Index (Gemma 1.31.3-SNAPSHOT Test API)

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

A

AbstractArrayDesignProcessingTest - Class in ubic.gemma.core.loader.expression.arrayDesign: Base test for tests that need persistent array design with sequences.
AbstractArrayDesignProcessingTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.AbstractArrayDesignProcessingTest
AbstractDaoIntegrationTest - Class in ubic.gemma.persistence.service
AbstractDaoIntegrationTest() - Constructor for class ubic.gemma.persistence.service.AbstractDaoIntegrationTest
AbstractDaoTest - Class in ubic.gemma.persistence.service
AbstractDaoTest() - Constructor for class ubic.gemma.persistence.service.AbstractDaoTest
AbstractDaoTest.MyDao - Class in ubic.gemma.persistence.service
AbstractDaoTest.MyEntity - Class in ubic.gemma.persistence.service
AbstractDwrReplyMatchers - Class in ubic.gemma.web.util.dwr
AbstractDwrReplyMatchers(String, int, int) - Constructor for class ubic.gemma.web.util.dwr.AbstractDwrReplyMatchers
AbstractDwrReplyParser - Class in ubic.gemma.web.util.dwr
AbstractDwrReplyParser(String, int, int) - Constructor for class ubic.gemma.web.util.dwr.AbstractDwrReplyParser
AbstractFetcherTest - Class in ubic.gemma.core.loader.util.fetcher
AbstractFetcherTest() - Constructor for class ubic.gemma.core.loader.util.fetcher.AbstractFetcherTest
AbstractFileServiceTest - Class in ubic.gemma.core.analysis.service
AbstractFileServiceTest() - Constructor for class ubic.gemma.core.analysis.service.AbstractFileServiceTest
AbstractFilteringVoEnabledDaoTest - Class in ubic.gemma.persistence.service
AbstractFilteringVoEnabledDaoTest() - Constructor for class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest
AbstractFilteringVoEnabledDaoTest.FakeEnum - Enum in ubic.gemma.persistence.service
AbstractGeoServiceTest - Class in ubic.gemma.core.loader.expression.geo
AbstractGeoServiceTest() - Constructor for class ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest
AbstractServiceTest - Class in ubic.gemma.persistence.service
AbstractServiceTest() - Constructor for class ubic.gemma.persistence.service.AbstractServiceTest
AbstractServiceTest.ExceptionWithMessage - Exception in ubic.gemma.persistence.service
AbstractServiceTest.ExceptionWithoutMessage - Exception in ubic.gemma.persistence.service
accessDecisionManager() - Method in class ubic.gemma.rest.SearchWebServiceTest.SearchWebServiceTestContextConfiguration
AclAdviceTest - Class in ubic.gemma.core.security.authorization.acl: Tests of ACL management: adding and removing from objects during CRUD operations.
AclAdviceTest() - Constructor for class ubic.gemma.core.security.authorization.acl.AclAdviceTest
AclAuthorizationTest - Class in ubic.gemma.core.security.authorization.acl
AclAuthorizationTest() - Constructor for class ubic.gemma.core.security.authorization.acl.AclAuthorizationTest
AclCollectionBeforeTest - Class in ubic.gemma.core.security.authorization.acl: Test the AclCollectionEntryVoter.
AclCollectionBeforeTest() - Constructor for class ubic.gemma.core.security.authorization.acl.AclCollectionBeforeTest
AclCriteriaUtilsTest - Class in ubic.gemma.persistence.util
AclCriteriaUtilsTest() - Constructor for class ubic.gemma.persistence.util.AclCriteriaUtilsTest
aclDao(SessionFactory) - Method in class ubic.gemma.core.util.test.BaseDatabaseTest.BaseDatabaseTestContextConfiguration
AclQueryUtilsTest - Class in ubic.gemma.persistence.util
AclQueryUtilsTest() - Constructor for class ubic.gemma.persistence.util.AclQueryUtilsTest
aclService - Variable in class ubic.gemma.core.util.test.BaseDatabaseTest
aclService(AclDao) - Method in class ubic.gemma.core.util.test.BaseDatabaseTest.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
addTestAnalyses(ExpressionExperiment) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Create test Analysis for the given expression experiment.
