unit tests for RoundingUtils, the JSON-side counterpart of TsvUtils.format(double).

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

RoundingUtilsTest.Holder - Class in ubic.gemma.core.util

roundTripBackward() - Method in class ubic.gemma.persistence.util.CursorTest

roundTripCompoundKeyForward() - Method in class ubic.gemma.persistence.util.CursorTest

roundTripSingleIdForward() - Method in class ubic.gemma.persistence.util.CursorTest

RowLevelFilterTest - Class in ubic.gemma.core.analysis.preprocess.filter

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

RowMissingFilterTest - Class in ubic.gemma.core.util.matrix.datafilter

Unit tests for RowMissingFilter: removes matrix rows that have too many missing values (NaN, by the matrix's own isMissing contract).

RowMissingFilterTest() - Constructor for class ubic.gemma.core.util.matrix.datafilter.RowMissingFilterTest

runAsAdmin() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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.BaseSpringContextTest5

Deprecated.

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.BaseSpringContextTest5

Deprecated.

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.BaseSpringContextTest5

Deprecated.

runAsUser(String, boolean) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

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

Run as a regular user.

runProvenance_roundTrips() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

runSecuredMethodOnSchedule() - Method in class ubic.gemma.core.job.SchedulerSecurityTest

runSecuredMethodOnScheduleMultiGroup() - Method in class ubic.gemma.core.job.SchedulerSecurityTest

runUnauthorizedMethodOnSchedule() - Method in class ubic.gemma.core.job.SchedulerSecurityTest

S

sameArray(int[], int[]) - Static method in class ubic.gemma.core.util.RegressionTesting

Test whether two int arrays contain the same items in the same order.

sameCuratorReacquires() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockPersistenceIT

sameJudgeTwice_upsertsInPlace() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriagePersistenceIT

sameMillisecondTie_breaksOnId() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

sample() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.NegativeBinomialDistribution

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

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

SampleCorrelationAttritionMappingTest - Class in ubic.gemma.persistence.service.analysis.expression.sampleCoexpression

Pins the shape of the filter attrition recorded on SampleCorrelationAnalysisEvent.

SampleCorrelationAttritionMappingTest() - Constructor for class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCorrelationAttritionMappingTest

SampleMexDataset - Class in ubic.gemma.core.loader.expression.singleCell

Sample a given MEX file.

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

SamplePayload(int, String) - Constructor for record class ubic.gemma.core.security.audit.AuditedAspectTest.SamplePayload

Creates an instance of a SamplePayload record class.

ScaleTypeConversionUtilsTest - Class in ubic.gemma.core.analysis.preprocess.convert

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

scbrainMatcher_hitsOn10xTechMention() - Method in class ubic.gemma.core.geoscrape.MatchersTest

scbrainMatcher_hitsWhenSingleCellAndBrain() - Method in class ubic.gemma.core.geoscrape.MatchersTest

scbrainMatcher_missesWhenBrainButNotSingleCell() - Method in class ubic.gemma.core.geoscrape.MatchersTest

scbrainMatcher_missesWhenSingleCellButNotBrain() - Method in class ubic.gemma.core.geoscrape.MatchersTest

ScheduledSearchReindexerTest - Class in ubic.gemma.core.search.indexer

Pins the two staleness signals in ScheduledSearchReindexer.

ScheduledSearchReindexerTest() - Constructor for class ubic.gemma.core.search.indexer.ScheduledSearchReindexerTest

SchedulerSecurityTest - Class in ubic.gemma.core.job

Tests security of methods run by Quartz.

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

SchedulerSecurityTest.TestSecureJob - Class in ubic.gemma.core.job

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

One-off Flyway baseline generator.

scopeAndSubject_mustAgree() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionPersistenceIT

scopeIsPartOfTheKey() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionPersistenceIT

scrape_cancelledMidLoop_doesNotOpenTicket() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

scrape_explicitSince_overridesTheWatermark() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

scrape_explicitUntil_beatsStartAt() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

scrape_forwardsSinceAndUntilToGeoBrowser() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

scrape_happyPath_createsPreboardedsAndOneTicketWithEnrichedMetadata() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

scrape_omittedSince_resumesFromLastCompletedWatermark() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

scrape_startAt_resolvesAccessionToTheWindowUpperBound() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

scrape_unresolvableStartAt_failsInsteadOfRescanningFromTheTop() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

scrape_zeroMatches_doesNotOpenTicket() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

scratchpadRoute_isNotSwallowedByTheIdTemplate() - Method in class ubic.gemma.rest.TicketsWebServiceScratchpadRoutingTest

scratchpads_areExcludedOutrightWhenTheCallerIsUnknown() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketSearchQueryTest

Another curator's scratchpad is not somewhere to file work, so it is not offered; when nobody is identified, no scratchpad is.

scratchpads_areOfferedToTheCuratorWhoReportedThem() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketSearchQueryTest

screeningResult_roundTripsUncoupledAndLogged() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

screeningResultReason_absentKeyLeavesReasonUntouched() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

screeningType_roundTripsAsName() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

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

search_byIdFindsTheTicketOrNothing() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

search_openOnlyExcludesResolvedTickets() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

search_scratchpadIsScopedToItsReporter() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

search_targetCountIsCountedNotLoaded() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

search_titleHitsAreOrderedByUpdatedAtDesc() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

search_titleMatchesCaseInsensitiveSubstring() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

search_wildcardsInTheQueryAreEscaped() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

searchDir - Variable in class ubic.gemma.core.config.SettingsConfigTest

searchEmptyIndexReturnsEmptyMap() - Method in class ubic.gemma.core.search.SearchServiceImplTest

searchEmptyQueryReturnsEmptyMap() - Method in class ubic.gemma.core.search.SearchServiceImplTest

SearchResultSetTest - Class in ubic.gemma.core.search

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

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.rest.AnnotationsUsageCountCacheTest.ContextConfig

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

SearchServiceImplTest - Class in ubic.gemma.core.search

Unit-level smoke tests for SearchServiceImpl.

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

searchTickets_acceptsALimitAtTheMaximum() - Method in class ubic.gemma.rest.TicketsWebServiceTest

searchTickets_anonymousCallerIsServedWithNoContactId() - Method in class ubic.gemma.rest.TicketsWebServiceTest

searchTickets_blankQuery_returnsNothingAndQueriesNothing() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

searchTickets_digitsFollowedByText_isTitleTextNotAnId() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

"Verbatim" excludes text that merely starts with digits: "6 samples" is a title, and reading it as ticket 6 would put an unrelated ticket at the top of the list.

searchTickets_doesNotListTheIdMatchTwiceWhenItAlsoMatchesTheTitle() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

A ticket whose title is also the number typed would otherwise be listed twice — once as the id match, once as a title match.

searchTickets_idThatNamesNoTicket_yieldsNoHitRatherThanAnError() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

A number that parses but names no ticket is a non-hit, not an error — the caller must not turn it into a 404, because the same string is still a legitimate title search.

searchTickets_listsTheVerbatimIdMatchFirst() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

searchTickets_nonNumericQuery_neverRunsTheIdLookup() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

searchTickets_openOnlyDefaultsToTrueOnTheWire() - Method in class ubic.gemma.rest.TicketsWebServiceTest

The default lives in the @DefaultValue annotation, which JAX-RS applies during parameter binding — calling the method directly never sees it, so it is asserted on the wire contract itself.

searchTickets_openOnlyFalseIsPassedThrough() - Method in class ubic.gemma.rest.TicketsWebServiceTest

searchTickets_passesOpenOnlyAndTheCallersContactIdToBothQueries() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

searchTickets_passesTheCallersContactId_forScratchpadScoping() - Method in class ubic.gemma.rest.TicketsWebServiceTest

The caller's identity decides whose scratchpad is worth offering, so it has to reach the service.

searchTickets_refusesALimitAboveTheMaximum_ratherThanClampingIt() - Method in class ubic.gemma.rest.TicketsWebServiceTest

A limit the endpoint will not honour is refused, not quietly reduced — a silent clamp teaches the client nothing about why it got 100 rows back when it asked for 500.

searchTickets_requiresAQuery() - Method in class ubic.gemma.rest.TicketsWebServiceTest

searchTickets_returnsTheHitsInTheOrderTheServiceGaveThem() - Method in class ubic.gemma.rest.TicketsWebServiceTest

searchTickets_truncatesToTheLimit() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

secondCuratorRefusedWithoutSteal() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockPersistenceIT

securedChild_withSecurityOwner_inheritsFromOwnerAcl() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest

securedNotChildBackRef_isUsedAsParent_whenNoSecuredChildCandidate() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest

securedNotChildInCascadeCollection_isNotClaimedAsChild() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest

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

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

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

SecurityUtilsTest - Class in ubic.gemma.core.security

SecurityUtilsTest() - Constructor for class ubic.gemma.core.security.SecurityUtilsTest

seed() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

seed() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriagePersistenceIT

seed() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionPersistenceIT

seed() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockPersistenceIT

A PreboardedExperiment rather than a full ExpressionExperiment: it is an Investigation, which is all the lock needs, and it carries no Taxon or ArrayDesign — so the seed does not depend on reference data that a schema rebuilt from the entities does not have.

seed() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationPersistenceIT

seededShortcutsReturnSameRowAcrossCalls() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactoryTest

seedExperiment() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

seedFixtures() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentInCurationFilterIT

seedPreboarded() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

seedReporter() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

SendfileProviderTest - Class in ubic.gemma.rest.providers

Pins the sendfile-vs-content-encoding interaction in SendfileProvider.

SendfileProviderTest() - Constructor for class ubic.gemma.rest.providers.SendfileProviderTest

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

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

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

servesTheStoredHistogramVerbatimAt100Bins() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServicePvalueDistributionTest

ServiceBasedValueObjectConverterTest - Class in ubic.gemma.persistence.util

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

ServiceBasedValueObjectConverterTest.VoConverterTestContextConfiguration - Class in ubic.gemma.persistence.util

sessionFactory - Variable in class ubic.gemma.core.util.test.BaseDatabaseTest5

sessionFactory(DataSource, Flyway) - Method in class ubic.gemma.core.util.test.BaseDatabaseTest5.BaseDatabaseTestContextConfiguration

setApplicationContext(ApplicationContext) - Method in class ubic.gemma.rest.util.BaseJerseyTest5

setArguments(String[]) - Method in class ubic.gemma.cli.util.TestCLIContext

setCommandNameOrAliasUsed(String) - Method in class ubic.gemma.cli.util.TestCLIContext

setConsole(Console) - Method in class ubic.gemma.cli.util.TestCLIContext

setDs(DataSource) - Method in class ubic.gemma.core.security.acl.domain.AclDaoImplParentPersistenceTest

setEnvironment(Map) - Method in class ubic.gemma.cli.util.TestCLIContext

setErrorStream(PrintStream) - Method in class ubic.gemma.cli.util.TestCLIContext

setExitStatus(int, Exception) - Method in class ubic.gemma.cli.util.TestCLIContext

setGroupDescription(String, String) - Method in class ubic.gemma.core.security.GroupManagerImpl

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

Set the resource used for loading Homologene.

setInputStream(InputStream) - Method in class ubic.gemma.cli.util.TestCLIContext

setIsPublic(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest.ItemVO

setIsPublic(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest.ItemVO

setIsPublic(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest.ItemVO

setIsPublic(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest.ItemVO

setIsShared(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest.ItemVO

setIsShared(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest.ItemVO

setIsShared(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest.ItemVO

setIsShared(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest.ItemVO

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

Set whether to load homologene or not.

setMaxFractionRemoved_rejectsOutOfRange() - Method in class ubic.gemma.core.util.matrix.datafilter.RowMissingFilterTest

setMinPresentCount_rejectsNegative() - Method in class ubic.gemma.core.util.matrix.datafilter.RowMissingFilterTest

setMinPresentFraction_rejectsOutOfRange() - Method in class ubic.gemma.core.util.matrix.datafilter.RowMissingFilterTest

setOutputStream(PrintStream) - Method in class ubic.gemma.cli.util.TestCLIContext

setParentObjectDoesNotNPEOnUninitializedInstance() - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentityTest

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

Set the seed to use to generate random data.

setSeed(long) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomBulkDataUtils

setSeed(long) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils

setSeed(long) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomSingleCellDataUtils

Set the seed used to generate random single-cell vectors.

setSeed(long) - Static method in class ubic.gemma.persistence.service.expression.experiment.RandomExperimentalDesignUtils

setTableMaintenanceUtil(TableMaintenanceUtil) - Method in class ubic.gemma.core.job.SchedulerSecurityTest.TestSecureJob

setTestCollectionSize(int) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

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

setTimeZoneToAmericaVancouver() - Static method in class ubic.gemma.cli.util.OptionsUtilsTest

SettingsConfigTest - Class in ubic.gemma.core.config

SettingsConfigTest() - Constructor for class ubic.gemma.core.config.SettingsConfigTest

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.apps.DifferentialExpressionAnalysisCliTest

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

setUp() - Method in class ubic.gemma.apps.RNASeqDataAddCliTest

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.DiffExAnalyzerUtilsSampleSelectionTest

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.ExpressionExperimentBatchCorrectionServiceImplTest

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.convert.QuantitationTypeConversionUtilsTest

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

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

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

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

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

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

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

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

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

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.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceTest

setUp() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceTest

setUp() - Method in class ubic.gemma.core.context.LazyInitByDefaultPostProcessorTest

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

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

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

setUp() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImplTest

setUp() - Static method in class ubic.gemma.core.goldenpath.GoldenPathQueryTest

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

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.cellxgene.CellXGeneConverterTest

setUp() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest2

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

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

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

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

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.expression.singleCell.MexSingleCellDataLoaderTest

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

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

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

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

setUp() - Method in class ubic.gemma.core.metrics.binder.VirtualThreadExecutorMetricsTest

setUp() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionServiceTest

setUp() - Method in class ubic.gemma.core.ontology.OntologyCacheTest

setUp() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

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

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

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

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

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

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

setUp() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest

setUp() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProviderTest

setUp() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProviderTest

setUp() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapFilteringProviderTest

setUp() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapValueFilteringProviderTest

setUp() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationOwnedCollectionFilteringProviderTest

setUp() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationPrivateCollectionFilteringProviderTest

setUp() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationProviderTest

setUp() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationStreamFilteringProviderTest

setUp() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest

setUp() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest

setUp() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest

setUp() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest

setUp() - Method in class ubic.gemma.core.security.acl.domain.AclDaoImplParentPersistenceTest

setUp() - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest

setUp() - Method in class ubic.gemma.core.security.acl.voter.AclEntryVoterTest

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

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

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

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.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.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskImplTest

setUp() - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserMetadataWriterTest

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

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

setUp() - Method in class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVectorTest

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

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

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

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

setUp() - Method in class ubic.gemma.persistence.audit.AuditTrailEventListenerTest

setUp() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceTest

setUp() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceTest

setUp() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceTest

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

setUp() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplCuratableDispatchTest

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

setUp() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableValueObjectTest

setUp() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

setUp() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

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

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

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

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

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

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

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

setUp() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

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

setUp() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoTest

setUp() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceTest

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

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

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

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

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentBatchInformationServiceTest

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceTest

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentFilterRewriteHelperServiceTest

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceAnnotationsTest

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceDetachedEntityTest

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

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

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperImplTest

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

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoTest

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceTest

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceIntegrationTest

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceTest

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellIntegrationTest

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellStreamingAddTest

setUp() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowServiceTest

setUp() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

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

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

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

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

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

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

setUp() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

setUp() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest

setUp() - Method in class ubic.gemma.rest.AdminWebServiceTest

setUp() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceCursorTest

setUp() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServicePvalueDistributionTest

setUp() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4ProviderTest

setUp() - Method in class ubic.gemma.rest.DatasetsWebServiceAuditEventsCursorTest

setUp() - Method in class ubic.gemma.rest.DatasetsWebServiceBlacklistedCursorTest

setUp() - Method in class ubic.gemma.rest.DatasetsWebServiceByIdsCursorTest

setUp() - Method in class ubic.gemma.rest.DatasetsWebServiceExpressionLevelsForGeneCursorTest

setUp() - Method in class ubic.gemma.rest.DatasetsWebServiceSamplesCursorTest

setUp() - Method in class ubic.gemma.rest.DatasetsWebServiceSubSetSamplesCursorTest

setUp() - Method in class ubic.gemma.rest.DatasetsWebServiceTicketsCursorTest

setUp() - Method in class ubic.gemma.rest.GeneWebServiceCursorTest

setUp() - Method in class ubic.gemma.rest.GeneWebServiceOverviewTest

setUp() - Method in class ubic.gemma.rest.GeneWebServiceProbesCursorTest

setUp() - Method in class ubic.gemma.rest.GroupsWebServiceTest

setUp() - Method in class ubic.gemma.rest.OpenApiWebServiceTest

Bridge Jersey's JUnit 4 lifecycle into Jupiter's, as in WebApplicationExceptionMapperTest.

setUp() - Method in class ubic.gemma.rest.PlatformsWebServiceBlacklistedCursorTest

setUp() - Method in class ubic.gemma.rest.PlatformsWebServiceByIdsCursorTest

setUp() - Method in class ubic.gemma.rest.PlatformsWebServiceCursorTest

setUp() - Method in class ubic.gemma.rest.PlatformsWebServiceDatasetsCursorTest

setUp() - Method in class ubic.gemma.rest.PlatformsWebServiceElementCursorTest

setUp() - Method in class ubic.gemma.rest.PlatformsWebServiceElementGenesCursorTest

setUp() - Method in class ubic.gemma.rest.PlatformsWebServiceElementsCursorTest

setUp() - Method in class ubic.gemma.rest.PlatformsWebServiceMappingSummaryTest

setUp() - Method in class ubic.gemma.rest.PlatformsWebServicePslTrackTest

setUp() - Method in class ubic.gemma.rest.PlatformsWebServiceTicketsCursorTest

setUp() - Method in class ubic.gemma.rest.PreboardedWebServiceTest

setUp() - Method in class ubic.gemma.rest.providers.OntologyTermValidationExceptionMapperTest

setUp() - Method in class ubic.gemma.rest.providers.SendfileProviderTest

setUp() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterDisabledTest

setUp() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest

setUp() - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapperTest

Bridge Jersey's JUnit 4 lifecycle into Jupiter's.

setUp() - Method in class ubic.gemma.rest.TaxaWebServiceCursorTest

setUp() - Method in class ubic.gemma.rest.TaxaWebServiceGeneProbesCursorTest

setUp() - Method in class ubic.gemma.rest.TaxaWebServiceGenesCursorTest

setUp() - Method in class ubic.gemma.rest.TicketsWebServiceCursorTest

setUp() - Method in class ubic.gemma.rest.TicketsWebServiceEventsCursorTest

setUp() - Method in class ubic.gemma.rest.TicketsWebServiceScratchpadRoutingTest

setUp() - Method in class ubic.gemma.rest.TicketsWebServiceTest

setUp() - Method in class ubic.gemma.rest.util.BaseJerseyTest5

Bridge the Jersey test-container setUp into Jupiter's lifecycle.

setUp() - Method in class ubic.gemma.rest.WorkflowWebServiceTest

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

setUpAuthentication() - Method in class ubic.gemma.core.util.test.BaseIntegrationTest5

Setup the authentication for the test.

setUpAuthentication() - Method in class ubic.gemma.rest.util.BaseJerseyIntegrationTest5

setUpFixture() - Method in class ubic.gemma.rest.DatasetVisualizationWebServiceTest

setUpFixtureAuthentication() - Method in class ubic.gemma.persistence.util.AclSemanticsContractTest

setUpFixtures() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

setUpFixtures() - Method in class ubic.gemma.rest.DatasetsPlatformsRestTest

setupMocks() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

setupMocks() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

setupMocks() - Method in class ubic.gemma.rest.util.args.GeneArgServiceTest

setUpMocks() - Method in class ubic.gemma.rest.AnalysisResultSetsJerseyTest

setUpMocks() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

setUpMocks() - Method in class ubic.gemma.rest.DatasetsRestTest

setUpMocks() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

setUpMocks() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

setUserCanWrite(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest.ItemVO

setUserCanWrite(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest.ItemVO

setUserCanWrite(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest.ItemVO

setUserCanWrite(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest.ItemVO

setUserOwned(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest.ItemVO

setUserOwned(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest.ItemVO

setUserOwned(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest.ItemVO

setUserOwned(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest.ItemVO

sha1HexUsernameSalt_helperMatchesFixtures() - Method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoderTest

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

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

ShellUtilsTest - Class in ubic.gemma.core.util

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

shortDownload_isRejectedAndTheFileRemoved(Path) - Method in class ubic.gemma.core.util.NetUtilsTest

shutdownBlatServer() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlatTest

SideEffectConfigurationEagerTest - Class in ubic.gemma.core.context

Guards the trap described in LazyInitByDefaultPostProcessor.

SideEffectConfigurationEagerTest() - Constructor for class ubic.gemma.core.context.SideEffectConfigurationEagerTest

sidRetrievalForAdmin_includesGroupAdminAuthoritySid() - Method in class ubic.gemma.core.security.acl.AdminAclEvaluationTest

Sanity check: the role-hierarchy-aware sid retrieval really does emit a GrantedAuthoritySid("GROUP_ADMIN") for an admin user, so the ACE sid and the user sid should match.

sidRetrievalStrategy() - Method in class ubic.gemma.core.util.test.BaseDatabaseAclConfig

sidRetrievalStrategy() - Method in class ubic.gemma.core.util.test.BaseDatabaseTest5.BaseDatabaseTestContextConfiguration

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

simpleRemove_writesTypedEventWithLiteralMessage_andPublishesSpringEvent() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

SINGLE_CELL - Enum constant in enum class ubic.gemma.core.util.test.fixture.ExperimentFactory.Modality

singleAnnotation_defaultFilter_firesForAnyThrowable() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C (repeatable): a single AuditedOnError declaration with a default Throwable.class filter (back-compat) still fires for everything.

singleAnnotation_specificFilter_firesForMatchingThrowable() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C (repeatable): a single AuditedOnError declaration with a specific exception filter fires when the throwable matches.

singleAnnotation_specificFilter_skipsForNonMatchingThrowable() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase C (repeatable): a single AuditedOnError declaration with a specific exception filter SKIPS when the throwable doesn't match — the original exception still propagates (Spring AOP re-throws regardless).

singleCell() - Method in class ubic.gemma.core.util.test.fixture.ExperimentFactory

Start building a single-cell expression experiment.

singleCell_defaults_returnsPersistentEEWithoutBulkQts() - Method in class ubic.gemma.core.util.test.fixture.ExperimentFactoryTest

SingleCell10xMexFilterTest - Class in ubic.gemma.core.loader.expression.singleCell.transform

SingleCell10xMexFilterTest() - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.SingleCell10xMexFilterTest

SingleCellDataLoaderServiceIntegrationTest - Class in ubic.gemma.core.loader.expression.singleCell

Complete integration tests for loading single-cell data.

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

SingleCellDataTransformationPipelineParserTest - Class in ubic.gemma.core.loader.expression.singleCell.transform

SingleCellDataTransformationPipelineParserTest() - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationPipelineParserTest

SingleCellDataTransformationsTest - Class in ubic.gemma.core.loader.expression.singleCell

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

SingleCellDataTransformationsTest.Config - Class in ubic.gemma.core.loader.expression.singleCell

SingleCellDataVectorAggregatorUtilsTest - Class in ubic.gemma.core.analysis.singleCell.aggregate

SingleCellDataVectorAggregatorUtilsTest() - Constructor for class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtilsTest

SingleCellDescriptiveTest - Class in ubic.gemma.core.analysis.singleCell

SingleCellDescriptiveTest() - Constructor for class ubic.gemma.core.analysis.singleCell.SingleCellDescriptiveTest

SingleCellDimensionCacheStalenessTest - Class in ubic.gemma.persistence.service.expression.bioAssayData

HB6 cascade audit #9 regression guard: SingleCellDimension family (Pattern C — mutable="false" class + child collection + cache directive).

SingleCellDimensionCacheStalenessTest() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.SingleCellDimensionCacheStalenessTest

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

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

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

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

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

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

SingleCellExpressionExperimentAggregateServiceTest - Class in ubic.gemma.core.analysis.singleCell.aggregate

SingleCellExpressionExperimentAggregateServiceTest() - Constructor for class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceTest

SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceTest - Class in ubic.gemma.core.analysis.singleCell.aggregate

SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceTest() - Constructor for class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceTest

SingleCellExpressionExperimentServiceTest - Class in ubic.gemma.persistence.service.expression.experiment

Tests covering integration of single-cell.

SingleCellExpressionExperimentServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

SingleCellExpressionExperimentSubSetServiceTest - Class in ubic.gemma.core.analysis.singleCell.aggregate

SingleCellExpressionExperimentSubSetServiceTest() - Constructor for class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetServiceTest

SingleCellIntegrationTest - Class in ubic.gemma.persistence.service.expression.experiment

SingleCellIntegrationTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.SingleCellIntegrationTest

SingleCellMaskUtilsTest - Class in ubic.gemma.core.analysis.singleCell

SingleCellMaskUtilsTest() - Constructor for class ubic.gemma.core.analysis.singleCell.SingleCellMaskUtilsTest

SingleCellSlicerUtilsTest - Class in ubic.gemma.core.analysis.singleCell

SingleCellSlicerUtilsTest() - Constructor for class ubic.gemma.core.analysis.singleCell.SingleCellSlicerUtilsTest

SingleCellStreamingAddTest - Class in ubic.gemma.persistence.service.expression.experiment

Tests for the streaming overload of SingleCellExpressionExperimentService.addSingleCellDataVectors(ExpressionExperiment, QuantitationType, SingleCellDimension, Stream, String, boolean, boolean).

SingleCellStreamingAddTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.SingleCellStreamingAddTest

SingleExperimentAnalysisTest - Class in ubic.gemma.model.analysis

Unit tests for SingleExperimentAnalysis.getSecurityOwner(), the hook the ACL machinery consults to decide which ACL an analysis inherits.

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

singleFilterSubqueryIsUnchanged() - Method in class ubic.gemma.persistence.util.SubqueryConjunctionTest

A single-filter subquery must render and bind exactly as it did before conjunctions existed.

singleIdentifier_stillWorks() - Method in class ubic.gemma.apps.AclLinterCliTest

size() - Method in class ubic.gemma.core.security.acl.InMemoryAclService

Snapshot of currently-stored ACL count, for size assertions.

skippedClassGetsNoMarker() - Method in class ubic.gemma.core.search.indexer.ScheduledSearchReindexerTest

Per-class isolation: the marker is what carries the audit cutoff forward, and a class that was never rebuilt must not get one.

SlackAppenderTest - Class in ubic.gemma.core.logging

SlackAppenderTest() - Constructor for class ubic.gemma.core.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

snapshot_appendOnly() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

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

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

SortValueObjectTest - Class in ubic.gemma.rest.util

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

SparseArrayListTest - Class in ubic.gemma.core.datastructure.sparse

SparseArrayListTest() - Constructor for class ubic.gemma.core.datastructure.sparse.SparseArrayListTest

SparseListUtilsTest - Class in ubic.gemma.core.datastructure.sparse

SparseListUtilsTest() - Constructor for class ubic.gemma.core.datastructure.sparse.SparseListUtilsTest

SparseRangeArrayListTest - Class in ubic.gemma.core.datastructure.sparse

SparseRangeArrayListTest() - Constructor for class ubic.gemma.core.datastructure.sparse.SparseRangeArrayListTest

spearmanRankCorrelation_pairs_mismatchedSizes_throws() - Method in class ubic.gemma.core.util.math.DistanceTest

spearmanRankCorrelation_pairs_perfectAgreement_isOne() - Method in class ubic.gemma.core.util.math.DistanceTest

spearmanRankCorrelation_pairs_perfectDisagreement_isNegativeOne() - Method in class ubic.gemma.core.util.math.DistanceTest

spearmanRankCorrelation_pairs_tooFewNonNaN_returnsNaN() - Method in class ubic.gemma.core.util.math.DistanceTest

spearmanRankCorrelation_singleArg_ascendingIsOne() - Method in class ubic.gemma.core.util.math.DistanceTest

spearmanRankCorrelation_singleArg_descendingIsNegativeOne() - Method in class ubic.gemma.core.util.math.DistanceTest

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

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

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

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

splitsTheOrdinaryCaseAtTheFirstColon() - Method in class ubic.gemma.core.loader.expression.geo.GeoColonSplitTest

SpringContextUtilsTest - Class in ubic.gemma.core.context

SpringContextUtilsTest() - Constructor for class ubic.gemma.core.context.SpringContextUtilsTest

SraFetcherTest - Class in ubic.gemma.core.loader.expression.sra

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

standardError() - Method in class ubic.gemma.cli.util.test.CliAssert

standardOutput() - Method in class ubic.gemma.cli.util.test.CliAssert

startJavaProcess(Class, String...) - Static method in class ubic.gemma.core.util.test.TestProcessUtils

Start a Java process that inherits the current process's environment and classpath.

stateMachine_canTransitionToIsStrict() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowServiceTest

stateMachine_transitionTableMatchesHandoff() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowServiceTest

statement_populatesAllRelationalFields() - Method in class ubic.gemma.model.common.description.AnnotationValueObjectTest

statementsAreAbsentRatherThanEmptyWhenExcluded() - Method in class ubic.gemma.model.expression.bioAssay.BioAssaySamplePayloadShapeTest

Statements are on by default.

StatementTagPersistenceTest - Class in ubic.gemma.persistence.service.expression.experiment

A statement-shaped experiment tag must survive the round trip as a Statement.

StatementTagPersistenceTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.StatementTagPersistenceTest

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

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

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

Guards the design read path's provenance surface.

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

statementWithOnlyFirstPair_leavesSecondPairNull() - Method in class ubic.gemma.model.common.description.AnnotationValueObjectTest

StaticCacheKeyLockTest - Class in ubic.gemma.persistence.cache

StaticCacheKeyLockTest() - Constructor for class ubic.gemma.persistence.cache.StaticCacheKeyLockTest

status_defaultsToPendingOnProposalsOnly() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

A queue is ordered by when the RUN happened, not by when the row was stored, and the two disagree: a set carrying August's run can be written today.

status_isNotAClosedSet() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

stealSucceedsAndRecordsTheDisplacedHolder() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockPersistenceIT

stillSplitsAGenuineMultiPairLine() - Method in class ubic.gemma.core.loader.expression.geo.GeoColonSplitTest

StopWatchUtilsTest - Class in ubic.gemma.core.util

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

strategy_declares_it_needs_the_prior_and_not_the_usage_counts() - Method in class ubic.gemma.rest.ranking.CommonalityRankingStrategyTest

stressTest() - Method in class ubic.gemma.core.context.AsyncFactoryTest

StrictBeanDefinitionValidatorTest - Class in ubic.gemma.core.util

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

StrictBeanDefinitionValidatorTest.TestAnnotatedVo - Class in ubic.gemma.core.util

StrictBeanDefinitionValidatorTest.TestImplicitValueObject - Class in ubic.gemma.core.util

StringArrayArgTest - Class in ubic.gemma.rest.util.args

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

StringArrayArgTest.Api - Class in ubic.gemma.rest.util.args

stringArrayRoundTrip_explicitCharset_preservesNonAscii() - Method in class ubic.gemma.persistence.util.ByteArrayUtilsTest

stringArrayRoundTrip_utf8_default() - Method in class ubic.gemma.persistence.util.ByteArrayUtilsTest

StringUtilsTest - Class in ubic.gemma.core.util

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

submitCallableThatThrows_incrementsFailed() - Method in class ubic.gemma.core.metrics.binder.VirtualThreadExecutorMetricsTest

submitGeoScrape_dryRunTrue_returnsSyncCandidateList() - Method in class ubic.gemma.rest.AdminWebServiceTest

submitGeoScrape_happyPath_submits202() - Method in class ubic.gemma.rest.AdminWebServiceTest

submitGeoScrape_nullBody_submitsDefaults() - Method in class ubic.gemma.rest.AdminWebServiceTest

submitMultifunctionalityRecompute_happyPath_submitsTaskWithResolvedTaxon() - Method in class ubic.gemma.rest.AdminWebServiceTest

submitRunnable_incrementsSubmittedAndCompleted() - Method in class ubic.gemma.core.metrics.binder.VirtualThreadExecutorMetricsTest

SubqueryConjunctionTest - Class in ubic.gemma.persistence.util

A Subquery may carry several conjoined filters, so that they bind to the SAME element of a to-many relation.

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

SubqueryUtilsTest - Class in ubic.gemma.persistence.util

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

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

SubsettedAnalysis4Test - Class in ubic.gemma.core.analysis.expression.diff

This test covers subset analysis with pre-existing EE subset structure.

SubsettedAnalysis4Test() - Constructor for class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysis4Test

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

A subset analysis has to describe itself with the factors it actually modelled.

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

succeeds() - Method in class ubic.gemma.cli.util.test.CliAssert

Asserts that the command succeeds with a zero exit status.

suffixIsOnlyStrippedAtTheEnd() - Method in class ubic.gemma.core.analysis.sequence.BlatResult2PslTest

A name that merely contains the suffix mid-string is untouched.

summariesProjection() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

supportedResultTypesIsTheCanonicalEight() - Method in class ubic.gemma.core.search.SearchServiceImplTest

surplusDocumentsTriggerAReindexWithNoAuditedUpdates() - Method in class ubic.gemma.core.search.indexer.ScheduledSearchReindexerTest

The gap this signal exists to close: nothing was updated, but the index holds more documents than the database holds rows, so entities were deleted since the last rebuild.

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

SymbolFontPuaTest - Class in ubic.gemma.core.util

The three corpus strings uib read out of production, plus the cases where doing nothing is the correct behaviour.

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

systematic_chemical_names_are_demoted_when_the_corpus_is_silent() - Method in class ubic.gemma.rest.ranking.CommonalityRankingStrategyTest

T

tabbedStringRoundTrip_preservesTokens() - Method in class ubic.gemma.persistence.util.ByteArrayUtilsTest

TableMaintenanceUtilIntegrationTest - Class in ubic.gemma.persistence.service.maintenance

TableMaintenanceUtilIntegrationTest() - Constructor for class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilIntegrationTest

TableMaintenanceUtilTest - Class in ubic.gemma.persistence.service.maintenance

TableMaintenanceUtilTest() - Constructor for class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilTest

TabularMatrixWriterTest - Class in ubic.gemma.core.datastructure.matrix.io

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

Tag - Section in class ubic.gemma.persistence.util.HqlSmokeIT

tagEventsAreNotFlattenedIntoTheirAnnotationParent() - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObjectTest

tagsArePresentOnAllMeters() - Method in class ubic.gemma.core.metrics.binder.VirtualThreadExecutorMetricsTest

takingOverALapsedClaimIsNotASteal() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockPersistenceIT

targetCountIsCountedBySql_andTheTargetsCollectionIsNeverNamed() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketSearchQueryTest

The reason this endpoint exists rather than GET /tickets?query=: a picker showing 20 hits must not fetch 500 target rows for one of them.

targetsCarryTheirDatasetsNames() - Method in class ubic.gemma.rest.TicketsWebServiceTargetLabelsTest

targetSizeFallsBackWhenTheChromosomeHasNoSequenceLength() - Method in class ubic.gemma.core.analysis.sequence.BlatResult2PslTest

The target size falls back to the target sequence, then to targetEnd + 1, when the chromosome carries no sequence length -- the alignment is still placeable.

TaskExecutorThreadContextInheritPostProcessorTest - Class in ubic.gemma.core.logging.log4j

TaskExecutorThreadContextInheritPostProcessorTest() - Constructor for class ubic.gemma.core.logging.log4j.TaskExecutorThreadContextInheritPostProcessorTest

taskRunningService() - Method in class ubic.gemma.rest.TasksWebServiceTest.TasksWebServiceContextConfiguration

TasksRestTest - Class in ubic.gemma.rest

TasksRestTest() - Constructor for class ubic.gemma.rest.TasksRestTest

tasksWebService() - Method in class ubic.gemma.rest.TasksWebServiceTest.TasksWebServiceContextConfiguration

TasksWebServiceContextConfiguration() - Constructor for class ubic.gemma.rest.TasksWebServiceTest.TasksWebServiceContextConfiguration

TasksWebServiceTest - Class in ubic.gemma.rest

TasksWebServiceTest() - Constructor for class ubic.gemma.rest.TasksWebServiceTest

TasksWebServiceTest.TasksWebServiceContextConfiguration - Class in ubic.gemma.rest

TaskUtilsTest - Class in ubic.gemma.core.job

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

TaxaWebServiceCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to TaxaWebService.getTaxonDatasets(TaxonArg, FilterArg, OffsetArg, LimitArg, SortArg, CursorArg) as step 1d of CURSOR_PAGINATION_STEP1_PLAN.md, following the same pattern as PlatformsWebServiceCursorTest (step 1c) and GeneWebServiceCursorTest (step 1b).

TaxaWebServiceCursorTest() - Constructor for class ubic.gemma.rest.TaxaWebServiceCursorTest

TaxaWebServiceGeneProbesCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to TaxaWebService.getTaxonGeneProbes(TaxonArg, GeneArg, OffsetArg, LimitArg, CursorArg) as step 1n of CURSOR_PAGINATION_STEP1_PLAN.md.

TaxaWebServiceGeneProbesCursorTest() - Constructor for class ubic.gemma.rest.TaxaWebServiceGeneProbesCursorTest

TaxaWebServiceGenesCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to TaxaWebService.getTaxonGenes(TaxonArg, OffsetArg, LimitArg, CursorArg) as step 1g of CURSOR_PAGINATION_STEP1_PLAN.md.

TaxaWebServiceGenesCursorTest() - Constructor for class ubic.gemma.rest.TaxaWebServiceGenesCursorTest

TaxaWebServiceTest - Class in ubic.gemma.rest

TaxaWebServiceTest() - Constructor for class ubic.gemma.rest.TaxaWebServiceTest

taxonArgService(TaxonService, GeneService) - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

taxonArgService(TaxonService, GeneService) - Method in class ubic.gemma.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

TaxonArgServiceTest - Class in ubic.gemma.rest.util.args

TaxonArgServiceTest() - Constructor for class ubic.gemma.rest.util.args.TaxonArgServiceTest

TaxonArgTest - Class in ubic.gemma.rest.util.args

TaxonArgTest() - Constructor for class ubic.gemma.rest.util.args.TaxonArgTest

TaxonFactory - Class in ubic.gemma.core.util.test.fixture

Typed factory for persistent Taxon test fixtures.

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

TaxonFactory.AdHocBuilder - Class in ubic.gemma.core.util.test.fixture

Builder for a newly-created ad-hoc taxon.

TaxonFactory.ResolveBuilder - Class in ubic.gemma.core.util.test.fixture

Builder for a resolved (seeded) taxon.

TaxonFactoryTest - Class in ubic.gemma.core.util.test.fixture

Verifies the Phase 3 typed TaxonFactory.

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

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.BaseSpringContextTest5

Deprecated.

taxonService() - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest.ContextConfig

taxonService() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration

TaxonServiceImplTest - Class in ubic.gemma.persistence.service.genome

TaxonServiceImplTest() - Constructor for class ubic.gemma.persistence.service.genome.TaxonServiceImplTest

TaxonUtilsTest - Class in ubic.gemma.persistence.service.genome

TaxonUtilsTest() - Constructor for class ubic.gemma.persistence.service.genome.TaxonUtilsTest

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.apps.AclLinterCliTest

tearDown() - Method in class ubic.gemma.apps.ArrayDesignMergeCliTest

tearDown() - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCliTest

tearDown() - Method in class ubic.gemma.apps.RNASeqDataAddCliTest

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.ProcessedExpressionDataCreateServiceTest

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.TwoChannelExpressionDataDoubleMatrixTest

tearDown() - Method in class ubic.gemma.core.analysis.preprocess.VectorMergingServiceTest

tearDown() - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceTest

tearDown() - Static method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest

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

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

tearDown() - Static method in class ubic.gemma.core.goldenpath.GoldenPathQueryTest

tearDown() - Method in class ubic.gemma.core.job.progress.ProgressDataTest

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.homology.HomologeneServiceTest

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() - Method in class ubic.gemma.core.mail.MailEngineImplTest

tearDown() - Method in class ubic.gemma.core.metrics.binder.VirtualThreadExecutorMetricsTest

tearDown() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

tearDown() - Method in class ubic.gemma.core.search.MassIndexerSmokeIntegrationTest

tearDown() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest

tearDown() - Method in class ubic.gemma.core.security.acl.AdminAclEvaluationTest

tearDown() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest

tearDown() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProviderTest

tearDown() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapFilteringProviderTest

tearDown() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapValueFilteringProviderTest

tearDown() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationOwnedCollectionFilteringProviderTest

tearDown() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationPrivateCollectionFilteringProviderTest

tearDown() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationStreamFilteringProviderTest

tearDown() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest

tearDown() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProviderTest

tearDown() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProviderTest

tearDown() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest

tearDown() - Method in class ubic.gemma.core.security.acl.domain.AclDaoImplParentPersistenceTest

tearDown() - Method in class ubic.gemma.core.security.util.ActingIdentityTest

tearDown() - Method in class ubic.gemma.core.util.locking.FileLockManagerTest

tearDown() - Method in class ubic.gemma.core.util.MailServiceTest

tearDown() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.DetachedCuratableValueObjectTest

tearDown() - Method in class ubic.gemma.model.common.DescribableUtilsTest

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

tearDown() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceTest

tearDown() - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceTest

tearDown() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplTest

tearDown() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableValueObjectTest

tearDown() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

tearDown() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceTest

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

tearDown() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

tearDown() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoTest

tearDown() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceGeoTest

tearDown() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

tearDown() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceTest

tearDown() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceTest

tearDown() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperTest

tearDown() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionServiceTest

tearDown() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceIntegrationTest

tearDown() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellIntegrationTest

tearDown() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImplTest

tearDown() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceTest

tearDown() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceTest

tearDown() - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationServiceTest

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

tearDown() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

tearDown() - Method in class ubic.gemma.persistence.util.PointcutsTest

tearDown() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest

tearDown() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4ProviderTest

tearDown() - Method in class ubic.gemma.rest.OpenApiWebServiceTest

tearDown() - Method in class ubic.gemma.rest.providers.OntologyTermValidationExceptionMapperTest

tearDown() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterDisabledTest

tearDown() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest

tearDown() - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapperTest

tearDown() - Method in class ubic.gemma.rest.TicketsWebServiceScratchpadRoutingTest

tearDown() - Method in class ubic.gemma.rest.util.args.TaxonArgServiceTest

tearDown() - Method in class ubic.gemma.rest.util.BaseJerseyTest5

Bridge the Jersey test-container tearDown into Jupiter's lifecycle.

tearDownFixtures() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

tearDownFixtures() - Method in class ubic.gemma.rest.DatasetsPlatformsRestTest

tearDownSecurityContext() - Method in class ubic.gemma.core.util.test.BaseIntegrationTest5

Clear the SecurityContextHolder so that subsequent tests don't inherit authentication.

tearDownSecurityContext() - Method in class ubic.gemma.rest.util.BaseJerseyIntegrationTest5

Clear the SecurityContextHolder so that subsequent tests don't inherit authentication.

terminalStatesMapToTypedEvents_table() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

termTextIsNormalizedOnWrite() - Method in class ubic.gemma.model.common.description.CharacteristicTest

Free-text term fields carry the submitter's spacing.

test() - Method in class ubic.gemma.apps.ArrayDesignMergeCliTest

test() - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCliTest

test() - Method in class ubic.gemma.apps.FindObsoleteTermsCliTest

test() - Method in class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLITest

test() - Method in class ubic.gemma.apps.ProtocolAdderCliTest

test() - Method in class ubic.gemma.apps.ProtocolDeleterCliTest

test() - Method in class ubic.gemma.cli.metrics.MeterRegistryCliConfigurerTest

test() - Method in class ubic.gemma.cli.util.EnumConverterTest

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

test() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterTest

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.convert.RepresentationConversionUtilsTest

test() - Method in class ubic.gemma.core.analysis.preprocess.filter.LowVarianceFilterTest

test() - Method in class ubic.gemma.core.analysis.preprocess.filter.ZeroVarianceFilterTest

test() - Method in class ubic.gemma.core.analysis.preprocess.SampleCoexpressionAnalysisServiceTest

test() - Method in class ubic.gemma.core.analysis.preprocess.slice.BulkDataSlicerUtilsTest

test() - Method in class ubic.gemma.core.analysis.preprocess.SplitExperimentNameGeneratorTest

test() - Method in class ubic.gemma.core.analysis.preprocess.VectorMergingServiceTest

test() - Method in class ubic.gemma.core.analysis.service.ExpressionMetadataChangelogFileServiceTest

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

test() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetServiceTest

test() - Method in class ubic.gemma.core.analysis.singleCell.SingleCellMaskUtilsTest

test() - Method in class ubic.gemma.core.config.BaseCodeConfigurerTest

test() - Method in class ubic.gemma.core.config.SettingsConfigTest

test() - Method in class ubic.gemma.core.context.LazyInitByDefaultPostProcessorTest

test() - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixBundlerTest

test() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrixTest

test() - Method in class ubic.gemma.core.datastructure.sparse.SparseArrayListTest

test() - Method in class ubic.gemma.core.datastructure.sparse.SparseRangeArrayListTest

test() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneConverterTest

test() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneDataLoaderServiceTest

test() - Method in class ubic.gemma.core.loader.expression.geo.GeoTermReplacementTest

test() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoUtilsTest

test() - Method in class ubic.gemma.core.loader.expression.SequencingMetadataFileDataLoaderTest

test() - Method in class ubic.gemma.core.loader.expression.singleCell.GenericMetadataSingleCellDataLoaderTest

test() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderPersistenceTest

test() - Method in class ubic.gemma.core.loader.util.anndata.AnnDataTest

test() - Method in class ubic.gemma.core.loader.util.mapper.CellIdOverlapBioAssayMapperTest

test() - Method in class ubic.gemma.core.loader.util.mapper.EnsemblIdDesignElementMapperTest

test() - Method in class ubic.gemma.core.logging.log4j.BuildInfoThreadContextPopulatorTest

test() - Method in class ubic.gemma.core.logging.log4j.TaskExecutorThreadContextInheritPostProcessorTest

test() - Method in class ubic.gemma.core.logging.LoggingTest

test() - Method in class ubic.gemma.core.logging.SlackAppenderTest

test() - Method in class ubic.gemma.core.mail.MailEngineImplTest

test() - Method in class ubic.gemma.core.metrics.GenericMeterRegistryConfigurerTest.MyService

test() - Method in interface ubic.gemma.core.metrics.GenericMeterRegistryConfigurerTest.MyService2

test() - Method in class ubic.gemma.core.metrics.GenericMeterRegistryConfigurerTest.MyService2Impl

test() - Method in class ubic.gemma.core.ontology.OntologyExternalLinksTest

test() - Method in class ubic.gemma.core.ontology.providers.CellLineOntologyTest

test() - Method in class ubic.gemma.core.ontology.providers.GemmaOntologyServiceTest

test() - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactoryTest

test() - Method in class ubic.gemma.core.ontology.providers.PatoOntologyServiceTest

test() - Method in class ubic.gemma.core.scheduler.BatchInfoRepopulationJobTest

test() - Method in class ubic.gemma.core.search.SearchResultSetTest

test() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationProviderTest

test() - Method in class ubic.gemma.core.security.acl.ObjectIdentityRetrievalStrategyImplTest

test() - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationServiceBasedSecurityContextFactoryTest

test() - Method in class ubic.gemma.core.security.authorization.acl.AclClassMetadataTest

test() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterServiceTest

test() - Method in class ubic.gemma.core.security.concurrent.DelegatingSecurityContextTaskExecutorTest

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

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

test() - Method in class ubic.gemma.core.util.locking.ReadWriteFileLockTest

Relies on the /proc/locks pseudo-file, which only exists on Linux.

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

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

test() - Method in class ubic.gemma.core.util.runtime.ExtendedRuntimeTest

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

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

test() - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserMetadataWriterTest

test() - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixWriterTest

test() - Method in class ubic.gemma.core.visualization.HeatmapTest

test() - Method in class ubic.gemma.model.analysis.expression.diff.BaselineTest

test() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastTest

test() - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventTypeTest

test() - Method in class ubic.gemma.model.expression.experiment.FactorValueUtilsTest

test() - Method in class ubic.gemma.persistence.cache.StaticCacheKeyLockTest

test() - Method in class ubic.gemma.persistence.initialization.BootstrappedDataSourceFactoryTest

test() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest

test() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceTest

test() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentBatchInformationServiceTest

test() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentFilterRewriteHelperServiceTest

test() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellIntegrationTest

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

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

test() - Method in class ubic.gemma.persistence.util.EntityUrlBuilderTest

test() - Method in class ubic.gemma.persistence.util.FiltersTest

test() - Method in class ubic.gemma.persistence.util.QueryUtilsTest

test() - Method in class ubic.gemma.persistence.util.SubqueryUtilsTest

test() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4ProviderTest

test() - Method in class ubic.gemma.rest.RootWebServiceTest

test() - Method in class ubic.gemma.rest.serializers.FactorValueValueObjectSerializerTest

test() - Method in class ubic.gemma.rest.servlet.RestapidocsIndexRewriteFilterTest

test() - Method in class ubic.gemma.rest.util.SortValueObjectTest

test(Collection) - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest.MyService

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

testABackgroundIsAFactAboutTheLineAndImpliesOnlyDownwards() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

A cell line or strain's genetic background is a fact about that line, not about the experiment that used it, and the implication runs one way: a knockout line implies C57BL/6, while C57BL/6 implies nothing about which of the thousands of lines on it is in hand.

testABadChangeLogPathIsRefusedBeforeAnythingIsLoaded() - Method in class ubic.gemma.apps.VerifyPublicationEvidenceCliTest

🛑 Refused while it is still an argument.

testAbbreviate() - Method in class ubic.gemma.core.util.StringUtilsTest

testAbbreviateUtf16() - Method in class ubic.gemma.core.util.StringUtilsTest

testAbbreviateWithSuffix() - Method in class ubic.gemma.core.util.StringUtilsTest

testABlankTokenPostsNothing() - Method in class ubic.gemma.core.logging.SlackAppenderTest

Same for a deployment that set the property to nothing at all.

testABroadObjectIsDroppedWhenACallerSetsABar() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

🛑 An object that relates to many subjects identifies none of them.

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

testAbsentRelationServiceIsHarmless() - Method in class ubic.gemma.core.search.source.OntologySearchSourceInferredRelationsTest

With no relation service wired the widening is a no-op rather than a failure — several contexts construct this source by hand.

testAbsentSupportingEvidenceIsNull() - Method in class ubic.gemma.model.common.description.CharacteristicValueObjectTest

Nothing recorded is the expected reading for most rows, and must arrive as null rather than as an error.

testAbsentSupportingEvidenceIsNull() - Method in class ubic.gemma.model.expression.experiment.StatementValueObjectTest

Nothing recorded is the expected reading, and must arrive as null rather than as an empty or an error.

testAbstainOnCollectionContainingTransientObject() - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest

testAbstainOnTransientObject() - Method in class ubic.gemma.core.security.acl.voter.AclEntryVoterTest

testAbstractEntityType() - Method in class ubic.gemma.persistence.util.EntityUrlBuilderTest

testABulkDatasetKeepsCellTypeSubjects() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

🛑 The control that keeps the cut honest.

testACharacteristicSurvivesBeingReTermedInsideASet() - Method in class ubic.gemma.model.common.description.CharacteristicTest

testACommandWithNoAnalysisIsRefused() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskImplTest

Positive control off the same wiring: the guard above still rejects a command with nothing to remove, so a task that quietly did nothing at all cannot pass the test above.

testACompleteFactorIsModelled() - Method in class ubic.gemma.core.analysis.expression.diff.IncompleteFactorBaselineTest

The positive control, off the same fixture: with every sample assigned a sex, nothing is dropped and both factors are modelled.

testAConclusionTheDatasetAlreadyCarriesIsNotOfferedBackToIt() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

A conclusion the dataset already carries is not an inference, so it is not offered back to it.

testACuratedStatementIsNotHarvestedIntoARelation() - Method in class ubic.gemma.persistence.service.maintenance.AnnotationRelationHarvestTest

🛑 The rule, and the reason this class no longer tests a harvest: a curated statement does NOT become a relation.

testACuratorsAssertionIsNotWrittenOver() - Method in class ubic.gemma.apps.VerifyPublicationEvidenceCliTest

A curator outranks GEO, and apply() declines such a write in silence — so a run that reports what it changed must not attempt one and assume it landed.

testACuratorSeesTroubledWithoutAskingForThem() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDaoTest

🛑 A curator sees troubled entities without asking.

testADatasetCanHaveMoreThanOneOriginalPlatform() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest

More than one submitted platform is legitimate — the assays need not have come from a single one.

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

testAddAllByNameIgnoreExisting() - Method in class ubic.gemma.model.common.DescribableUtilsTest

testAddAllByNameIgnoreExisting2() - Method in class ubic.gemma.model.common.DescribableUtilsTest

testAddAllByNameReplaceExisting() - Method in class ubic.gemma.model.common.DescribableUtilsTest

testAddByName() - Method in class ubic.gemma.model.common.DescribableUtilsTest

testAddByNameWithDuplicate() - Method in class ubic.gemma.model.common.DescribableUtilsTest

testAddData() - Method in class ubic.gemma.core.loader.expression.DataUpdaterTest

testAddDatasetAnnotation() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testAddDatasetAnnotationCarriesSupportingEvidence() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testAddDatasetAnnotationCarriesSupportingEvidenceOnAStatement() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testAddDatasetAnnotationCreatesCharacteristicWhenNoStatementFieldsSet() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testAddDatasetAnnotationCreatesStatementWhenPredicateOrObjectSet() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testAddDatasetAnnotationDuplicateReturns409() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testAddDatasetAnnotationRejectsBadEvidenceCode() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testAddDatasetAnnotationRejectsBlankCategory() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testAddDatasetAnnotationRejectsSecondPredicateWithoutFirst() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testAddDatasetAnnotationTag() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testAddDatasetAnnotationTagAcceptsAndDropsAnnotationSetId() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testAddDatasetAnnotationTagDuplicateReturnsConflict() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testAddDatasetAnnotationWithoutEvidenceLeavesSupportingEvidenceNull() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testAddDoesNotNeedsAttentionEvent() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplTest

testAddDuplicatedCellLevelCharacteristics() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testAddEventWhenTransactionIsRolledBack() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplTest

testAddEventWhenTransactionIsRolledBack2() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplTest

testAddExceptionEventOnTransientEntity() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplTest

testAddingExperimentOfWrongTaxonUpdate() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceTest

testAddingExperimentOfWrongTaxonUpdateDatabaseEntityMembers() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceTest

testAddMember_byUserId() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testAddMember_byUsername() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testAddMember_neitherUsernameNorUserId_throws400() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testAddMember_unknownUser_throws404() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testAddNeedsAttentionEvent() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplTest

testAddOKEvent() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplTest

testAddRawDataVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testAddRawDataVectorsWithNumberOfCells() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testAddSingleCellDataVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testAddSingleCellDataVectorsTwice() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testAddSingleCellDataVectorsWhenThereIsAlreadyAPreferredSetOfVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testAddSingleCellDataVectorsWithInteger() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testAddTroubledEventOnAlreadyTroubledEntity() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.CuratableDaoTest

testAddTroubledEventOnPlatform() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.CuratableDaoTest

testAddTroubleEvent() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplTest

testAddTroubleEventOnTransientEntity() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplTest

testAddTroubleEventWhenCurationDetailsAreModified() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplTest

testAddUpdateEventAuditableAuditEventTypeString() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplTest

testAddUpdateEventAuditableString() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplTest

testAddUpdateEventOnTransientEntity() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplTest

testAddWhenMaxResultsIsReached() - Method in class ubic.gemma.core.search.SearchResultSetTest

testADeclaredStrategyIsNotSecondGuessed() - Method in class ubic.gemma.core.loader.expression.geo.GeoLibraryStrategyTest

A DECLARED strategy is believed, whatever the sample happens to be called.

testADirectHitIsNotDemotedByAlsoBeingInferred() - Method in class ubic.gemma.core.search.source.OntologySearchSourceInferredRelationsTest

A term the query already matched directly keeps its own score.

testAdminChangePasswordEncodesAndStores() - Method in class ubic.gemma.core.security.authentication.UserManagerTest

testAdminChangePasswordRejectsTooShortPassword() - Method in class ubic.gemma.core.security.authentication.UserManagerTest

testAdminChangePasswordUnknownUser() - Method in class ubic.gemma.core.security.authentication.UserManagerTest

testADryRunSignDoesNotReleaseTheLock() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A dry run predicts; it must not release anything.

testAFailedSignKeepsTheLock() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A sign that fails keeps the lock.

testAFlaggedSampleIsBlankedInBothDirections() - Method in class ubic.gemma.persistence.service.expression.experiment.GeeqCormatMaskingTest

testAGenotypeSeedStillReachesTheDiseaseItStandsFor() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

The shape the two rules must NOT cost us, measured on GSE28044.

testAgentAndCuratorVerdictsCoexistWithTheRightKinds() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The agent's own verdict and a curator's relayed one coexist on the same set, and the curator's is recorded as CURATOR rather than as the agent that transmitted it.

testAgentDraftsForTwoCuratorsDoNotCollapseOntoOneRow() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The bug this gate exists for.

testAgentReadsTheNamedCuratorsDraft() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

Reading is delegated for the same reason writing is: an agent that asks for "the draft" without naming a curator gets its own, which is never what it means.

testAgentRunningAsAdminStillRecordsItsOwnVerdictAsAgent() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The agent authenticates as whichever account runs it, which today is a human administrator.

testAggregate() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtilsTest

testAggregatedAssaysInheritFromTheirExperiment() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceTest

Aggregation must leave every assay and sample it creates inheriting from the experiment.

testAggregateToNonPreferredVectors() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceTest

testAggregateWithMask() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceTest

testAggregateWithUnknown() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtilsTest

testAggregationWithUnmappedFactorValue() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceTest

This cover the case where a FV was removed by a curator.

testAHumanHeldLockNamesNoJob() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A person takes a lock without naming a job, and it reads as a person: no run id.

testALabelSpelledTwoWaysIsOneRelation() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

🛑 A vocabulary label spelled two ways is one relation, not two.

testALabelThatMerelyResemblesAnAccessionStillResolves() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

A genuine label that merely looks id-ish must still resolve — the guard keys on the URI's own local name.

testAListEnumeratingSubjectIsDroppedWhenACallerSetsASubjectBreadthBar() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

The bar, on the same fixture.

testAll() - Method in class ubic.gemma.rest.DatasetsRestTest

testAll() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

testAll() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testAllAddByName() - Method in class ubic.gemma.model.common.DescribableUtilsTest

testAllFilterById() - Method in class ubic.gemma.rest.DatasetsRestTest

testAllFilterByIdIn() - Method in class ubic.gemma.rest.DatasetsRestTest

testAllFilterByIdInOrShortNameIn() - Method in class ubic.gemma.rest.DatasetsRestTest

testAllFilterByShortName() - Method in class ubic.gemma.rest.DatasetsRestTest

testAllFilterByShortNameIn() - Method in class ubic.gemma.rest.DatasetsRestTest

testAllowMissing() - Method in class ubic.gemma.core.analysis.preprocess.slice.BulkDataSlicerUtilsTest

testAllParents() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test

testAllParents() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testAllParents2() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testAllWithTooLargeLimit() - Method in class ubic.gemma.rest.DatasetsRestTest

testAlreadyShorterThanFourDigitsIsUnchanged() - Method in class ubic.gemma.core.util.RoundingUtilsTest

testAMatrixWithNoFlaggedSamplesIsUntouched() - Method in class ubic.gemma.persistence.service.expression.experiment.GeeqCormatMaskingTest

testAmount() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtilsTest

testAMultiTermCellBecomesOneCharacteristicPerTerm() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderTest

🛑 A cell annotated with two ontology terms must become two characteristics, each carrying ONE URI.

testAnAbsentRecordThrowsRatherThanLookingLikeNoPublication() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest

Likewise for an accession GEO has no record of: we have learned nothing about its publications, which is not the same as learning that it has none.

testAnAdministratorStillSeesTroubled() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDaoTest

An administrator is unchanged by the widening.

testAnAgentAuthorityAloneDoesNotSeeTroubled() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDaoTest

And the widening does not reach anyone else: GROUP_AGENT on its own is not a curating role, so an agent that holds only it is still shown the ordinary view.

testAnalysisAcl() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

testAnalysisAclOnReanalysis() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

Re-running an analysis deletes the old one and persists a new one in the same call.

testAnalysisWithAutomaticallySelectedFactors() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testAnalysisWithAutomaticallySelectedFactorsWhenBatchFactorIsPresent() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testAnalysisWithAutomaticallySelectedFactorsWhenDeExcludeAndBatchFactorsArePresent() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

GSE13367's shape: two real factors, the DE_Include/DE_Exclude marker and a batch factor.

testAnalysisWithAutomaticallySelectedFactorsWhenDeExcludeFactorIsPresent() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

The DE_Include/DE_Exclude marker is not a biological factor.

testAnalysisWithAutomaticallySelectedFactorsWithBatchFactorIsPresentAndIncluded() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testAnalysisWithManuallySelectedFactors() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testAnalysisWithManuallySelectedFactorsWhenFactorDoesNotExist() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testAnalysisWithManuallySelectedFactorsWhenFactorsAreRepeated() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testAnalysisWithManuallySelectedFactorsWithInteractionOfContinuousFactor() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testAnalysisWithManuallySelectedFactorsWithNoInteraction() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testAnalysisWithManuallySelectedInteraction() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testAnalysisWithManuallySelectedInteractionOfContinuousFactor() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testAnalysisWithManuallySelectedInteractionWhenInteractionIsRepeated() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

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

testAnAssertionAndARefutationOfOneTripleDoNotCollapse() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

An assertion and a refutation of the same triple are two things a source said, so the grain must keep them apart.

testAnEmptyArmDoesNotAbortTheExperiment() - Method in class ubic.gemma.core.analysis.expression.diff.EmptySubSetIsSkippedTest

The rule, on the path production took.

testAnEmptyArmWithAStoredSubsetIsSkipped() - Method in class ubic.gemma.core.analysis.expression.diff.EmptySubSetIsSkippedTest

The other entry point, run(ee, subsets, dmatrix, config), is handed subsets that already exist rather than deriving them from the matrices — AnalysisSelectionAndExecutionService reuses stored ones.

testAnEmptyEvidenceArrayClearsStoredEvidence() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

An EMPTY evidence array means "the row should have none", so it CLEARS.

testAnExperimentSeedMustSupplyTheEndThatImplies() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

🛑 An experiment seed may only walk FORWARDS: the dataset has to supply the end that implies.

testAnExperimentThatProducedNoAnalysisFails() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

An experiment that produced no analysis is not a success.

testAnExplicitZeroTurnsTheSubjectBreadthBarOff() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

...and a caller who asks for 0 gets 0.

testAnIncompleteFactorDoesNotLeaveABaselineBehind() - Method in class ubic.gemma.core.analysis.expression.diff.IncompleteFactorBaselineTest

The rule: the dropped factor leaves the model AND the baseline map, and the analysis runs.

testAnInducerIsNeverHandedTheDiseaseEvenForAHumanExperiment() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

🛑 An inducer is never handed the disease, whatever the taxon.

testAnInferredTermScoresBelowTheTermActuallyAskedFor() - Method in class ubic.gemma.core.search.source.OntologySearchSourceInferredRelationsTest

An inferred hit must never outrank a dataset actually annotated with the query.

testAnnotatedRouteAcceptsAnythingItIsGiven() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest

TestAnnotatedVo() - Constructor for class ubic.gemma.core.util.StrictBeanDefinitionValidatorTest.TestAnnotatedVo

testANonGeoExperimentIsSkippedRatherThanFailed() - Method in class ubic.gemma.apps.UpdateGeoSourceMetadataCliTest

A non-GEO experiment has no record to store.

testANonNumericIdIsSkippedRatherThanFatal() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest

testANonSeriesAccessionIsEmpty() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest

testANonTranscriptomicSampleIsNotPromoted() - Method in class ubic.gemma.core.loader.expression.geo.GeoLibraryStrategyTest

A non-transcriptomic source is never reinterpreted, however it is named.

testANoOpCommitKeepsNoSnapshot() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A commit that changes nothing displaced nothing, so it keeps nothing.

testANoopSwitchIsNotAnOriginalPlatform() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest

🛑 A no-op switch — the original recorded as the platform already in use — must NOT come back.

testAnOrdinarySampleIsAnalyzed() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsSampleSelectionTest

testAnotherAliasDoesNotDisarmIt() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDaoTest

A filter on a DIFFERENT alias must not disarm the rule for this one.

testAnUngroundedRelatedTermIsDropped() - Method in class ubic.gemma.core.search.source.OntologySearchSourceInferredRelationsTest

An ungrounded related term is dropped rather than matched on its label.

testAnUnknownSetIs404() - Method in class ubic.gemma.rest.ExperimentSetsWebServiceTest

testAnUnknownSpellingIsNotGuessedAt() - Method in class ubic.gemma.core.loader.expression.geo.GeoLibraryStrategyTest

testAnUnmappedTermIsReturnedUnchanged() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsUriMigrationTest

The overwhelmingly common case: a term nobody remapped comes back untouched.

testAnUnreadableGeoThrowsRatherThanLookingLikeNoPublication() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest

The distinction the reCAPTCHA incident turned on.

testAnUnresolvedTokenPostsNothing() - Method in class ubic.gemma.core.logging.SlackAppenderTest

🛑 An unresolved placeholder is not a token, and posting with it is worse than not posting.

testAnUnseededQueryReturnsNothing() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

Refuse to enumerate the table.

testAny() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testAPaperGeoDoesNotListAtAllIsNotWritten() - Method in class ubic.gemma.apps.VerifyPublicationEvidenceCliTest

A paper GEO does not link to the series at all IS the disagreement, and nothing is written for it: it splits into "a curator corrected GEO" and "GEO is wrong", which no rule separates.

testAPaperGeoListsSecondIsReportedNotCertified() - Method in class ubic.gemma.apps.VerifyPublicationEvidenceCliTest

🛑 GEO listing several papers is not GEO disagreeing.

testAPlainCuratorMayNotWriteAsSomeoneElse() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A plain curator claiming another identity is refused rather than silently rewritten to their own — storing a different fact from the one they asked for is worse than declining.

testAppendWithDelimiter() - Method in class ubic.gemma.core.util.StringUtilsTest

testApplyAddressesIdenticalLabelFactorValuesById() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

W10 — two factor values under one factor whose statements serialize identically (distinguished only by a zygosity statement the curation side adds).

testApplyAddressesSameCategorySameNameFactorsById() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

W9 — two factors sharing both category and name.

testApplyBaselineOnlyChangeIsAppliedAndReflected() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

Setting only a factor value's baseline flag is a real change: it must NOT be short-circuited as a no-op, must be written to the entity, and must be reflected in the rebuilt design returned by the apply.

testApplyClearsEvidenceWhenThePayloadOmitsIt() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

🛑 This service applies FULL-RECORD REPLACEMENT, so an omitted supportingEvidence CLEARS a stored one and counts as a change.

testApplyClearsTheEvidenceCodeWhenThePayloadOmitsIt() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

The evidence code replaces on the same terms as supporting evidence: an omitted one CLEARS a stored code and counts as a change.

testApplyDesignatingBaselineLeavesSiblingAlone() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

Designating a baseline leaves its siblings alone.

testApplyEditingAFlattenedStatementKeepsItsSecondObject() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

The curator edits the subject and nothing else.

testApplyEvidenceCodeOnlyEditIsNotANoOp() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

An evidence code is as invisible to the structural summary and to statementsChanged as supporting evidence is, so a code-only edit needs the same dedicated check or it is swallowed as a no-op.

testApplyEvidenceOnlyEditIsNotANoOp() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

Attaching evidence to an otherwise-unchanged statement leaves every content key identical, so the structural summary and statementsChanged both see nothing.

testApplyFactorCategoryOnlyEditIsNotANoOp() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

W11 / W1 — a factor category re-term with the factor values left in place.

testApplyFactorDescriptionOnlyEditIsNotANoOp() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

W11 — a factor description-only edit is a real change.

testApplyFactorNameOnlyEditIsNotANoOp() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

W11 — same gap, reached through the factor name.

testApplyMeasurementEditOnKeptFactorValueIsApplied() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

W14 — editing the measurement on a kept continuous factor value.

testApplyNoChangeIsIdempotentNoOp() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testApplyPreservesNonAsciiCuratedText() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

W16 — non-ASCII in curated text survives the apply byte-exact.

testApplyPreservesUngroundedFreeTextStatement() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

W8 — a factor value carrying deliberately ungrounded free text (JAX strain nomenclature, hybrid backgrounds with no ontology term in existence) round-trips with the text intact.

testApplyRejectsBlockerWithIllegalArgumentException() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testApplyRemovesNoAnalysisForALabelOnlyEdit() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

The other half of the same contract: the one excluded edit removes nothing.

testApplyRemovesTheAnalysesThePreflightEnumerated() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

The apply side executes the report's list instead of deriving its own.

testApplyStatementOnlyEditIsAppliedAndReflected() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

Editing only a kept factor value's statement (no structural add/delete) is a real change: it must not be short-circuited as a no-op, and the edit must reach the entity.

testApplyWritesEvidenceCodeOntoAStatement() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

An evidence code stated on a factor-value statement reaches the entity, so a design write can say how it was decided.

testApplyWritesSupportingEvidenceOntoAStatement() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

W13 — supporting evidence attached to a factor-value statement reaches the entity.

testAQuantityValuedPredicateIsNotARelationBetweenConcepts() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

A predicate whose object is a quantity does not relate two concepts, so the harvest does not store it at all — 9,606 of 36,073 curated rows, whose objects are 10 uM and 10 mg/kg.

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

testARecordWithNoPubMedListIsEmpty() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest

A record that carries no PubMed list at all is GEO stating none, not a failure.

testARedoThatProducedNoAnalysisFails() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

Same for a redo: the CLI reports what came back, and nothing coming back is not something to report as done.

testARefutedRelationIsExcludedUnlessAskedForAndNeverInfers() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

🛑 A refutation is not weak support — it is the opposite — so it stays out of ordinary reads and out of every inference.

testARepeatedIdIsOnePaper() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest

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

The other half: the report still reaches the platform it was written for.

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

A report is one file per database id, so an id that comes to mean a different platform hands that platform the previous occupant's counts — silently, because they are plausible numbers either way.

testARoundTripDoesNotMigrateARetiredTermUri() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

🛑 A design round-trip must not perform the parked term-URI migration.

testArrayDesignAcls() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

testArrayDesignAclsUser() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

testArrayIsCopiedNotRoundedInPlace() - Method in class ubic.gemma.core.util.RoundingUtilsTest

Rounding in place would corrupt the loaded entity's array or the cached matrix's backing store, which is the hazard the sample-correlation rounding was written around.

testARunRemovesCuratedRowsAndLeavesEveryOtherBasis() - Method in class ubic.gemma.persistence.service.maintenance.AnnotationRelationHarvestTest

A run still REMOVES the curated rows already in the table -- that is how the ones harvested before the rule changed leave -- and the ONTOLOGY row beside it is the control: the delete is scoped to CURATED and is not a table wipe.

testAsAdmin() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

testAsAnonymous() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

testASetWithNoTaxonMaySpanThem() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceTest

A set that declares a taxon keeps the constraint: no mice in a rat set.

testASingleCellDatasetDropsCellTypeSubjects() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

On a single-cell dataset the cell types belong to the CELLS, so what they imply is not a fact about the experiment.

testASingleTermCellKeepsOneCharacteristic() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderTest

The ordinary single-term case, which took the working branch all along.

testAskingAboutTroubleIsNotNegated() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDaoTest

🛑 ...but a caller who asks about trouble is not contradicted.

testAsRegularGoId() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testAsRegularGoId() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyUtilsTest

testAssertedRelationIsNotFilteredByDatasetPermissions() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

An ontology's claim is about a term, not about anything Gemma holds, so no dataset permission can be relevant to it.

testAssertionOutranksAttestation() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

A curator's statement outranks any amount of co-occurrence.

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

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

testAsStatementCarriesEveryField() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsTest

The converter must carry every field Characteristic declares, not just category and value.

testAsStatementReturnsAStatementUnchanged() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsTest

An already-persistent Statement must keep its identity, not be replaced by a copy.

testAStatementTagPersistsAsAStatement() - Method in class ubic.gemma.persistence.service.expression.experiment.StatementTagPersistenceTest

testAStrainOrGenotypeSubjectLicensesNoDiseaseClaim() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

🛑 An OBJECT_IMPLIES_SUBJECT licence resolves to has role in modeling or has disease — a claim ABOUT DISEASE — so it may only run where the subject is one.

testASubjectsVocabularyOutranksAMiscategorizedRow() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

🛑 The curated CATEGORY is the unreliable half of the row; the subject's VOCABULARY is the reliable half.

testASubsetsBaselineIsReassignedWithinTheSubset() - Method in class ubic.gemma.core.analysis.expression.diff.IncompleteFactorBaselineTest

🛑 A subset's baseline must be REASSIGNED within that subset, not inherited from the whole experiment.

testASubsetThatCanBeModelledStillRuns() - Method in class ubic.gemma.core.analysis.expression.diff.NoSubSetAnalysisIsNotSuccessTest

Positive control off the same fixture: let treatment vary within each arm and both subsets are analyzed, so an analyzer that had simply become unable to analyze anything could not pass the two tests above.

testASubsetThatCanModelEveryFactorKeepsThemAll() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysisFactorConsistencyTest

The positive control on its own: with both subsets carrying both sexes, nothing is dropped anywhere and both analyses keep the interaction.

testASubsetThatCannotModelAFactorDoesNotCarryItsInteraction() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysisFactorConsistencyTest

The rule.

testAsUser() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

testATermSeededReadIsNeverCellTypeFiltered() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

A term-seeded read carries no dataset, so there is nothing to call single-cell and no cut.

testATermSeededReadIsNotBarredByDefault() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

Positive control for the two above: a term-seeded read is NOT barred.

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

testAttestedRelationOnAPrivateDatasetIsHidden() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

An attested row names a dataset, so a private one must not contribute a count or an example.

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

testAUriNothingUsesIsCachedToo() - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest

A URI nothing uses is the common case in a broad candidate set, and it is the one a naive cache drops: with only non-zero counts stored, every uninformative candidate goes back to the database on the next keystroke, which is most of them.

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

testAutoOption() - Method in class ubic.gemma.cli.util.OptionsUtilsTest

testAutowiredBean() - Method in class ubic.gemma.core.context.AsyncBeanAutowiringTest

testAutowiredList() - Method in class ubic.gemma.core.context.AsyncBeanAutowiringTest

testAutowiredListOfFactories() - Method in class ubic.gemma.core.context.AsyncBeanAutowiringTest

testAutowiredMap() - Method in class ubic.gemma.core.context.AsyncBeanAutowiringTest

testAVerySmallPvalueSurvives() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionResultPrecisionTest

Four significant digits still resolves a p-value at the bottom of the double range, which is why the rule is significant digits rather than decimal places.

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

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

testBackwardCompatibleProps() - Method in class ubic.gemma.core.config.BaseCodeConfigurerTest

testBackwardCursorReturnsPreviousPage() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoCursorTest

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

testBareCurieExpandsToAnIri() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsUriMigrationTest

A bare CURIE is not an IRI; it expands to the OBO form.

testBase64EncodedFilter() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testBase64EncodedFilter() - Method in class ubic.gemma.rest.util.args.StringArrayArgTest

testBaseline() - Method in class ubic.gemma.core.analysis.expression.diff.BaselineSelectionTest

testBaselineRelevanceRoundTripsAndAnOverrideOnlyCommitIsNotANoOp() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The baseline-relevance hint round-trips, and a commit that carries ONLY the hint is applied.

testBash() - Method in class ubic.gemma.cli.util.CompletionGeneratorTest

testBashCompletions() - Method in class ubic.gemma.cli.util.CompletionGeneratorTest

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

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

testBatchMarkOutliersMarksAndUnmarksAtomically() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

POST /samples/outliers atomically marks one assay and unmarks another.

testBatchMarkOutliersReturns400WhenIdDoesntBelongToDataset() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

POST /samples/outliers must reject ids that don't belong to the path-derived dataset with HTTP 400, AND must not mutate any state.

testBatchMarkOutliersReturns400WhenIdInBothMarkAndUnmark() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

POST /samples/outliers rejects an id that appears in BOTH mark and unmark (ambiguous caller-side delta) with HTTP 400.

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

testBatchParameterList() - Method in class ubic.gemma.persistence.util.QueryUtilsTest

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

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

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

testBinarySearchFirst() - Method in class ubic.gemma.core.util.ArrayUtilsTest

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

testBioMaterialIdBindsOnBothCommitSections() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The field binds at all — a payload carrying it is not rejected as an unknown property.

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

testBlacklist() - Method in class ubic.gemma.persistence.service.blacklist.BlacklistTest

testBlacklistedExperimentAsNonAdmin() - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceTest

testBlacklistExperiment() - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceTest

testBlacklistPlatformProperlyCascadeThroughAllExperiments() - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceTest

testBlankCategoryLabelFilledWithTheUnmarkedName() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

A category URI with no label fills in the unmarked name rather than minting obsolete_disease.

testBlankFillRecordedAsCanonicalization() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testBlankLabelWithResolvableUriIsFilledIn() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testBlankMeasurementId() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4ProviderTest

testBlankValueParsesToNullNotAnEmptyString() - Method in class ubic.gemma.core.loader.expression.geo.GeoCharacteristicParseTest

🛑 A submitter who writes "Strain:" with nothing after the colon has given a category and no value.

testBlockCompleteSeesOnlyTheSamplesGiven() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsSampleSelectionTest

A design that is block-complete over every sample need not be over the modelled ones.

testBothDirectionsAreAsked() - Method in class ubic.gemma.core.search.source.OntologySearchSourceInferredRelationsTest

Both directions are consulted: which end of a relation the user typed is not something to guess.

testBoxedOverloadPassesNullThrough() - Method in class ubic.gemma.core.util.RoundingUtilsTest

testBreadthCountsDistinctSubjects() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

Breadth counts subjects, not rows.

testBrowse() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceTest

testBrowseWithInvalidField() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceTest

testBuildAssignmentPassWiresNewFvToBiomaterial() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testBulkDelete() - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDaoImplTest

testBulkLockGrantsAFreeDatasetAndTheClaimIsVisible() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A free dataset is granted, and the claim is then visible to the single-dataset read.

testBulkLockReadAcceptsAlargeListInAbody() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The same answer with the ids in a body.

testBulkLockReadOmitsDatasetsNobodyHolds() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

🛑 An unheld dataset is ABSENT from the map rather than present with locked:false.

testBulkLockReadReportsWhoHoldsEachDataset() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The read uib asked for: the curation queue pages up to 1000 rows and needs one request per screen, not one per row.

testBulkLockReportsPerDatasetRatherThanFailingTheBatch() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The batch never fails as a unit.

testBulkReleaseDropsTheCallersOwnClaims() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The companion a finished run has to call.

testCacheEntriesAreScopedToTheReader() - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest

The tally is ACL-restricted, so an entry computed for one reader must not be reachable by another.

testCacheInvalidationWhenACharacteristicIsDeleted() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testCallerDeathDoesNotAbortTheCacheBuild() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceTest

The caller going away mid-stream must not abort the cache build — otherwise an impatient client re-cools the cold path forever.

testCancelToReopen_lifecycle() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testCanDeleteDelegatesToResultSetDao() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceTest

testCanDeleteReturnsFalse() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceTest

testCandidatesWithinTheBudgetAllGoIn() - Method in class ubic.gemma.core.search.source.OntologySearchSourceInferredRelationsTest

Within the per-seed budget, ambiguity survives: nothing picks one of the candidates.

testCanonicalTgemoUriUnchanged() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testCanonicalUrisAnswersForATwinTheCorpusNeverUsed() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

🛑 The regression guard for the whole point of this endpoint: a twin the CORPUS HAS NEVER USED must still be answered for.

testCanonicalUrisAreQueryable() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

The canonicalization table has to be reachable by a client that resolves terms before asking Gemma — cab seeded a two-row local redirect table because ours was not queryable, and two authorities on one question is the thing this endpoint exists to prevent.

testCanonicalUrisCarryTheDecidingRule() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

Every row says which rule decided it, so a consumer can tell an ontology-intrinsic answer (R3 xref, R4 definition) from one that rests on our curators' spelling habits (R5 usage).

testCanonicalUrisFilterByUri() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

Filtering by URI returns that one row, and an unmapped URI returns none rather than a guess.

testCascadeCreateCompositeSequences() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testCaseNearMatchAcceptedAndCanonicalized() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testCaseNearMatchRecordedAsCanonicalization() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testCategoryExclusionRemovesAndReportsOutOfCategoryHits() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

An excluded namespace leaves data but is REPORTED, not deleted — a gene symbol answered with the disease it causes is the measured failure, and an over-firing rule has to be visible rather than silent.

testCategoryPromotionSurvivesTheRankingStrategy() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testCategoryResolvesFromGemmasOwnCategoryVocabulary() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

A category is likewise checked against Gemma's category vocabulary before anything external.

testCategorySentWithTheOntologysObsoleteSpellingIsCanonicalized() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

The ontology's own spelling still validates, and is rewritten to the name Gemma stores.

testCategorySlotValidated() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testCategoryUsageIsIncludedInTheExperimentCount() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

The count must include the category slot, otherwise a category-only term reports zero experiments and reads as harmless.

testCellosaurusIsNotOnThePurl() - Method in class ubic.gemma.core.ontology.OntologyUtilsTest

Cellosaurus is off the PURL and on https, so it needs its own base in both directions.

testCELnameregex() - Method in class ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarizeTest

testChangeMyPasswordEndToEnd() - Method in class ubic.gemma.rest.RootWebServiceTest

End-to-end confirmation that an authenticated user can rotate their own password: PUT /users/me/password with the correct current password re-encodes the credential.

testChangeMyPasswordMissingFieldsIs400() - Method in class ubic.gemma.rest.RootWebServiceTest

testChangeMyPasswordTooShortIs400() - Method in class ubic.gemma.rest.RootWebServiceTest

A new password below the minimum length is rejected with 400.

testChangeMyPasswordWrongCurrentIs400() - Method in class ubic.gemma.rest.RootWebServiceTest

A wrong current password must be rejected with 400 — a hijacked session can't rotate the credential without proving knowledge of the existing one.