addTestAnalyses(ExpressionExperiment) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
AffyChipTypeExtractorTest - Class in ubic.gemma.core.loader.expression.arrayDesign
AffyChipTypeExtractorTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractorTest
AffyPowerToolsProbesetSummarizeTest - Class in ubic.gemma.core.loader.expression
AffyPowerToolsProbesetSummarizeTest() - Constructor for class ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarizeTest
AffyProbeReaderTest - Class in ubic.gemma.core.loader.expression.arrayDesign
AffyProbeReaderTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReaderTest
AffyScanDateExtractorTest - Class in ubic.gemma.core.analysis.preprocess.batcheffects
AffyScanDateExtractorTest() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractorTest
after() - Method in class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceTest
after() - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceTest
after() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVectorServiceTest
afterPropertiesSet() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test
afterPropertiesSet() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest
afterPropertiesSet() - Method in class ubic.gemma.core.util.test.BaseDatabaseTest.DataSourceInitializer
afterPropertiesSet() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
afterPropertiesSet() - Method in class ubic.gemma.core.util.test.TestAuthenticationUtilsImpl
afterPropertiesSet() - Method in class ubic.gemma.persistence.retry.RetryTest
afterPropertiesSet() - Method in class ubic.gemma.rest.util.BaseJerseyTest
afterPropertiesSet() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupControllerTest
afterPropertiesSet() - Method in class ubic.gemma.web.util.BaseSpringWebTest
afterPropertiesSet() - Method in class ubic.gemma.web.util.BaseWebTest
afterTestMethod(TestContext) - Method in class org.springframework.security.test.context.support.WithSecurityContextTestExecutionListener: Clears out the TestSecurityContextHolder and the SecurityContextHolder after each test method.
AgilentScanDateExtractorTest - Class in ubic.gemma.core.analysis.preprocess.batcheffects: Tests of parsing various flat file formats used for Agilent slides (and possibly other types)
AgilentScanDateExtractorTest() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractorTest
AllenBrainAtlasServiceTest - Class in ubic.gemma.core.image.aba: Alan brain Atlas service test.
AllenBrainAtlasServiceTest() - Constructor for class ubic.gemma.core.image.aba.AllenBrainAtlasServiceTest
AllenBrainAtlasTest - Interface in ubic.gemma.core.util.test.category: Mark tests that require the Allen Brain Atlas RESTful API.
AllTests - Class in ubic.gemma.core.util.test.suite: Test suite consisting of all the tests in the current classpath.
AllTests() - Constructor for class ubic.gemma.core.util.test.suite.AllTests
AnalysisResultSetsJerseyTest - Class in ubic.gemma.rest: Integration test for the result sets endpoint.
AnalysisResultSetsJerseyTest() - Constructor for class ubic.gemma.rest.AnalysisResultSetsJerseyTest
AnalysisResultSetsWebServiceTest - Class in ubic.gemma.rest
AnalysisResultSetsWebServiceTest() - Constructor for class ubic.gemma.rest.AnalysisResultSetsWebServiceTest
analyticsProvider() - Method in class ubic.gemma.rest.SearchWebServiceTest.SearchWebServiceTestContextConfiguration
AnchorTagUtilTest - Class in ubic.gemma.web.util
AnchorTagUtilTest() - Constructor for class ubic.gemma.web.util.AnchorTagUtilTest
AncovaTest - Class in ubic.gemma.core.analysis.expression.diff: Tests of ANCOVA: using linear models with mixtures of fixed level and continuous parameters.
AncovaTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.AncovaTest
and(Object...) - Method in class ubic.gemma.web.util.dwr.DwrRequestBuilder: Chain one additional DWR call.