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

testChangePasswordRejectsTooShortNewPassword() - Method in class ubic.gemma.core.security.authentication.UserManagerTest

testChangePasswordRejectsWrongCurrentPassword() - Method in class ubic.gemma.core.security.authentication.UserManagerTest

testChannelsAgreeing() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterMoleculeTest

testCheckValidForLmSeesOnlyTheAnalyzedSamples() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsSampleSelectionTest

The point of dropping early: a factor whose second level exists only on samples that will not be modelled must not read as analyzable.

testChildren() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testChildrenMarksWhetherTheTermWasReachedBySubClassOfAlone() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

The children walk carries the same marker, on the same two-walk mechanism.

testChildrenPopulatesUsageCount() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testClearNeedsAttentionFlag_noOpWhenNoOpenTickets() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionServiceTest

testClearNeedsAttentionFlag_resolvesOpenFvTickets() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionServiceTest

testClearNeedsAttentionFlag_skipsAlreadyResolvedAndCancelledTickets() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionServiceTest

TestCli - Class in ubic.gemma.apps

TestCli() - Constructor for class ubic.gemma.apps.TestCli

testCliBeanIsPrototype() - Method in class ubic.gemma.cli.util.MarkCLIsAsPrototypesTest

TestCLIContext - Class in ubic.gemma.cli.util

A simple implementation of CLIContext for testing purposes.

TestCLIContext(String, String[]) - Constructor for class ubic.gemma.cli.util.TestCLIContext

testClient() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlatTest

testCloTwinResolvesToTheKeptTerm() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsUriMigrationTest

A CLO twin: the retired spelling resolves to the one we keep, and the label follows.

testCollection() - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest

testCollectionAbstainWhenOneEntryIsNull() - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest

testCollectionDenyAccessWhenOneEntryDoesNotGrant() - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest

testCollectionWithNullElement() - Method in class ubic.gemma.persistence.util.FilterTest

testCollectionWithSubclass() - Method in class ubic.gemma.persistence.util.FilterTest

testColonFormIsRepairedToUnderscore() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsUriMigrationTest

OBO IRIs separate with an underscore; a colon in that position is malformed.

testColumnMapping() - Method in class ubic.gemma.core.datastructure.matrix.MatrixConversionTest

testComBat() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImplTest

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

testComBatWithAnOutlier() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImplTest

Outlier samples are sliced out before ComBat runs and their original values put back afterwards.

testCommitAcceptsDeletedIdThatIsOnThatFactorValue() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The id that IS on the factor value is accepted, so the refusal is about membership, not about deleting.

testCommitAdvancesLastUpdated() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

testCommitAndPreflightAcceptOnBehalfOf() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The commit and the preflight accept onBehalfOf.

testCommitByTheLockHolderIsNotGated() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

Holding it yourself is not being blocked by it.

testCommitContinuousFactorValueCarriesMeasurementAndUnit() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

W14 — a continuous factor value keeps its measurement AND its unit.

testCommitCurationAcceptsADeclaredFreeTextTagThatIsHooked() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Declaring it accepts the same tag — the gate is the declaration, not the absence of a URI.

testCommitCurationAcceptsAFreeTextTagHookedOnItsSecondPair() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The hook may sit in the row's SECOND predicate/object pair — a tag whose first claim is ungrounded and whose second reaches a term is still hooked.

testCommitCurationBasics() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testCommitCurationDesignCreatesFactor() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testCommitCurationDesignDeletesByDeletedIds() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testCommitCurationDesignEmptySamplesClearsAssignment() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testCommitCurationDesignForceGateIs409() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testCommitCurationDesignNullSamplesLeavesAssignmentUntouched() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testCommitCurationDesignPreflightIsGivenTheDeferredBindings() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The preflight has to be handed the PLAN, not only the design payload.

testCommitCurationDesignStatementCarriesEvidenceCode() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A design factor-value statement carries its own code, normalized to the enum name.

testCommitCurationDetailsFlagsAre400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testCommitCurationDetailsNote() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testCommitCurationDryRunRefreshesNothing() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

A preflight computes the same tallies without writing, so it must not rebuild EE2C either — the rebuild would publish annotations the dry run did not apply.

testCommitCurationNote() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

testCommitCurationPublications() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testCommitCurationRefreshesEe2cAtTheBioMaterialLevelForASampleCharacteristicChange() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

A per-sample characteristic change reaches EE2C at the BioMaterial level and at no other.

testCommitCurationRefreshesEe2cAtTheDesignLevelForAStatementReTerm() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

Re-terming a statement on a kept factor value reaches EE2C at the ExperimentalDesign level.

testCommitCurationRefreshesEe2cAtTheExperimentLevelForATagChange() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

A tag add/remove reaches EE2C at the ExpressionExperiment level and at no other.

testCommitCurationRefusesAGemmaIdStatementWithNoSubject() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A partial statement item is refused rather than applied.

testCommitCurationRefusesBothSpellingsOfATagsSecondPair() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Both spellings of the same pair on one tag is ambiguous, so it is a 400 rather than a silent winner.

testCommitCurationRefusesHalfASecondPair() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Half a pair is not a claim: a dangling predicate would sit on a production row with nothing to render it.

testCommitCurationRejectsADeclaredFreeTextTagWithNoHook() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A declared free-text tag that hangs off nothing is refused.

testCommitCurationRejectsAFreeTextTagWhoseHookObjectIsUngrounded() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

🛑 The hook has to reach a TERM.

testCommitCurationRejectsAnUndeclaredUngroundedTag() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

An experiment tag with no value.uri is refused unless the caller says the free text is deliberate.

testCommitCurationRejectsAThirdStatementOnATag() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A row holds two pairs, so a third claim is refused rather than silently dropped.

testCommitCurationRejectsUnknownEvidenceCode() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

An unknown code is a 400, not a silent drop.

testCommitCurationRejectsUnknownEvidenceCodeOnADesignStatement() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A bad code inside the design tree is rejected too, located in the design tree.

testCommitCurationRejectsUnknownSection() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testCommitCurationSampleCharacteristics() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testCommitCurationSampleCharacteristicsUnknownSampleIs400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testCommitCurationStaleBaselineIs409() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testCommitCurationTagAcceptsAnExplicitSecondPair() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A tag's second pair can be spelled explicitly too, which is the only way to state one on a tag whose statement is new.

testCommitCurationTagCarriesEvidenceCode() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A stated evidence code reaches the Characteristic instead of being left to the add path's default.

testCommitCurationTagCarriesSupportingEvidence() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The tag's supportingEvidence reaches the Characteristic handed to the service.

testCommitCurationTagKeepsBothStatements() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A tag carrying two statements must store BOTH pairs.

testCommitCurationTags() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testCommitCurationTagWithoutEvidenceCodeLeavesItUnset() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Omitting the field leaves the Characteristic's code null, which is what hands the row to ExpressionExperimentWriteServiceImpl#addCharacteristic's IC fallback — the code every tag written through this route has carried.

testCommitCurationTagWithStatementsReachesTheCommitAsAStatement() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A tag carrying nested statements must reach the commit as a Statement, not a bare Characteristic.

testCommitCurationWithNoChangeRefreshesNothing() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

A commit whose sections all matched what was already stored pays for no rebuild.

testCommitCurationWritesASecondPairOnANewStatement() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A NEW statement can carry a second predicate-object pair.

testCommitDeletesContinuousFactorWithItsMeasurementValues() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

W3 — deleting a continuous factor takes its measurement-bearing factor values with it.

testCommitDeletesFactorAndRecreatesItInOneCommit() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

W1 — a factor is re-categorized by replacing it wholesale: the old factor goes out via deletedIds and a new one arrives with clientRef, in ONE commit.

testCommitDesignCreatesFactorAssignsSampleAndBaseline() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

testCommitFactorDescriptionOnlyEditPersists() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

W11 — a factor description-only edit reaches the database.

testCommitKeepsWhatItDisplacedAndTheReportPointsAtIt() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The restore point nobody had to remember to ask for.

testCommitMovesSamplesFromAnExistingFactorValueToANewOne() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

W6 — the most foreign-key-sensitive case on the list: within one factor, some samples move OUT of an existing factor value INTO a newly created one, while the donor factor value survives (it is neither deleted nor recreated) and a sibling is relabelled in place.

testCommitNamingANonProposalParentIsRejected() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A COMMIT may only name a PROPOSAL as the thing it applied.

testCommitOnAnUnheldDatasetIsNotGated() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

🛑 The non-breaking guarantee.

testCommitPersistsFactorAndFactorValueSupportingEvidence() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

Provenance at the FACTOR and FACTOR VALUE levels survives the commit.

testCommitPersistsStatementSupportingEvidence() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

W13 — a curated statement's justification survives the real persist.

testCommitPersistsTagSupportingEvidenceAndEvidenceCode() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The tags section had no transaction-boundary coverage for either provenance slot: the only guard was DatasetsCurationCommitRestTest.testCommitPersistsStatementSupportingEvidence(), on design statements.

testCommitPreservesUngroundedAndNonAsciiFreeText() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

W8 / W16 — deliberately ungrounded free text (JAX strain nomenclature has no ontology term, and the curation side files these as free text on purpose) survives with its characters intact.

testCommitRecordsTheBasisGivenForAPublication() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The evidence a commit is given is recorded, not dropped.

testCommitRefusesDeletedIdThatIsNotOnThatFactorValue() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A deletedIds entry naming a statement that is not on that factor value is refused.

testCommitRefusesFactorDeletedIdThatIsNotOnThisDataset() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A factor deletedIds naming a factor of another dataset is refused the same way.

testCommitRefusesOmittedEvidenceCodeOnAStatementThatHasOne() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Omitting evidenceCode on a statement that has one is refused.

testCommitRefusesOmittedEvidenceOnAStatementThatHasSome() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Omitting evidence on a row that HAS evidence is refused; sending [] clears it deliberately.

testCommitRefusesStatementDeletedIdThatIsNotOnThatFactorValue() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A statement deletedIds entry naming a row that is not on that factor value is refused rather than absorbed.

testCommitRejectsDecoratedKeepMarkersInEverySectionAtOnce() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

sampleCharacteristics has the same add/delete-only shape and discarded decoration the same way, so it gets the same refusal — bioassayShortName included, which on a keep-marker reads like "move this characteristic to that sample" and does nothing.

testCommitRejectsDecoratedTagKeepMarker() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A tags item bearing a gemmaId is a keep-marker: the section is add/delete only, so the mapper reads the id and nothing else.

testCommitRejectsUngroundedDesignStatementTerm() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A design-section factor-value statement with an ungrounded term is rejected, located in the design tree.

testCommitRejectsUngroundedTerm() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A tag whose label doesn't match its URI is rejected with a structured, per-slot 400.

testCommitRetermsOneFactorValueLeavingSiblingsUntouched() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

W4 — one factor value is re-termed in place and every sibling is left alone.

testCommitSampleCharacteristic() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

testCommitStrandingASubsetRequiresForce() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A change that would strand a subset on deleted factor values needs the same explicit consent as the analysis cascade: 409 without force, applied with it.

testCommitTagsAddThenDeleteById() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

testCommitWhileAnotherCuratorHoldsTheLockIsRefused() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The gate: someone else holds it, so the write is refused and names them.

testCommitWithoutAnEvidenceCodeStillRecordsIC() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

Omitting the code leaves the add path's IC in place — the behaviour every tag on this route has had.

testCommitWithoutRunRefMintsNothing() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

Provenance is sparse on purpose: an ordinary curator commit names no run and mints nothing.

testCommitWithRunRefMintsCommitAnnotationSet() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

Naming a run mints a COMMIT annotation set carrying that run's build, and the report points at it.

testComparator() - Method in class ubic.gemma.model.common.description.CharacteristicTest

testCompareTerm() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsTest

testCompareToCategory() - Method in class ubic.gemma.model.common.description.CharacteristicValueObjectTest

testCompareToNull() - Method in class ubic.gemma.model.common.description.CharacteristicValueObjectTest

testCompareToOrdering() - Method in class ubic.gemma.model.common.description.CharacteristicValueObjectTest

testCompareToTaxon() - Method in class ubic.gemma.model.common.description.CharacteristicValueObjectTest

testCompareToValue() - Method in class ubic.gemma.model.common.description.CharacteristicValueObjectTest

testCompareToValueUri() - Method in class ubic.gemma.model.common.description.CharacteristicValueObjectTest

testCompleteFactors() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testCompleteSubSetFactors() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testComplexClause() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testCompositeSequenceArrayArg() - Method in class ubic.gemma.rest.util.args.EntityArrayArgsTest

testCompoundSortRejected() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoCursorTest

testCompressedEndpoint() - Method in class ubic.gemma.core.util.GemmaRestApiClientTest

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

testConcatenatedIdIsRepaired() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsUriMigrationTest

An id concatenated with itself resolves to nothing; the repair was label-verified.

testConcurrent() - Method in class ubic.gemma.core.util.locking.FileLockManagerTest

testConcurrentReadersDoNotRaceTheOsLock() - Method in class ubic.gemma.core.util.locking.ReadWriteFileLockTest

Concurrent readers must not race the OS-level lock acquisition.

testConcurrentReadWriteAccess() - Method in class ubic.gemma.core.util.locking.ReadWriteFileLockTest

testConcurrentWriterDegradesToPlainStream() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceTest

A concurrent builder holding the cache file degrades the call to a plain stream.

testConjunction() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testConjunctionOfDisjunctions() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testConsiderCandidatesDoNotMakeATermAutoCorrectable() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

oboInOwl:consider is advice to a human, not an assertion of equivalence, so it must never make a term auto-correctable however many candidates it lists.

testConstructExpressionDataDoubleMatrix() - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelExpressionDataDoubleMatrixTest

Tests the construction of an ExpressionDataDoubleMatrix

testConstructExpressionDataDoubleMatrixWithGeoValues() - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelExpressionDataDoubleMatrixTest

This is a self-contained test.

testContinuous() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastTest

testContinuousFactor() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest

testContrastsSurviveFlushClearReload() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.AnalysisResultSetCacheStalenessTest

Companion read-only assertion for the inner level — DifferentialExpressionAnalysisResult.getContrasts().

testContrastStatisticsSerializeRounded() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionResultPrecisionTest

testConvertCollection() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest

testConvertCollectionOfIds() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest

testConvertCollectionToListSuperType() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest

testConvertCollectionToSuperType() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest

testConvertCountingData() - Method in class ubic.gemma.core.analysis.preprocess.convert.ScaleTypeConversionUtilsTest

testConvertDataDoubles() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertDataIntegers() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertEntitiesFromIds() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest

testConvertEntityFromId() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest

testConvertGenePix() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

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

testConvertGSE235534() - 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

testConvertMultiSeriesPerSample() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertMultiTaxonDatasetGSE7540() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testConvertNullEntity() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest

testConvertSingleEntity() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest

testConvertSingleEntityById() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest

testConvertSingleEntityFromSubType() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest

testConvertSingleEntityToSuperType() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest

testConvertToEntity() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperTest

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

testConvertToLightValueObject() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperTest

Tests loading 'light' value objects - VOs without EEIds

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

testConvertToValueObject() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperTest

Tests loading value objects with EEIds.

testConvertUnknownType() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest

testConvertWithLotsOfPlatforms() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testCopyDelegates() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceTest

testCopyMetadata() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceTest

testCorrelateNewDesignIdsMapsNewFactorsAndValues() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testCorrelateNewFactorValueUnderExistingFactor() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testCount() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtilsTest

testCountAgreesWithTheFullReport() - Method in class ubic.gemma.core.analysis.report.WhatsNewServiceTest

countNewExpressionExperiments exists so the daily HomeStats snapshot can skip getReport's platform / taxon / biomaterial passes.

testCountAll() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testCountBioSequencesById() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testCountBlatResultsById() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testCountByValueLike() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testCountByValueUriIn() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testCountConversion() - Method in class ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionUtilsTest

testCountData() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExTest

Test differential expression analysis on RNA-seq data.

testCountDataAsDoubles() - Method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptiveTest

testCountDataAsFloats() - Method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptiveTest

testCountDataAsInts() - Method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptiveTest

testCountDataAsLongs() - Method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptiveTest

testCountExperimentsByUrisAgreesWithFindExperimentsByUris() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

The aggregate count has to agree with the number the callers used to derive by loading every matching experiment and sizing a Set of their ids.

testCountExperimentsByUrisAsAdminWithExclusions() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoMySqlIntegrationTest

testCountExperimentsByUrisAsAnonymous() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoMySqlIntegrationTest

testCountExperimentsByUrisAsLoggedInUser() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoMySqlIntegrationTest

testCountExperimentsByUrisCountsAnExperimentOnceAcrossColumns() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

Count an experiment once even when its EE2C row carries the URI in more than one column.

testCountExperimentsByUrisExcludesExperiments() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testCountExperimentsByUrisRespectsAcl() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

The count is what a curator is shown as a term's corpus usage, so it must not include experiments they cannot read — the aggregate carries the same ACL restriction as the row-returning lookup it replaced.

testCountExpressionExperiments() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest

testCountGenes() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testCountMissing() - Method in class ubic.gemma.core.analysis.stats.DataVectorDescriptiveTest

testCounts() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testCounts() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceTest

testCountsAsFloats() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceTest

testCountsAsInts() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceTest

testCountsAsLongs() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceTest

testCountsWhenPlatformIsMicroarrayThenReportAsLinear() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testCountsWhenPlatformIsNotSequencing() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testCountsWhenValueIsNegativeTreatAsLogbaseUnknown() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testCountWithAdjustedLibrarySize() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceTest

testCountWithBooleans() - Method in class ubic.gemma.core.analysis.stats.DataVectorDescriptiveTest

testCountWithChars() - Method in class ubic.gemma.core.analysis.stats.DataVectorDescriptiveTest

testCountWithPresentAbsent() - Method in class ubic.gemma.core.analysis.stats.DataVectorDescriptiveTest

testCountWithStrings() - Method in class ubic.gemma.core.analysis.stats.DataVectorDescriptiveTest

testCreate() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceTest

testCreate() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDaoTest

testCreateAnalysisWithoutContrasts() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDaoTest

testCreateAnalysisWithoutResults() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDaoTest

testCreateAnalysisWithResultSetAndPvalueDistribution() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDaoTest

testCreateCellTypeFactor() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testCreateCellTypeFactorIgnoreCompatibleFactor() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testCreateCircularBioMaterial() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoTest

testCreateDatabaseEntry() - Method in class ubic.gemma.persistence.service.common.description.DatabaseEntryDaoImplTest

testCreateFactorValueCarriesMeasurementUnit() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

W14 — a newly created continuous factor value must keep its unit.

testCreateGroup_existingName_throws400() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testCreateGroup_happyPath() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testCreateGroup_missingName_throws400() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testCreateGroup_nullBody_throws400() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testCreateGroup_systemGroupName_throws400() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testCreateInvalidAnalysis() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDaoTest

testCreateLoadAndRemove() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceTest

Test of cascade create

testCreatePassesTheMembersAndLeavesTheTaxonAlone() - Method in class ubic.gemma.rest.ExperimentSetsWebServiceTest

🛑 The taxon is NOT sent unless the caller declared one.

testCreateProcessedDataVectors() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorCreationHelperServiceTest

testCreateProcessedDataVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testCreateProcessedDataVectorsFromLog2Data() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorCreationHelperServiceTest

testCreateProcessedDataVectorsFromLog2RatiometricData() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorCreationHelperServiceTest

testCreateProcessedDataVectorsWithNonPersistentQt() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testCreateRequiresAName() - Method in class ubic.gemma.rest.ExperimentSetsWebServiceTest

A create is a create: the name is the only thing the caller must supply, and a blank one is refused here rather than reaching the service, which would throw IllegalArgumentException and surface as a less specific error.

testCreateSetWithAccession() - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoTest

This is an example of modeling a GEO super-series.

testCreateStatement() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceTest

testCreateStatementWithDetachedFactorValue() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceTest

testCreateSubSetsSkipsSamplesNotInSingleCellDimension() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetServiceTest

testCreateSubSetsWhenMissingFactorValue() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetServiceTest

testCreateTicket_carriesTheScreenPayload() - Method in class ubic.gemma.rest.TicketsWebServiceTest

A screening agent opens a ticket and says what its screen asked.

testCreateTicket_GEO_SCRAPE_WATERMARK_target() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testCreateTicket_happyPath() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testCreateTicket_missingTitle_throws400() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testCreateTicket_multiTargetMixedTypes_passesAllThrough() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testCreateTicket_nullBody_throws400() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testCreateTicket_withBodyAndMode_persistsBoth() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testCreateTicket_withoutAPayloadLeavesItUnset() - Method in class ubic.gemma.rest.TicketsWebServiceTest

An ordinary ticket carries none, and creating one must not invent an empty payload.

testCreateTicket_withTargetStatus_seedsUNDERWAY() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testCreateTicketFromAccession_aSplitAccessionTargetsEveryPart() - Method in class ubic.gemma.rest.TicketsWebServiceTest

🛑 ONE ACCESSION CAN NAME SEVERAL DATASETS, and all of them become targets.

testCreateTicketFromAccession_fallsBackToShortName() - Method in class ubic.gemma.rest.TicketsWebServiceTest

Nothing carries the accession as an accession, so the short name is tried before giving up.

testCreateTicketFromAccession_resolvesAndOpens() - Method in class ubic.gemma.rest.TicketsWebServiceTest

A caller holding a GEO accession opens a ticket in one call, and the type defaults to the category the curation store's own REVIEW maps onto.

testCreateTicketFromAccession_unknownAccessionOpensNothing() - Method in class ubic.gemma.rest.TicketsWebServiceTest

An accession naming nothing is a 404 and opens NO ticket.

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

Tests creating a UserGroup

testCreateWithMultipleFactorValueForSameExperimentalFactor() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoTest

testCuratableValueObjectCreation() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableValueObjectTest

testCuratableValueObjectInteraction() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableValueObjectTest

testCurationDetailsTroubledIsRejected() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

testCursorWalkProducesDisjointPages() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoCursorTest

testCyclicReplacedByChainIsNotAutoCorrectable() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

A cyclic replaced-by chain must stop rather than spin, and must not be presented as correctable.

testDailyReportIsContainedInTheWeeklyReport() - Method in class ubic.gemma.core.analysis.report.WhatsNewServiceTest

The daily window is contained in the weekly one.

testDanglingOperatorIsNotTreatedAsASeparator() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyQueryRewriteTest

A DANGLING operator is left alone on purpose.

testDatabaseEntryArrayArg() - Method in class ubic.gemma.rest.util.args.EntityArrayArgsTest

testDatasetArrayArg() - Method in class ubic.gemma.rest.util.args.EntityArrayArgsTest

testDatasetArrayArgEmptyRaises() - Method in class ubic.gemma.rest.util.args.EntityArrayArgsTest

testDatasetArrayArgTrimsWhitespace() - Method in class ubic.gemma.rest.util.args.EntityArrayArgsTest

testDatasetCompletionsEmptyPrefixReturnsAll() - Method in class ubic.gemma.rest.CompletionsWebServiceTest

testDatasetCompletionsHonourLimit() - Method in class ubic.gemma.rest.CompletionsWebServiceTest

testDatasetGroupCompletions() - Method in class ubic.gemma.rest.CompletionsWebServiceTest

testDatasetsCanBeFilteredByVisibility() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

🛑 `isPublic` is not a mapped attribute — it is read off the ACL entries when the value object is built — so the metamodel walk that enumerates filterable properties could not see it and `filter=isPublic = false` answered 400 "the property of isPublic is unknown".

testDateCreatedComesFromTheCreationAuditEvent() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

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

testDatesToBatchE() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceTest

testDeclaredParametersAreAccepted() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest

testDeExcludedSampleIsNotAnalyzed() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsSampleSelectionTest

testDeExcludeFactorCanStillBeRequestedExplicitly() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

The marker is still selectable by ID, so a curator can inspect that design deliberately.

testDeferredTermIsActedOnWhenNamedExplicitly() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionServiceTest

testDeferredTermIsSkippedByABlanketRun() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionServiceTest

testDefinitionFallsBackToCommentWhenTheOntologyUsesOne() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

CLO does not use the OBO definition property.

testDefinitionIsNullWhenTheTermDescribesItselfNowhere() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

A term with neither still reports nothing, rather than an empty string a caller would render as a definition that exists and is blank.

testDegradedSharedLockCanStillBeUpgraded() - Method in class ubic.gemma.core.util.locking.FileLockManagerTest

A degraded shared lock upgrades into a real one: toExclusive() re-acquires from scratch, which is how a probe that decides to write still coordinates properly.

testDelete() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testDelete() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceIntegrationTest

testDeleteAll() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceTest

testDeleteAll() - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImplTest

testDeleteAnalysis() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testDeleteAnalysisJoinsACallersTransaction() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceTest

The curation cascade reaches deleteAnalysis from inside its own transaction (ExpressionExperimentServiceImpl step 2, which routes there so the analysis takes its diffex archive and result-set TSV caches with it).

testDeleteDatasetProcessedDataHappyPath() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testDeleteDatasetProcessedDataWithoutConfirmIs400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testDeleteDatasetRawDataHappyPath() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testDeleteDatasetRawDataWithoutConfirmIs400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testDeleteExperimentalFactor() - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorServiceTest

testDeleteExperimentalFactorUsedByASample() - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorServiceTest

testDeleteGroup_happyPath() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testDeleteGroup_notFound() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testDeleteGroup_systemGroup_throws400() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testDeleteMetadata() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceTest

testDeleteRawVectorsWithNumberOfCells() - Method in class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVectorTest

testDeleteTicket_alreadyCancelled_noTransition() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testDeleteTicket_notFound_throws404() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testDeleteTicket_softCancels() - Method in class ubic.gemma.rest.TicketsWebServiceTest

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

Test for deleting a user group

testDeploymentInDifferentTimeZone() - Method in class ubic.gemma.persistence.util.DateStorageTest

Simulate a case where Gemma is used/deployed in a different timezone than America/Vancouver.

testDerivesFromNeedsSomebodyToHaveSaidWhatTheObjectIs() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

🛑 RO_0001000 derives from licenses nothing until some source has said what its object IS.

testDescendingCursorWalk() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoCursorTest

testDetect10xUnfiltered10XData() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurerTest

testDirectionParsing() - Method in class ubic.gemma.rest.util.args.SortArgTest

testDisableInference() - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactoryTest

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

testDiscriminator() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testDisjunction() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testDoubleMangledTgemoNormalized() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testDoubleMatrix() - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrixTest

testDoubleMatrixToVectors() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrixUtilsTest

testDownloadDatasetAsset() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcherTest

testDownloadSingleCellDataInCellXGene() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testDownloadSingleCellDataInCellXGeneWithoutACollectionId() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testDownloadSingleSampleAccession() - Method in class ubic.gemma.apps.GeoSingleCellDataDownloaderCliTest

testDroppedFactorIsStillInItsDesignWhenTheSecuredRemoveIsCalled() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

🛑 A dropped factor is STILL IN its design's factor collection when experimentalFactorService.remove is called.

testDropsBothDeExcludedAndOutlierSamples() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsSampleSelectionTest

testDrosophilaBicistronicReattachment() - Method in class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceTest

Quirk 4.1 (migration plan): drosophila bicistronic — a GeneProduct found-by-BK to belong to gene A is reattached to gene B during a gene update.

testDryRunRefusesTheSameUnmatchedDeletedId() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The dry run refuses it too, so a client can find out its document is stale without writing anything.

testDryRunWritesNothing() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionServiceTest

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

testDuplicateElements() - Method in class ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrixTest

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

testEditingAStatementDoesNotDuplicateTheSampleFactorValueRow() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

Editing a factor value's statements must not duplicate its BIO_MATERIAL_FACTOR_VALUES row.

testEe2cDesignLevelOmitsTheIndexHintOnH2() - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilTest

H2 — what the unit tests run on, MODE=MYSQL and all — rejects FORCE INDEX with a syntax error, and the constraint name it does carry is not an index name anyway.

testEe2cDesignLevelPinsTheFactorAnnotationsIndexOnMysql() - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilTest

The deprecated factor-annotations branch joins CHARACTERISTIC on a column that is NULL on all 10.8M production rows, so its index reports cardinality 1 and MySQL costs the ref lookup at the whole table — it full-scans instead, which measured 12.1 s per experiment regardless of size.

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

testEmpty() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderTest

testEmptyArray() - Method in class ubic.gemma.core.datastructure.sparse.SparseArrayListTest

testEmptyArray() - Method in class ubic.gemma.core.datastructure.sparse.SparseRangeArrayListTest

testEmptyArray() - Method in class ubic.gemma.rest.util.args.StringArrayArgTest

testEmptyBase64EncodedArray() - Method in class ubic.gemma.rest.util.args.StringArrayArgTest

testEmptyBioAssayDimensionRoundTrip() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionCacheStalenessTest

A mutable="false" BioAssayDimension with an empty bioAssays list persists and survives a flush + clear + reload.

testEmptyCollectionShouldGrant() - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest

testEmptyFilter() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testEmptyMatrix() - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrixTest

testEmptyMatrix() - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrixTest

testEmptyMembershipEmptiesTheSet() - Method in class ubic.gemma.rest.ExperimentSetsWebServiceTest

Replacing membership is a replace.

testEmptyPath() - Method in class ubic.gemma.persistence.util.SubqueryUtilsTest

testEmptySingleCellDimensionRoundTrip() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.SingleCellDimensionCacheStalenessTest

Pattern C smoke test: a mutable="false" parent (SingleCellDimension) persisted with empty child sets survives a flush + clear + reload.

testEmptySortArg() - Method in class ubic.gemma.rest.util.args.SortArgTest

testEmptySubClause() - Method in class ubic.gemma.persistence.util.FiltersTest

testEmptyWindowCountsZero() - Method in class ubic.gemma.core.analysis.report.WhatsNewServiceTest

A window that ended before Gemma existed has nothing in it — guards against the count silently ignoring its date argument and returning the whole corpus.

testEndpointDeclaringNoParametersSaysSo() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest

testEndpoints_requireAuthentication() - Method in class ubic.gemma.rest.GroupsWebServiceTest

Annotation-level guard: all endpoints (incl.

testEndpointThatRequiresCredentials() - Method in class ubic.gemma.core.util.GemmaRestApiClientTest

testEndpointWithIncorrectCredentials() - Method in class ubic.gemma.core.util.GemmaRestApiClientTest

testEndpointWithParameters() - Method in class ubic.gemma.core.util.GemmaRestApiClientTest

testEndpointWithRedirection() - Method in class ubic.gemma.core.util.GemmaRestApiClientTest

testEnsemblId() - Method in class ubic.gemma.rest.util.args.GeneArgServiceTest

testEnsureInSession() - Method in class ubic.gemma.persistence.service.AbstractServiceTest

testEnsureInSessionPreserveInputOrder() - Method in class ubic.gemma.persistence.service.AbstractServiceTest

testEnsureInSessionReturnsOriginalCollectionIfAlreadyInSession() - Method in class ubic.gemma.persistence.service.AbstractServiceTest

testEnsureInSessionWhenSomeElementsAreNotInSessionOnlyLoadThoseElements() - Method in class ubic.gemma.persistence.service.AbstractServiceTest

testEnsureThatAllEndpointHaveADefaultGetResponseOrIsARedirection() - Method in class ubic.gemma.rest.OpenApiTest

testEnsureThatAllErrorResponsesUseResponseErrorObjectWithJsonMediaType() - Method in class ubic.gemma.rest.OpenApiTest

testEnum() - Method in class ubic.gemma.core.loader.util.anndata.AnnDataTest

testEnvironmentVariableFiltering12FactorStyle() - Method in class ubic.gemma.core.config.SettingsConfigTest

testEqual() - Method in class ubic.gemma.model.expression.experiment.StatementTest

testEquality() - Method in class ubic.gemma.persistence.util.FiltersTest

testEquals() - Method in class ubic.gemma.model.common.description.CharacteristicTest

testEquals() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsTest

testEquals() - Method in class ubic.gemma.model.expression.experiment.FactorValueTest

testEquals() - Method in class ubic.gemma.model.util.ModelUtilsTest

testEqualsA() - Method in class ubic.gemma.model.common.description.CharacteristicValueObjectTest

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

testEqualsAndHashCodeAgreeForTwoInstancesOfOneRow() - Method in class ubic.gemma.model.common.description.CharacteristicTest

testEqualsB() - Method in class ubic.gemma.model.common.description.CharacteristicValueObjectTest

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

testEqualsByName() - Method in class ubic.gemma.model.common.DescribableUtilsTest

testEqualsC() - Method in class ubic.gemma.model.common.description.CharacteristicValueObjectTest

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

testEqualsD() - Method in class ubic.gemma.model.common.description.CharacteristicValueObjectTest

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

testEqualsE() - Method in class ubic.gemma.model.common.description.CharacteristicValueObjectTest

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

testEqualsF() - Method in class ubic.gemma.model.common.description.CharacteristicValueObjectTest

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

testEqualsWithDifferentCharacteristics() - Method in class ubic.gemma.model.expression.experiment.FactorValueTest

testEqualsWithDifferentValues() - Method in class ubic.gemma.model.expression.experiment.FactorValueTest

testErrorOnCollectionContainingTransientObjectWhenAttributeIsMissing() - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest

testErrorOnTransientObjectWhenAttributeIsMissing() - Method in class ubic.gemma.core.security.acl.voter.AclEntryVoterTest

testEscapeMarkdown() - Method in class ubic.gemma.core.util.MarkdownUtilsTest

testEveryCellLineMergeCitesItsCellosaurusAccession() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsUriMigrationTest

🛑 Every cell-line merge in the shipped table names the Cellosaurus accession that decided it.

testEveryPubMedIdIsReadableNotJustTheFirst() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest

A series listing two papers has a primary and a follow-up, and the second one has somewhere to go: the other-relevant slot.

testEverySlotIsRewrittenNotJustTheSubject() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionServiceTest

testEverySpellingResolves() - Method in class ubic.gemma.core.loader.expression.geo.GeoLibraryStrategyTest

🛑 Every constant must round-trip from GEO's own spelling.

testEverySubsetSkippedIsAFailure() - Method in class ubic.gemma.core.analysis.expression.diff.NoSubSetAnalysisIsNotSuccessTest

The rule.

testEveryUnknownParameterIsNamedNotJustTheFirst() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest

testExactIdentifierMatchDefaultsFalse() - Method in class ubic.gemma.core.search.SearchResultTest

testExactIdentifierMatchPreservedAcrossWithMethods() - Method in class ubic.gemma.core.search.SearchResultTest

testExactLabelDoesNotSuppressNegativeEvidence() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

exact_label filters the POSITIVE list; negativeEvidence reports the VERDICT.

testExactMatchPasses() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testExactMatchRecordsNoCanonicalization() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testExactMatchTierSurvivesTheRankingStrategy() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

The exact tier has the same problem the category promotion had: it is established on the candidate list and then thrown away by strategy.rank(), which re-sorts everything on its own score.

testExactSynonymEarnsTheExactTier() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

Reported by CAB 2026-08-11: `H1` is a declared exact synonym of EFO_0003042 ("H1-hESC", 18 corpus uses), but the relevance tiers read the hit's LABEL only, so on "h1-hesc" it scored as a prefix match and came back at rank 7 -- behind two CHEBI histamine-receptor ligands with no corpus use at all.

testExamplesFromClasspath() - Method in class ubic.gemma.rest.OpenApiTest

testExcludedSubjectCategoryDropsOnlyThatCategory() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

The complement of subjectCategoryUris: everything except one kind of implying term.

testExcludingADatasetRemovesItsOwnEvidence() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

Excluding a dataset removes its contribution, which is what makes "this tag is inferable, so it can be dropped" a claim about the rest of the corpus rather than about the dataset itself.

testExclusiveLockStillCreatesItsDirectoryChain() - Method in class ubic.gemma.core.util.locking.FileLockManagerTest

The counterpart: an exclusive acquirer still gets its directory chain.

testExistingAndSeparatorsDoNotWeldOperands() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyQueryRewriteTest

The defect: the separator replacement yielded the empty string, so the operands were welded into one token and the rejoin pass had nothing left to split on.

testExistingCuratorEvidenceSurvives() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionServiceTest

testExistingFvWithNullSamplesKeepsAssignments() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

testExonArrayInfo() - Method in class ubic.gemma.core.loader.expression.geo.GeoPlatformTest

testExpansionKeepsAmbiguityInsteadOfResolvingIt() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

Expansion returns the whole candidate set and resolves nothing.

testExplicitIsBaselineAlwaysDecides() - Method in class ubic.gemma.core.analysis.expression.diff.BaselineSelectionTest

An explicit isBaseline decides on its own, whatever else the factor value carries.

testExpressionExperimentAcls() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

testExpressionExperimentFindAll() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

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

This test applies to fixtures found in init-entities.sql.

testExternalDocumentationUrlIsReplaced() - Method in class ubic.gemma.rest.OpenApiTest

testExtractAgilent() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractorTest

testExtractAgilent2() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractorTest

testExtractFetchIds() - Method in class ubic.gemma.core.loader.entrez.EntrezXmlUtilsTest

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

testExtractKeywords() - Method in class ubic.gemma.apps.GeoGrabberCliTest

testExtractLinkIds() - Method in class ubic.gemma.core.loader.entrez.EntrezXmlUtilsTest

testExtractLongDate() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest

testExtractSearchIds() - Method in class ubic.gemma.core.loader.entrez.EntrezXmlUtilsTest

testFabricatedTgemoStillRejectedAfterNormalization() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testFacSorted(String) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest2

testFactorIsStillAttachedToItsDesignWhenFindByFactorIsCalled() - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorServiceTest

🛑 The factor is STILL IN its design's factor collection when bioMaterialService.findByFactor is called.

testFactorValueOntologyUrl() - Method in class ubic.gemma.persistence.util.EntityUrlBuilderTest

testFactorValueSamplesCanBeNamedByBioMaterialId() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A factor value can name its samples by BioMaterial id.

testFactorValueStatementsNotListedInOldStyleCharacteristics() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoTest

testFailedTaskClassifiesSuperSeriesGateFromMessage() - Method in class ubic.gemma.rest.TasksWebServiceTest

testFailedTaskReportsAlreadyExistsWithExistingExperimentId() - Method in class ubic.gemma.rest.TasksWebServiceTest

testFailedTaskReportsNetworkErrorFromBuriedIOException() - Method in class ubic.gemma.rest.TasksWebServiceTest

testFailedTaskWithoutCapturedExceptionStillReportsGenericError() - Method in class ubic.gemma.rest.TasksWebServiceTest

testFailsFastWhenFileSuffixPointsToMissingFile(Path) - Method in class ubic.gemma.core.config.ConfigUtilsTest

testFallsBackToDirectEnvVarWhenFileSuffixIsBlank() - Method in class ubic.gemma.core.config.ConfigUtilsTest

testFallsBackToDirectEnvVarWhenFileSuffixUnset() - Method in class ubic.gemma.core.config.ConfigUtilsTest

testFetch() - Method in class ubic.gemma.core.loader.entrez.EutilFetchTest

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.expression.sra.SraFetcherTest

testFetch() - Method in class ubic.gemma.core.loader.util.HttpFetcherTest

testFetch() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoTest

testFetchAllCollectionMetadata() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcherTest

testFetchAllDatasetMetadata() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcherTest

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

testFetchCollectionMetadata() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcherTest

testFetchDatasetMetadata() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcherTest

testFetchDetailedGeoSeries() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserTest

There are two strategies to retrieve detailed GEO series and those should produce identical documents.

testFetchDetailedGeoSeriesWithInvalidUtf8Characters() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserTest

testFetchNothingThere() - Method in class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcherTest

testFetchProject() - Method in class ubic.gemma.core.loader.expression.sra.SraFetcherTest

testFetchProjectRunInfo() - Method in class ubic.gemma.core.loader.expression.sra.SraFetcherTest

testFetchRunInfo() - Method in class ubic.gemma.core.loader.expression.sra.SraFetcherTest

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

testFilterableProperties() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceTest

testFilterAndCountByArrayDesign() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testFilterArgSchemas() - Method in class ubic.gemma.rest.OpenApiTest

testFilterBulkData() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterTest

testFilterByAllCharacteristics() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testFilterByGeeqQualityScore() - Method in class ubic.gemma.rest.DatasetsRestTest

testFilterByGeeqScore() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testFilterBySize() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceTest

There's a few quirks for the Criteria API when it comes to treating size.

testFilterDataWithOutliers() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterTest

testFilteredProperties() - Method in class ubic.gemma.core.config.SettingsConfigTest

testFilterEmptyMatrix() - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilterTest

testFilteringByAllFilterableProperties() - Method in class ubic.gemma.persistence.service.FilteringVoEnabledServiceIntegrationTest

testFilterLog2cpmData() - Method in class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilterTest

testFilterMatrixFilledWithNaNs() - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilterTest

testFilterMatrixFilledWithZeroes() - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilterTest

testFilterMatrixWithOutliers() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterTest

testFilterMicroarrayData() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterTest

testFilterProbesByPlatformEmptyArrayDesignsShortCircuits() - Method in class ubic.gemma.persistence.util.CommonQueriesTest

testFilterProbesByPlatformEmptyProbesShortCircuits() - Method in class ubic.gemma.persistence.util.CommonQueriesTest

testFilterSingleCellMatrix() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterTest

testFilterSingleCellMatrix() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterTest

testFilterSingleCellMatrixWithAssayLevelCellCounts() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterTest

testFilterVosByNumberOfCharacteristics() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceTest

testFilterVosByNumberOfResults() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceTest

testFilterWithCustomValues() - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilterTest

testFilterWithHighCut() - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilterTest

testFilterWithHighCutAsFraction() - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilterTest

testFilterWithLowCut() - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilterTest

testFilterWithLowCutAndHighCut() - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilterTest

testFilterWithLowCutAndHighCutAsFraction() - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilterTest

testFilterWithLowCutAsFraction() - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilterTest

testFilterWithLowCutForDroppingZeros() - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilterTest

testFilterWithMissingValues() - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilterTest

testFilterWithNonLogScaleData() - Method in class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilterTest

testFilterWithNumberOfCellsInAssays() - Method in class ubic.gemma.core.analysis.preprocess.filter.MinimumCellsFilterTest

testFilterWithNumberOfCellsInMatrix() - Method in class ubic.gemma.core.analysis.preprocess.filter.MinimumCellsFilterTest

testFilterWithSliceColumns() - Method in class ubic.gemma.core.analysis.preprocess.filter.MinimumCellsFilterTest

testFilterWithStatementSecondObject() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testfind() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceTest

testFind() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoTest

testFind() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoTest

testFind() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoTest

testFind() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceTest

testFind() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoTest

testFindAll() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImplTest

testFindAllByExperiment() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoTest

testFindAllByNameAndVectorTypeDelegates() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testFindAllDoesNotServePrivateResultSetsToAnonymousCallers() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

🔒 The LISTING is ACL-filtered, not just the id-taking loaders.

testFindAllWhenDatabaseEntryDoesNotExistThenRaise404NotFound() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

testFindAllWhenDatasetDoesNotExistThenRaise404NotFound() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

testFindAllWhenNoDatasetsAreProvidedThenReturnLatestAnalysisResults() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

testFindAllWithDatabaseEntriesThenReturnLatestAnalysisResults() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

testFindAllWithDatasetIdsThenReturnLatestAnalysisResults() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

testFindAllWithFilters() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

testFindAllWithFiltersAndCollections() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

testFindAllWithInvalidFilters() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

testFindBioAssayDimensionsLong() - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceTest

Tests HQL

testFindBioMaterial() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceTest

Test method for BioMaterialDaoImpl.find(ubic.gemma.model.expression.biomaterial.BioMaterial) .

testFindBioMaterialByAccessionOnly() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceTest

testFindBioMaterialByNameOnly() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceTest

testFindBioSequence() - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationServiceTest

testFindBlatResultByBioSequence() - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultServiceTest

testFindByAccession() - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceTest

testFindByAccession() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testFindByAccessionDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testFindByAccessionNcbi() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceTest

testFindByAccessionNcbiWithSource() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceTest

testFindByAccessionNoSource() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImplTest

testFindByAccessionNullSourceDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testFindByAccessionOther() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceTest

testFindByAliasDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testFindByBioSequenceDelegates() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testFindByBioSequenceNameDelegates() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testFindByCategoryLike() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testFindByCategoryLike_returnsPlainAndStatement() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoMySqlIntegrationTest

testFindByCategoryUri_returnsPlainAndStatement() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoMySqlIntegrationTest

testFindByCursorWithFilterOnAliasedBaselineGroupCharacteristic() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoTest

testFindByEnsemblIdDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testFindByExperimentAndAnalysisIdDelegates() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceTest

testFindByExperimentDelegates() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceTest

testFindByExperimentDelegates() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceTest

testFindByExperimentsDelegates() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceTest

testFindByExpressionExperimentAndDimensionDelegates() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testFindByExpressionExperimentAndDimensionWithVectorTypesDelegates() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testFindByExpressionExperimentMapDelegates() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testFindByExpressionExperimentMultipleVectorTypesUnions() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testFindByExpressionExperimentSingleVectorTypeDelegates() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testFindByExternalId() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImplTest

testFindByExternalIdentString() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceTest

testFindByExternalIdToleratesDuplicates() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceTest

Prod has duplicate BibliographicReference rows for the same PubMed accession; the external-id lookups must return one (the lowest-id) rather than throwing NonUniqueResultException (which surfaced as a 500 on PUT /datasets/{id}/publications), and find must too so findOrCreate doesn't add yet another duplicate.

testFindByFactor() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDaoTest

testFindByFactor() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testFindByFactorDelegates() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceTest

testFindByFactorDelegates() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceTest

testFindByFactors() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDaoTest

testFindByFactorValue() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testFindByFactorValueId() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testFindByFilterOnAliasedBaselineGroupCharacteristic() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoTest

testFindByFilterOnAliasedSubsetFactorValueCharacteristic() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoTest

testFindByGene() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoTest

testFindByGene() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest

testFindByGene() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceTest

testFindByGeneAndExperimentAnalyzed() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoTest

testFindByGeneAndExperimentAnalyzed() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceTest

This test mainly exercise the ACL annotation for filtering DEA results.

testFindByGeneAndExperimentAnalyzedGroupingBySourceExperiment() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoTest

testFindByGeneAndPlatform() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest

testFindByGeneAndPlatformWithGene2Cs() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest

testFindByGeneAndThreshold() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoTest

testFindByGeneDelegates() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testFindByGenesDelegates() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testFindByGeneSlice() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest

testFindByGeneSliceWithGene2Cs() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest

testFindByGenesWithPlatformDelegates() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testFindByGeneWithGene2Cs() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest

testFindByGeneWithPlatformDelegates() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testFindByGoId() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceTest

No @DirtiesContext, deliberately.

testFindByIdThenReturn200Success() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

testFindByIdToTsv() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

testFindByIdWhenExcludeResultsThenReturn200Success() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

testFindByIdWhenInvalidIdentifierThenThrowMalformedArgException() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

testFindByIdWhenResultSetDoesNotExistsThenReturn404NotFoundError() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

testFindByInvestigation() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceTest

testFindByInvestigations() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceTest

testFindByName() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceTest

testFindByNameAndVectorType() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoTest

testFindByNameAndVectorTypeDelegates() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testFindByNameAndVectorTypeWrapsNonUniqueResultException() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testFindByNameDefaultsToRawAndDelegates() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testFindByNameDelegates() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceTest

testFindByNameDelegates() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testFindByNameExact() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceTest

testFindByNameInPlatformDelegates() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testFindByNameRecent() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceTest

testFindByNamesInArrayDesignsResolvesAndDedupes() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testFindByNamesInArrayDesignsReturnsNullWhenAllUnknown() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testFindByNameWhenNameIsNonUnique() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoTest

testFindByNameWrapsNonUniqueResultException() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testFindByNcbiId() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImplTest

testFindByNcbiId() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceTest

testFindByNCBIIdDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testFindByNcbiIdsBuildsVoMap() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testFindByNCBIIdValueObjectReturnsNullWhenMissing() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testFindByNCBIIdValueObjectWrapsGene() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testFindByOfficialName() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImplTest

testFindByOfficialNameDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testFindByOfficialSymbol() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImplTest

testFindByOfficialSymbol() - Method in class ubic.gemma.rest.util.args.GeneArgServiceTest

testFindByOfficialSymbolAndTaxon() - Method in class ubic.gemma.rest.util.args.GeneArgServiceTest

testFindByOfficialSymbolInexact() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImplTest

testFindByOfficialSymbolsBuildsVoMap() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testFindByOfficialSymbolWithTaxonDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testFindByParentClasses_returnsPlainAndStatement() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoMySqlIntegrationTest

testFindByPhysicalLocationDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testFindByQt() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceGeoTest

testFindByResultSets() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoTest

testFindBySortOnAliasedBaselineGroupCharacteristic() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoTest

testFindByUri() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testFindByUri_returnsPlainAndStatement() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoMySqlIntegrationTest

testFindByValueLike() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testFindByValueLike_returnsPlainAndStatement() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoMySqlIntegrationTest

testFindByValueStartingWith() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoTest

testFindByValueStartingWithDelegates() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

testFindByVectorType() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoTest

testFindDatabaseEntry() - Method in class ubic.gemma.persistence.service.common.description.DatabaseEntryDaoImplTest

testFindEeCountsByUriForOriginalValue() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testFindEeCountsByUriForOriginalValueRefusesQuantities() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testFindEeCountsByUriForOriginalValueTreatsWildcardsLiterally() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testFindEvenThoughHaveSameSymbol() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceTest

testFindExperimentsByUris() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testFindExperimentsByUris() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceTest

testFindExperimentsByUrisAsAdmin() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testFindExperimentsByUrisAsAnonymous() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testFindExperimentsByUrisAsAnonymousUser() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceTest

testFindExperimentsByUrisAsProxies() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceTest

testFindExperimentsByUrisAsUser() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceTest

testFindExperimentsWithAnalysesDelegates() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceTest

testFindGDSGrouping() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testFindGene() - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationServiceTest

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

testFindGSEForGDS() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testFindIdsByBioMaterial_resolvesThroughASubset() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

A sample whose only route to an experiment is subset -> sourceExperiment must still resolve.

testFindOrCreate() - Method in class ubic.gemma.persistence.service.genome.TaxonServiceImplTest

Situation where the secondary id is treated as the primary, we must not make a new taxon!

testFindPriorCurationByOriginalValue() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testFindRepresentativeUsageByValueUris() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testFindSiblingsRemovesSelf() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceTest

testFindSiblingsReturnsEmptyWhenNoSource() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceTest

testFindSubBioMaterialsDelegates() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceTest

testFindTerm() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testFindTermInexact() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

testFindTerms() - Method in class ubic.gemma.core.ontology.OntologyCacheTest

testFindTermWithEmptyQuery() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testFindTermWithMultipleTerms() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testFindValueGroupedByValueUri() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testFindWithExternalReference() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testFindWithExternalReferenceNotFound() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testFindWrapsSingletonVectorType() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testFirstPageEmitsNextCursor() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoCursorTest

testFish() - Method in class ubic.gemma.cli.util.CompletionGeneratorTest

testFishCompletions() - Method in class ubic.gemma.cli.util.CompletionGeneratorTest

testFixingATopLevelSecurableGrantsAdministration() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterServiceTest

Repairing a top-level Securable must leave it editable.

testForcedBaseline() - Method in class ubic.gemma.core.analysis.expression.diff.BaselineSelectionTest

testForceIsNotABypassForANonAdmin() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

force=true is not a bypass.

testForceRefetchesEvenWhenOneIsStored() - Method in class ubic.gemma.apps.UpdateGeoSourceMetadataCliTest

...

testFormAclJoinClauseAsAdmin() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

testFormAclJoinClauseAsNonAdminIncludesAoiEntriesInnerJointure() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

testFormat() - Method in class ubic.gemma.core.util.TsvUtilsTest

testFormatArray() - Method in class ubic.gemma.core.util.TsvUtilsTest

testFormatComment() - Method in class ubic.gemma.core.util.TsvUtilsTest

testFormatLong() - Method in class ubic.gemma.core.util.TsvUtilsTest

testFormatMarkdownCodeSpan() - Method in class ubic.gemma.core.util.MarkdownUtilsTest

testFormatNumber() - Method in class ubic.gemma.core.util.TsvUtilsTest

testFormNativeRestrictionClause() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

testFormNativeRestrictionClauseAsAnonymous() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

testFormRestriction() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testFormRestrictionAndGroupByAndOrderByClauses() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testFraction() - Method in class ubic.gemma.core.analysis.sequence.RepeatScanTest

testFreeTextLiteralIsNotMistakenForAReplacement() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

The literal branch must not turn arbitrary annotation text into a replacement — only something shaped like a term URI counts.

testFreeTextSkipped() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testFromCollection() - Method in class ubic.gemma.core.datastructure.sparse.SparseArrayListTest

testFromCollection() - Method in class ubic.gemma.core.datastructure.sparse.SparseRangeArrayListTest

testFromExactIdentifierTagsResult() - Method in class ubic.gemma.core.search.SearchResultTest

testFromManifest() - Method in class ubic.gemma.core.util.BuildInfoTest

testFutureEvent() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4ProviderTest

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

testGDS186() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testGeneArrayArg() - Method in class ubic.gemma.rest.util.args.EntityArrayArgsTest

testGeneArrayArgEmptyRaises() - Method in class ubic.gemma.rest.util.args.EntityArrayArgsTest

testGeneDifferentialExpression() - Method in class ubic.gemma.rest.GeneWebServiceTest

testGeneDifferentialExpressionRejectsOutOfRangeThreshold() - Method in class ubic.gemma.rest.GeneWebServiceTest

testGeneDifferentialExpressionWithThreshold() - Method in class ubic.gemma.rest.GeneWebServiceTest

testGeneGoTerms() - Method in class ubic.gemma.rest.GeneWebServiceTest

testGeneListPlatformGeneCountsComeFromTheElementCount() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

Ask 4, RNA-seq case.

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

testGeneLocations() - Method in class ubic.gemma.rest.GeneWebServiceTest

testGeneOntologyTermsAreSkipped() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

GO annotations are gene annotations; their obsolescence is a separate problem and the CLI skipped them, so the report must not start reporting them just because it changed how it enumerates URIs.

testGeneProbes() - Method in class ubic.gemma.rest.GeneWebServiceTest

testGeneProbesSummary() - Method in class ubic.gemma.rest.GeneWebServiceTest

testGeneProbesWhenIdentifierIsAmbiguous() - Method in class ubic.gemma.rest.GeneWebServiceTest

testGeneProductAccessionHistoryRotation() - Method in class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceTest

Gene-product history rotation: when a GeneProduct already in the DB receives an updated DatabaseEntry accession, the new one must be APPENDED to the accessions collection, not replace the old one.

testGenerate() - Method in class ubic.gemma.core.loader.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().

testGeneric() - Method in class ubic.gemma.core.security.acl.voter.AclEntryMapValueVoterTest

testGeneric() - Method in class ubic.gemma.core.security.acl.voter.AclEntryMapVoterTest

testGeneric(Collection) - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest.MyService

testGeneric2(Collection) - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest.MyService

testGenericCellLevelCharacteristicsRoundTrip() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.SingleCellDimensionCacheStalenessTest

Standalone GenericCellLevelCharacteristics create + reload, exercising the mutable="false" + cache shape on the child class directly.

testGenericCollection() - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest

testGenericCollection2() - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest

testGenes() - Method in class ubic.gemma.rest.GeneWebServiceTest

testGenesByCompositeSequence() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest

testGenesByIds() - Method in class ubic.gemma.rest.GeneWebServiceTest

testGenesByIdsIncludesAliases() - Method in class ubic.gemma.rest.GeneWebServiceTest

testGeneValueObjectWithoutTaxon() - Method in class ubic.gemma.model.genome.GeneValueObjectTest

testGenomicDnaIsAReferenceChannelAndNotTheSample() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterMoleculeTest

🛑 The GSE9164 case.

testGeoEmptyMINiML() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserTest

GEO returns an empty document when retrieving the samples for this document.

testGeqWithNullRequiredValue() - Method in class ubic.gemma.persistence.util.FilterTest

testGetAllAnnotations() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetAllChildren() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testGetAllGeoRecords() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserTest

testGetAnnotationCategories() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testGetAnnotationCategoriesEmpty() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testGetAnnotationCategoriesReturnsList() - Method in class ubic.gemma.rest.AnnotationsRestTest

testGetAnnotationPredicates() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testGetAnnotationPredicatesEmpty() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testGetAnnotationPredicatesReturnsList() - Method in class ubic.gemma.rest.AnnotationsRestTest

testGetAnnotationsById() - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtilsTest

testGetAnnotationsByLevel() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetAnnotationsIncludeFreeText() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testGetAnnotationsUsageFrequency() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceTest

testGetAnnotationsUsageFrequencyWithFilters() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceTest

testGetAnnotationTerm() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testGetAnnotationTermExpandsCurieValuedReplacement() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

A CURIE-valued literal (CLO:0000457) is canonicalised, not dropped.

testGetAnnotationTermExposesConsiderCandidates() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

A term that was split rather than merged names candidates, not a replacement.

testGetAnnotationTermExposesReplacementForObsoleteTerm() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

The EFO case that motivated the field (uib, 2026-08-16): EFO_0000408 obsolete_disease names MONDO_0000001 as its successor, and EFO's OWL carries a label for that class, so no second lookup is needed.

testGetAnnotationTermIncludesSynonymsAndAlternativeIds() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testGetAnnotationTermNotFound() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testGetAnnotationTermPopulatesParents() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testGetAnnotationTermReportsZeroWhenNoExperimentsMatch() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testGetAnnotationTermResolvesLiteralReplacementAndItsLabel() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

Same axiom written as a literal rather than an rdf:resource — the OBO→OWL conversions disagree on this, and reading only the resource form empties the field for whole ontologies.

testGetAnnotationTermSkipsCountLookupWhenTermHasNoUri() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testGetAnnotationTermSkipsObsolescenceLookupForLiveTerm() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

A live term is never probed for obsolescence axioms — it declares none, and probing would cost a successor lookup per call for a field that is always null.

testGetAnnotationTermWhenLookupTimesOut() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testGetAnnotationTermWithBlankUriIs400() - Method in class ubic.gemma.rest.AnnotationsRestTest

testGetAnnotationTermWithBlankUriIs400() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testGetAnnotationTermWithholdsLiteratureCitationsUnlessAsked() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

🛑 Literature citations are withheld from dbXrefs unless asked for, and always counted.

testGetAnnotationTermWithMissingUriIs400() - Method in class ubic.gemma.rest.AnnotationsRestTest

testGetAnnotationTermWithMissingUriIs400() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testGetAnnotationTermWithUnknownUriIs404() - Method in class ubic.gemma.rest.AnnotationsRestTest

testGetAnnotationUsageFrequency() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetAnnotationUsageFrequencyAsAnonymous() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetAnnotationUsageFrequencyExcludingFreeTextCategories() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetAnnotationUsageFrequencyExcludingFreeTextTerms() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetAnnotationUsageFrequencyExcludingUncategorizedTerms() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetAnnotationUsageFrequencyRetainMentionedTerm() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetAnnotationUsageFrequencyWithIds() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

No ACL filtering is done when explicit IDs are provided, so this should work without WithMockUser.

testGetAnnotationUsageFrequencyWithLargeBatch() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetAnnotationUsageFrequencyWithUncategorizedCategory() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetArrayDesignUsageFrequency() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetArrayDesignUsed() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetAspect() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test

testGetAspect() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testGetAspect2() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test

testGetBaselineConditionsRefusesAFactorTheSamplesDoNotCarry() - Method in class ubic.gemma.core.analysis.expression.diff.BaselineSelectionTest

A factor none of the given samples carries has no baseline to pick, and getBaselineConditions says so by throwing.

testGetBatchConfounds() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentBatchInformationServiceTest

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

Test of creating batch factor.

testGetBean() - Method in class ubic.gemma.core.context.AsyncFactoryTest

testGetBean() - Method in class ubic.gemma.core.context.AsyncSingletonFactoryTest

testGetBeanAndGetBeanAsync() - Method in class ubic.gemma.core.context.AsyncSingletonFactoryTest

testGetBeanAsync() - Method in class ubic.gemma.core.context.AsyncFactoryTest

testGetBeanAsync() - Method in class ubic.gemma.core.context.AsyncSingletonFactoryTest

testGetBeanAsyncThenCancel() - Method in class ubic.gemma.core.context.AsyncFactoryTest

testGetBeanAsyncThenCancel() - Method in class ubic.gemma.core.context.AsyncSingletonFactoryTest

testGetBeanAsyncThenWait() - Method in class ubic.gemma.core.context.AsyncFactoryTest

testGetBeanThenCancel() - Method in class ubic.gemma.core.context.AsyncSingletonFactoryTest

testGetBioAssay() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionTest

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

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

testGetBioMaterialCount() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testGetBlacklistedDatasets() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetBlacklistedPlatforms() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

testGetBlacklistedPlatformsAsNonAdmin() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

testGetByGeneAlias() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceTest

testGetByTaxon() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testGetCategoriesUsageFrequencyAsAnonymous() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetCategoriesUsageFrequencyWithIds() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

No ACL filtering is done when explicit IDs are provided, so this should work without WithMockUser.

testGetCategoriesWithUsageFrequency() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetCellLevelCharacteristics() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testGetChildren() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testGetChildrenPartOf() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testGetCompositeSequenceCountByIdDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testGetCompositeSequenceCountDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testGetCompositeSequences() - Method in class ubic.gemma.persistence.service.genome.GeneDaoTest

testGetCompositeSequencesByGeneId() - Method in class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperServiceFastTest

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

testGetCompositeSequencesWithArrayDesignDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testGetCount() - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceTest

testGetCs2GeneIdMapForGenesEmptyArrayDesignsShortCircuits() - Method in class ubic.gemma.persistence.util.CommonQueriesTest

testGetCs2GeneIdMapForGenesEmptyGenesShortCircuits() - Method in class ubic.gemma.persistence.util.CommonQueriesTest

testGetCs2GeneMapForProbesEmptyShortCircuits() - Method in class ubic.gemma.persistence.util.CommonQueriesTest

testGetDataset() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtilsTest

testGetDatasetAllPublications() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetAnnotations() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetAnnotationsExcludingFreeText() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetAuditEvents() - Method in class ubic.gemma.rest.DatasetsRestTest

testGetDatasetAuditEvents() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetAuditEventsByShortName() - Method in class ubic.gemma.rest.DatasetsRestTest

testGetDatasetAuditEventsCompactAlternatingTypesProducesAllSolo() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetAuditEventsCompactCollapsesConsecutiveSameTypeAndPerformer() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetAuditEventsCompactFalseReturnsFullList() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetAuditEventsCompactMixedAABA() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetAuditEventsCompactOnEmptyIsEmpty() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetAuditEventsExcludeEmptyComposesWithCompact() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetAuditEventsExcludeEmptyDropsTypelessBlankEvents() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetAuditEventsWhenEmpty() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetAuditEventsWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsRestTest

testGetDatasetAuditEventsWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetCurationDetails() - Method in class ubic.gemma.rest.DatasetsRestTest

testGetDatasetCurationDetails() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetCurationDetailsExposesCurationNoteForAdmin() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetCurationDetailsHidesCurationPendingFromNonAdmins() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A non-administrator does not learn that curation is under way.

testGetDatasetCurationDetailsReportsCurationPendingWhileLocked() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

curationPending is the curation lock's unexpired lease and nothing else: it must read true while a lock is held, and the response must still name nobody.

testGetDatasetCurationDetailsReportsNoCurationPendingWhenUnlocked() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A free dataset reads false, not null: the GET always consults the lock, so the reader can tell "nobody is curating" from "this path did not look".

testGetDatasetCurationDetailsWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsRestTest

testGetDatasetCurationDetailsWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetDataMatrix() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtilsTest

testGetDatasetDescription() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtilsTest

testGetDatasetDesignDefaultIsJson() - Method in class ubic.gemma.rest.DatasetsRestTest

testGetDatasetDesignDefaultIsJson() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetDesignJson() - Method in class ubic.gemma.rest.DatasetsRestTest

testGetDatasetDesignJson() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetDesignJsonReturnsNotFoundWhenDesignMissing() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetDesignJsonWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsRestTest

testGetDatasetDesignJsonWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetDesignTsvViaAcceptHeader() - Method in class ubic.gemma.rest.DatasetsRestTest

testGetDatasetGeeq() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetGeeqWhenNotComputedIs404() - Method in class ubic.gemma.rest.DatasetsRestTest

testGetDatasetGeeqWhenNotComputedIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetGeeqWithoutEvent() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetGeeqWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsRestTest

testGetDatasetGeeqWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetMeanVariance() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetMeanVarianceCollapsesAHeavilyOverplottedDataset() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The size guard: 30,000 points drawn from ten distinct coordinates come back as ten.

testGetDatasetMeanVarianceDropsNonFinitePoints() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A point whose mean or variance is not finite has no position on the scatter, so it is dropped rather than keyed into the grid.

testGetDatasetMeanVarianceHttp200() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

Wire-shape check: the HTTP response is 200 with a JSON body containing the means array.

testGetDatasetMeanVarianceIsRoundedAndLeavesTheEntityArrayAlone() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Mean-variance is the heaviest diagnostics payload — one mean and one variance per probe.

testGetDatasetMeanVarianceIsThinnedOnTheWire() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The thinned arrays are what actually goes on the wire.

testGetDatasetMeanVarianceKeepsOnePointPerCellAndStaysIndexParallel() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Two points that land in the same grid cell collapse to the first of them, and the pairing survives: the fixture makes every variance twice its mean, so an entry dropped from one array and not the other would re-pair every point after it and break that relation.

testGetDatasetMeanVarianceLeavesWellSeparatedPointsAlone() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Points that each get their own cell come back untouched — thinning only ever removes a point that would be drawn on top of one already sent.

testGetDatasetMeanVarianceReturnsArrays() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

Regression guard: calling the handler must not throw LazyInitializationException.

testGetDatasetMeanVarianceWhenDatasetMissingIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetMeanVarianceWhenNoneIs404() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

Negative case: a dataset without an MVR returns 404 (NotFoundException from the handler).

testGetDatasetMeanVarianceWhenNoneIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetMeanVarianceWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

testGetDatasetMetadataFileForDirectoryTypeIs400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetMetadataFileServesPayload() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetMetadataFileWhenAbsentIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetMetadataFileWhenDatasetMissingIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetMetadataFileWithUnknownTypeIs400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetPipelineStatus() - Method in class ubic.gemma.rest.DatasetsRestTest

testGetDatasetPipelineStatusAdminSeesCurationNote() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetPipelineStatusCarriesFilterAttrition() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The sample-correlation step carries the filter attrition recorded when the matrix was computed.

testGetDatasetPipelineStatusCarriesProcessedVectorDetails() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The preprocess step carries what the processed-vector creation did to the data.

testGetDatasetPipelineStatusIncludesConvenienceFields() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetPipelineStatusMissingValueApplicableForTwoColor() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetPipelineStatusNonAdminDoesNotSeeCurationNote() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetPipelineStatusPcaFailed() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetPipelineStatusPicksLatestEvent() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetPipelineStatusPreprocessOk() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetPipelineStatusReturnsAllStepsWithNotRunOrNotApplicable() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetPipelineStatusSurvivesAnUnparseableAuditPayload() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A payload that does not parse must not take the status read down with it.

testGetDatasetPipelineStatusWithoutFilterAttritionStillReportsTheStep() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Every correlation matrix computed before the payload existed carries no payload at all.

testGetDatasetPipelineStatusWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsRestTest

testGetDatasetPipelineStatusWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetProcessedExpression() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetProcessedExpressionWhenNoProcessedVectorsExist() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetQcMetricsServesTheDatabaseReadCountWithoutAReport() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

Most RNA-seq assays carry a read count in the database while only a minority of datasets have a MultiQC report, so a read count alone has to answer 200 — with reportPresent false so the caller can tell the two apart.

testGetDatasetQcMetricsWhenThereIsNothingIs404() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

A dataset with no MultiQC report and no sequencing read counts has nothing to show, so the endpoint 404s rather than returning an empty row per assay.

testGetDatasetQuantitationTypes() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetRawExpression() - Method in class ubic.gemma.rest.DatasetsRestTest

testGetDatasetRawExpression() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetRawExpressionByQuantitationType() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetRawExpressionByQuantitationTypeWhenQtIsNotFromTheDataset() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasets() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtilsTest

testGetDatasets() - Method in class ubic.gemma.rest.AnalysisResultSetsJerseyTest

testGetDatasets() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSampleCorrelation() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSampleCorrelationIsWithheldForSingleCell() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

🛑 Temporary, pending the per-cell-type design.

testGetDatasetSampleCorrelationStillServedWhenNotSingleCell() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The same dataset, not single-cell, still serves the matrix — the gate is the flag, not the route.

testGetDatasetSampleCorrelationWhenDatasetMissingIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSampleCorrelationWhenNoneIs404() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

GET /sample-correlation returns 404 when the dataset has no SampleCoexpressionAnalysis.

testGetDatasetSampleCorrelationWhenNoneIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSamplesCanExcludeStatements() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

sample.statements is 21.5% of the samples response and carries the same rows as sample.characteristics plus a predicate and object, so a client that renders only subjects can decline it.

testGetDatasetSamplesDoesNotComputePredictedOutliersByDefault() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The predicted-outlier flag costs the dataset's whole N×N sample-correlation matrix to compute, which is why it is opt-in: the cost is set by the correlation analysis, not the page size, and on the largest datasets it exceeds the request timeout.

testGetDatasetSamplesIsCompressed() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

🛑 The route was not compressed, and that — not any single field — was the size of the problem.

testGetDatasetSamplesRejectsALimitItCannotHonour() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

🛑 limit was bound by the route and then used only on the cursor branch, so a client asking for a page got the whole dataset instead, with nothing in the body saying so.

testGetDatasetSamplesRejectsAnUnsupportedExclusion() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

An exclusion the route does not offer is a 400, not a silently ignored parameter.

testGetDatasetsAnalysisResultSets() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetsAnnotations() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetsAnnotationsForUncategorizedTerms() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetsAnnotationsWhenMaxFrequencyIsSuppliedLimitMustUseMaximum() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetsAnnotationsWithLimitIsSupplied() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetsAnnotationsWithRetainMentionedTerms() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetsAnnotationWhenLimitExceedHardCap() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetsCategories() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetsCategories() - Method in class ubic.gemma.rest.OpenApiTest

testGetDatasetsDifferentialAnalysisResultsExpressionForGene() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetsDifferentialAnalysisResultsExpressionForGeneInTaxa() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetsExpressionLevelsForGeneIsRoundedUnlessPreciseIsAsked() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Expression levels are a data-download surface, so rounding here is the default and precise=true is the opt-out.

testGetDatasetSingleCellData() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSingleCellDataAsDownload() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSingleCellDataAsMex() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSingleCellDataWhenCacheIsCold() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Cold cache: the tabular single-cell data is generated ONCE, streaming to the caller and populating the cache file in the same pass — never by racing a fire-and-forget background build against an in-band stream of the same data, which on this endpoint meant two concurrent full scans of the largest payloads in the system.

testGetDatasetsOrderedByGeeqScore() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSourceMetadata() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The document is served as an object, not as the string it is stored as.

testGetDatasetSourceMetadataForAnUnknownDataset() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A dataset that does not exist is still a 404, which is what the null case must not look like.

testGetDatasetSourceMetadataWhenNoneHasBeenHarvested() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

🛑 Nothing harvested is the normal state for most of the corpus, not an error.

testGetDatasetsPipelineStatusReturnsAnEntryPerDatasetAlongsideTheSingleRoute() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The bulk route lives at the LITERAL `/datasets/pipelineStatus` with ids in a query param.

testGetDatasetsPlatformsUsageStatistics() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSubSet() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSubSetGroup() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSubSetGroups() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSubSets() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSubSetSamples() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSvdIsRoundedAndLeavesTheResultArraysAlone() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

SVD loadings serialize at a mean of ~20 characters each and nothing consumes the digits below it, so this route rounds with no opt-out.

testGetDatasetSvdLoadings() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSvdLoadingsWhenNoSvdIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSvdLoadingsWithMissingPcIs400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSvdLoadingsWithPcZeroIs400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSvdLoadingsWithTopOverCapIs400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetSvdLoadingsWithUnknownDirectionIs400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetsWhenInferenceTimeoutThenProduce503ServiceUnavailable() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetsWhenSliceHasNoLimit() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetsWithEmptyQuery() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetsWithQuery() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetsWithQueryAndSort() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testGetDatasetUrl() - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserServiceImplTest

testGetDataVectorType() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoTest

testGetDataVectorTypeDelegates() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testGetDataVectorTypesAggregates() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testGetDesignElementDataVectorsByQt() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testGetDetailedGeoRecord() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserTest

testGetEnhancedFilters() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceTest

testGetEnhancedFiltersWhenANegativeQueryIsPerformed() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceTest

testGetEnhancedFiltersWhenAPredicateOrObjectIsUsed() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceTest

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

Excluded by default: this downloads a file from BioMart on every run, 25.6 s cold, the largest single item in the fast suite.

testGetEntitiesWithEvent() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplTest

testGetEvents() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoTest

testGetExperimentalFactorCategoriesIgnoreAclsDelegates() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

testGetExperimentDataFileResult() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLITest

testGetExperimentOfInitializedExperiment() - Method in class ubic.gemma.persistence.util.CommonQueriesTest

testGetExperimentOfInitializedSubsetReturnsItsSource() - Method in class ubic.gemma.persistence.util.CommonQueriesTest

testGetExperimentOfLazyProxiedExperiment() - Method in class ubic.gemma.persistence.util.CommonQueriesTest

testGetExperimentOfLazyProxiedSubsetReturnsItsSource() - Method in class ubic.gemma.persistence.util.CommonQueriesTest

testGetExperimentsWithAnalysisDelegates() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceTest

testGetExplicitBaselinesIgnoresInferredOnes() - Method in class ubic.gemma.core.analysis.expression.diff.BaselineSelectionTest

🛑 Only the explicit flag counts.

testGetExplicitBaselinesReturnsEveryMarkedValue() - Method in class ubic.gemma.core.analysis.expression.diff.BaselineSelectionTest

More than one explicitly marked baseline on a factor is legitimate — a dataset holding two experiments has a reference level per experiment.

testGetExpressionExperimentsById() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testGetExpressionExperimentsDelegates() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceTest

testGetExpressionExperimentsIgnoreAclsDelegates() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

testGetFactorValueMap() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignUtilsTest

testGetFactorValueMapWithMultipleValues() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignUtilsTest

testGetFactorValueMapWithUnassignedFactors() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignUtilsTest

testGetFilter() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest

testGetFilter() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

EE service has a few extensions for supporting various filtering strategies in the frontend, so we need to test them here.

testGetFilterableProperties() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest

testGetFilterableProperties() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetFilterableProperties() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testGetFilterablePropertyType() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testGetFilters() - Method in class ubic.gemma.rest.util.args.TaxonArgServiceTest

testGetFiltersWithCategories() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceTest

testGetFilterTechnologyType() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest

testGetFilterWhenPropertyDoesNotExist() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest

testGetFilterWhenPropertyExceedsMaxDepth() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest

testGetFilterWithStatementObject() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetFtpClientWithIncompleteUserInfo() - Method in class ubic.gemma.core.loader.util.FTPClientFactoryImplTest

testGetGenes() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest

testGetGenes() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest

testGetGenesCollectionDelegates() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testGetGenesForCompositeSequence() - Method in class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperServiceFastTest

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

Tests finding all genes for a given composite sequence.

testGetGenesSingleUsesSliceWithUnboundedLimit() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testGetGenesSlicedDelegates() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testGetGenesUsedByProcessedVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetGenesWithGene2Cs() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest

testGetGenesWithSpecificityDelegates() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testGetGeoRecordB() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserTest

testGetGeoRecordGSE93825() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserTest

testGetGeoRecordWithMeshHeadings() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserTest

This dataset has MESH headings.

testGetGroup_notFound() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testGetGroup_summariesOff() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testGetGroup_summariesOn_includesMembers() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testGetGroups_paginates() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testGetGroups_queryFilter() - Method in class ubic.gemma.rest.GroupsWebServiceTest

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

testGetLastEvent() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoTest

testGetLastEvents() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoTest

testGetLastEventsByType() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoTest

testGetLastEventsByType2() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoTest

testGetLastEventsWholeCorpusSqlSideMax() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoTest

testGetLockInfo() - Method in class ubic.gemma.core.util.locking.FileLockManagerTest

testGetMappedDataVectorTypeDelegates() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testGetMappedDataVectorTypes() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoTest

testGetMetadata() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceTest

testGetMicroRnaByTaxon() - Method in class ubic.gemma.persistence.service.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

testGetMyselfAsAdminExposesAdminAuthority() - Method in class ubic.gemma.rest.RootWebServiceTest

/users/me must carry the user's Spring Security authorities so the curation-UI can gate admin surfaces on GROUP_ADMIN membership.

testGetMyselfAsRegularUserExposesUserAuthorityOnly() - Method in class ubic.gemma.rest.RootWebServiceTest

testGetNewSinceDate() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoTest

testGetOriginalPlatformUsageFrequency() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetParentIdentity_returnsExistingAoi() - Method in class ubic.gemma.core.security.authorization.acl.ParentIdentityRetrievalStrategyTest