annotationsWebService(OntologyService, SearchService, CharacteristicService, ExpressionExperimentService, DatasetArgService, TaxonArgService) - 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
Api() - Constructor for class ubic.gemma.rest.util.args.StringArrayArgTest.Api
appDataHome - Variable in class ubic.gemma.persistence.util.SettingsConfigTest
applicationContext - Variable in class ubic.gemma.web.util.BaseSpringWebTest
ArrayDesignControllerTest - Class in ubic.gemma.web.controller.expression.arrayDesign
ArrayDesignControllerTest() - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerTest
ArrayDesignDaoTest - Class in ubic.gemma.persistence.service.expression.arrayDesign
ArrayDesignDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest
arrayDesignMergeCli() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration
ArrayDesignMergeCliTest - Class in ubic.gemma.core.apps
ArrayDesignMergeCliTest() - Constructor for class ubic.gemma.core.apps.ArrayDesignMergeCliTest
ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration - Class in ubic.gemma.core.apps
ArrayDesignMergeCliTestContextConfiguration() - Constructor for class ubic.gemma.core.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration
arrayDesignMergeService() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration
ArrayDesignMergeServiceTest - Class in ubic.gemma.core.loader.expression.arrayDesign
ArrayDesignMergeServiceTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeServiceTest
arrayDesignReportService() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration
ArrayDesignReportServiceTest - Class in ubic.gemma.core.analysis.report
ArrayDesignReportServiceTest() - Constructor for class ubic.gemma.core.analysis.report.ArrayDesignReportServiceTest
ArrayDesignSequenceAlignmentandMappingTest - Class in ubic.gemma.core.loader.expression.arrayDesign
ArrayDesignSequenceAlignmentandMappingTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentandMappingTest
ArrayDesignSequenceProcessorFastacmdTest - Class in ubic.gemma.core.loader.expression.arrayDesign: Test exercises the fastacmd - requires executable.
ArrayDesignSequenceProcessorFastacmdTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorFastacmdTest
ArrayDesignSequenceProcessorTest - Class in ubic.gemma.core.loader.expression.arrayDesign
ArrayDesignSequenceProcessorTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorTest
arrayDesignService() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration
arrayDesignService() - Method in class ubic.gemma.rest.SearchWebServiceTest.SearchWebServiceTestContextConfiguration
ArrayDesignServiceTest - Class in ubic.gemma.model.expression.arrayDesign
ArrayDesignServiceTest() - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
asHeader() - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.CsrfRequestPostProcessor: Instead of using the CsrfToken as a request parameter (default) will populate the CsrfToken as a header.
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.rest.util: Entrypoint for custom AssertJ 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
assumeThatResourceIsAvailable(String) - Static method in class ubic.gemma.core.util.test.Assumptions: Assume that a resource identified by a URL is available.
Assumptions - Class in ubic.gemma.core.util.test: Reusable assumptions for tests.
Assumptions() - Constructor for class ubic.gemma.core.util.test.Assumptions
AsyncBeanAutowiringTest - Class in ubic.gemma.persistence.util
AsyncBeanAutowiringTest() - Constructor for class ubic.gemma.persistence.util.AsyncBeanAutowiringTest
AsyncBeanAutowiringTest.MyService - Class in ubic.gemma.persistence.util
AsyncBeanAutowiringTest.MyService2 - Class in ubic.gemma.persistence.util
AsyncBeanAutowiringTest.MyService2Factory - Class in ubic.gemma.persistence.util
AsyncBeanAutowiringTest.MyServiceFactory - Class in ubic.gemma.persistence.util
AsyncFactoryTest - Class in ubic.gemma.persistence.util
AsyncFactoryTest() - Constructor for class ubic.gemma.persistence.util.AsyncFactoryTest
AsyncFactoryTest.MyService - Class in ubic.gemma.persistence.util
AsyncFactoryTest.MyServiceFactory - Class in ubic.gemma.persistence.util
AsyncSingletonFactoryTest - Class in ubic.gemma.persistence.util
AsyncSingletonFactoryTest() - Constructor for class ubic.gemma.persistence.util.AsyncSingletonFactoryTest
AsyncSingletonFactoryTest.MyService - Class in ubic.gemma.persistence.util
AsyncSingletonFactoryTest.MyServiceFactory - Class in ubic.gemma.persistence.util
AuditAdviceTest - Class in ubic.gemma.core.security.audit: Test of adding audit events when objects are created, updated or deleted.
AuditAdviceTest() - Constructor for class ubic.gemma.core.security.audit.AuditAdviceTest
AuditControllerTest - Class in ubic.gemma.web.remote
AuditControllerTest() - Constructor for class ubic.gemma.web.remote.AuditControllerTest
AuditEventDaoTest - Class in ubic.gemma.model.common.auditAndSecurity
AuditEventDaoTest() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEventDaoTest
AuditEventServiceTest - Class in ubic.gemma.model.common.auditAndSecurity
AuditEventServiceTest() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEventServiceTest
AuditEventTypeTest - Class in ubic.gemma.model.common.auditAndSecurity.eventType
AuditEventTypeTest() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventTypeTest
AuditTrailDaoTest - Class in ubic.gemma.model.common.auditAndSecurity
AuditTrailDaoTest() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditTrailDaoTest
auditTrailService() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration
AuditTrailServiceImplTest - Class in ubic.gemma.model.common.auditAndSecurity
AuditTrailServiceImplTest() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest
authenticated() - Static method in class org.springframework.security.test.web.servlet.response.SecurityMockMvcResultMatchers: ResultMatcher that verifies that a specified user is authenticated.
authentication(Authentication) - Static method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors: Establish a SecurityContext that uses the specified Authentication for the Authentication.getPrincipal() and a custom UserDetails.
authorities() - Method in annotation type org.springframework.security.test.context.support.WithMockUser: The authorities to use.
authorities(Collection<? extends GrantedAuthority>) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.UserRequestPostProcessor: Populates the user's GrantedAuthority's.
authorities(GrantedAuthority...) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.UserRequestPostProcessor: Populates the user's GrantedAuthority's.

B

BAR - ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest.FakeEnum
BaseAnalyzerConfigurationTest - Class in ubic.gemma.core.analysis.expression.diff: Other tests can extend this class if they want an expression experiment with complete block design and biological replicates.
BaseAnalyzerConfigurationTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.BaseAnalyzerConfigurationTest
BaseCliTest - Class in ubic.gemma.core.util.test: Minimal setup
BaseCliTest() - Constructor for class ubic.gemma.core.util.test.BaseCliTest
BaseDatabaseTest - Class in ubic.gemma.core.util.test: Minimalist test setup with an in-memory database and transactional test cases.
BaseDatabaseTest() - Constructor for class ubic.gemma.core.util.test.BaseDatabaseTest
BaseDatabaseTest.BaseDatabaseTestContextConfiguration - Class in ubic.gemma.core.util.test
BaseDatabaseTest.DataSourceInitializer - Class in ubic.gemma.core.util.test
BaseDatabaseTestContextConfiguration() - Constructor for class ubic.gemma.core.util.test.BaseDatabaseTest.BaseDatabaseTestContextConfiguration
BaseJerseyIntegrationTest - Class in ubic.gemma.rest.util: Base class for Jersey-based integration tests.
BaseJerseyIntegrationTest() - Constructor for class ubic.gemma.rest.util.BaseJerseyIntegrationTest
BaseJerseyTest - Class in ubic.gemma.rest.util: Base class for Jersey-based tests that needs a WebApplicationContext for loading and configuring or mocking Spring components.
BaseJerseyTest() - Constructor for class ubic.gemma.rest.util.BaseJerseyTest
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
BaseSpringContextTest - Class in ubic.gemma.core.util.test: subclass for tests that need the container and use the database
BaseSpringContextTest() - Constructor for class ubic.gemma.core.util.test.BaseSpringContextTest
BaseSpringWebTest - Class in ubic.gemma.web.util: Class to extend for tests of controllers et al.
BaseSpringWebTest() - Constructor for class ubic.gemma.web.util.BaseSpringWebTest
BaseWebTest - Class in ubic.gemma.web.util: Base class for a Web-based unit test.
BaseWebTest() - Constructor for class ubic.gemma.web.util.BaseWebTest
BaseWebTest.BaseWebTestContextConfiguration - Class in ubic.gemma.web.util
BaseWebTestContextConfiguration() - Constructor for class ubic.gemma.web.util.BaseWebTest.BaseWebTestContextConfiguration
batch(int) - Static method in class ubic.gemma.web.util.dwr.MockDwrResultMatchers: Match a batch of DWR results.
BatchInfoPopulationServiceIntegrationTest - Class in ubic.gemma.core.analysis.preprocess.batcheffects: Test fetching and loading the batch information from raw files.
BatchInfoPopulationServiceIntegrationTest() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceIntegrationTest
BatchInfoPopulationServiceTest - Class in ubic.gemma.core.analysis.preprocess.batcheffects: Unit tests.
BatchInfoPopulationServiceTest() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceTest
before() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceTest
before() - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationProcessingTest
before() - Method in class ubic.gemma.core.security.principal.PrincipalTest
before() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVectorServiceTest
beforeTestMethod(TestContext) - Method in class org.springframework.security.test.context.support.WithSecurityContextTestExecutionListener: Sets up the SecurityContext for each test method.