Seed an acl_class + acl_object_identity row for ExpressionExperiment id=4242, then drive the strategy with a synthetic BioAssay whose owning EE id is 4242.

testGetParentIdentity_returnsNullWhenNoAoi() - Method in class ubic.gemma.core.security.authorization.acl.ParentIdentityRetrievalStrategyTest

If no acl_object_identity row exists for the resolved parent type+identifier, the strategy must return null (matching the prior HQL uniqueResult() behavior).

testGetParentIdentity_returnsNullWhenParentIdentifierIsNull() - Method in class ubic.gemma.core.security.authorization.acl.ParentIdentityRetrievalStrategyTest

If the upstream lookup returns a null identifier (e.g.

testGetParents() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testGetParents() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testGetParents() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceTest

testGetParentsForMultiParent() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testGetParentsPartOf() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testGetPerTaxonCount() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetPerTaxonCount() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testGetPhysicalLocationsValueObjectsNullGene() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testGetPlatforms() - Method in class ubic.gemma.rest.AnalysisResultSetsJerseyTest

testGetPreferredCellTypeLabellingWhenNonUnique() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

This a behaviour test when the labelling is not unique.

testGetPreferredQuantitationType() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testGetPreferredRawDataVectorsDelegates() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceTest

testGetProcessedDataMatrices() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceTest

Test method for ProcessedExpressionDataVectorService.getProcessedDataArrays(java.util.Collection, java.util.Collection) .

testGetProcessedVectors() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoTest

testGetProductsBuildsVos() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testGetProductsThrowsOnNullId() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testGetProductsThrowsWhenGeneMissing() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testGetQuantitationTypeCount() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testGetQuantitationTypes() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testGetRandomRawVectors() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoTest

testGetRandomRawVectorsEmptyWhenNoVectors() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoTest

testGetRawDataVectorCount() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testGetRawDataVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetRawDataVectorsDelegates() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceTest

testGetRawExpressionDataVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testGetRawSummaryArrayDesignDelegates() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testGetRawSummaryDelegates() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testGetRelatedExperiments() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceTest

testGetResultSets() - Method in class ubic.gemma.rest.AnalysisResultSetsJerseyTest

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

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

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

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

testGetSingleCellDataMatrix() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testGetSingleCellDataVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testGetSingleCellDimensionWithoutCellIds() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testGetSort() - Method in class ubic.gemma.rest.util.args.SortArgTest

testGetSortWhenFieldDoesNotExistThenRaiseMalformedArgumentException() - Method in class ubic.gemma.rest.util.args.SortArgTest

testGetSubSetsByExpressionExperimentsBatched() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetSubSetsByExpressionExperimentsEmpty() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetSubSetsStillReusesWhenASampleWasDropped() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

Reuse still works when a sample has been DROPPED — the case that decides between the two possible fixes.

testGetSubSetsToleratesATransientBioAssayDimension() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

🛑 A TRANSIENT BioAssayDimension is a normal input here, and it must not throw.

testGetTaskStatus() - Method in class ubic.gemma.rest.TasksWebServiceTest

testGetTaskStatusFallsBackToProgressQueueWhenLastIsEmpty() - Method in class ubic.gemma.rest.TasksWebServiceTest

testGetTaskStatusForCompletedTask() - Method in class ubic.gemma.rest.TasksWebServiceTest

testGetTaskStatusReportsUnknownWhenStatusIsNull() - Method in class ubic.gemma.rest.TasksWebServiceTest

testGetTaskStatusWithUnknownTaskIdIs404() - Method in class ubic.gemma.rest.TasksRestTest

testGetTaskStatusWithUnknownTaskIdIs404() - Method in class ubic.gemma.rest.TasksWebServiceTest

testGetTaxaFromBioSequencesMultipleTaxonForArray() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

Test retrieving multiple taxa for an arraydesign where hibernate query is not restricted to return just 1 taxon.

testGetTaxaFromBioSequencesOneTaxonForArray() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testGetTaxon() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testGetTechnologyTypeUsageFrequency() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testGetTermForId() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest

testGetTermResolvesAGeneOntologyUri() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

A GO URI resolves through getTerm, even though GO stays out of the search fan-out.

testGetTermsResolvesAGeneOntologyUri() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

The same URI through the batch path, which is what fills in a cross-vocabulary parent's label.

testGetTicket_includesEvents() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testGetTicket_notFound() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testGetTicketEvents_notFound() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testGetTicketEvents_returnsEventList() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testGetTickets_defaultsAreNullFilters() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testGetTickets_passesFiltersThrough() - Method in class ubic.gemma.rest.TicketsWebServiceTest

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

testGetUnprefixedName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSetUtilsTest

testGetUnprefixedNameFromOldDeaName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSetUtilsTest

testGetUpdatedSinceDate() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoTest

testGetUri() - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtilsTest

testGetValueExceedsCustomMaximumRaises() - Method in class ubic.gemma.rest.util.args.LimitArgTest

testGetValueExceedsDefaultMaximumRaises() - Method in class ubic.gemma.rest.util.args.LimitArgTest

testGetValueNoMaximumAllowsLarge() - Method in class ubic.gemma.rest.util.args.LimitArgTest

testGetValueWithAllowedSetReturnsSubset() - Method in class ubic.gemma.rest.util.args.ExcludeArgTest

testGetValueWithCustomMaximum() - Method in class ubic.gemma.rest.util.args.LimitArgTest

testGetValueWithDisallowedFieldRaises() - Method in class ubic.gemma.rest.util.args.ExcludeArgTest

testGetVectors() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.CachedProcessedExpressionDataVectorServiceTest

testGetVectorsForSubBioAssays() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.CachedProcessedExpressionDataVectorServiceTest

This test exercise the ability of the service to retrieve vector for a subset of sub-bioassays.

testGetVectorsForSubset() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.CachedProcessedExpressionDataVectorServiceTest

testGetVectorTypesDelegates() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testGetVersion() - Method in class ubic.gemma.core.loader.util.hdf5.H5UtilsTest

testGiRotationInPlace() - Method in class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceTest

Quirk 4.2 (migration plan): GI rotation — same Gene, same product name, GeneProduct's GI rotates to a new value because NCBI bumped the sequence version.

testGPL6096ExonArray() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testGrantOnCollectionContainingTransientObject() - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest

testGrantOnTransientObject() - Method in class ubic.gemma.core.security.acl.voter.AclEntryVoterTest

testGSE109774() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This series has numerous TAR archives with numerous small files within.

testGSE125708() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This series has samples lacking data.

testGSE125708(Path) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderTest

This GEO series includes cell types in the barcodes.tsv.gz files.

testGSE125708OverTheWire() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderTest

Truth-source variant of MexSingleCellDataLoaderTest.testGSE125708(Path).

testGSE132188() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This is an AnnData dataset that uses the .h5ad.h5 extension.

testGSE132355() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurerTest

testGSE141552(Path) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderTest

This dataset does not filter empty droplets and thus many barcodes are simply unused and can be discarded.

testGSE141552OverTheWire() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderTest

Truth-source variant of MexSingleCellDataLoaderTest.testGSE141552(Path).

testGSE14285OneBatch() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testGSE143355() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurerTest

testGSE147495() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This is a case of a MEX dataset where files are located in the series.

testGSE148611() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testGSE155499() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This example has some additional supplementary materials that are inside a TAR archive that contains MEX data.

testGSE155695() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This dataset has technical replicates, this is not supported.

testGSE156689NoBatchinfo() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest

testGSE158184() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This is a curious example of a SOFT file that has NONE indicators in its supplementary materials.

testGSE159416() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This is a Loom dataset with a single file in the series.

testGSE1611() - Method in class ubic.gemma.core.datastructure.matrix.io.ExperimentalDesignWriterTest

testGSE162631() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This is a pathologic case with nested zip and gzipped files.

testGSE162807() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This is a custom H5 attachment that is unsupported.

testGSE165635() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

The SRA metadata does not use the "TRANSCRIPTOMIC SINGLE CELL" library source, but keywords in the protocol indicate it is single-cell.

testGSE165635() - Method in class ubic.gemma.core.loader.expression.sra.SraFetcherTest

testGSE169285() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testGSE174574() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

Interesting case because it uses genes.tsv instead of features.tsv.

testGSE178226() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

MEX dataset stored in ZIP archives.

testGSE178226() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurerTest

testGSE179516() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This is a Loom dataset with files in individual samples

testGSE184506() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This series has complete MEX files at the sample-level, but also provide MEX files in the series.

testGSE185737() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This dataset as a mix of scRNA-Seq and ATAC-Seq

testGSE193884() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testGSE196516() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This file has a large TAR attachment in its ATAC-seq samples that should be ignored.

testGSE198033() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurerTest

testGSE199762() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This one uses non-standard file names.

testGSE200202() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This files produces "java.util.zip.ZipException: invalid block type" apparently...

testGSE200218() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This dataset does not use 'single-cell transcriptomic' as a library source, so we have to rely on keywords.

testGSE201032() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testGSE201263() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

Similar case here with large TAR attachments, but in this case it has a lot of samples to skip.

testGSE201814() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This is a case of a MEX dataset where files are bundled in a per-sample TAR archive.

testGSE201814DownloadAll() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testGSE202051() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This dataset has multiple .h5ad supplementary files.

testGSE208742() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This dataset has MEX data at both series and sample-levels.

testGSE208742() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderServiceIntegrationTest

testGSE216457() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderTest

AnnData on-disk format was formalized in the 0.8.x series.

testGSE217511() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurerTest

This is an older single-cell dataset with many typos in the GEO record.

testGSE218621() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This is a MEX dataset with a barcode_metadata.tsv.gz file.

testGSE221042() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurerTest

testGSE221522() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testGSE221593() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This AnnData file has invalid columns and numerical categorical arrays and uses a dense matrix.

testGSE223423() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurerTest

testGSE224438() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

Typical MEX format: 3 supplementary files per sample

testGSE224438() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderTest

testGSE225158() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

AnnData (and also Seurat Disk, but the former is preferred)

testGSE225158() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderIntegrationTest

This test requires a fairly large input file which must be located in the download directory.

testGSE225158() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderTest

testGSE228370() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testGSE230440() - Method in class ubic.gemma.core.loader.expression.sra.SraFetcherTest

testGSE235314() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This series contains large TAR attachment that should be skipped when inspecting for MEX.

testGSE237862() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This dataset has a mixture of Loom and MEX, the latter should take precedence because Loom is not supported yet.

testGSE242423() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This is a case of a MEX dataset that has matrix and barcodes at the sample-level (as we support it!), but genes at the series level.

testGSE244451() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This dataset as an array of ENUM, a raw.X and needs to be transposed.

testGSE246121() - Method in class ubic.gemma.core.loader.expression.geo.fetcher2.GeoFetcherTest

testGSE246121ViaGeoQuery() - Method in class ubic.gemma.core.loader.expression.geo.fetcher2.GeoFetcherTest

This is a fallback if we encounter issues with the FTP server.

testGSE251724() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testGSE254569() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testGSE255369() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurerTest

testGSE256105() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testGSE2569() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserTest

This dataset has incorrect UTF-8 characters in its MINiML file on GEO FTP server.

testGSE269482() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurerTest

testGSE274772() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testGSE280175() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurerTest

testGSE295078() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurerTest

testGSE35930() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExTest

Test where probes have constant values.

testGSE36025() - Method in class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchTest

for bug 3451

testGSE44903() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testGSE465() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest

testGSE71585() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testGSE8579() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserTest

THis dataset has invalid 1-byte UTF-8 sequence (0x1b)

testGSE8872() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testGSE97948() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserTest

This GEO record has ~1000 samples with hundreds of characteristics each.

testGSM3559978() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCell10xMexFilterTest

testGSM4282408() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

This sample has duplicated cell IDs.

testGSM4871780() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCell10xMexFilterTest

This example uses 3 GEMs.

testGSM6925121() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCell10xMexFilterTest

testGSM8316309() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCell10xMexFilterTest

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

testHandleAddEventAuditableAuditEvent() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDaoTest

testHandleGetNewSinceDate() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceTest

testHandleGetUpdatedSinceDate() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceTest

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

testHasSingleCellDataInCellXGene() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testHasSingleCellDataInSra() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testHasSourceMetadata() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

The backfill asks this once per experiment across the corpus to decide whether to skip it, so it must not read the document to answer — SOURCE_METADATA is a LONGTEXT holding the whole GEO record.

testHeatmapBase64Encoding_roundTrips() - Method in class ubic.gemma.rest.DatasetVisualizationWebServiceTest

testHeatmapByGenes_shapesAndFactorCoverage() - Method in class ubic.gemma.rest.DatasetVisualizationWebServiceTest

testHeatmapByProbes_routesThroughProbeSelector() - Method in class ubic.gemma.rest.DatasetVisualizationWebServiceTest

testHeatmapDefault_routesThroughRandomSample() - Method in class ubic.gemma.rest.DatasetVisualizationWebServiceTest

testHeatmapFactorsHaveStatementsAndMeasurements() - Method in class ubic.gemma.rest.DatasetVisualizationWebServiceTest

testHeatmapNonProcessedQt_maskOutliersFalse_returnsStoredOutlierValues() - Method in class ubic.gemma.rest.DatasetVisualizationWebServiceTest

testHeatmapNonProcessedQt_rejectsResultSetMode() - Method in class ubic.gemma.rest.DatasetVisualizationWebServiceTest

testHeatmapNonProcessedQt_servesFromRawVectors() - Method in class ubic.gemma.rest.DatasetVisualizationWebServiceTest

testHeatmapNonProcessedQt_servesRandomFallbackFromRawVectors() - Method in class ubic.gemma.rest.DatasetVisualizationWebServiceTest

testHeatmapProcessedQt_maskOutliersFalse_noOpWhenStoredValueMasked() - Method in class ubic.gemma.rest.DatasetVisualizationWebServiceTest

testHeatmapProcessedQt_maskOutliersFalse_restoresFromStoredEntityWhenValuePresent() - Method in class ubic.gemma.rest.DatasetVisualizationWebServiceTest

testHeatmapSubSet_columnsAndMatrixFilteredToSubsetBioAssays() - Method in class ubic.gemma.rest.DatasetVisualizationWebServiceTest

testHeatmapSubSet_rejectsForeignSubset() - Method in class ubic.gemma.rest.DatasetVisualizationWebServiceTest

testHelper - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest5

Deprecated.

testHitListSizesSurviveFlushClearReload() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.AnalysisResultSetCacheStalenessTest

Cross-session-reload pin for the third leg of the 02c87a91ed fix: the hitListSizes child bag on ExpressionAnalysisResultSet.

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

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

testIdentifiable() - Method in class ubic.gemma.persistence.util.QueryUtilsTest

testIdentifyOutliers() - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetectionServiceTest

testIgnoreFailingSubsetsDoesNotSuppressIt() - Method in class ubic.gemma.core.analysis.expression.diff.NoSubSetAnalysisIsNotSuccessTest

-ignoreFailingSubsets is about carrying on when SOME subsets succeed; it does not make "none of them did" a success.

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

TestImplicitValueObject() - Constructor for class ubic.gemma.core.util.StrictBeanDefinitionValidatorTest.TestImplicitValueObject

testImpliesRefusesRefutedEvenWhenTheParameterIsSent() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

🛑 The gate reads /relations/implies.

testIn() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentFilterRewriteHelperServiceTest

testIncludeCellTypeSubjectsTurnsTheSingleCellCutOff() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

...and a caller who asks for them gets them back.

testIndexing() - Method in class ubic.gemma.core.loader.util.anndata.AnnDataTest

testIndexOfCaseInsensitiveStringElements() - Method in class ubic.gemma.core.util.ListUtilsTest

testIndexOfElements() - Method in class ubic.gemma.core.util.ListUtilsTest

testInducedByOnACellTypeSubjectLicensesNothing() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

🛑 uib, 2026-08-18: a curator's term card carried induced pluripotent stem cell line cell --has disease--> lower motor neuron.

testInferenceInGemma() - Method in class ubic.gemma.core.ontology.GemmaAndExperimentalFactorOntologyTest

testInferredLogbaseDifferFromQuantitations() - Method in class ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionUtilsTest

testInferringFromScratchStillReadsNegativeValuesAsLogTransformed() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

The flags live on the quantitation type being checked, so a type being built from scratch cannot consult them.

testInfixNotMakesTheFallbackSitTheQueryOut() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyQueryRewriteTest

NOT is NOT a separator: stripping it would invert the query into a match for the very thing the caller excluded.

testInfixOrIsASeparatorAndNeverBecomesAnOperand() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyQueryRewriteTest

The defect oganm reported on gemma-ui PR #11: only AND was stripped, so an infix OR survived the rejoin as an OPERAND — `tumour OR normal` came out `tumour AND OR AND normal`, which does not parse.

testInfoMatchContentOfOpenApiConfiguration() - Method in class ubic.gemma.rest.OpenApiTest

testInitializeAllOntologies() - Method in class ubic.gemma.core.ontology.OntologyLoadingTest

testInjectBeanDirectly() - Method in class ubic.gemma.core.context.AsyncBeanAutowiringTest

testInjectViaBeanFactory() - Method in class ubic.gemma.core.context.AsyncBeanAutowiringTest

testInjectViaServiceFactory() - Method in class ubic.gemma.core.context.AsyncBeanAutowiringTest

testInSubquery() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentFilterRewriteHelperServiceTest

testIntegrationWithFilterEnvironmentVariables(Path) - Method in class ubic.gemma.core.config.ConfigUtilsTest

testInteraction() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastTest

testInteractionBaseline() - Method in class ubic.gemma.model.analysis.expression.diff.BaselineTest

testIntMatrixToVectors() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrixUtilsTest

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

testInvalidEvent() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4ProviderTest

testInvalidFilter() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testIsAdmin() - Method in class ubic.gemma.core.security.SecurityUtilsTest

testIsAutomaticallyGenerated() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceTest

testIsBaselineA() - Method in class ubic.gemma.core.analysis.expression.diff.DetectFactorBaselineTest

testIsBaselineB() - Method in class ubic.gemma.core.analysis.expression.diff.DetectFactorBaselineTest

testIsBatchFactor() - Method in class ubic.gemma.model.expression.experiment.ExperimentFactorUtilsTest

testIsDeIncludeExcludeFactor() - Method in class ubic.gemma.model.expression.experiment.ExperimentFactorUtilsTest

testIsFreeText() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsTest

testIsFreeTextCategory() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsTest

testIsGoId() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyUtilsTest

testIsHuman() - Method in class ubic.gemma.persistence.service.genome.TaxonUtilsTest

testIsLog10Ratiometric() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testIsMouse() - Method in class ubic.gemma.persistence.service.genome.TaxonUtilsTest

testIsNotBaselineA() - Method in class ubic.gemma.core.analysis.expression.diff.DetectFactorBaselineTest

testIsPubliclyReadableExpressionIsBoundForAdmin() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

The isPublic filter emits AclQueryUtils.formIsPubliclyReadableExpression(String), which declares :aclQueryUtils_aoiClassId for every caller — including an administrator, whose restriction clause is only the (1=1) placeholder.

testIsPubliclyReadableExpressionIsBoundForAnonymous() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

testIsRat() - Method in class ubic.gemma.persistence.service.genome.TaxonUtilsTest

testIsSingleCellOnADetachedExperiment() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceDetachedEntityTest

testIsSingleNuclei() - Method in class ubic.gemma.core.loader.expression.geo.GeoSingleCellDetectorTest

testIsUserLoggedIn() - Method in class ubic.gemma.core.security.SecurityUtilsTest

testItReadsTheAccessionFromTheThawedExperiment() - Method in class ubic.gemma.apps.UpdateGeoSourceMetadataCliTest

🛑 The accession must be read from a THAWED experiment.

testItRefusesToRunWithoutBeingToldWhichHalf() - Method in class ubic.gemma.apps.VerifyPublicationEvidenceCliTest

🛑 There is no default mode, deliberately.

testItSkipsAnExperimentThatAlreadyHasOne() - Method in class ubic.gemma.apps.UpdateGeoSourceMetadataCliTest

Resumable: what already has a document is not refetched, so an interrupted run continues.

testItStoresTheDocumentAndNothingElse() - Method in class ubic.gemma.apps.UpdateGeoSourceMetadataCliTest

🛑 The safety rule.

testJson() - Method in class ubic.gemma.rest.OpenApiWebServiceTest

testJsonRepresentation() - Method in class ubic.gemma.rest.providers.OntologyTermValidationExceptionMapperTest

testJsonRepresentation() - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapperTest

testJvmStandardPropertiesIncludesTmpdir() - Method in class ubic.gemma.core.config.SettingsConfigTest

testKeepingTheDisplacedCurationCostsNoAuditEvent() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

Keeping the displaced curation has to be free in audit events.

testKeepPooledSample() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderTest

Trimmed fixture derived from the CELLxGENE "HypoMap" atlas (a unified single-cell atlas of the murine hypothalamus), which contains a "pooled" donor alongside the individual SRR donors.

testLabelEqualToTheTermsOwnAccessionIsNotAResolution() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

A resolver that hands back the term's own accession as its label has not resolved anything — it has told us it does not know the term.

testLabelMismatchRejected() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testLargeValuesKeepTheirMagnitude() - Method in class ubic.gemma.core.util.RoundingUtilsTest

testLastPageHasNoNextCursor() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoCursorTest

testLayeredAnnDataFile() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderTest

testLengthyDetail() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImplTest

Length audit event detail get abbreviated.

testLexicalCatalogueHitAlsoSinksBelowANonExactOntologyHit() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testLexicalCatalogueHitIsWorthOneTierLessThanAnOntologyHit() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testLike() - Method in class ubic.gemma.persistence.util.FilterTest

testLikeEscapesTheEscapeCharacterItself() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

The escape character must itself be escaped when it occurs in user data, or a value containing a tilde would silently change meaning.

testLikeRestrictionClause() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testLikeWithInvalidPropertyType() - Method in class ubic.gemma.persistence.util.FilterTest

testLikeWithUnderscoreEmitsAMatchingEscapeClause() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

A value containing an underscore must still match its own literal text.

testLimitArgIs5000ForGetDatasetsAnnotations() - Method in class ubic.gemma.rest.OpenApiTest

testLinearConversion() - Method in class ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionUtilsTest

testLinkingAParentTurnsOnEntriesInheriting() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterParentInheritanceTest

A child whose identity has entries_inheriting off gains nothing from a parent link — Spring only walks to the parent when the flag is on — so the linter has to set both.

testLintAclObjectIdentityLackingSecurable_emptyPath() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterServiceTest

Phase 3 gsec HQL deprecation: empty path for lintAclObjectIdentityLackingSecurable.

testLintAclObjectIdentityLackingSecurable_reportsDangling() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterServiceTest

Phase 3 gsec HQL deprecation: regression coverage for the converted JdbcTemplate-backed lintAclObjectIdentityLackingSecurable (dangling-AOI variant).

testLintChildWithoutParentAlsoSeesAPresentParentThatIsNotInherited() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterServiceTest

🛑 A SecuredChild whose parent is present AND CORRECT but which does not inherit reaches no other predicate, and grants nothing.

testLintSecurableLackingObjectIdentity_emptyAndHappyPath() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterServiceTest

Phase 3 gsec HQL deprecation: regression coverage for the converted JdbcTemplate-backed lintSecurableLackingObjectIdentity (bulk variant).

testLintSecurableLackingObjectIdentity_singleId() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterServiceTest

Phase 3 gsec HQL deprecation: regression coverage for the single-id variant of lintSecurableLackingObjectIdentity.

testLintSecuredNotChildWithParent_reportsWhenParentSet() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterServiceTest

Phase 3 gsec HQL deprecation: regression coverage for the converted JdbcTemplate-backed lintSecuredNotChildWithParent (bulk variant).

testLintSecuredNotChildWithParent_singleId_noAoi() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterServiceTest

Phase 3 gsec HQL deprecation: regression coverage for the single-id variant of lintSecuredNotChildWithParent.

testListDatasetMetadataFilesEmpty() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testListDatasetMetadataFilesReturnsAvailable() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testListIsSortedAndPaged() - Method in class ubic.gemma.rest.ExperimentSetsWebServiceTest

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

testLoad() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest

testLoadAllIdsDelegates() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

testLoadAllIdsOffsetLimitDelegates() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

testLoadAllOffsetLimitDelegates() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

testLoadAllTaxonDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testLoadAllValueObjects() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testLoadAllValueObjects() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testLoadAllValueObjectsOneTaxon() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

Test to ensure that if one taxon is present on an array only 1 string is returned with taxon name

testLoadAnalysisOnSubset() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoTest

This test covers the application of ACLs on the source experiment when a subset analysis is retrieved.

testLoadAndThawOrFailReturnsBmWhenFound() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceTest

testLoadAndThawOrFailThrowsWhenMissing() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceTest

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

testLoadBlacklistedValueObjects() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testLoadByIdAndVectorType() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoTest

testLoadByIdAndVectorTypeDelegates() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testLoadByIdDelegates() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testLoadCommandConsoleFormat() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceIntegrationTest

testLoadCompositeSequences() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testLoadContrastDetails() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoTest

testLoadData() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneConverterTest

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

testLoadFactorValueWithRegularCharacteristic() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoTest

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

testLoadGenes() - Method in class ubic.gemma.persistence.service.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

testLoadIds() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest

testLoadIdsWithNumberOfOldStyleCharacteristicsDelegates() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

testLoadIgnoreAclsDelegates() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

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

testLoadMetadata() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCliTest

testLoadMetadataFileLackingHeader() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCliTest

Convers old-style files that lack a header.

testLoadMetadataWithoutData() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCliTest

testLoadMicroRNAsDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testLoadMPSNames() - Method in class ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarizeTest

testLoadMultipleReferences() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testLoadOrFail() - Method in class ubic.gemma.persistence.service.AbstractServiceTest

testLoadOriginalPlatformValueObjectsForEE() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest

A dataset switched to a generic platform must be able to say what it was submitted on WITHOUT anyone walking its assays — the field lives on BioAssay, and reading it through the sample list costs the whole list for one line of header.

testLoadReference() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testLoadRNASeqData() - Method in class ubic.gemma.core.loader.expression.DataUpdaterTest

testLoadRNASeqDataWithMissingSamples() - Method in class ubic.gemma.core.loader.expression.DataUpdaterTest

testLoadSampleInDifferentOrder() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderTest

testLoadSpecificSamples() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderTest

testLoadSpecificSamples() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderTest

testLoadValueObject() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceTest

testLoadValueObject() - Method in class ubic.gemma.persistence.service.genome.TaxonServiceImplTest

testLoadValueObjectByIdReturnsNullWhenMissing() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testLoadValueObjectCarriesTheOtherPartsOfASplitStudy() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

A split part names its siblings on the dataset itself.

testLoadValueObjectLite() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceTest

testLoadValueObjectNamesThePlatformsAndTheSwitch() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

The dataset VO has to name the platform, not merely count it: a curator reading a dataset in the UI sees a blank platform line otherwise, and originalPlatform is the field that says a dataset was switched, which is a thing they check for.

testLoadValueObjectOfSetWithoutTaxon() - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoTest

A set whose members disagree on taxon is stored with no taxon at all, which is what lets a set span them.

testLoadValueObjectOfSetWithTaxon() - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoTest

Control: a set that DOES declare a taxon still reports it.

testLoadValueObjectOtherPartsIsEmptyForAnUnsplitDataset() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

An unsplit dataset gets an empty list, not null — one shape for every dataset.

testLoadValueObjectReportsNoSwitchWhenThereWasNone() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

The other half: a dataset nobody switched reports no original platform at all.

testLoadValueObjects() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceTest

testLoadValueObjects() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoTest

testLoadValueObjectsByBioAssay() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testLoadValueObjectsByCharacteristic() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testLoadValueObjectsByFactorValueCharacteristic() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testLoadValueObjectsByIds() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testLoadValueObjectsBySampleUsedCharacteristic() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testLoadValueObjectsExposesPrimaryPublicationDoi() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

A preprint primary publication (bioRxiv/DOI-namespace pubAccession, no PubMed ID) surfaces on the dataset VO as doi rather than pubmedId.

testLoadValueObjectsExposesPrimaryPublicationPubmedId() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

A PubMed-indexed primary publication surfaces on the dataset VO as pubmedId (and never doi), across both the filtered-list path (which join-fetches the publication) and the by-ids-with-relations path (which initializes it post-fetch).

testLoadValueObjectsWithExpressionExperimentDelegates() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testLoadValueObjectsWithPagination() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceTest

testLoadValueObjectWithoutSingleCellDataIsNotSingleCell() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

And an ordinary dataset says so, rather than leaving the client to infer it.

testLoadValueObjectWithSingleCellData() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

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

testLoadWithEmptyCollection() - Method in class ubic.gemma.persistence.service.common.description.DatabaseEntryDaoImplTest

testLoadWithExperimentalFactorDelegates() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

testLoadWithExperimentalFactorOrFailNeverLooksAtFactor_whenMissing() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

testLoadWithExperimentalFactorOrFailReturnsFv() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

testLoadWithExperimentalFactorOrFailThrowsWhenMissing() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

testLoadWithExperimentalFactorReturnsNullWhenMissing() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

testLoadWithExperimentAnalyzedReturnsNullWhenMissing() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceTest

testLoadWithOldStyleCharacteristicsDelegates() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceTest

testLoadWithRefreshCacheMode() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

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

testLocalLabelEqualToTheTermsOwnAccessionIsNotAResolution() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

The same guard for a local hit: a loaded ontology that has no rdfs:label often falls back to the id.

testLocalNameToTermId() - Method in class ubic.gemma.core.ontology.OntologyUtilsTest

The underscore spelling of an identifier, which is what a URI's tail and a term card both show.

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.ExpressionExperimentBibRefFinderNetworkTest

testLocatePubMedId() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderNetworkTest

The id behind the assertion above, without the second PubMed round trip.

testLock() - Method in class ubic.gemma.persistence.cache.StaticCacheKeyLockTest

testLockInterruptibly() - Method in class ubic.gemma.persistence.cache.StaticCacheKeyLockTest

testLockIsFreeThenHeldThenReleased() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

testLog() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrixTest

On a log-scale, zero is mapped to negative infinity.

testLog10Conversion() - Method in class ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionUtilsTest

testLog1p() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrixTest

In log1p, 0 is mapped back to 0.

testLog1PData() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceTest

testLog2Ratiometric() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testLog2ShouldDoNothing() - Method in class ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionUtilsTest

testLoggingInProgressUpdateCallbackDoesNotResultInLoggingRecursion() - Method in class ubic.gemma.core.logging.log4j.ProgressUpdateAppenderTest

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

testLogTransformedData() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceTest

testLogTransformedData() - Method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptiveTest

testLookupByMaximalSubset() - Method in class ubic.gemma.core.ontology.OntologyCacheTest

testLookupByMaximalSubsetWhenMinSubsetSizeIsSet() - Method in class ubic.gemma.core.ontology.OntologyCacheTest

testLowercaseKeywordsAreOrdinaryTokens() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyQueryRewriteTest

Lucene treats only UPPERCASE as operators, so lowercase is an ordinary token and must survive as one — `cell or` is a search for two words, and it answers 200 today.

testMain() - Method in class ubic.gemma.apps.PubMedSearcherIntegrationTest

Test method for AbstractCLI.executeCommand(CLIContext).

testMakeDatasetPrivateOnAlreadyPrivateIsNoOpNoEvent() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testMakeDatasetPrivateRecordsMakePrivateEvent() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testMakeDatasetPublicFlipsTheAcl() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testMakeDatasetPublicOnAlreadyPublicIsNoOpNoEvent() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

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

testMappingSurvivesTheFirstAcquirersKeyBeingCollected() - Method in class ubic.gemma.core.util.locking.FileLockManagerTest

The path→lock mapping must survive as long as any holder does — regardless of WHICH Path instance each caller used and of what the garbage collector decides.

testMarkAsNeedsAttention_idempotentWhenOpenTicketAlreadyExists() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionServiceTest

testMarkAsNeedsAttention_noEeNoTicket() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionServiceTest

testMarkAsNeedsAttention_opensTicketTargetingBothFvAndEe() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionServiceTest

testMarkedFactorValueWinsOverATermMatch() - Method in class ubic.gemma.core.analysis.expression.diff.BaselineSelectionTest

A marked factor value wins the baseline for its factor even when another value matches a control term, regardless of which of the two the factor happens to iterate first.

testMarkSampleOutlierViaPutEndpointFlipsIsOutlier() - Method in class ubic.gemma.rest.DatasetsDiagnosticsRestTest

PUT /samples/{bioAssayId}/outlier flips isOutlier=true on the targeted BioAssay.

testMas5() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testMas6() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest

testMaskedMatrix() - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrixTest

testMaskWithUnassignedCells() - Method in class ubic.gemma.core.analysis.singleCell.SingleCellMaskUtilsTest

testMatrixConversion() - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelExpressionDataDoubleMatrixTest

testMatrixIsCopiedRowByRow() - Method in class ubic.gemma.core.util.RoundingUtilsTest

testMatrixIsUntouchedWhenThereIsNothingToDrop() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsSampleSelectionTest

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

testMeasurement() - Method in class ubic.gemma.model.expression.experiment.FactorValueUtilsTest

testMeasurementWithCategory() - Method in class ubic.gemma.model.expression.experiment.FactorValueUtilsTest

testMeasurementWithoutCategory() - Method in class ubic.gemma.model.expression.experiment.FactorValueUtilsTest

testMerge() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeServiceTest

testMergedTermIsResolvedByItsAlternativeIdRecord() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

An ontology that MERGES X into Y frequently writes nothing on X — it records X in Y's hasAlternativeId.

testMergeQuantitationTypes() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtilsTest

testMergingHighlightWhenReplacingAResult() - Method in class ubic.gemma.core.search.SearchResultSetTest

testMergingHighlightWhenRetainingAnExistingResult() - Method in class ubic.gemma.core.search.SearchResultSetTest

testMessageSpelEvaluation() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Phase B-2: messageSpel must be evaluated against the method arguments (by parameter name) and the resolved string passed through to AuditTrailService.addUpdateEventWithPayload(Auditable, Class, String, String).

testMicroarrayGeneCountsAreNullWithoutAReport() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

Ask 4, microarray case.

testMineAsksForMineRatherThanFilteringAll() - Method in class ubic.gemma.rest.ExperimentSetsWebServiceTest

testMismatchedCursorSortSpecRejected() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoCursorTest

testMismatchRecordsNoCanonicalization() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testMissingBatchInformation() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentBatchInformationServiceTest

Cover various edge cases of missing batch information.

testMissingMembershipIsRefused() - Method in class ubic.gemma.rest.ExperimentSetsWebServiceTest

A missing datasetIds is not the same as an empty one, and must not silently empty the set.

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

testMultiAssay() - Method in class ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrixTest

testMultiAssayWithUnequalSize() - Method in class ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrixTest

testMultipleBaselinesInFactorIsAllowed() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

A factor MAY designate more than one baseline: a dataset holding two experiments has a reference level per experiment, and a curator has to be able to record that.

testMultipleStatements() - Method in class ubic.gemma.model.expression.experiment.FactorValueUtilsTest

testNamingARunCostsNoExtraAuditEvent() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

Naming a run must not cost an extra audit event.

testNative() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

testNativeAsAnonymous() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

testNativeAsUser() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest

testNcbiGeneUriSkipped() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testNcbiId() - Method in class ubic.gemma.rest.util.args.GeneArgServiceTest

testNcbiIdMergeRefusedWhenPreviousIdDoesNotMatch() - Method in class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceTest

Quirk 4.3 negative case: if previousNcbiGeneId does NOT contain our existing id, the service must refuse the update with IllegalStateException — we never silently overwrite an NCBI ID we didn't expect.

testNcbiIdMergeWithCommaListPreviousId() - Method in class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceTest

Quirk 4.3 (migration plan): NCBI ID merge with comma-separated previousNcbiGeneId.

testNegativeEvidenceAbsentForDescriptiveQuery() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

The confident negative must not be claimed when identity matching never ran — a descriptive query keeps its near-matches, so absence of a match there says nothing.

testNegativeIsRoundedNotTruncated() - Method in class ubic.gemma.core.util.RoundingUtilsTest

testNegativeValuesDoNotMeanLogTransformedWhenTheDataIsBackgroundSubtracted() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testNegativeValuesDoNotMeanLogTransformedWhenTheDataIsNormalized() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

Negative values are read as evidence of a log transformation.

testNegativeValuesStillMeanLogTransformedWhenNothingAccountsForThem() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

The narrowing must not swallow the case it was built for.

testNestedContrastsAreRoundedInsideAResult() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionResultPrecisionTest

The result value object carries its contrasts inline, so the nested statistics have to round too.

testNestedSubquery() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testNestedSubquery() - Method in class ubic.gemma.persistence.util.FilterTest

testNeverSwitchedHasNoOriginalPlatform() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest

A dataset that was never switched has no original at all.

testNewThread() - Method in class ubic.gemma.core.util.concurrent.ThreadUtilsTest

testNextAvailableName() - Method in class ubic.gemma.model.common.DescribableUtilsTest

testNoChannelReportsAMolecule() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterMoleculeTest

testNoColumnMatrix() - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrixTest

testNoExclusionKeepsEveryCategory() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

With no exclusion the same three rows all come back, so the filter is what removed the row above.

testNone() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testNonFiniteValuesAreLeftAlone() - Method in class ubic.gemma.core.util.RoundingUtilsTest

Math.round(NaN) is 0.0, which on a mean-variance or correlation payload reads as "this value is zero" rather than "not known".

testNonIdSortRejected() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoCursorTest

testNonParseOntologyFailureStaysAServerError() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

The converse: a failure with no parse error in the chain is a server fault and must stay a SearchException, so a broken index keeps answering 500 rather than blaming the query.

testNoOpCommitNamingARunStillMints() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A no-op commit that named a run still mints.

testNoOriginalPlatformLeavesTheFieldNull() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObjectTest

No switch, no original — the field stays absent rather than echoing the used platform.

testNoParametersAtAllIsAccepted() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest

testNoPublicationIsAnEmptyListNotAZero() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest

testNoPublicationIsMinusOneForTheSingleIdForm() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest

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

testNormalizeByValue() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

testNoSupportForIgnoringTransientIfNoStrategyIsSet() - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest

testNoSupportForIgnoringTransientIfNoStrategyIsSet() - Method in class ubic.gemma.core.security.acl.voter.AclEntryVoterTest

testNotEq() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentFilterRewriteHelperServiceTest

testNotEqualsID() - Method in class ubic.gemma.model.genome.biosequence.BioSequenceTest

testNotFound() - Method in class ubic.gemma.core.loader.expression.geo.fetcher2.GeoFetcherTest

testNotFoundEndpoint() - Method in class ubic.gemma.core.util.GemmaRestApiClientTest

testNotFoundFactory() - Method in class ubic.gemma.core.ontology.ols.OlsTermResolverImplTest

testNotIn() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentFilterRewriteHelperServiceTest

testNotInSubquery() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentFilterRewriteHelperServiceTest

testNoTwoSecuredChildrenShareAnOwnerQuery() - Method in class ubic.gemma.core.security.authorization.acl.AclClassMetadataTest

No two secured children may resolve their owner through the same query.

testNullArraysArePassedThrough() - Method in class ubic.gemma.core.util.RoundingUtilsTest

testNullCollection() - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoterTest

testNullIsPassedThrough() - Method in class ubic.gemma.persistence.service.expression.experiment.GeeqCormatMaskingTest

testNullIsTolerated() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsUriMigrationTest

Null in, null out — the VOs call this on nullable columns.

testNullPrecedenceOnCriteriaDao() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest

Exercises null-precedence (FIRST/LAST) via the Hibernate-6 JpaOrder vendor extension.

testNullStatisticsAreStillNull() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionResultPrecisionTest

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

testNumberOfCellsIsDeletedWhenOrphaned() - Method in class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVectorTest

This test ensures that the RawExpressionDataVectorNumberOfCells is properly deleted when orphaned (e.g.

testNumberOfCellsObjectIsReusedWhenAssigned() - Method in class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVectorTest

testNumCompositeSequencesArrayDesign() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testNumExperiments() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

testOboDefinitionWinsOverComment() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

The fallback is a fallback: an ontology that states a definition properly still wins, so a MONDO or UBERON term never reports an editorial comment as its definition.

testObsoletedCategoryAcceptsTheNameGemmaUses() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

EFO_0000408 is on Gemma's category list as disease, but EFO has obsoleted it and getCategoryTerms hands back EFO's live term, labelled obsolete_disease.

testObsoletedCategoryOffTheListAcceptsItsPreObsolescenceName() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

EFO_0000322 is NOT on the category list — CLO_0000031 is the canonical cell-line category — so it resolves through the loaded ontologies, and to obsolete_cell line.

testObsoleteMarkerIsNotStrippedInTheValueSlot() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

Categories only.

testObsoleteReplacementIsNotAutoCorrectable() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

A replacement that is itself obsolete is a chain for a curator to walk, not one to follow automatically.

testObsoleteTermUsedOnlyAsACategoryIsReported() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

A term used only as a CATEGORY has to be found too.

testObsoleteTermWithAssertedReplacementIsAutoCorrectable() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

The real shape of the problem: EFO obsoleted EFO_0000408 and named MONDO_0000001 as its replacement, so the correction is derivable rather than a curator's guess.

testOlsUnavailableYieldsUnverified() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testOmittingEvidenceOnARowThatHasSomeIsRefused() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A commit that omits supportingEvidence CLEARS it — the design section is full-record replacement.

testOneProlificSeedCannotSwampTheQuery() - Method in class ubic.gemma.core.search.source.OntologySearchSourceInferredRelationsTest

🛑 One seed may not swamp the query.

testOnlyTheNewlyProposedUriReachesTheDatabase() - Method in class ubic.gemma.rest.AnnotationsUsageCountCacheTest

The point of the cache: a keystroke that re-proposes a URI already counted must not send that URI back to the database.