BibliographicReferenceServiceImplTest - Class in ubic.gemma.core.annotation.reference
BibliographicReferenceServiceImplTest() - Constructor for class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImplTest
BibliographicReferenceServiceTest - Class in ubic.gemma.core.annotation.reference: This class tests the bibliographic reference data access object.
BibliographicReferenceServiceTest() - Constructor for class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceTest
BibRefControllerTest - Class in ubic.gemma.web.controller.common.description.bibref: Tests the BibliographicReferenceController
BibRefControllerTest() - Constructor for class ubic.gemma.web.controller.common.description.bibref.BibRefControllerTest
BioAssayServiceTest - Class in ubic.gemma.model.expression.bioAssay
BioAssayServiceTest() - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayServiceTest
BioMartEnsemblNcbiFetcherTest - Class in ubic.gemma.core.util.biomart: Tests that biomart fetcher works correctly.
BioMartEnsemblNcbiFetcherTest() - Constructor for class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiFetcherTest
BioMartEnsemblNcbiObjectGeneratorTest - Class in ubic.gemma.core.util.biomart: Class to test BioMartEnsemblNcbiObjectGeneration.
BioMartEnsemblNcbiObjectGeneratorTest() - Constructor for class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiObjectGeneratorTest
BioMartEnsemblNcbiParserTest - Class in ubic.gemma.core.util.biomart: Tests the parsing of a BioMart file.
BioMartEnsemblNcbiParserTest() - Constructor for class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiParserTest
BioMaterialDaoTest - Class in ubic.gemma.persistence.service.expression.biomaterial
BioMaterialDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoTest
BioMaterialServiceTest - Class in ubic.gemma.model.expression.biomaterial
BioMaterialServiceTest() - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterialServiceTest
BioSequencePersistTest - Class in ubic.gemma.model.genome
BioSequencePersistTest() - Constructor for class ubic.gemma.model.genome.BioSequencePersistTest
BioSequenceTest - Class in ubic.gemma.model.genome.biosequence
BioSequenceTest() - Constructor for class ubic.gemma.model.genome.biosequence.BioSequenceTest
BlacklistedEntityDaoImplTest - Class in ubic.gemma.persistence.service.expression.experiment
BlacklistedEntityDaoImplTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDaoImplTest
BlacklistedEntityServiceTest - Class in ubic.gemma.persistence.service.expression.experiment
BlacklistedEntityServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityServiceTest
BlacklistTest - Class in ubic.gemma.model.expression
BlacklistTest() - Constructor for class ubic.gemma.model.expression.BlacklistTest
BlatAssociationScorerTest - Class in ubic.gemma.core.analysis.sequence: BlatAssociationScorer tests
BlatAssociationScorerTest() - Constructor for class ubic.gemma.core.analysis.sequence.BlatAssociationScorerTest
BlatAssociationServiceTest - Class in ubic.gemma.model.genome.sequenceAnalysis
BlatAssociationServiceTest() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociationServiceTest
BlatResultParserTest - Class in ubic.gemma.core.loader.genome
BlatResultParserTest() - Constructor for class ubic.gemma.core.loader.genome.BlatResultParserTest
BlatResultServiceTest - Class in ubic.gemma.model.genome.sequenceAnalysis
BlatResultServiceTest() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatResultServiceTest
BlatResultTest - Class in ubic.gemma.model.genome
BlatResultTest() - Constructor for class ubic.gemma.model.genome.BlatResultTest
BuildInfoTest - Class in ubic.gemma.core.util
BuildInfoTest() - Constructor for class ubic.gemma.core.util.BuildInfoTest
buildRequest(ServletContext) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestBuilders.FormLoginRequestBuilder
buildRequest(ServletContext) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestBuilders.LogoutRequestBuilder
buildRequest(ServletContext) - Method in class ubic.gemma.web.util.dwr.DwrRequestBuilder

C

cacheManager() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test.GeneOntologyService2TestContextConfiguration
callback() - Method in class ubic.gemma.web.util.dwr.DwrBatchMatchers
callback() - Static method in class ubic.gemma.web.util.dwr.MockDwrResultMatchers
callback(int) - Method in class ubic.gemma.web.util.dwr.DwrBatchMatchers: Match a DWR callback.
callback(int) - Static method in class ubic.gemma.web.util.dwr.MockDwrResultMatchers: Match a DWR callback.