TestOntologyConfig - Class in ubic.gemma.core.ontology

This class contains configuration for the ontology services used in tests

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

testOntologyTermCompletionsExpandToTermId() - Method in class ubic.gemma.rest.CompletionsWebServiceTest

testOntologyTermCompletionsPrefixMatchesOboId() - Method in class ubic.gemma.rest.CompletionsWebServiceTest

testOpenApiEndpoint() - Method in class ubic.gemma.rest.AnalysisResultSetsJerseyTest

The spec is ~600 kB, so it is gzipped — but only when the client asks.

testOpenApiEndpointIsNotCompressedWhenTheClientDoesNotAskForIt() - Method in class ubic.gemma.rest.AnalysisResultSetsJerseyTest

The other half of the contract: a client that does not advertise gzip is not sent a gzipped body.

testOpenFileThatDoesNotExist() - Method in class ubic.gemma.core.loader.util.hdf5.H5FileTest

testOpenTicketsForArrayDesign_delegatesToService() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testOpenTicketsForExpressionExperiment_delegatesToService() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testOrderBasicExperiment() - Method in class ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceTest

testOrderByExperimentalDesignB() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSortTest

testOrderExperimentSubSet() - Method in class ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceTest

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

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

testOrderSingleCellData() - Method in class ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceTest

testOriginalPlatformComesFromTheCacheWhenItIsThere() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObjectTest

And when the cache does know the original, it is reused rather than rebuilt.

testOriginalPlatformIsNotTakenFromTheUsedPlatformsCacheEntry() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObjectTest

The regression.

testOutlierSampleIsNotAnalyzed() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsSampleSelectionTest

testOverlappingLocks() - Method in class ubic.gemma.core.util.locking.ReadWriteFileLockTest

Locks are not allowed to overlap within the same JVM.

testOverwriteValueFromDelegate() - Method in class ubic.gemma.core.loader.expression.SequencingMetadataFileDataLoaderTest

testPack() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataTransformationsTest

testPadToNextPowerOfTwo() - Method in class ubic.gemma.core.util.ListUtilsTest

testPaired() - Method in class ubic.gemma.apps.RNASeqDataAddCliTest

testParallelAndSequentialCli() - Method in class ubic.gemma.apps.BatchProcessingCliTest

testParallelCli() - Method in class ubic.gemma.apps.BatchProcessingCliTest

testParallelFiltering() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurerTest

testParametersAnnotatedWithExplode() - Method in class ubic.gemma.rest.util.args.StringArrayArgTest

testParents() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test

testParents() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testParentsLeavesViaSubClassOfNullOnAUrilessTerm() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

No URI, nothing to match against the subClassOf-only walk — unknown, not "reached by a role".

testParentsMarksWhetherTheTermWasReachedBySubClassOfAlone() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

CHEBI's shape: vancomycin reaches glycopeptide by rdfs:subClassOf and antibacterial drug only by has_role, which Gemma follows as an additional property.

testParentsPopulatesUsageCount() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testParentsReportsZeroWhenNoExperimentsMatch() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testParentsSkipsCountLookupWhenAllTermsLackUris() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testParentsWhenInferenceTimeout() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testParentsWhenTermIsNotFound() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

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

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

testParse() - Method in class ubic.gemma.core.util.TsvUtilsTest

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.FilterTest

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

testParseCollection() - Method in class ubic.gemma.persistence.util.FilterTest

testParseCollection() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testParseCollectionOfDates() - Method in class ubic.gemma.persistence.util.FilterTest

testParseCollectionOfDateTimes() - Method in class ubic.gemma.persistence.util.FilterTest

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

testParseDataset() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtilsTest

testParseDatasets() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtilsTest

testParseDate() - Method in class ubic.gemma.persistence.util.FilterTest

testParseDate() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testParseDateTime() - Method in class ubic.gemma.persistence.util.FilterTest

testParseDateTimeWithNonUtcTimeZone() - Method in class ubic.gemma.persistence.util.FilterTest

testParseDateTimeWithoutZuluSuffix() - Method in class ubic.gemma.persistence.util.FilterTest

testParseDouble() - Method in class ubic.gemma.core.util.TsvUtilsTest

testParseDouble() - Method in class ubic.gemma.persistence.util.FilterTest

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

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

testParseEmptyCollection() - Method in class ubic.gemma.persistence.util.FilterTest

testParseEmptyCollectionRaisesMalformedArgException() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testParseEmptyTermsReturnsNull() - Method in class ubic.gemma.core.ontology.ols.OlsTermResolverImplTest

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

testParseFallsBackToFirstWhenNoDefining() - Method in class ubic.gemma.core.ontology.ols.OlsTermResolverImplTest

testParseFuzzyDate() - Method in class ubic.gemma.cli.util.OptionsUtilsTest

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.FilterTest

testParseInvalidCollection() - Method in class ubic.gemma.persistence.util.FilterTest

testParseInvalidOperator() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testParseIso8601Date() - Method in class ubic.gemma.cli.util.OptionsUtilsTest

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

PMID 37094356 carries a publisher-supplied KeywordList Owner="NOTNLM" whose first entry is a 1417-character abbreviations glossary.

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

testParseMaven311BuildTimestamp() - Method in class ubic.gemma.core.util.BuildInfoTest

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

testParseMixtureOfDateAndDateTime() - Method in class ubic.gemma.persistence.util.FilterTest

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

testParseNoMatchReturnsNull() - Method in class ubic.gemma.core.ontology.ols.OlsTermResolverImplTest

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

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

testParsePrefersDefiningOntology() - Method in class ubic.gemma.core.ontology.ols.OlsTermResolverImplTest

testParsePropertiesCollectionForPredicate() - Method in class ubic.gemma.core.ontology.ols.OlsTermResolverImplTest

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.FilterTest

testParseString() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testParseStringUnescapeQuote() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testParseSubqueryWithEmptyCollectionRaisesMalformedArgException() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testParseTermWithoutLabelReturnsNull() - Method in class ubic.gemma.core.ontology.ols.OlsTermResolverImplTest

testParseUnsupportedType() - Method in class ubic.gemma.persistence.util.FilterTest

testParseUri() - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtilsTest

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

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

testParseValue() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

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

testParseWithInvalidUtf8Characters() - Method in class ubic.gemma.core.loader.entrez.EntrezXmlUtilsTest

testParseWords() - Method in class ubic.gemma.cli.util.OptionsUtilsTest

testPatchQuantitationTypeCorrectsTheScale() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The case this was expanded for: a pre-2018 Affymetrix `rma value` recorded as LINEAR when RMA output is log2.

testPatchQuantitationTypeDoesNotTouchPreference() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Preference did not change, so no preferred-data event may be emitted for it.

testPatchQuantitationTypeRefusesRepresentation() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

representation describes the stored values rather than how to read them, so patching it would misdescribe the vectors.

testPatchQuantitationTypeRejectsANoOp() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A patch that asks for what the record already says changes nothing, so it is a bad request rather than a 200 with an audit event nobody can interpret.

testPatchTicket_delegatesToUpdateTicket() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testPathParameterIsNotAnAcceptedQueryParameter() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest

A path parameter is bound from the path, so it must not be mistaken for a declared query parameter, and its presence must not widen what the query string may carry.

testPendingIsNotAVerdict() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

There is no `pending` verdict -- an un-ruled set has no row -- so a client sending one is told rather than silently given a verdict nobody chose.

testPercent() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

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

testPercent1() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testPersistBioSequence() - Method in class ubic.gemma.persistence.service.genome.BioSequencePersistTest

testPersistGene() - Method in class ubic.gemma.persistence.persister.GenomePersisterTest

testPersistGeneProduct() - Method in class ubic.gemma.persistence.persister.GenomePersisterTest

testPersistingAnAnalysisDoesNotStealTheExperimentsFactors() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

🛑 Persisting an analysis must NOT re-parent the EXPERIMENT's factors onto the ANALYSIS, and deleting that analysis must not take their ACLs with it.

testPersistNewArrayDesign() - Method in class ubic.gemma.persistence.persister.PersisterTest

testPersistStatement() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoTest

testPipeline() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataTransformationsTest

testPipelineStatusAFailedDeaStaysFailedAfterADesignChange() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A DEA that FAILED and was then followed by a design change stays `failed`.

testPipelineStatusBatchInfoIsNeverStale() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

batchInfo comes from scan dates and file headers.

testPipelineStatusCarriesTheEffectiveTriageVerdictAndJudgeKind() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testPipelineStatusDeaGoesStaleWhenTheDesignChangedAfterIt() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A DEA that succeeded and then had the design change under it is still there, and its own event still says it succeeded — but it no longer describes the design it was computed from.

testPipelineStatusDeaStaysOkWhenTheDesignChangedBeforeIt() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A design change BEFORE the analysis is the normal order: the DEA already reflects it.

testPipelineStatusEveryDataDerivedStepGoesStaleOnADesignChange() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Every step but batchInfo is computed from the samples and the design, so a design change makes all of them stale -- not just the DEA.

testPipelineStatusGoesStaleWhenAnOutlierWasFlaggedAfterTheRun() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Flagging an outlier changes the analyzed sample set and no longer reprocesses the dataset inline, so the SampleRemovalEvent it records is what marks the computed results as owed a re-run.

testPipelineStatusTriageIsNullWhenNothingHasBeenTriaged() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Nothing triaged leaves both fields null rather than defaulting — that is how a caller tells "not triaged" from "triaged Fine", which a boolean could not express.

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

testPlatformAnnotationsRejectsAnUnknownFileType() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

An unknown type is a 400 naming the accepted values, not a silent fallback to the standard file — a caller asking for bioProcess must not be handed every GO term with nothing in the response to say so.

testPlatformAnnotationsServesEachFileType() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

The endpoint served the standard flavour unconditionally until the type parameter existed, so the _bioProcess / _noParents files that create() writes on every GO-enabled run were unreachable.

testPlatformArrayArg() - Method in class ubic.gemma.rest.util.args.EntityArrayArgsTest

testPlatformArrayArgEmptyRaises() - Method in class ubic.gemma.rest.util.args.EntityArrayArgsTest

testPlatformCompletionsGenericFlagSwitchesSource() - Method in class ubic.gemma.rest.CompletionsWebServiceTest

testPlatformCompletionsIncludeAlternateNames() - Method in class ubic.gemma.rest.CompletionsWebServiceTest

testPlatformCompletionsPrefixOnShortName() - Method in class ubic.gemma.rest.CompletionsWebServiceTest

testPlatformDatasets() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

testPlatformElementRestrictsToTheRequestedProbe() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

Regression guard for the {probes} restriction being dropped.

testPlatformElements() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

testPlatformElementsHonoursNameFilter() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

A user filter= must narrow the listing.

testPlatformElementsWithGenesYieldsEmptyListNotNull() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

withGenes=true must set the field on every row, and to an EMPTY list rather than null for a probe with no gene mapping — otherwise NON_NULL elides it and the client cannot tell "maps to nothing" from "not requested".

testPlatformElementsWithoutGenesLeavesFieldNull() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

Without the opt-in the field stays null, so it elides from the wire entirely — the existing default response shape is unchanged for callers that never ask.

testPlatformElementsWithSequence() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

testPlatformsOriginalIsEmptyRatherThanEchoingTheCurrentPlatform() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

An unswitched dataset answers with an empty list, never with its current platform.

testPlatformsOriginalRoutesToTheOriginalPlatforms() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

`?original=true` must actually route.

testPlatformSwitchingWithExpressionData() - Method in class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchTest

testPlatformVoNamesItsMergeTargetAndItsMergees() - Method in class ubic.gemma.rest.PlatformsWebServiceTest

Ask 3: a mergee must be able to NAME its merge target.

testPopulateFactorValuesSeesOnlyTheSamplesGiven() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtilsSampleSelectionTest

Level counting must use the samples that will be modelled.

testPredicateOutsideTheVocabularyStillNeedsToResolve() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

A predicate URI that is NOT in the sanctioned list still has to ground somewhere.

testPredicateResolvesFromGemmasOwnRelationVocabulary() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

A predicate is checked against Gemma's OWN vocabulary, not against whatever ontologies happen to be loaded.

testPreflightAcceptsAnUnfamiliarBaselineRelevanceValue() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A word outside the three in use round-trips instead of 400ing.

testPreflightAcceptsTheBaselineRelevanceHint() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The baseline-relevance hint is accepted on the write side and reaches the design mapper.

testPreflightCurationDesignIsDryRun() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testPreflightCurationIsDryRun() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testPreflightDesignWritesNothing() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

testPreflightEmitsNoAuditEvent() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A preflight must not audit.

testPreflightIsNotGatedByAnotherCuratorsLock() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A preflight writes nothing, so it is deliberately exempt.

testPreflightIsNotRejected() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest

A CORS preflight is sent to the URL of the request it is asking about, query string included, so rejecting it would take the browser client down rather than the bad parameter.

testPreflightKeepsNoSnapshot() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A preflight writes nothing, so there is nothing to keep and no row left behind to explain.

testPreflightOmitsTheDesignReportWhenThereIsNoDesignSection() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

🛑 A commit with no design section reports designReport ABSENT, not empty.

testPreflightRejectsDecoratedTagKeepMarker() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The preflight shares the mapper, so it refuses exactly what the commit refuses.

testPreflightRejectsUngroundedTerm() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Preflight enforces the same gate, so a client catches the failure on the dry run.

testPreflightRejectsUnknownEvidenceCode() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The preflight enforces the same gate, so a client catches a bad code on the dry run.

testPreflightReportsTheForceGateItDoesNotTrip() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A preflight REPORTS the force gate it deliberately does not trip.

testPreflightRequest() - Method in class ubic.gemma.rest.servlet.CorsFilterTest

testPreflightRequestWithCredentials() - Method in class ubic.gemma.rest.servlet.CorsFilterTest

testPreflightRequestWithCredentialsAndInvalidOrigin() - Method in class ubic.gemma.rest.servlet.CorsFilterTest

testPreflightRequestWithMaxAge() - Method in class ubic.gemma.rest.servlet.CorsFilterTest

testPreflightWithRunRefMintsNothing() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A preflight writes nothing, so it mints no row either — the run reference is only shape-checked.

testPrepareContext() - Method in class ubic.gemma.core.context.SpringContextUtilsTest

testPrepareContextDoesNotFailFastWhenProfileExplicitlyActive() - Method in class ubic.gemma.core.context.SpringContextUtilsTest

testPrepareContextFailsFastWhenNoProfileActive() - Method in class ubic.gemma.core.context.SpringContextUtilsTest

testPrepareContextFallsBackToDevWhenAllowDevFallbackIsSet() - Method in class ubic.gemma.core.context.SpringContextUtilsTest

testPrepareContextWhenMoreThanOneEnvironmentProfileIsActive() - Method in class ubic.gemma.core.context.SpringContextUtilsTest

testPrepareContextWithIncorrectSecurityContextHolderStrategyIsSet() - Method in class ubic.gemma.core.context.SpringContextUtilsTest

testPresentAbsent() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtilsTest

testPreviewAddingAWholeFactorInvalidatesTheExistingAnalyses() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

Adding a WHOLE factor used to mark nothing: the old rule (c) only fired for a new value under an EXISTING factor, and a brand-new factor has no id and no analyses of its own.

testPreviewAddingNewFvFlagsAnalysesOnTheParentFactor() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testPreviewBlocksAssignmentReferencingUnknownFv() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testPreviewBlocksTypeChangeWhenFactorHasValues() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testPreviewBlocksUnknownBiomaterial() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testPreviewBlocksUnknownFactorId() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testPreviewBlocksUnknownFactorValueId() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testPreviewCountsABiomaterialOnceWhenItBothLosesAndGainsAFactorValue() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

A biomaterial that both loses a factor value in the payload and gains a deferred one from the plan is ONE changed biomaterial.

testPreviewCountsBiomaterialsBoundToAFactorValueTheCommitCreates() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

🛑 A biomaterial bound to a factor value the commit CREATES cannot be seen in the design payload at all: an assignment carries factor value ids, and a new factor value has none until the first apply pass makes it.

testPreviewDatasetDesignChangeNoOp() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testPreviewDatasetDesignChangeReportsDeletions() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testPreviewDatasetDesignChangeWithBlockers() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testPreviewDatasetDesignChangeWithEmptyBodyIs400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testPreviewDatasetDesignChangeWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testPreviewDeletingAFactorCascadesToItsValuesAndAnalyses() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testPreviewDeletingAFactorValueFlagsDependentAnalyses() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testPreviewDeletingContinuousFactorReportsItsMeasurementValues() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

W3 — deleting a continuous factor takes its measurement-bearing factor values with it, and the preflight says so before the caller commits.

testPreviewDoesNotReportAnEchoOfTheSerializedProjection() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

🛑 The shape an HTTP client actually round-trips.

testPreviewEchoingTheWireFormIsNotAnEdit() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

And the echo is a no-op: before the halves were re-joined, one entry became two content keys neither of which matched the stored statement, so an unedited round-trip counted as an edit on every compound statement in the design.

testPreviewEditingStatementOnKeptFvDoesNotFlagAnalyses() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testPreviewFlippingABaselineInvalidatesTheAnalyses() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

A baseline flip moves no structural counter, so it rode through as "safe" and quietly falsified the analysis: the stored result set still names the OLD reference, and every contrast is relative to it.

testPreviewIgnoresADeferredBindingForAForeignBiomaterial() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

The plan may name a biomaterial that is not part of this experiment.

testPreviewInvalidationIsDatasetWideNotPerFactor() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

Invalidation is DATASET-wide, not per-factor: a sibling factor's analyses go too, because the design they were fitted against changed.

testPreviewNoChange() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testPreviewReassigningBiomaterialFlagsAnalyses() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testPreviewRefusesAThirdEntryForOneStatementId() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

A statement holds two objects and no more, so a third entry for one id is refused rather than dropped.

testPreviewRelabellingAKeptFactorValueDoesNotInvalidateAnything() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

The exclusion, and the only one: relabelling a kept factor value does not move a sample, a level or a reference, so the analysis still describes what it described.

testPreviewReportsARenameOfAKeptFactor() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

The factor half of the same gap: renaming a kept factor touches no factor value at all.

testPreviewReportsAReTermOfAKeptFactorValue() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

A re-term of a kept factor value is a change the report has to be able to state.

testPreviewReportsNoUpdatesWhenNothingIsEdited() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

The other half of the rule: a proposal that changes nothing reports nothing.

testPreviewSubsetWithLostAnchorIsFlaggedButNotBlocked() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

Re-enabled 2026-08-16.

testPreviewSubsetWithLostAnchorRequiresForce() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

A stranded subset requires the same explicit consent as the analysis cascade.

testPreviewWithoutConsequencesDoesNotRequireForce() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

A change with no analyses to delete and no stranded subsets proceeds without consent.

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.FilterTest

testPriorCurationHonoursLeaveOneOut() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoTest

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

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

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

testProductionOverloadReadsSystemEnv() - Method in class ubic.gemma.core.config.ConfigUtilsTest

testProgressData() - Method in class ubic.gemma.core.job.progress.ProgressDataTest

testProgressLogging() - Method in class ubic.gemma.core.logging.log4j.ProgressUpdateAppenderTest

testPropertyPlaceholderConfigurer() - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test.GeneOntologyService2TestContextConfiguration

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

Minimalistic placeholder configurer for usage in tests.

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

testPropertyStartingWithGzipMagicNumber() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testProtocolCompletionsDedup() - Method in class ubic.gemma.rest.CompletionsWebServiceTest

testProvenanceRecordsWhatAssertedTheReplacement() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionServiceTest

testPvalueDistributionAdvertisesTheStoredHistogramContract() - Method in class ubic.gemma.rest.OpenApiTest

GET /resultSets/{id}/pvalueDistribution serves the stored histogram.

testQuantileNormalizedData() - Method in class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilterTest

testQuantitationTypeDedupWithinSingleEePersist() - Method in class ubic.gemma.persistence.persister.EeWriteServiceImplQtDedupTest

Three equal-by-(name, description) QT instances hitting the helper with one shared local map must all resolve to the SAME persistent QT entity, and only one QUANTITATION_TYPE row must be inserted.

testQuantitationTypesWithDifferentDescriptionsAreNotDeduped() - Method in class ubic.gemma.persistence.persister.EeWriteServiceImplQtDedupTest

Distinct-by-(name, description) QT instances hitting the helper with one shared map must each produce a separate persistent row — the dedup is keyed on (name, description), not on object identity.

testQueryEst() - Method in class ubic.gemma.core.goldenpath.GoldenPathQueryTest

testQueryMrna() - Method in class ubic.gemma.core.goldenpath.GoldenPathQueryTest

testQueryNoResult() - Method in class ubic.gemma.core.goldenpath.GoldenPathQueryTest

testQuiet() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationProviderTest

testRandomCountMatrix() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testRandomLinearMatrix() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testRandomLnTransformedCountMatrix() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testRandomLog1pTransformedCountMatrix() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testRandomLog2Matrix() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testRandomLogTransformedCountMatrix() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testRandomRatiometricLog2Matrix() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testRandomSuspiciousLog2Matrix() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

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

testRawDataset() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderTest

testRawX() - Method in class ubic.gemma.core.loader.util.anndata.AnnDataTest

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

testRecalculateBatchInfoWithMissingDesign() - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceTest

testRecalculateExperimentBatchInfoAsAdmin() - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceTest

testRecomputeDatasetGeeqDefaultModeIsAll() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRecomputeDatasetGeeqIncludesLastComputed() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRecomputeDatasetGeeqWithSpecificMode() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRecomputeDatasetGeeqWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsRestTest

testRecomputeDatasetGeeqWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRedirection() - Method in class ubic.gemma.rest.AnalysisResultSetsJerseyTest

testRedoAggregate() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceTest

testRedoAnalysis() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testRedoDatasetDifferentialAnalysis() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRedoDatasetDifferentialAnalysisWithUnknownAnalysisIs404() - Method in class ubic.gemma.rest.DatasetsRestTest

testRedoDatasetDifferentialAnalysisWithUnknownAnalysisIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testReentrant() - Method in class ubic.gemma.core.util.locking.FileLockManagerTest

testReentrantLocking() - Method in class ubic.gemma.core.util.locking.ReadWriteFileLockTest

testReentrantLockingWithConcurrency() - Method in class ubic.gemma.core.util.locking.ReadWriteFileLockTest

testRefreshDataset() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRefreshDatasetNotFound() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRefreshDatasetReportsOnly() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRefreshDatasetVectorsOnly() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRefreshDatasetWithDefaultsDoesNotEvictCaches() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRelabelCellTypes() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testRelatedButDifferentAssaysAreLeftAsOther() - Method in class ubic.gemma.core.loader.expression.geo.GeoLibraryStrategyTest

...and the detector stays narrow.

testRelationsAppliesTheSubjectBreadthBarByDefaultForADataset() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

The bar defaults ON for a dataset-seeded read, where the fan-out was measured.

testRelationsExcludesRefutedByDefault() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

And it stays off unless asked, so exposing it changed no existing caller's results.

testRelationsHonoursIncludeRefutedWhenAsked() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

The other half: on /relations the parameter does reach the query, or it is decorative.

testRelationsPassesTheSubjectBreadthBarToTheQuery() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

A query parameter that never reaches the query is decorative and nothing fails — the same shape the two tests above pin for includeRefuted.

testReloadDelegates() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceTest

testRemove() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDeleteTest

testRemove() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoTest

testRemove() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoTest

testRemove() - Method in class ubic.gemma.persistence.service.genome.GeneDaoTest

testRemoveAllRawDataVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testRemoveAllRawDataVectorsDelegates() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceTest

testRemoveByBasisClearsOnlyThatBasis() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

A rebuild clears the basis it is rebuilding, so a relation whose source annotation was deleted does not outlive it.

testRemoveByCompositeSequence() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoTest

testRemoveDatasetAnnotation() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testRemoveDatasetAnnotationNotFound() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testRemoveDatasetAnnotationTag() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRemoveDatasetAnnotationTagNotFound() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRemoveDatasetDifferentialAnalysis() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRemoveDatasetDifferentialAnalysisWithUnknownAnalysisIs404() - Method in class ubic.gemma.rest.DatasetsRestTest

testRemoveDatasetDifferentialAnalysisWithUnknownAnalysisIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRemovedCollectionElementsAreNotHashed() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProviderTest

Hashing an element triggers a proxy initialization with Hibernate, which is not desirable.

testRemoveDetachedStatementFromDetachedFactorValue() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceTest

testRemoveExperimentInSet() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testRemoveExperimentInSingletonSet() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testRemoveExperimentWithSharedBioMaterial() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testRemoveMember_happyPath() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testRemoveMember_unknownUser_throws404() - Method in class ubic.gemma.rest.GroupsWebServiceTest

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

testRemoveProcessedDataVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testRemoveProcessedDataVectorsDelegates() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceTest

testRemoveRawDataVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testRemoveRawDataVectorsTwoArgDefaultsKeepDimensionFalse() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceTest

testRemoveRawDataVectorsWhenQtIsUnknown() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testRemoveRawDataVectorsWithDimension() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testRemoveRawDataVectorsWithNumberOfCells() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testRemoveStatement() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceTest

testRemoveUnrelatedStatementRaisesAnException() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceTest

testRemoveVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testRemoveVectorsSharingADimension() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testRemoveWhenBioAssayIsInADimensionThatIndexesData() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoTest

The reverse: vectors index their values by the assay's position in the dimension, so neither the assay nor the dimension may be touched.

testRemoveWhenBioAssayIsInADimensionThatIndexesNoData() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoTest

A dimension that indexes no data is garbage once the subset that owns its assays is gone; leaving it behind strands the assays forever, since the guard below would then refuse to ever delete them.

testRemoveWhenBioAssayIsOwnedByTheSubset() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoTest

testRemoveWhenBioAssayIsUsedByAnotherSubSet() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoTest

An assay can sit in a cell-type subset and in a further subset of it.

testRemoveWhenBioMaterialIsUsedByAnotherBioAssay() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoTest

testRemoveWithDummyGeneProducts() - Method in class ubic.gemma.persistence.service.genome.GeneDaoTest

testRemoveWithSubBioMaterials() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoTest

testRemovingAnAnalysisTakesItsFilesWithIt() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskImplTest

The rule: the removal goes through deleteAnalysis, with this experiment and this analysis, and the row-only remove is not called at all.

testReorder() - Method in class ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataCreateServiceTest

testRepeatedDesignElements() - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrixTest

testRepeatedElements() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrixTest

testRepeatedMeasuredRegion() - Method in class ubic.gemma.core.util.StopWatchUtilsTest

testRepeatedReloadOfBioAssayDimension() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionCacheStalenessTest

Reloading the same mutable="false" BioAssayDimension twice after flush + clear must give equivalent state both times.

testRepeatScan() - Method in class ubic.gemma.core.analysis.sequence.RepeatScanTest

testRepetitiveValuesWithCountData() - Method in class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilterTest

testRepetitiveValuesWithNonZeroVariance() - Method in class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilterTest

testReplaceAllRawDataVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testReplaceAllRawDataVectorsCreatesTransientCollaborators() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceTest

testReplaceAllRawDataVectorsRejectsEmptyInput() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceTest

testReplaceAllRawDataVectorsRejectsMultiplePreferredQts() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceTest

testReplaceAllRawDataVectorsWithMoreThanOnePreferredQt() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImplTest

testReplaceDatasetAnnotationsAppliesDiff() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testReplaceDatasetAnnotationsCarriesSupportingEvidence() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testReplaceDatasetAnnotationsIdempotentNoOp() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testReplaceDatasetDesignHappyPath() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testReplaceDatasetDesignNoOpEcho() - Method in class ubic.gemma.rest.DatasetsRestTest

testReplaceDatasetDesignReturns409WhenForceRequired() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testReplaceDatasetDesignReturnsBadRequestOnBlockers() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testReplaceDatasetDesignWithEmptyBodyIs400() - Method in class ubic.gemma.rest.DatasetsRestTest

testReplaceDatasetDesignWithEmptyBodyIs400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testReplaceDatasetDesignWithForceAppliesEvenWithCascade() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testReplaceDatasetDesignWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsRestTest

testReplaceDatasetDesignWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testReplacedByChainIsFollowedToACurrentTerm() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

A term replaced by a term that was itself replaced is ordinary ontology housekeeping.

testReplacementWrittenAsALiteralIsRead() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

EFO writes IAO:0100001 as a LITERAL whose text is the URI, where MONDO/OBI/CL/CLO write a RESOURCE.

testReplaceProcessedDataVectors() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceTest

testReplaceProcessedDataVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testReplaceProcessedDataVectorsReusingTheSameQT() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testReplaceProcessedDataVectorsWithDetachedExperiment() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testReplaceRawDataVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testReplaceRawDataVectorsWithNewDimension() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testReplaceVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testReporting() - Method in class ubic.gemma.apps.BatchProcessingCliTest

testRequestWithCredentials() - Method in class ubic.gemma.rest.servlet.CorsFilterTest

testRequestWithOrigin() - Method in class ubic.gemma.rest.servlet.CorsFilterTest

testRequestWithoutOrigin() - Method in class ubic.gemma.rest.servlet.CorsFilterTest

testReservedEventName() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4ProviderTest

testReservedSliceIsReturnedToConventionalHitsWhenUnused() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

Reserving a slice must not cost a result when there is nothing to put in it: with no supplementary source contributing, the conventional hits still fill the whole window.

testResolveFabricatedTermReturnsNull() - Method in class ubic.gemma.core.ontology.ols.OlsTermResolverIntegrationTest

testResolveRealTerm() - Method in class ubic.gemma.core.ontology.ols.OlsTermResolverIntegrationTest

testResolvesFromFileWhenFileSuffixIsSet(Path) - Method in class ubic.gemma.core.config.ConfigUtilsTest

testRestByDefault() - Method in class ubic.gemma.persistence.util.EntityUrlBuilderTest

testRestoreAfterADeleteReturnsContentUnderANewId() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The identity caveat, pinned as behaviour rather than left in a doc comment.

testRestoreBringsBackADroppedPublicationWithItsBasis() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A commit that drops a paper is undone from its own backup, and the paper comes back with the basis it had.

testRestoreOfASnapshotWithSurvivingTagsIsNotRefusedAsDecorated() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

A restore replays a SNAPSHOT, and a snapshot records the content of every row — including the rows the restore only has to leave alone.

testRestoreRemovesAFactorTheAgentAddedAfterTheSnapshot() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A restore has to undo additions too, not just edits.

testRestoringANonSnapshotIsRejected() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

Only a SNAPSHOT can be restored — replaying some other tool's payload shape as a commit is a 400.

testRestoringAnUnchangedDatasetIsANoOp() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

Restoring an unchanged dataset changes nothing: the snapshot round-trips as a no-op.

testRestrictionClauseWithCollection() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testRestrictionClauseWithNullObjectAlias() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testRestrictionClauseWithNullRequiredValue() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testResultObject() - Method in class ubic.gemma.core.search.SearchResultTest

testResultObjectIsRetainedWhenReplacingAResult() - Method in class ubic.gemma.core.search.SearchResultSetTest

testResultObjectWithNullId() - Method in class ubic.gemma.core.search.SearchResultTest

testResultSetOfPrivateExperimentIsNotReadableAnonymously() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

A result set of a private experiment must not be readable anonymously.

testResultSetReflectsLaterAddedResultAcrossSessions() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.AnalysisResultSetCacheStalenessTest

Reproduction of HB6 audit finding #6: ensure that a DifferentialExpressionAnalysisResult written to an existing ExpressionAnalysisResultSet after a flush+clear is visible when the result set is reloaded from a fresh session.

testResultStatisticsSerializeRounded() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionResultPrecisionTest

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

testRetrieveDetailedGeoRecords() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserTest

Exercises getting details

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

testRetryableMethod() - Method in class ubic.gemma.persistence.util.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

testReturnsFirstWhenMultiple() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest

testReturnsNullWhenNeitherIsSet() - Method in class ubic.gemma.core.config.ConfigUtilsTest

testReuseIsRefusedWhenTheExistingSubSetDoesNotCoverTheSamples() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetServiceTest

Reuse is refused when the existing subset does not cover the samples being aggregated — aggregating over the wrong assays is worse than the duplicate row the reuse prevents.

testRewrite() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataTransformationsTest

testRewriteIsIdempotentAndCollapsesWhitespace() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyQueryRewriteTest

Idempotent, and surrounding/repeated whitespace collapses — the rewrite runs on whatever the caller sent, including a query that already reads as an AND chain.

testRibosomeProfilingSubmittedAsOther() - Method in class ubic.gemma.core.loader.expression.geo.GeoLibraryStrategyTest

🛑 The GSE288755 case: titled … Ribo-seq replicate #1, declared OTHER.

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

testRoundedValueSerializesShort() - Method in class ubic.gemma.core.util.RoundingUtilsTest

The point of the exercise: four significant digits has to actually shorten the serialized form, or the bytes on the wire do not move.

testRouteHoldingUriInfoAcceptsAnythingItIsGiven() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest

testRunAsAdmin() - Method in class ubic.gemma.core.security.SecurityUtilsTest

testRunDatasetBatchInformationFetch() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRunDatasetBatchInformationFetchWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsRestTest

testRunDatasetDiagnosticsSetsFlag() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRunDatasetDiagnosticsWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsRestTest

testRunDatasetDifferentialAnalysisRejectsSubsetFactorInFactorIds() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRunDatasetDifferentialAnalysisRejectsUnknownFactorId() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRunDatasetDifferentialAnalysisWithoutBodyUsesAllNonBatchFactors() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRunDatasetDifferentialAnalysisWithoutDesignIs400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRunDatasetDifferentialAnalysisWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsRestTest

testRunDatasetGeeqWithModeBatch() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRunDatasetPreprocess() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRunDatasetPreprocessWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsRestTest

testRunDatasetPreprocessWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRunDatasetSwitchPlatformUnknownShortNameIs400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRunDatasetSwitchPlatformWithoutBodyAutoDetectsMerged() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRunDatasetSwitchPlatformWithTargetShortName() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testRunProvenanceWithoutRunIdIsRejected() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

Provenance with no run to hang it off cannot be stored.

testSameJudgeRulingTwiceLeavesOneRow() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A judge has one standing ruling, so changing your mind edits rather than accumulates.

testSameRunCommittingTwiceKeepsOneRow() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

One run committing the same dataset twice keeps one row.

testSameTagComparesContentNotType() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsTest

Identity is the content, not the Java type.

testSameTagPlain() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsTest

testSameTagStatementComparesPredicateAndObject() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsTest

testSameTagStatementComparesSecondPair() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsTest

testSample() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataTransformationsTest

testSampleCorrelationBestFallsBackToFullAndSaysSo() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

No regressed matrix: `best` falls back to the full one and says so, rather than implying regression.

testSampleCorrelationFullIsServedOnRequestEvenWhenRegressedExists() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

`matrix=full` takes the full one even when a regressed one exists — that is the whole point.

testSampleCorrelationRegressedDoesNotFallBack() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

`matrix=regressed` never silently substitutes the full one; a dataset without one 404s.

testSampleCorrelationSaysWhichMatrixItReturned() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The default is `best`, and the response says which of the two it actually got.

testSampleCorrelationValuesAreRoundedAndKeepNaN() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

Three decimals, and a masked cell stays masked.

testSaveStatement() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceTest

testSaveWithTransientEntity() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testSavingADraftDoesNotTakeALockYouDoNotHold() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A save by someone who holds no lock takes none -- a refresh must never become an acquire.

testSavingADraftExtendsTheCuratorsLock() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

Editing holds the lease.

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

testSearchableProperties() - Method in class ubic.gemma.rest.OpenApiTest

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

testSearchAndSearchAndRetrieveByDoi() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearchTest

testSearchAnnotationsAttributesAFreeTextRowFromItsOwnLabel() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsAttributesLabelPrefixForTypeahead() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsAttributesLabelTokensForNonEqualPartialLabel() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsAttributesPreferredLabelMatch() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsAttributesSynonymMatch() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsAttributesSynonymTokensWhenLabelLacksTokens() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsBatchEmptyReturns400() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsBatchResolvesEachLabelIndependently() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsCanonicaliesInputOrderByUri() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsCanonicaliseDoesNotRegressNonHyphenatedQueries() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsCellLineTiebreakerDoesNotAffectNonCellLineQueries() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsDedupesGenesAcrossProbes() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsDefaultLimitIs20() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsDropsGeneFanoutWhenURIAlreadyInOntologyResults() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsEnrichesTopNWithDefinitionAndParents() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsExactLabelFilterRespectsHyphenAndCellSuffixCanonicalForm() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsExactOntologyLabelOutranksGeneAliasCollision() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsHyphenInsensitiveMec2DashFindsEfoBareLabel() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsHyphenInsensitiveMec2FindsCloCellLine() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsIncludeGenesFalseSkipsGeneFanout() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsLeavesEnrichmentNullForPostTopN() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsLimitBelow1Returns400() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsLimitOver100Returns400() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsPopulatesPriorCategoriesFromCorpusHistory() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsPopulatesUsageCount() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsPrefersCloOverEfoForBareCellLineQuery() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsPrefersCloOverEfoForCellSuffixQuery() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsPrefixesFilterAppliesBeforeRanking() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsPrefixesFilterRespectsLimit() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsRejectsEmptyQuery() - Method in class ubic.gemma.rest.AnnotationsRestTest

testSearchAnnotationsReportsTheTallyItIsGiven() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

Counting one experiment once, however many annotation rows or levels carry the term, is now the database's job — countExperimentsByUris does it with a count(distinct ...) over the union of URI columns, so there is no per-class map left for this layer to collapse.

testSearchAnnotationsRespectsExplicitLimit() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsReturnsUsageCountField() - Method in class ubic.gemma.rest.AnnotationsRestTest

testSearchAnnotationsSurfacesGeneByAlias() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsSurfacesGeneByOfficialName() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsSymbolMatchStillPrependsAboveOntologyHits() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsUnknownRankReturns400() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchAnnotationsUpstreamReturns400WhenUrlUnset() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSearchGenes() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSearchTest

testSearchGeoRecords() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserTest

testSearchGeoRecordWithMeshHeadings() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserTest

testSearchingADiseaseReachesTheGenotypeThatStandsForIt() - Method in class ubic.gemma.core.search.source.OntologySearchSourceInferredRelationsTest

The acceptance criterion: searching the disease reaches the genotype that stands for it.

testSearchTaxonDatasets() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

testSecondCuratorIsRefusedByNameThenMaySteal() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A second curator is refused with a 409 that NAMES the holder, then gets it with ?steal=true.

testSecondPredicateResolvesFromGemmasOwnRelationVocabulary() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

The same for the second predicate slot — statements carry two.

testSecondRunReusesSubSetsInsteadOfCreatingASecondSet() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetServiceTest

A second aggregation run must reuse the subsets the first run left behind.

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

testSecureJob() - Method in class ubic.gemma.core.job.SchedulerSecurityTest

TestSecureJob() - Constructor for class ubic.gemma.core.job.SchedulerSecurityTest.TestSecureJob

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

testSeedsCoverSubjectObjectAndSecondObject() - Method in class ubic.gemma.core.ontology.providers.chebi.ChebiSeedResolverSlotsTest

testSeedsStayBoundedToChebiUrisTheCorpusUses() - Method in class ubic.gemma.core.ontology.providers.chebi.ChebiSeedResolverSlotsTest

Widening the slots must not widen the seed set beyond what the corpus actually annotates — that is the whole bargain of a slim.

testSelectColumns() - Method in class ubic.gemma.core.datastructure.sparse.CompRowMatrixUtilsTest

testSelectRows() - Method in class ubic.gemma.core.datastructure.sparse.CompRowMatrixUtilsTest

testSendAccountCreatedEmail() - Method in class ubic.gemma.core.util.MailServiceTest

testSendPasswordResetEmail() - Method in class ubic.gemma.core.util.MailServiceTest

testSendTaskCompletedEmail() - Method in class ubic.gemma.core.util.MailServiceTest

testSendWithNullReference() - Method in class ubic.gemma.core.mail.MailEngineImplTest

testSendWithUnresolvableTemplate() - Method in class ubic.gemma.core.mail.MailEngineImplTest

testSendWithUnresolvableVariables() - Method in class ubic.gemma.core.mail.MailEngineImplTest

testSeparateSampleFromAssayIdentifiers() - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserMetadataWriterTest

testSequentialCli() - Method in class ubic.gemma.apps.BatchProcessingCliTest

testSerializerEmitsRoundedNumberAndSkipsNull() - Method in class ubic.gemma.core.util.RoundingUtilsTest

testSerializerLeavesTheInMemoryValueExact() - Method in class ubic.gemma.core.util.RoundingUtilsTest

testServer() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlatTest

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.job.progress.ProgressDataTest

testSetDone() - Method in class ubic.gemma.core.job.progress.ProgressDataTest

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

testSetPercent() - Method in class ubic.gemma.core.job.progress.ProgressDataTest

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

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

testSettingsDescriptions() - Method in class ubic.gemma.core.config.SettingsConfigTest

testSharedLockIsARealFileLockOnceTheDirectoryExists() - Method in class ubic.gemma.core.util.locking.FileLockManagerTest

Once the directory exists a writer can be mid-copy into it, so the real file lock comes back and reader/writer coordination is what it always was.

testSharedLockOnAMissingDirectoryCreatesNothing() - Method in class ubic.gemma.core.util.locking.FileLockManagerTest

🛑 A shared lock is often taken only to ask "does this file exist?", and it must not answer by creating the directory the file would have lived in.

testSharedLockUnderAReadOnlyDirectoryDoesNotThrow() - Method in class ubic.gemma.core.util.locking.FileLockManagerTest

A read-only directory is a read-only directory, not an error.

testSignAppliesWhatAPlainCommitRefuses() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The point of the endpoint.

testSignup() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest

testSignWhileAnotherCuratorHoldsTheLockIsRefused() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

Someone else's lock is not yours.

testSignWithNoBodyAndNoDraftIsRejected() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

...

testSignWithNoBodySignsTheDraft() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

With no body, what gets signed is the caller's own draft — the held-back delta.

testSignWithoutTheLockIsRefused() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The whole gate: no lock, no sign, nothing written.

testSimpleEquality() - Method in class ubic.gemma.rest.util.args.FilterArgTest

testSingleCellDimensionWithCellLevelCharacteristicsRoundTrip() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.SingleCellDimensionCacheStalenessTest

Pattern C primary repro: persist an SCD with a non-empty cellLevelCharacteristics set (cascade=all-delete-orphan) where each GenericCellLevelCharacteristics itself is mutable="false" with a mutable="false" characteristics list.

testSingleCellSubSetAnalysis() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysis4Test

testSingleCharacterQueryIsStillRefused() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

One character stays out: that is where the candidate set stops being a name and becomes a scan of the index, and nothing we annotate is designated by a single character.

testSingleExperimentMode() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLITest

testSingleTaxonOnArrayWithNoOrganismColumn() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testSingletonShouldNotBeInitializedEagerly() - Method in class ubic.gemma.cli.util.MarkCLIsAsPrototypesTest

testSizeFilterOnCriteriaDao() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest

Exercises the .size-suffix filter path on the JPA-Criteria filtering DAO.

testSlice() - Method in class ubic.gemma.core.analysis.singleCell.SingleCellSlicerUtilsTest

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

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

A sample the matrix does not hold must be refused by name.

testSlicePartiallyInitializedDimension() - Method in class ubic.gemma.core.analysis.singleCell.SingleCellSlicerUtilsTest

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

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

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

testSnapshotThenRelabelThenRestoreReturnsTheOriginalLabel() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The basic loop: snapshot, relabel a factor value, then restore and find the original label back.

testSomeById() - Method in class ubic.gemma.rest.DatasetsRestTest

testSomeByShortName() - Method in class ubic.gemma.rest.DatasetsRestTest

testSortArgSchemas() - Method in class ubic.gemma.rest.OpenApiTest

testSortArgWithoutField() - Method in class ubic.gemma.rest.util.args.SortArgTest

testSortByCollectionSize() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testSortByJoinedIdKeepsNullOrdering() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testSortByJoinedIdResolvedThroughGetSortKeepsNullOrdering() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testSortByNullablePropertyKeepsNullOrdering() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testSortByOwnIdOmitsNullOrdering() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testSortByOwnIdResolvedThroughGetSortOmitsNullOrdering() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testSortBySample() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataTransformationsTest

testSortCharacteristics() - Method in class ubic.gemma.core.ontology.CharacteristicSortTest

testSortingByAllFilterableProperties() - Method in class ubic.gemma.persistence.service.FilteringVoEnabledServiceIntegrationTest

testSparseRangeArray() - Method in class ubic.gemma.core.datastructure.sparse.SparseListUtilsTest

testSpellingIsCaseAndWhitespaceInsensitive() - Method in class ubic.gemma.core.loader.expression.geo.GeoLibraryStrategyTest

testSplitByPlatform() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testSplitGivesEachNewExperimentAnAcl() - Method in class ubic.gemma.core.analysis.preprocess.SplitExperimentTest

Every experiment a split produces must come out editable.

testSplitGSE123753ByCollectionOfMaterial() - Method in class ubic.gemma.core.analysis.preprocess.SplitExperimentTest

testSplitGSE17183ByOrganismPart() - Method in class ubic.gemma.core.analysis.preprocess.SplitExperimentTest

testStaleStepsDropsACandidateTheCallerCannotRead() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The candidate ids come from an audit query that has no ACL clause, so what keeps a private dataset out of the response is the ACL-filtered load it is passed through.

testStaleStepsListsADatasetWhoseRunPredatesTheDesignChange() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The corpus-wide read of the same stale rule the per-dataset route applies: which datasets owe pipeline work, and which steps.

testStaleStepsOmitsADatasetWhoseRunPostdatesTheDesignChange() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

The disconfirming half: the same two events in the other order.

testStatementPredicateAndObjectValidated() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testSteal() - Method in class ubic.gemma.core.util.locking.FileLockManagerTest

testStealWithPath() - Method in class ubic.gemma.core.util.locking.FileLockManagerTest

testStreamAndWriteTeesOneBuildIntoStreamAndCache() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceTest

testStreamExperiments() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testStreamingAddAcceptsPersistentDimensionFromPriorAdd() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellStreamingAddTest

Covers the scdJustCreated branch of the streaming validator: re-adding vectors against a dimension that is already wired to existing vectors must be allowed.

testStreamingAddAppliesSparsityMetricsForPreferredQt() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellStreamingAddTest

testStreamingAddConsumesSourceExactlyOnce() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellStreamingAddTest

Single-pass consumption is the whole point of the streaming overload: if the implementation ever materialises the source internally (a toList() slipped into the path, say), the memory saving evaporates silently and only this test notices.

testStreamingAddCreatesCellTypeFactorWhenPreferred() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellStreamingAddTest

testStreamingAddDoesNotApplySparsityForNonPreferredQt() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellStreamingAddTest

testStreamingAddMatchesCollectionVariant() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellStreamingAddTest

testStreamingAddPersistsAllVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellStreamingAddTest

testStreamingAddRejectsDuplicateQuantitationTypeName() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellStreamingAddTest

testStreamingAddRejectsEmptyStream() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellStreamingAddTest

testStreamingAddRejectsWrongQuantitationType() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellStreamingAddTest

testStreamingAddRejectsWrongSingleCellDimension() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellStreamingAddTest

testString() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtilsTest

testStringCannotContainSpace() - Method in class ubic.gemma.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

testSubjectBreadthCountsObjectsUnderOnePredicateOnly() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

🛑 Subject breadth counts objects under ONE predicate, and the unscoped number it used to report cannot do the job the field was added for.

testSubquery() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testSubquery() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testSubquery() - Method in class ubic.gemma.persistence.util.FilterTest

testSubqueryWithEmptyPrefix() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest

testSubqueryWithGuessedAliases() - Method in class ubic.gemma.persistence.util.SubqueryUtilsTest

testSubqueryWithMultipleJointures() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testSubqueryWithRootAlias() - Method in class ubic.gemma.persistence.util.SubqueryUtilsTest

testSubsetAnalysisResultSetsAreVisibleViaTheSourceExperiment() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest

🛑 A SUBSET analysis's result sets must be visible to a caller who can read the SOURCE experiment.

testSubSetAnalysisWithAutomaticallySelectedFactorsAndContinuousFactor() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testSubSetAnalysisWithAutomaticallySelectedFactorsWhenContinuousFactorIsPresent() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testSubSetAnalysisWithManuallySelectedFactors() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testSubSetAnalysisWithManuallySelectedFactorsAndContinuousFactor() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testSubSetAnalysisWithManuallySelectedFactorsAndNoInteraction() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testSubSetAnalysisWithManuallySelectedFactorsWhenSubSetFactorIsSelected() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCliTest

testSubsetOfGSE225158() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderTest

testSubsetRelevanceRoundTripsAndAnOverrideOnlyCommitIsNotANoOp() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

The subset-relevance hint round-trips, and a commit that carries ONLY the hint is applied.

testSubsetWithNoFactorValuesYieldsAnEmptyListNotANullPointer() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

🛑 A subset with no factor values is normal, not an error.

testSubstantiaNigraInUberon() - Method in class ubic.gemma.core.ontology.providers.UberonOntologyTest

testSummariesForGroupNames_emptyInput() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testSummariesForGroupNames_skipsUnknown() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testSupplementaryHitDoesNotSuppressTheGeneOntologyFallback() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

GO is consulted only when the other ontologies come up empty.

testSupplementarySourceRanksBelowConventionalOntologies() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

A supplementary source scores against its own Lucene index and applies a large exact-name boost, so its raw score dwarfs a conventional ontology's.

testSupplementarySourceStillSurfacesWhenOntologiesFindNothing() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

The gap-fill case: when no conventional ontology matches, the supplementary hit is still returned and is still first.

testSupplementaryTierIsReachableWhenConventionalHitsFillTheWindow() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

Ranking below must not mean "only if there is room left over".

testSupportedSecuredConfigAttributes() - Method in class ubic.gemma.core.security.ApplicationContextTest

Test all the supported Secured config attribute.

testSupportingEvidenceAffectsNeitherEqualityNorOrdering() - Method in class ubic.gemma.model.expression.experiment.StatementValueObjectTest

Evidence is provenance, not identity.

testSupportingEvidenceDoesNotAffectEquality() - Method in class ubic.gemma.model.common.description.CharacteristicValueObjectTest

Evidence is provenance, not identity.

testSupportingEvidenceIsReadBackFromTheCharacteristic() - Method in class ubic.gemma.model.common.description.CharacteristicValueObjectTest

The SUPPORTING_EVIDENCE column has always existed on every characteristic; this value object simply never surfaced it, which left the design read path unable to answer "where did this come from" even for rows that recorded it.

testSupportingEvidenceIsReadBackFromTheStatement() - Method in class ubic.gemma.model.expression.experiment.StatementValueObjectTest

testSupportOrdersWithinABasis() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

🛑 Within a basis, support has to order — the score used to be a constant.

testSuppressedDesignationReportsWhatItRuledOut() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest

A designation query that retrieves only near-matches must report WHICH terms it ruled out, not merely that nothing matched.

testSvd() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImplTest

testSvdGapped() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImplTest

testTakingASnapshotDoesNotMarkTheDatasetAsUpdated() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A backup must not modify what it backs up.

testTaxonArrayArg() - Method in class ubic.gemma.rest.util.args.EntityArrayArgsTest

testTaxonArrayArgEmptyRaises() - Method in class ubic.gemma.rest.util.args.EntityArrayArgsTest

testTaxonByCommonName() - Method in class ubic.gemma.rest.TaxaWebServiceTest

testTaxonById() - Method in class ubic.gemma.rest.TaxaWebServiceTest

testTaxonByNcbiId() - Method in class ubic.gemma.rest.TaxaWebServiceTest

testTaxonByScientificName() - Method in class ubic.gemma.rest.TaxaWebServiceTest

testTaxonCompletionsCaseInsensitivePrefix() - Method in class ubic.gemma.rest.CompletionsWebServiceTest

testTaxonCompletionsFanOut() - Method in class ubic.gemma.rest.CompletionsWebServiceTest

testTaxonCompletionsLimitClampedToMax() - Method in class ubic.gemma.rest.CompletionsWebServiceTest

testTaxonDatasetsByNcbiId() - Method in class ubic.gemma.rest.TaxaWebServiceTest

testTaxonGeneGoTerms() - Method in class ubic.gemma.rest.TaxaWebServiceTest

testTaxonGeneLocations() - Method in class ubic.gemma.rest.TaxaWebServiceTest

testTaxonGeneProbes() - Method in class ubic.gemma.rest.TaxaWebServiceTest

testTaxonGenes() - Method in class ubic.gemma.rest.TaxaWebServiceTest

testTaxonGenesByIds() - Method in class ubic.gemma.rest.TaxaWebServiceTest

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

testTaxonPropertyResolutionInGetFilter() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest

testTechnologyTypeIsNullWhenThePlatformsDisagree() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

🛑 A dataset run on two kinds of platform IS both, so it has no single technology and the field says so by being null.

testTermIdOrUriToUri() - Method in class ubic.gemma.core.ontology.OntologyUtilsTest

🛑 The ingestion-boundary normalizer: whatever spelling a source file uses, what gets STORED is a URI.

testTermIdToUri() - Method in class ubic.gemma.core.ontology.OntologyUtilsTest

testTermLackingLabelIsIgnored() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

testTermNeedingAJudgementIsNeverTouched() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionServiceTest

testTermsDiscouragedByTheCurationGuideAreStillDetected() - Method in class ubic.gemma.core.analysis.expression.diff.BaselineSelectionTest

The curation guide's "do not use, Gemma won't pick them up" list.

testTextRepresentation() - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapperTest

testThatChebiDoesNotHaveInferenceEnabled() - Method in class ubic.gemma.core.ontology.OntologyLoadingTest

testThatConnectivityAndConnectiveAreExcludedFromStemmingInClo() - Method in class ubic.gemma.core.ontology.OntologyLoadingTest

testThatTGEMODoesNotProcessImports() - Method in class ubic.gemma.core.ontology.OntologyLoadingTest

testThaw() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest

testThaw() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testThaw() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorCreationHelperServiceTest

testThaw() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoTest

testThaw() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testThawAliasesDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testThawBioMaterialsForBioAssaysEmpty() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoTest

testThawBioMaterialsForBioAssaysWarmsSourceChain() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoTest

testThawCollection() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceTest

testThawCollectionEmpty() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceTest

testThawCollectionEmpty() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceTest

testThawCollectionReloadsByIdsAndThaws() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testThawDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testThawLite() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testThawLiteCollectionDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testThawLiter() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testThawLiterDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testThawLiteSingleDelegates() - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceTest

testThawSingleReloadsAndThaws() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testThawSingleThrowsWhenMissing() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceTest

testThawTransientEntity() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

testTheAdvertisedShortAliasDisarmsItToo() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDaoTest

🛑 The short spelling counts too.

testTheBreadthCutRunsBeforeTheRowCap() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

🛑 The breadth cut runs BEFORE the row cap, or a threshold thins the answer instead of improving it.

testTheCapKeepsTheBestCandidatesNotTheAlphabeticalOnes() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

The cap has to keep the BEST candidates, not merely the same ones every time.

testTheDefaultRunVisitsEveryExperiment() - Method in class ubic.gemma.apps.UpdateGeoSourceMetadataCliTest

🛑 The corpus sweep is the point of this command, and it is what you get by default.

testTheDerivedClaimIsItsOwnTripleWithATaxonChosenVerb() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

The derived claim is its own triple, and taxon picks its verb.

testTheDirectTargetsAreTheOnesGeoKnows() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoUtilsTest

🛑 acc.cgi's targets are self / gsm / gpl / gse / all.

testTheImplicationRunsOnlyOneWayAndTheWayDependsOnThePredicate() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

testTheInMemoryStatisticIsNotRounded() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionResultPrecisionTest

Rounding happens at serialization, so the in-memory value the diff-ex ranking sorts on stays exact.

testTheLastEventForeignKeyDeletesToNull() - Method in class ubic.gemma.persistence.hibernate.AuditTrailForeignKeyIntegrationTest

Plain JDBC rather than a Hibernate session: the schema is what is under test, so nothing here needs a persistence context, and reading it through one would only add a transaction to get wrong.

testTheListDoesNotLoadMembersUnlessAsked() - Method in class ubic.gemma.rest.ExperimentSetsWebServiceTest

🛑 Members are off by default on the list.

testTheLockSaysWhatIsHoldingItNotJustWho() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

uib's ask: a blocked curator gets a name and has to choose wait-or-steal, and a batch mid-run looks exactly like a person at lunch.

testTheMappingHasNoChains() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsUriMigrationTest

Every mapping must be a fixed point: no from-URI may also be a to-URI, or the resolved answer depends on how many times you resolve.

testTheMappingResourceActuallyLoads() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsUriMigrationTest

testTheParentWalkStillDoesNotEnterGeneOntology() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

🛑 The parent/child walk is deliberately NOT extended to GO.

testThePostCarriesATextFallback() - Method in class ubic.gemma.core.logging.SlackAppenderTest

The fallback Slack renders where blocks cannot be — notifications, screen readers.

testTheRelationReadsFromEitherEnd() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

The same rows read from either end.

testTheReportHandsBackTheTokenForTheNextCommit() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

A client that has just committed knows the state — its own write produced it — so it should be able to keep editing and commit again.

testTheRetiredSpellingIsNotSuggested() - Method in class ubic.gemma.rest.CompletionsWebServiceTest

🛑 The picker must not hand out a term the read path is going to rewrite.

testTheSeriesPubMedIdIsTheAuthoritativeLink() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest

testTheShortAliasSaysNothingAboutAnAssociatedEntity() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDaoTest

...but only for the entity it belongs to: it is this dataset's flag, not its platform's.

testTheSingleSubsetPathDropsAFactorWithMissingValues() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysisFactorConsistencyTest

The single-subset overload, run(ExpressionExperimentSubSet, ...), is a separate path -- it is what a redo of one subset analysis takes -- and it drops incomplete factors itself.

testTheSingleSubsetPathKeepsACompleteFactor() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysisFactorConsistencyTest

Positive control for the single-subset path, off the same fixture: with nothing missing, ct1 models both factors and keeps the interaction, so an analysis that simply modelled less cannot pass the test above.

testTheSpellingsAlreadySeenInProd() - Method in class ubic.gemma.core.loader.expression.geo.GeoLibraryStrategyTest

The spellings that were already in the corpus before the vocabulary was completed.

testTheSummaryAgreesWithTheStatementsItSummarizes() - Method in class ubic.gemma.model.expression.experiment.FactorValueUtilsTest

🛑 The summary must say what the statements beside it say.

testTheThreeFormerlyCopyPastedRegistrations() - Method in class ubic.gemma.core.security.authorization.acl.AclClassMetadataTest

The three that carried the wrong query, pinned explicitly: a subset names its source experiment, while the design and the mean-variance relation are named BY the experiment.

testTheUndecidablePairsAreNotMerged() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsUriMigrationTest

The six pairs Cellosaurus could not decide by name are not in the table.

testThreeMoleculesStayUnset() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterMoleculeTest

Three disagreeing channels are not the two-colour shape either, DNA present or not.

testTiedAssertedRowsAreOrderedSpecificFirst() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

🛑 An asserted basis carries no support, so every row of it scores the same and the sort used to fall through to alphabetical.

testTimedMethod() - Method in class ubic.gemma.core.metrics.GenericMeterRegistryConfigurerTest

testTimedMethodAtInterfaceLevel() - Method in class ubic.gemma.core.metrics.GenericMeterRegistryConfigurerTest

testToExclusive() - Method in class ubic.gemma.core.util.locking.FileLockManagerTest

testToOriginalString() - Method in class ubic.gemma.persistence.util.FilterTest

testToOriginalStringWhenOriginalPropertyIsNull() - Method in class ubic.gemma.persistence.util.FilterTest

testTopRankedProbeWithDistinctValuesIsKept() - Method in class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilterTest

A probe that is the highest-expressed in every sample holds one single rank throughout, because ranking runs within a column across design elements.

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

testToShared() - Method in class ubic.gemma.core.util.locking.FileLockManagerTest

testTransactionalService() - Method in class ubic.gemma.persistence.util.PointcutsTest

testTranspose() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataTransformationsTest

testTriageDoesNotTouchTheCuratorNeedsAttentionFlag() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

needsAttention is the pre-agent curator flag and must NOT move with triage: the two are separate signals, and collapsing them was the thing this design turned down.

testTrimsLeadingAndTrailingWhitespace(Path) - Method in class ubic.gemma.core.config.ConfigUtilsTest

testTroubledAreHiddenByDefault() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDaoTest

The default is unchanged: an ordinary caller does not see troubled entities.

testTwoCellLinesThatMerelyPunctuateAlikeAreNotMerged() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsUriMigrationTest

🛑 KMH-2 and KM-H2 are not the same cell line, and the shim used to say they were.

testTwoCharacterQueryReachesTheOntologies() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

A two-character query is a real term name — H1, H7 and H9 are among the most-used human embryonic stem cell lines, and EFO_0003042 (H1-hESC) carries `H1` as an exact synonym.

testTwoFramingsOfTheSameFactBothSurvive() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

Two bases naming different terms are reported side by side, not merged and not treated as a disagreement.

testTwoManagers() - Method in class ubic.gemma.core.util.locking.FileLockManagerTest

testTwoRelationsDerivingOneClaimShareAnImpliedTripleKey() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoTest

🛑 Two different stored relations converging on one claim must key the same.

testTwoRnaFlavoursStayUnset() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterMoleculeTest

...but only genomic DNA earns that treatment.

testTypingTheRetiredIdStillFindsTheTerm() - Method in class ubic.gemma.rest.CompletionsWebServiceTest

...and typing the retired id still finds the term.

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

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

testUncategorized() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsTest

testUndefinedProperty() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest

testUnknownJudgeKindIsRejected() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

An unknown judgeKind is refused rather than silently defaulted to a judge nobody named.

testUnknownParameterIsIgnoredWhenDisabled() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterDisabledTest

testUnknownParameterIsRejectedAndNamed() - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest

The reported case: ids is not a parameter of /datasets, was dropped, and the whole corpus came back reported as the caller's selection.

testUnmappedRoute() - Method in class ubic.gemma.rest.AnalysisResultSetsJerseyTest

testUnmatchedSample() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderTest

testUnpaired() - Method in class ubic.gemma.apps.RNASeqDataAddCliTest

testUnparseableEvidenceIsPreservedRatherThanDiscarded() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionServiceTest

testUnparseableQuerySurfacesAsParseSearchException() - Method in class ubic.gemma.core.ontology.OntologyServiceTest

A query Lucene cannot parse is caller input, so it must surface as a ParseSearchException — the type every search endpoint already maps to 400.

testUnparseableSupportingEvidenceYieldsNullRatherThanThrowing() - Method in class ubic.gemma.model.expression.experiment.StatementValueObjectTest

A malformed payload must not propagate a parse failure into a read response.

testUnraw() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataTransformationsTest

testUnrawAndTranspose() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderTest

This test exercise the ability of the Configurer to detect datasets that need to be unrawed and transposed.

testUnrelatedBeanIsSingleton() - Method in class ubic.gemma.cli.util.MarkCLIsAsPrototypesTest

testUnresolvedEverywhereRejected() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testUnresolvedLocallyThenOlsResolves() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testUnsupportedTransformation() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceTest

testUpdate() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceTest

testUpdate() - Method in class ubic.gemma.persistence.service.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.persister.GenomePersisterTest

testUpdateDatasetAnnotations() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetAnnotationsAcceptsEmptyListAsClear() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetAnnotationsCarriesSupportingEvidence() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetAnnotationsConstructsStatementWhenPredicateAndObjectPresent() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetAnnotationsConstructsStatementWithSecondPair() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetAnnotationsMissingBody() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetAnnotationsNoEvidenceLeavesSupportingEvidenceNull() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetAnnotationsRejectsBlankCategory() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetAnnotationsRejectsBlankValue() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetAnnotationsStaysPlainCharacteristicWhenNoStatementFields() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetBasics() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetBasicsDescriptionOnly() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetBasicsRejectsBlankName() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetBasicsRejectsEmptyBody() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetCurationDetailsAppliesMultipleChanges() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetCurationDetailsClearsNeedsAttention() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetCurationDetailsClearsTroubled() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetCurationDetailsSetsNeedsAttention() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetCurationDetailsSetsTroubled() - Method in class ubic.gemma.rest.DatasetsRestTest

testUpdateDatasetCurationDetailsSetsTroubled() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetCurationDetailsSkipsNoOpTroubled() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetCurationDetailsUpdatesCurationNote() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetCurationDetailsWithEmptyBodyIs400() - Method in class ubic.gemma.rest.DatasetsRestTest

testUpdateDatasetCurationDetailsWithEmptyBodyIs400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetCurationDetailsWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPermissionsMakePublicOnAlreadyPublicRecordsNoEvent() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPermissionsMakesPrivate() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPermissionsMakesPublic() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPermissionsMakesPublicThenPrivate() - Method in class ubic.gemma.rest.DatasetsRestTest

testUpdateDatasetPermissionsReturnsCurrentStateWhenIsPublicOmitted() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPermissionsReturnsStateWhenIsPublicOmitted() - Method in class ubic.gemma.rest.DatasetsRestTest

testUpdateDatasetPermissionsWithEmptyBodyIs400() - Method in class ubic.gemma.rest.DatasetsRestTest

testUpdateDatasetPermissionsWithEmptyBodyIs400() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPermissionsWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsRestTest

testUpdateDatasetPermissionsWithUnknownDatasetIs404() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPublications() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPublicationsByDoi() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPublicationsCarriesEvidence() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPublicationsClearAll() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPublicationsEmptyRejectedListStillClearsThem() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPublicationsMissingOtherList() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPublicationsOmittingRejectedLeavesThemUntouched() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPublicationsRecordsRejection() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPublicationsRejectedByHigherAuthorityIsConflict() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPublicationsRejectsBlankPubMedId() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPublicationsRejectsBothPubMedIdAndDoi() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPublicationsRejectsUnknownSource() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateDatasetPublicationsUnresolvablePubMedIdIsBadRequest() - Method in class ubic.gemma.rest.DatasetsWebServiceTest

testUpdateEE2CAsUser() - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilIntegrationTest

testUpdateExpressionExperiment2ArrayDesignEntries() - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilIntegrationTest

testUpdateExpressionExperiment2CharacteristicEntries() - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilIntegrationTest

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

testUpdateGroup_nullBody_throws400() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testUpdateGroup_rename() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testUpdateGroup_systemGroupCannotRename() - Method in class ubic.gemma.rest.GroupsWebServiceTest

testUpdateGroups() - Method in class ubic.gemma.core.security.authentication.UserManagerTest

testUpdateMeanVarianceRelation_deletesTheOneItReplaces() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

Replacing an experiment's mean-variance relation must delete the one it replaces.

testUpdateMembersOfSetWithoutTaxonAcceptsMixedTaxa() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperImplTest

testUpdateMembersOfSetWithTaxonRefusesAnother() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperImplTest

Control: a set that declares a taxon still refuses a member of another.

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

testUpdateSparsityMetrics() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceTest

testUpdateSubsumingStatus() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testUpdateSubsumingStatusTrue() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceTest

testUpdateTargetStatus_delegatesToService() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testUpdateTargetStatus_missingBody_returns400() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testUpdateTargetStatus_unknownTarget_returns404() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testUpdateTicket_addComment() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testUpdateTicket_bodyAbsent_doesNotClearExisting() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testUpdateTicket_clearAssignee() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testUpdateTicket_clearBody_explicitNull() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testUpdateTicket_notFound_throws404() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testUpdateTicket_setsBodyAndMode() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testUpdateTicket_setsTitle() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testUpdateTicket_stateTransition() - Method in class ubic.gemma.rest.TicketsWebServiceTest

testUpdateUser() - Method in class ubic.gemma.core.security.authentication.UserManagerTest

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

Tests updating the UserGroup

testUpdateUsername() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserDaoTest

Usernames are immutable, but Hibernate should be configured to disregard any changes.

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

testUpdateWithTransientEntity() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceIntegrationTest

testUriToTermId() - Method in class ubic.gemma.core.ontology.OntologyUtilsTest

testUseBuiltSubClause() - Method in class ubic.gemma.persistence.util.FiltersTest

testUserAddedToGroup() - Method in class ubic.gemma.core.util.MailServiceTest

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

testUseRawColumnNames() - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserMetadataWriterTest

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

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

testUserRemovedFromGroup() - Method in class ubic.gemma.core.util.MailServiceTest

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

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

testValueObject() - Method in class ubic.gemma.core.security.acl.ObjectIdentityRetrievalStrategyImplTest

testValueOf() - Method in class ubic.gemma.rest.util.args.SortArgTest

testValueOfAvg() - Method in class ubic.gemma.rest.util.args.ExpLevelConsolidationArgTest

testValueOfBlankRaises() - Method in class ubic.gemma.rest.util.args.CompositeSequenceArgTest

testValueOfBlankRaises() - Method in class ubic.gemma.rest.util.args.DatabaseEntryArgTest

testValueOfBlankRaises() - Method in class ubic.gemma.rest.util.args.DatasetArgTest

testValueOfBlankRaises() - Method in class ubic.gemma.rest.util.args.FactorValueArgTest

testValueOfBlankRaises() - Method in class ubic.gemma.rest.util.args.GeneArgTest

testValueOfBlankRaises() - Method in class ubic.gemma.rest.util.args.PlatformArgTest

testValueOfBlankRaises() - Method in class ubic.gemma.rest.util.args.TaxonArgTest

testValueOfBogusRaises() - Method in class ubic.gemma.rest.util.args.ExpLevelConsolidationArgTest

testValueOfEmptyRaises() - Method in class ubic.gemma.rest.util.args.CompositeSequenceArgTest

testValueOfEmptyRaises() - Method in class ubic.gemma.rest.util.args.DatabaseEntryArgTest

testValueOfEmptyRaises() - Method in class ubic.gemma.rest.util.args.DatasetArgTest

testValueOfEmptyRaises() - Method in class ubic.gemma.rest.util.args.ExcludeArgTest

testValueOfEmptyRaises() - Method in class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArgTest

testValueOfEmptyRaises() - Method in class ubic.gemma.rest.util.args.FactorValueArgTest

testValueOfEmptyRaises() - Method in class ubic.gemma.rest.util.args.GeneArgTest

testValueOfEmptyRaises() - Method in class ubic.gemma.rest.util.args.PlatformArgTest

testValueOfEmptyRaises() - Method in class ubic.gemma.rest.util.args.QueryArgTest

testValueOfEmptyRaises() - Method in class ubic.gemma.rest.util.args.TaxonArgTest

testValueOfEnsemblIdDispatchesToEnsemblArg() - Method in class ubic.gemma.rest.util.args.GeneArgTest

testValueOfLargeNumberDispatchesToNcbiIdArg() - Method in class ubic.gemma.rest.util.args.TaxonArgTest

testValueOfMaximumIsAllowed() - Method in class ubic.gemma.rest.util.args.LimitArgTest

testValueOfMouseEnsemblIdDispatchesToEnsemblArg() - Method in class ubic.gemma.rest.util.args.GeneArgTest

testValueOfMultiple() - Method in class ubic.gemma.rest.util.args.ExcludeArgTest

testValueOfNameDispatchesToNameArg() - Method in class ubic.gemma.rest.util.args.TaxonArgTest

testValueOfNegativeRaises() - Method in class ubic.gemma.rest.util.args.LimitArgTest

testValueOfNegativeRaises() - Method in class ubic.gemma.rest.util.args.OffsetArgTest

testValueOfNonBlank() - Method in class ubic.gemma.rest.util.args.QueryArgTest

testValueOfNonNumericRaises() - Method in class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArgTest

testValueOfNonNumericRaises() - Method in class ubic.gemma.rest.util.args.LimitArgTest

testValueOfNonNumericRaises() - Method in class ubic.gemma.rest.util.args.OffsetArgTest

testValueOfNumeric() - Method in class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArgTest

testValueOfNumeric() - Method in class ubic.gemma.rest.util.args.LimitArgTest

testValueOfNumeric() - Method in class ubic.gemma.rest.util.args.OffsetArgTest

testValueOfNumericDispatchesToByIdArg() - Method in class ubic.gemma.rest.util.args.QuantitationTypeArgTest

testValueOfNumericDispatchesToIdArg() - Method in class ubic.gemma.rest.util.args.CompositeSequenceArgTest

testValueOfNumericDispatchesToIdArg() - Method in class ubic.gemma.rest.util.args.DatabaseEntryArgTest

testValueOfNumericDispatchesToIdArg() - Method in class ubic.gemma.rest.util.args.DatasetArgTest

testValueOfNumericDispatchesToIdArg() - Method in class ubic.gemma.rest.util.args.FactorValueArgTest

testValueOfNumericDispatchesToIdArg() - Method in class ubic.gemma.rest.util.args.PlatformArgTest

testValueOfNumericDispatchesToNcbiIdArg() - Method in class ubic.gemma.rest.util.args.GeneArgTest

testValueOfNumericIsTrimmed() - Method in class ubic.gemma.rest.util.args.DatasetArgTest

testValueOfPickMax() - Method in class ubic.gemma.rest.util.args.ExpLevelConsolidationArgTest

testValueOfPickVar() - Method in class ubic.gemma.rest.util.args.ExpLevelConsolidationArgTest

testValueOfSingle() - Method in class ubic.gemma.rest.util.args.ExcludeArgTest

testValueOfSmallNumberAtBoundaryDispatchesToIdArg() - Method in class ubic.gemma.rest.util.args.TaxonArgTest

testValueOfSmallNumberDispatchesToIdArg() - Method in class ubic.gemma.rest.util.args.TaxonArgTest

testValueOfStringDispatchesToByNameArg() - Method in class ubic.gemma.rest.util.args.QuantitationTypeArgTest

testValueOfStringDispatchesToNameArg() - Method in class ubic.gemma.rest.util.args.CompositeSequenceArgTest

testValueOfStringDispatchesToStringArg() - Method in class ubic.gemma.rest.util.args.DatabaseEntryArgTest

testValueOfStringDispatchesToStringArg() - Method in class ubic.gemma.rest.util.args.DatasetArgTest

testValueOfStringDispatchesToStringArg() - Method in class ubic.gemma.rest.util.args.PlatformArgTest

testValueOfStringDispatchesToValueArg() - Method in class ubic.gemma.rest.util.args.FactorValueArgTest

testValueOfSymbolDispatchesToSymbolArg() - Method in class ubic.gemma.rest.util.args.GeneArgTest

testValueOfWhitespaceRaises() - Method in class ubic.gemma.rest.util.args.QueryArgTest

testValueOfZero() - Method in class ubic.gemma.rest.util.args.OffsetArgTest

testValueOfZeroRaises() - Method in class ubic.gemma.rest.util.args.LimitArgTest

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

testVerySmallValuesSurvive() - Method in class ubic.gemma.core.util.RoundingUtilsTest

The reason the rule is significant digits and not decimal places: a corrected p-value of 1e-300 has to come back as 1e-300, and any fixed number of decimals flattens it to zero.

testWebByDefault() - Method in class ubic.gemma.persistence.util.EntityUrlBuilderTest

testWhenCollectionContainNullOrIncompatibleEntries() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProviderTest

testWhenNotGranted() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationProviderTest

testWhenPairednessIsUnknown() - Method in class ubic.gemma.apps.RNASeqDataAddCliTest

testWhenProtocolWithNameAlreadyExists() - Method in class ubic.gemma.apps.ProtocolAdderCliTest

testWhenSlackApiRaisesException() - Method in class ubic.gemma.core.logging.SlackAppenderTest

testWhenSlackFailsToClose() - Method in class ubic.gemma.core.logging.SlackAppenderTest

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

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

testWhitespaceNearMatchAcceptedAndCanonicalized() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testWhitespaceSeparatedTokensAreJoinedOnAnd() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyQueryRewriteTest

testWideningDoesNotHappenUnlessAskedFor() - Method in class ubic.gemma.core.search.source.OntologySearchSourceInferredRelationsTest

Off by default: an existing search must not change shape because this feature landed.

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

testWireNamesAreCamelCaseEverywhere() - Method in class ubic.gemma.rest.OpenApiTest

The wire speaks one language, and it is camelCase.

testWithBarcodeCollisions() - Method in class ubic.gemma.core.loader.expression.singleCell.GenericMetadataSingleCellDataLoaderTest

testWithContextData() - Method in class ubic.gemma.core.logging.SlackAppenderTest

testWithContextStack() - Method in class ubic.gemma.core.logging.SlackAppenderTest

testWithDefault() - Method in class ubic.gemma.core.loader.expression.SequencingMetadataFileDataLoaderTest

testWithDefaultValue() - Method in class ubic.gemma.core.loader.expression.singleCell.GenericMetadataSingleCellDataLoaderTest

testWithDelegateThatProducesLibrarySize() - Method in class ubic.gemma.core.loader.expression.SequencingMetadataFileDataLoaderTest

testWithDifferentPath() - Method in class ubic.gemma.rest.servlet.RestapidocsIndexRewriteFilterTest

testWithdrawReturnsTheSetToUntriaged() - Method in class ubic.gemma.rest.DatasetsCurationCommitRestTest

Withdrawing returns the set to un-triaged, and withdrawing again is not an error -- a withdrawal that finds nothing has still achieved what it asked for.

testWithDuplicateCellId() - Method in class ubic.gemma.core.loader.expression.singleCell.GenericMetadataSingleCellDataLoaderTest

testWithDuplicateCellIdButDifferentValues() - Method in class ubic.gemma.core.loader.expression.singleCell.GenericMetadataSingleCellDataLoaderTest

testWithImageNoGenbank() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testWithImages() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest

testWithMissingSampleId() - Method in class ubic.gemma.core.loader.expression.singleCell.GenericMetadataSingleCellDataLoaderTest

testWithoutTrailingSlash() - Method in class ubic.gemma.rest.servlet.RestapidocsIndexRewriteFilterTest

testWithPreviousFireTime() - Method in class ubic.gemma.core.scheduler.BatchInfoRepopulationJobTest

testWithQuery() - Method in class ubic.gemma.rest.servlet.RestapidocsIndexRewriteFilterTest

testWithStacktrace() - Method in class ubic.gemma.core.logging.SlackAppenderTest

testWithUnmatchedSampleId() - Method in class ubic.gemma.core.loader.expression.singleCell.GenericMetadataSingleCellDataLoaderTest

testWrapperIsApplicationListenerAndForwardsContextClosedEvent() - Method in class ubic.gemma.core.security.concurrent.DelegatingSecurityContextSchedulingTaskExecutorTest

testWrapperToPrimitiveConversion() - Method in class ubic.gemma.persistence.util.FilterTest

testWriteAndConvertMatrixToStream() - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriterTest

testWriteConvertedFloatVectorsToDisk() - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriterTest

testWriteConvertedIntVectorsToDisk() - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriterTest

testWriteDoubleVectorsToDisk() - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriterTest

testWriteEndpoints_requireAuthentication() - Method in class ubic.gemma.rest.TicketsWebServiceTest

Annotation-level auth guard: the write-side endpoints must carry @PreAuthorize("isAuthenticated()").

testWriteFloatVectors() - Method in class ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriterTest

testWriteFloatVectorsToDisk() - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriterTest

testWriteIntVectors() - Method in class ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriterTest

testWriteIntVectorsToDisk() - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriterTest

testWriteLongVectors() - Method in class ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriterTest

testWriteLongVectorsToDisk() - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriterTest

testWriteMatrix() - Method in class ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriterTest

testWriteMatrixToDisk() - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriterTest

testWriteMatrixToStream() - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriterTest

testWritePValuesHistogram() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest

testWriteToDiskAndConvert() - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriterTest

testWriteToRdf() - Method in class ubic.gemma.core.ontology.FactorValueOntologyServiceTest

testWriteVectors() - Method in class ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriterTest

testWrongBaseTgemoNormalizedResolvesAndCanonicalizesUri() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

testWrongLabelOnAnObsoletedCategoryIsStillRejected() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

The carve-out drops a marker, it does not stop checking: a different category's name is still a mismatch.

testWrongLabelOnASanctionedPredicateIsStillRejected() - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImplTest

Gemma's vocabulary is the authority: a wrong label on a sanctioned predicate is still a mismatch.

testYaml() - Method in class ubic.gemma.rest.OpenApiWebServiceTest

testZeroKeepsItsSign() - Method in class ubic.gemma.core.util.RoundingUtilsTest

testZscore() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtilsTest

testZtransformed() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testZTransformedByMedian() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

testZtransformedInLogSpace() - Method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtilsTest

tfMatcher_doesNotMatchTfAsSubstring() - Method in class ubic.gemma.core.geoscrape.MatchersTest

tfMatcher_hitsOnCrisprKoOfTp53() - Method in class ubic.gemma.core.geoscrape.MatchersTest

tfMatcher_hitsOnKnockdownPlusTfSymbol() - Method in class ubic.gemma.core.geoscrape.MatchersTest

tfMatcher_missesOnNullOrEmpty() - Method in class ubic.gemma.core.geoscrape.MatchersTest

tfMatcher_missesWhenPerturbationButNoTf() - Method in class ubic.gemma.core.geoscrape.MatchersTest

tfMatcher_missesWhenTfPresentButNoPerturbation() - Method in class ubic.gemma.core.geoscrape.MatchersTest

thawCurationDetailsInitializesEveryLastEventAssociation() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.DetachedCuratableValueObjectTest

thawCurationDetailsToleratesAbsentEvents() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.DetachedCuratableValueObjectTest

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

Helpers for tests that need to assert lazy-association initialization state before and after a service's thaw(...) call.

theContributingSamplesKeepTheirResiduals() - Method in class ubic.gemma.core.util.math.linearmodels.FittedValuesForExcludedSamplesTest

The samples that did take part keep exactly the residuals they had.

theCreationFallbackSaysLoadedNotPublished() - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObjectTest

🛑 action='C' means the dataset was loaded into Gemma.

theFilterAlsoCounts() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentInCurationFilterIT

The count query joins differently from the id query, so a predicate can work in one and blow up in the other — and the dashboard panel uib wants this for reads the count, not the page.

theSourceMetadataBlobUsesTheSameRule() - Method in class ubic.gemma.core.loader.expression.geo.GeoColonSplitTest

theTicketHalfAgreesWithThePerDatasetLookup() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentInCurationFilterIT

The filter's ticket half and the per-dataset ticket route must name the same datasets, or the list says a dataset is in curation and its own ticket drawer shows nothing.

theWireDefaultsAreRawAnd20Bins() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServicePvalueDistributionTest

The wire default has to be raw.

ThreadUtilsTest - Class in ubic.gemma.core.util.concurrent

ThreadUtilsTest() - Constructor for class ubic.gemma.core.util.concurrent.ThreadUtilsTest

three_arg_overload_still_works_for_callers_that_have_no_prior() - Method in class ubic.gemma.rest.ranking.CommonalityRankingStrategyTest

TicketPersistenceIT - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Integration test for the V19 migration (TICKET.MODE + TICKET_TARGET.STATUS) and the corresponding Ticket/TicketTarget entity mappings.

TicketPersistenceIT() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

TicketSearchQueryTest - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Query construction behind GET /tickets/search: the HQL TicketDaoImpl.buildSearchHitHql(boolean, boolean, boolean) emits, the LIKE pattern TicketDaoImpl.searchLikePattern(String) builds, and the row projection TicketSearchHitValueObject.fromRow(Object[]).

TicketSearchQueryTest() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketSearchQueryTest

TicketServiceImplTest - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Lightweight Mockito unit tests for TicketServiceImpl covering the Phase B-1 happy paths (open / assign / addComment / transition) and verifying that each mutating call appends the correct TicketEventType to the ticket's append-only event log.

TicketServiceImplTest() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

TicketsWebServiceCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to TicketsWebService#getTickets(boolean, Long, TicketPriority, OffsetArg, LimitArg, CursorArg) as step 1o of CURSOR_PAGINATION_STEP1_PLAN.md.

TicketsWebServiceCursorTest() - Constructor for class ubic.gemma.rest.TicketsWebServiceCursorTest

TicketsWebServiceEventsCursorTest - Class in ubic.gemma.rest

Unit tests for the cursor-pagination branch added to TicketsWebService.getTicketEvents(Long, CursorArg, LimitArg) as step 1r of CURSOR_PAGINATION_STEP1_PLAN.md.

TicketsWebServiceEventsCursorTest() - Constructor for class ubic.gemma.rest.TicketsWebServiceEventsCursorTest

TicketsWebServiceScratchpadRoutingTest - Class in ubic.gemma.rest

Real JAX-RS path matching for GET /tickets/scratchpad — the one thing the mocked TicketsWebServiceTest cannot see, since it calls the handler methods directly and a literal route swallowed by @Path("/{id}") would still pass there.

TicketsWebServiceScratchpadRoutingTest() - Constructor for class ubic.gemma.rest.TicketsWebServiceScratchpadRoutingTest

TicketsWebServiceTargetLabelsTest - Class in ubic.gemma.rest

displayLabel / displayName on ticket targets.

TicketsWebServiceTargetLabelsTest() - Constructor for class ubic.gemma.rest.TicketsWebServiceTargetLabelsTest

TicketsWebServiceTest - Class in ubic.gemma.rest

Pure Mockito unit tests for TicketsWebService covering the read-only endpoints introduced in Phase B-2 of AUDIT_AS_WORKFLOW_RECCE.md.

TicketsWebServiceTest() - Constructor for class ubic.gemma.rest.TicketsWebServiceTest

timeoutMillis() - Element in annotation interface ubic.gemma.core.util.test.NetworkAvailable

Timeout in milliseconds for the connection attempt if a resource URL is specified via NetworkAvailable.url().

titleQuery_matchesACaseInsensitiveSubstringOfTheTitle() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketSearchQueryTest

titleQuery_ordersByUpdatedAtDescending() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketSearchQueryTest

tmp - Variable in class ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurerTest

tokenCoverage_handlesEmptyQuery() - Method in class ubic.gemma.rest.AnnotationSearchRankingStrategyTest

tokenCoverage_putsBothTokensFirst() - Method in class ubic.gemma.rest.AnnotationSearchRankingStrategyTest

TooFewDistinctValuesFilterTest - Class in ubic.gemma.core.analysis.preprocess.filter

Contract-level unit tests for TooFewDistinctValuesFilter: pins the threshold-validation invariants (constructor rejects out-of-range values) and the appliesTo short-circuit (threshold zero -> no-op filter).

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

toString() - Method in record class ubic.gemma.core.security.audit.AuditedAspectTest.SamplePayload

Returns a string representation of this record class.

toString_includesPercentFormattedThreshold() - Method in class ubic.gemma.core.analysis.preprocess.filter.TooFewDistinctValuesFilterTest

toString_renderingForZeroThreshold() - Method in class ubic.gemma.core.analysis.preprocess.filter.TooFewDistinctValuesFilterTest

toStringIsNonNull() - Method in class ubic.gemma.persistence.util.CursorTest

toStringRendersTheConjunction() - Method in class ubic.gemma.persistence.util.SubqueryConjunctionTest

totalElementsForwardedWhenPresent() - Method in class ubic.gemma.rest.util.CursorPaginatedResponseDataObjectTest

trackCarriesProvenanceBrowserPositionAndOnePslLinePerAlignment() - Method in class ubic.gemma.core.analysis.sequence.BlatResult2PslTest

trackLineKeepsItsQuotes() - Method in class ubic.gemma.core.analysis.sequence.BlatResult2PslTest

The track line keeps its quotes -- track name="..." is UCSC's own syntax for that line, unlike the PSL data rows.

trackNameDefaultsToTheQuerySequenceName() - Method in class ubic.gemma.core.analysis.sequence.BlatResult2PslTest

transactionManager(SessionFactory) - Method in class ubic.gemma.core.util.test.BaseDatabaseTest5.BaseDatabaseTestContextConfiguration

transientAnalysis_omitsTheAnalysisId() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtilsTest

transition_IN_PROGRESS_to_RESOLVED_emitsResolved() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

transition_noop_is_silent() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

transition_OPEN_to_CANCELLED_emitsCancelled() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

transition_OPEN_to_IN_PROGRESS_emitsStateChanged() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

transition_RESOLVED_to_OPEN_emitsReopened() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

TriageVerdictTest - Class in ubic.gemma.model.common.auditAndSecurity.curation

The wire form of TriageVerdict.

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

troubled_genericOnly_isFalse() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

troubled_noOpenTickets_isFalse() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

troubled_qualityReviewOpen_isTrue() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImplTest

TsvUtilsTest - Class in ubic.gemma.core.util

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

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

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

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

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

twoColor() - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactory

Start building a two-color (dual-channel, cDNA) array design.

twoColor_setsTechnologyType() - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactoryTest

twoFindingsOnOneSet_ruledIndependently() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

twoFindingsOnOneTarget_ruledIndependently() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

twoJudgesCoexist() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriagePersistenceIT

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

U

uberonOntologyService(TaskExecutor) - Method in class ubic.gemma.core.ontology.TestOntologyConfig

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

Loads a ROBOT STAR-extracted module of Uberon (substantia-nigra subhierarchy) from a classpath fixture so the test runs in the default surefire pass.

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

ubic.gemma.apps - package ubic.gemma.apps

ubic.gemma.cli.metrics - package ubic.gemma.cli.metrics

ubic.gemma.cli.util - package ubic.gemma.cli.util

ubic.gemma.cli.util.test - package ubic.gemma.cli.util.test

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.convert - package ubic.gemma.core.analysis.preprocess.convert

ubic.gemma.core.analysis.preprocess.detect - package ubic.gemma.core.analysis.preprocess.detect

ubic.gemma.core.analysis.preprocess.filter - package ubic.gemma.core.analysis.preprocess.filter

ubic.gemma.core.analysis.preprocess.slice - package ubic.gemma.core.analysis.preprocess.slice

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.analysis.singleCell - package ubic.gemma.core.analysis.singleCell

ubic.gemma.core.analysis.singleCell.aggregate - package ubic.gemma.core.analysis.singleCell.aggregate

ubic.gemma.core.analysis.stats - package ubic.gemma.core.analysis.stats

ubic.gemma.core.architecture - package ubic.gemma.core.architecture

ubic.gemma.core.config - package ubic.gemma.core.config

ubic.gemma.core.context - package ubic.gemma.core.context

ubic.gemma.core.datastructure.matrix - package ubic.gemma.core.datastructure.matrix

ubic.gemma.core.datastructure.matrix.io - package ubic.gemma.core.datastructure.matrix.io

ubic.gemma.core.datastructure.sparse - package ubic.gemma.core.datastructure.sparse

ubic.gemma.core.geoscrape - package ubic.gemma.core.geoscrape

ubic.gemma.core.goldenpath - package ubic.gemma.core.goldenpath

ubic.gemma.core.job - package ubic.gemma.core.job

ubic.gemma.core.job.progress - package ubic.gemma.core.job.progress

ubic.gemma.core.loader.association - package ubic.gemma.core.loader.association

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.cellxgene - package ubic.gemma.core.loader.expression.cellxgene

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.fetcher2 - package ubic.gemma.core.loader.expression.geo.fetcher2

ubic.gemma.core.loader.expression.geo.service - package ubic.gemma.core.loader.expression.geo.service

ubic.gemma.core.loader.expression.geo.singleCell - package ubic.gemma.core.loader.expression.geo.singleCell

ubic.gemma.core.loader.expression.simple - package ubic.gemma.core.loader.expression.simple

ubic.gemma.core.loader.expression.singleCell - package ubic.gemma.core.loader.expression.singleCell

ubic.gemma.core.loader.expression.singleCell.transform - package ubic.gemma.core.loader.expression.singleCell.transform

ubic.gemma.core.loader.expression.sra - package ubic.gemma.core.loader.expression.sra

ubic.gemma.core.loader.expression.ucsc.cellbrowser - package ubic.gemma.core.loader.expression.ucsc.cellbrowser

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.anndata - package ubic.gemma.core.loader.util.anndata

ubic.gemma.core.loader.util.biomart - package ubic.gemma.core.loader.util.biomart

ubic.gemma.core.loader.util.fetcher - package ubic.gemma.core.loader.util.fetcher

ubic.gemma.core.loader.util.hdf5 - package ubic.gemma.core.loader.util.hdf5

ubic.gemma.core.loader.util.mapper - package ubic.gemma.core.loader.util.mapper

ubic.gemma.core.logging - package ubic.gemma.core.logging

ubic.gemma.core.logging.log4j - package ubic.gemma.core.logging.log4j

ubic.gemma.core.mail - package ubic.gemma.core.mail

ubic.gemma.core.metrics - package ubic.gemma.core.metrics

ubic.gemma.core.metrics.binder - package ubic.gemma.core.metrics.binder

ubic.gemma.core.ontology - package ubic.gemma.core.ontology

ubic.gemma.core.ontology.ols - package ubic.gemma.core.ontology.ols

ubic.gemma.core.ontology.providers - package ubic.gemma.core.ontology.providers

ubic.gemma.core.ontology.providers.chebi - package ubic.gemma.core.ontology.providers.chebi

ubic.gemma.core.scheduler - package ubic.gemma.core.scheduler

ubic.gemma.core.search - package ubic.gemma.core.search

ubic.gemma.core.search.indexer - package ubic.gemma.core.search.indexer

ubic.gemma.core.search.source - package ubic.gemma.core.search.source

ubic.gemma.core.security - package ubic.gemma.core.security

ubic.gemma.core.security.acl - package ubic.gemma.core.security.acl

ubic.gemma.core.security.acl.afterinvocation - package ubic.gemma.core.security.acl.afterinvocation

ubic.gemma.core.security.acl.domain - package ubic.gemma.core.security.acl.domain

ubic.gemma.core.security.acl.voter - package ubic.gemma.core.security.acl.voter

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.concurrent - package ubic.gemma.core.security.concurrent

ubic.gemma.core.security.principal - package ubic.gemma.core.security.principal

ubic.gemma.core.security.util - package ubic.gemma.core.security.util

ubic.gemma.core.tasks.analysis.diffex - package ubic.gemma.core.tasks.analysis.diffex

ubic.gemma.core.util - package ubic.gemma.core.util

ubic.gemma.core.util.concurrent - package ubic.gemma.core.util.concurrent

ubic.gemma.core.util.locking - package ubic.gemma.core.util.locking

ubic.gemma.core.util.math - package ubic.gemma.core.util.math

ubic.gemma.core.util.math.linearmodels - package ubic.gemma.core.util.math.linearmodels

ubic.gemma.core.util.matrix.datafilter - package ubic.gemma.core.util.matrix.datafilter

ubic.gemma.core.util.runtime - package ubic.gemma.core.util.runtime

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.fixture - package ubic.gemma.core.util.test.fixture

ubic.gemma.core.visualization - package ubic.gemma.core.visualization

ubic.gemma.core.visualization.cellbrowser - package ubic.gemma.core.visualization.cellbrowser

ubic.gemma.model.analysis - package ubic.gemma.model.analysis

ubic.gemma.model.analysis.expression.diff - package ubic.gemma.model.analysis.expression.diff

ubic.gemma.model.common - package ubic.gemma.model.common

ubic.gemma.model.common.auditAndSecurity.curation - package ubic.gemma.model.common.auditAndSecurity.curation

ubic.gemma.model.common.auditAndSecurity.eventType - package ubic.gemma.model.common.auditAndSecurity.eventType

ubic.gemma.model.common.description - package ubic.gemma.model.common.description

ubic.gemma.model.common.quantitationtype - package ubic.gemma.model.common.quantitationtype

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.util - package ubic.gemma.model.util

ubic.gemma.persistence.audit - package ubic.gemma.persistence.audit

ubic.gemma.persistence.cache - package ubic.gemma.persistence.cache

ubic.gemma.persistence.hibernate - package ubic.gemma.persistence.hibernate

ubic.gemma.persistence.initialization - package ubic.gemma.persistence.initialization

ubic.gemma.persistence.persister - package ubic.gemma.persistence.persister

ubic.gemma.persistence.retry - package ubic.gemma.persistence.retry

ubic.gemma.persistence.service - package ubic.gemma.persistence.service

ubic.gemma.persistence.service.analysis.expression - package ubic.gemma.persistence.service.analysis.expression

ubic.gemma.persistence.service.analysis.expression.diff - package ubic.gemma.persistence.service.analysis.expression.diff

ubic.gemma.persistence.service.analysis.expression.pca - package ubic.gemma.persistence.service.analysis.expression.pca

ubic.gemma.persistence.service.analysis.expression.sampleCoexpression - package ubic.gemma.persistence.service.analysis.expression.sampleCoexpression

ubic.gemma.persistence.service.blacklist - package ubic.gemma.persistence.service.blacklist

ubic.gemma.persistence.service.common.auditAndSecurity - package ubic.gemma.persistence.service.common.auditAndSecurity

ubic.gemma.persistence.service.common.auditAndSecurity.curation - package ubic.gemma.persistence.service.common.auditAndSecurity.curation

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.arrayDesign - package ubic.gemma.persistence.service.expression.arrayDesign

ubic.gemma.persistence.service.expression.bioAssay - package ubic.gemma.persistence.service.expression.bioAssay

ubic.gemma.persistence.service.expression.bioAssayData - package ubic.gemma.persistence.service.expression.bioAssayData

ubic.gemma.persistence.service.expression.biomaterial - package ubic.gemma.persistence.service.expression.biomaterial

ubic.gemma.persistence.service.expression.designElement - package ubic.gemma.persistence.service.expression.designElement

ubic.gemma.persistence.service.expression.experiment - package ubic.gemma.persistence.service.expression.experiment

ubic.gemma.persistence.service.genome - package ubic.gemma.persistence.service.genome

ubic.gemma.persistence.service.genome.gene - package ubic.gemma.persistence.service.genome.gene

ubic.gemma.persistence.service.genome.sequenceAnalysis - package ubic.gemma.persistence.service.genome.sequenceAnalysis

ubic.gemma.persistence.service.maintenance - package ubic.gemma.persistence.service.maintenance

ubic.gemma.persistence.util - package ubic.gemma.persistence.util

ubic.gemma.rest - package ubic.gemma.rest

ubic.gemma.rest.analytics.ga4 - package ubic.gemma.rest.analytics.ga4

ubic.gemma.rest.providers - package ubic.gemma.rest.providers

ubic.gemma.rest.ranking - package ubic.gemma.rest.ranking

ubic.gemma.rest.serializers - package ubic.gemma.rest.serializers

ubic.gemma.rest.servlet - package ubic.gemma.rest.servlet

ubic.gemma.rest.util - package ubic.gemma.rest.util

ubic.gemma.rest.util.args - package ubic.gemma.rest.util.args

UcscCellBrowserUtilsTest - Class in ubic.gemma.core.loader.expression.ucsc.cellbrowser

UcscCellBrowserUtilsTest() - Constructor for class ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtilsTest

unconditionalGzipIsHandledBeforeTheEncoder() - Method in class ubic.gemma.rest.providers.GzipHeaderDecoratorTest

uncountableIndexTriggersAReindex() - Method in class ubic.gemma.core.search.indexer.ScheduledSearchReindexerTest

An unreadable index reports drift, which must reach the rebuild rather than being swallowed.

unFisherTransform_invertsFisherTransform() - Method in class ubic.gemma.core.util.math.CorrelationStatsTest

uninitializedLazyCollection_isSteppedOverAndTheWalkContinues() - Method in class ubic.gemma.core.security.acl.AclEventListenerTest

A lazy collection that was never loaded must be stepped over, not iterated.

unknownFormat_failsClosed() - Method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoderTest

UnknownQueryParameterFilterDisabledTest - Class in ubic.gemma.rest.providers

gemma.rest.rejectUnknownQueryParameters=false restores the JAX-RS default of ignoring an undeclared parameter.

UnknownQueryParameterFilterDisabledTest() - Constructor for class ubic.gemma.rest.providers.UnknownQueryParameterFilterDisabledTest

UnknownQueryParameterFilterDisabledTest.CustomResource - Class in ubic.gemma.rest.providers

UnknownQueryParameterFilterTest - Class in ubic.gemma.rest.providers

Pins the rejection of query parameters a resource method cannot bind, and — just as importantly — the four cases that must keep working: a declared parameter, a path parameter, a route that reads the query string itself, and a route that has been annotated to opt out.

UnknownQueryParameterFilterTest() - Constructor for class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest

UnknownQueryParameterFilterTest.CustomResource - Class in ubic.gemma.rest.providers

unlocked_readsAsFree() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockPersistenceIT

unplaceableAlignmentsAreDroppedRatherThanFailingTheTrack() - Method in class ubic.gemma.rest.PlatformsWebServicePslTrackTest

An alignment with no target chromosome cannot be placed in the browser.

unreadableDatasetsNeverReachTheTicketLookup() - Method in class ubic.gemma.rest.DatasetsWebServiceTicketsBulkTest

🛑 The ticket table carries no ACL of its own, so the readability filter has to run BEFORE the lookup, not after it.

unrecognizedShapeIsUnknownRatherThanZero() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetPayloadCountsTest

🛑 The distinction the whole class exists for.

unruled_hasNoRow() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionPersistenceIT

unsetByDefault() - Method in class ubic.gemma.core.security.util.ActingIdentityTest

unsupportedConfigAttribute_passesObjectThrough() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationStreamFilteringProviderTest

unsupportedConfigAttribute_returnsInputUnchanged() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProviderTest

unsupportedConfigAttribute_returnsInputUnchanged() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProviderTest

unsupportedConfigAttribute_returnsInputUnchanged() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapFilteringProviderTest

unsupportedConfigAttribute_returnsInputUnchanged() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapValueFilteringProviderTest

unsupportedConfigAttribute_returnsInputUnchanged() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationOwnedCollectionFilteringProviderTest

unsupportedConfigAttribute_returnsInputUnchanged() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationPrivateCollectionFilteringProviderTest

unsupportedConfigAttribute_returnsInputUnchanged() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProviderTest

unsupportedConfigAttribute_returnsInputUnchanged() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest

untriaged_hasNoRow() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriagePersistenceIT

update(MutableAcl) - Method in class ubic.gemma.core.security.authorization.acl.AclTestUtils

update(User) - Method in class ubic.gemma.core.security.UserServiceImpl

update(UserGroup) - Method in class ubic.gemma.core.security.UserServiceImpl

updateAcl(MutableAcl) - Method in class ubic.gemma.core.security.acl.InMemoryAclService

updateChildAclPersistsParentObjectFkAndEntriesInheriting() - Method in class ubic.gemma.core.security.acl.domain.AclDaoImplParentPersistenceTest

Reproduce the SecuredChild-with-parent-ACL update path used by ExperimentalDesignServiceImpl.update(Securable) in Gemma.

UpdateGeoSourceMetadataCliTest - Class in ubic.gemma.apps

The backfill writes the GEO document and nothing else, and it skips what is already done.

UpdateGeoSourceMetadataCliTest() - Constructor for class ubic.gemma.apps.UpdateGeoSourceMetadataCliTest

updateMetadata_auditOnly_noTicketEvent() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

updateMetadata_bumpsUpdatedAt_andDoesNotAppendTicketEvent() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

updateProvenance_blankClears() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

updateProvenance_correctsInPlace() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

The reason the route exists: correcting a mis-stamped envelope used to mean delete + recreate, which mints a new id, and set ids are quoted across handoffs.

updateProvenance_unknownId() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetPersistenceIT

updateTargetStatus_appendsTargetStatusChangedEvent_andBumpsUpdatedAt() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

updateTargetStatus_marksOneTargetDone() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

updateTargetStatus_noOp_whenAlreadyAtRequestedStatus() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

updateTargetStatus_unknownTargetId_throwsIAE() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImplTest

updateUser(UserDetails) - Method in class ubic.gemma.core.security.UserDetailsManagerImpl

urgent_cancelled_roundTrip() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketPersistenceIT

url() - Element in annotation interface ubic.gemma.core.util.test.NetworkAvailable

Assume that one (or multiple) resources identified by URLs are available.

usageWeighted_neverDisplacesTheTopLexicalHit() - Method in class ubic.gemma.rest.AnnotationSearchRankingStrategyTest

usageWeighted_pullsHighUsageForward() - Method in class ubic.gemma.rest.AnnotationSearchRankingStrategyTest

UserDaoTest - Class in ubic.gemma.persistence.service.common.auditAndSecurity

UserDaoTest() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.UserDaoTest

UserDetailsManagerImpl - Class in ubic.gemma.core.security

UserDetailsManagerImpl() - Constructor for class ubic.gemma.core.security.UserDetailsManagerImpl

userExists(String) - Method in class ubic.gemma.core.security.UserDetailsManagerImpl

UserGroupServiceTest - Class in ubic.gemma.core.security

Tests the Group facilities of the UserManager..

UserGroupServiceTest() - Constructor for class ubic.gemma.core.security.UserGroupServiceTest

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

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

UserServiceImpl - Class in ubic.gemma.core.security

UserServiceImpl() - Constructor for class ubic.gemma.core.security.UserServiceImpl

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

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

userWithEmailExists(String) - Method in class ubic.gemma.core.security.UserDetailsManagerImpl

V

validateSignupToken(String, String) - Method in class ubic.gemma.core.security.UserDetailsManagerImpl

value - Variable in class ubic.gemma.core.util.RoundingUtilsTest.Holder

valueObjectBuiltAfterAThawCarriesTheEvents() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.DetachedCuratableValueObjectTest

The refresh endpoint's shape: thaw in one transaction, build the value object in the next.

valueObjectBuiltWithoutAThawDropsTheEventsRatherThanThrowing() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.DetachedCuratableValueObjectTest

Same shape with the thaw missing, which is what production was doing.

valueOf(String) - Static method in enum class ubic.gemma.core.util.test.fixture.ExperimentFactory.Modality

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest.FakeEnum

Returns the enum constant of this class with the specified name.

values() - Static method in enum class ubic.gemma.core.util.test.fixture.ExperimentFactory.Modality

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest.FakeEnum

Returns an array containing the constants of this enum class, in the order they are declared.

valuesArePreservedAcrossFilter() - Method in class ubic.gemma.core.util.matrix.datafilter.RowMissingFilterTest

valueSpel_auditedConditionalSkipsWhenPredicateFalse() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

@AuditedConditional predicate false → no emission even if valueSpel would have resolved.

valueSpel_bothSetSpelChoiceWins() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Both value and valueSpel non-default: the SpEL choice wins when it resolves successfully (the literal value is the fallback for the broken-SpEL path).

valueSpel_brokenExpressionFallsBackToLiteralValue() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Broken valueSpel: the SpEL expression cannot evaluate.

valueSpel_noEventTypeResolvedSkips() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

Both value at its abstract default AND empty valueSpel: no concrete class to write, the aspect must skip emission entirely.

valueSpel_nullResultSkipsEmission() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

valueSpel returns null (the helper has no class for which == "x"); value() is at its abstract default.

valueSpel_resolvesToBranchA() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

valueSpel resolves to SampleRemovalEvent when which == "a".

valueSpel_resolvesToBranchB() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

valueSpel resolves to SampleRemovalReversionEvent when which == "b" — different concrete class from branch A, on the same annotated method.

valueSpel_worksOnAuditedConditional() - Method in class ubic.gemma.core.security.audit.AuditedAspectTest

@AuditedConditional also honours valueSpel: when the predicate fires, the event class is resolved at runtime.

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

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

VerifyPublicationEvidenceCliTest - Class in ubic.gemma.apps

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.

VerifyPublicationEvidenceCliTest() - Constructor for class ubic.gemma.apps.VerifyPublicationEvidenceCliTest

VirtualThreadExecutorMetricsTest - Class in ubic.gemma.core.metrics.binder

Verifies that VirtualThreadExecutorMetrics correctly increments its counters/gauges when wrapped tasks are submitted, complete, or throw.

VirtualThreadExecutorMetricsTest() - Constructor for class ubic.gemma.core.metrics.binder.VirtualThreadExecutorMetricsTest

VoConverterTestContextConfiguration() - Constructor for class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest.VoConverterTestContextConfiguration

voWithoutAcl_throwsAccessDeniedException() - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProviderTest

W

WebApplicationExceptionMapperTest - Class in ubic.gemma.rest.providers

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

WebApplicationExceptionMapperTest.CustomResource - Class in ubic.gemma.rest.providers

This is a very simplisitc example that produces two representation for the same resource.

WebApplicationExceptionMapperTest.CustomResource.MyModel - Class in ubic.gemma.rest.providers

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

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.

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

What this test catches - Section in class ubic.gemma.persistence.util.HqlSmokeIT

What this test does NOT catch - Section in class ubic.gemma.persistence.util.HqlSmokeIT

What went wrong - Section in class ubic.gemma.core.analysis.expression.diff.NoSubSetAnalysisIsNotSuccessTest

whenTripletIsDirectlyInSampleDir_thenItIsUsed() - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurerTest

whenTripletIsMissingEntirely_thenItThrows() - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurerTest

whenTripletIsNestedUnderCellRangerOuts_thenItIsResolved() - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurerTest

whenTripletIsNestedUnderRawMatrix_thenItIsResolved() - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurerTest

Why an arm can be empty - Section in class ubic.gemma.core.analysis.expression.diff.EmptySubSetIsSkippedTest

Why the cached entity is re-validated - Section in ubic.gemma.core.util.test.PersistentDummyObjectHelper.getTestPersistentTaxon()

Why the existing coverage missed it - Section in class ubic.gemma.core.security.acl.EventListenerRegistrationLazyContextTest

withAccession(boolean) - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactory.Builder

withAccessionFalse_skipsAccession() - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactoryTest

withArguments(String...) - Method in class ubic.gemma.cli.util.test.CliAssert

Set the arguments passed to the command.

withArrayDesign(ArrayDesign) - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactory.Builder

withArrayDesign(ArrayDesign) - Method in class ubic.gemma.core.util.test.fixture.CompositeSequenceFactory.Builder

withArrayDesign(ArrayDesign) - Method in class ubic.gemma.core.util.test.fixture.ExperimentFactory.Builder

withArrayDesign_usesSuppliedAD() - Method in class ubic.gemma.core.util.test.fixture.ExperimentFactoryTest

withBioMaterial(BioMaterial) - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactory.Builder

withBioSequence(boolean) - Method in class ubic.gemma.core.util.test.fixture.CompositeSequenceFactory.Builder

If true (default), attach a persistent BioSequence (with a GenBank DatabaseEntry) to the CS.

withBioSequenceFalse_skipsBioSequence() - Method in class ubic.gemma.core.util.test.fixture.CompositeSequenceFactoryTest

withCommandNameOrAlias(String) - Method in class ubic.gemma.cli.util.test.CliAssert

Set the command name or alias used to execute the command.

withCommonName(String) - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory.AdHocBuilder

withConsole(Console) - Method in class ubic.gemma.cli.util.test.CliAssert

Set the console to be used for interactive use.

withCustomArrayDesign_appliesOverride() - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactoryTest

withCustomArrayDesign_appliesOverride() - Method in class ubic.gemma.core.util.test.fixture.CompositeSequenceFactoryTest

withCustomBioMaterial_appliesOverride() - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactoryTest

withDescription(String) - Method in class ubic.gemma.core.util.test.fixture.CompositeSequenceFactory.Builder

withDescription_appliesOverride() - Method in class ubic.gemma.core.util.test.fixture.CompositeSequenceFactoryTest

withdraw_returnsToUntriaged() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriagePersistenceIT

withEnvironment(Map) - Method in class ubic.gemma.cli.util.test.CliAssert

Set the environment variables to be used when executing the command.

withErrorStream(OutputStream) - Method in class ubic.gemma.cli.util.test.CliAssert

withExternalAccession() - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactory.Builder

withExternalAccession() - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactory

Convenience: attach a GEO external accession (defaults elsewhere).

withExternalAccession_attachesGeoAccession() - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactoryTest

withGeneProducts(int) - Method in class ubic.gemma.core.util.test.fixture.GeneFactory.GeneBuilder

Attach N GeneProducts to the gene.

withGeneProducts_attachesAndPersistsThem() - Method in class ubic.gemma.core.util.test.fixture.GeneFactoryTest

withGeneProductsZero_isLegalAndProducesEmptyProducts() - Method in class ubic.gemma.core.util.test.fixture.GeneFactoryTest

withGenesUsable(boolean) - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory.AdHocBuilder

withInputStream(InputStream) - Method in class ubic.gemma.cli.util.test.CliAssert

Set the input stream to be used as standard input for the command.

withIsOutlier(boolean) - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactory.Builder

withName(String) - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactory.Builder

withName(String) - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactory.Builder

withName(String) - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactory.Builder

withName(String) - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactory

Convenience for the common "specify name, defaults elsewhere" case.

withName(String) - Method in class ubic.gemma.core.util.test.fixture.CompositeSequenceFactory.Builder

withName(String) - Method in class ubic.gemma.core.util.test.fixture.GeneFactory.GeneBuilder

withName_appliesOverride() - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactoryTest

withName_appliesOverride() - Method in class ubic.gemma.core.util.test.fixture.CompositeSequenceFactoryTest

withNcbiId(int) - Method in class ubic.gemma.core.util.test.fixture.GeneFactory.GeneBuilder

withNcbiId(Integer) - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory.AdHocBuilder

withNcbiId_appliesOverride() - Method in class ubic.gemma.core.util.test.fixture.GeneFactoryTest

withOfficialName(String) - Method in class ubic.gemma.core.util.test.fixture.GeneFactory.GeneBuilder

withOfficialSymbol(String) - Method in class ubic.gemma.core.util.test.fixture.GeneFactory.GeneBuilder

withOfficialSymbolAndName_appliesOverride() - Method in class ubic.gemma.core.util.test.fixture.GeneFactoryTest

withoutMissingValuesBothViewsAgree() - Method in class ubic.gemma.core.util.math.linearmodels.FittedValuesForExcludedSamplesTest

With nothing missing the two views are the same matrix of numbers, so no caller can be surprised by reaching for the new one.

withOutputStream(OutputStream) - Method in class ubic.gemma.cli.util.test.CliAssert

withPathParam(String, String) - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilterTest.CustomResource

withProbes(int) - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactory.Builder

Attach N composite sequences (probes) to the array design.

withProbes_producesExactlyNCompositeSequences() - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactoryTest

withRandomProbeNames(boolean) - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactory.Builder

If false, probes are named probeset_0, probeset_1, ...

withRandomProbeNamesFalse_namesAreDeterministic() - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactoryTest

withSamples(int) - Method in class ubic.gemma.core.util.test.fixture.ExperimentFactory.Builder

withSamples_producesExactlyNBioAssays() - Method in class ubic.gemma.core.util.test.fixture.ExperimentFactoryTest

withScientificName(String) - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory.AdHocBuilder

withSequencePairedReads(boolean) - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactory.Builder

withSequences(boolean) - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactory.Builder

If true, each probe is also given a BioSequence (persisted ahead of the AD).

withSequencesTrue_attachesBioSequencesToEveryProbe() - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactoryTest

withShortName(String) - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactory.Builder

withShortName(String) - Method in class ubic.gemma.core.util.test.fixture.ExperimentFactory.Builder

withShortName_appliesOverride() - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactoryTest

withSourceBioMaterial(BioMaterial) - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactory.Builder

withSourceBioMaterial(BioMaterial) - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactory

Convenience for the common "specify parent, defaults elsewhere" case.

withSourceBioMaterial_chainsParentCorrectly() - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactoryTest

withSourceBioMaterial_rejectsTransientParent() - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactoryTest

withTaxon(Taxon) - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactory.Builder

withTaxon(Taxon) - Method in class ubic.gemma.core.util.test.fixture.BioAssayFactory.Builder

Set the taxon to use when auto-creating the BioMaterial and ArrayDesign defaults.

withTaxon(Taxon) - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactory.Builder

withTaxon(Taxon) - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactory

Convenience for the common "specify taxon, defaults elsewhere" case.

withTaxon(Taxon) - Method in class ubic.gemma.core.util.test.fixture.CompositeSequenceFactory.Builder

Set the taxon used for the auto-created BioSequence.

withTaxon(Taxon) - Method in class ubic.gemma.core.util.test.fixture.ExperimentFactory.Builder

withTaxon(Taxon) - Method in class ubic.gemma.core.util.test.fixture.GeneFactory.GeneBuilder

withTaxon_appliesOverride() - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactoryTest

withTaxon_appliesOverride() - Method in class ubic.gemma.core.util.test.fixture.GeneFactoryTest

withTaxon_setsBioSequenceTaxon() - Method in class ubic.gemma.core.util.test.fixture.CompositeSequenceFactoryTest

withTaxon_usesSuppliedTaxon() - Method in class ubic.gemma.core.util.test.fixture.BioMaterialFactoryTest

withTechnologyType(TechnologyType) - Method in class ubic.gemma.core.util.test.fixture.ArrayDesignFactory

Start building an array design with a caller-supplied technology type.

work() - Method in interface ubic.gemma.persistence.retry.RetryTest.TestRetryDao

WorkflowServiceTest - Class in ubic.gemma.persistence.service.expression.experiment

Pure-Mockito unit tests for WorkflowServiceImpl: state-machine enforcement, idempotent no-op semantics, the disallowed-transition exception.

WorkflowServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.WorkflowServiceTest

WorkflowWebServiceTest - Class in ubic.gemma.rest

Pure-Mockito unit tests for WorkflowWebService: REST-shape validation, error mapping (404 / 400 / 409).

WorkflowWebServiceTest() - Constructor for class ubic.gemma.rest.WorkflowWebServiceTest

worm() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory

Resolve the seeded worm taxon (NCBI 6239).

wrappedStreamFallsBackToStreamingThroughTheEncoder() - Method in class ubic.gemma.rest.providers.SendfileProviderTest

The guard.

wrapsIllegalArgumentInMalformedArg() - Method in class ubic.gemma.rest.util.args.CursorArgTest

Y

yeast() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory

Resolve the seeded yeast taxon (NCBI 4932, secondary 559292).

Z

zebrafish() - Method in class ubic.gemma.core.util.test.fixture.TaxonFactory

Resolve the seeded zebrafish taxon (NCBI 7955).

zeroBytesPerSecond_rendersAsBytesPerSecond() - Method in class ubic.gemma.core.util.NetUtilsTest

ZeroVarianceFilterTest - Class in ubic.gemma.core.analysis.preprocess.filter

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

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