CharacteristicDaoImplTest - Class in ubic.gemma.persistence.service.common.description
CharacteristicDaoImplTest() - Constructor for class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest
characteristicService() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration
CharacteristicServiceTest - Class in ubic.gemma.model.common.description
CharacteristicServiceTest() - Constructor for class ubic.gemma.model.common.description.CharacteristicServiceTest
CharacteristicSortTest - Class in ubic.gemma.core.ontology
CharacteristicSortTest() - Constructor for class ubic.gemma.core.ontology.CharacteristicSortTest
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
CharacteristicValueObjectTest - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
CharacteristicValueObjectTest() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest
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
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
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
checkThatGeoIsAvailable() - Static method in class ubic.gemma.core.loader.expression.geo.GeoBrowserTest
cleanup() - Method in class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperServiceTest
Cleanup() - Method in class ubic.gemma.core.image.aba.AllenBrainAtlasServiceTest
clearContext() - Static method in class org.springframework.security.test.context.TestSecurityContextHolder: Clears the SecurityContext from TestSecurityContextHolder and SecurityContextHolder.
CliTest - Class in ubic.gemma.core.apps
CliTest() - Constructor for class ubic.gemma.core.apps.CliTest
CoexpressionNodeDegreeValueObjectTest - Class in ubic.gemma.model.analysis.expression.coexpression
CoexpressionNodeDegreeValueObjectTest() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.CoexpressionNodeDegreeValueObjectTest
ComBatTest - Class in ubic.gemma.core.analysis.preprocess.batcheffects
ComBatTest() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.ComBatTest
compassDir - Variable in class ubic.gemma.persistence.util.SettingsConfigTest
CompletionGeneratorTest - Class in ubic.gemma.core.util
CompletionGeneratorTest() - Constructor for class ubic.gemma.core.util.CompletionGeneratorTest
CompositeSequenceDaoTest - Class in ubic.gemma.persistence.service.expression.designElement
CompositeSequenceDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest
CompositeSequenceGeneMapperServiceTest - Class in ubic.gemma.core.analysis.service: This test makes use of the ArrayDesignProbeMapperServiceImpl.
CompositeSequenceGeneMapperServiceTest() - Constructor for class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperServiceTest
CompositeSequenceParserTest - Class in ubic.gemma.core.loader.expression.arrayDesign
CompositeSequenceParserTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParserTest
CompositeSequenceServiceTest - Class in ubic.gemma.persistence.service.expression.designElement
CompositeSequenceServiceTest() - Constructor for class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceTest
ConfigurationCookieTest - Class in ubic.gemma.web.util
ConfigurationCookieTest() - Constructor for class ubic.gemma.web.util.ConfigurationCookieTest
configure() - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapperTest
configure() - Method in class ubic.gemma.rest.util.BaseJerseyTest
configureClient(ClientConfig) - Method in class ubic.gemma.rest.util.BaseJerseyTest
ContinuousVariableDiffExTest - Class in ubic.gemma.core.analysis.expression.diff
ContinuousVariableDiffExTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.ContinuousVariableDiffExTest
cookies() - Method in class ubic.gemma.rest.util.ResponseAssert
CorsFilterTest - Class in ubic.gemma.rest.servlet
CorsFilterTest() - Constructor for class ubic.gemma.rest.servlet.CorsFilterTest
countRowsInTable(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Count the rows in the given table.
createCacheDirectory() - Static method in class ubic.gemma.core.util.test.HibernateConfigTest
createObject() - Method in class ubic.gemma.persistence.util.AsyncBeanAutowiringTest.MyService2Factory
createObject() - Method in class ubic.gemma.persistence.util.AsyncBeanAutowiringTest.MyServiceFactory
createObject() - Method in class ubic.gemma.persistence.util.AsyncFactoryTest.MyServiceFactory
createObject() - Method in class ubic.gemma.persistence.util.AsyncSingletonFactoryTest.MyServiceFactory
createSecurityContext(A) - Method in interface org.springframework.security.test.context.support.WithSecurityContextFactory: Create a SecurityContext given an Annotation.
csrf() - Static method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors: Creates a RequestPostProcessor that will automatically populate a valid CsrfToken in the request.
CuratableDaoTest - Class in ubic.gemma.persistence.service.common.auditAndSecurity
CuratableDaoTest() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.CuratableDaoTest
CuratableValueObjectTest - Class in ubic.gemma.web.controller.expression
CuratableValueObjectTest() - Constructor for class ubic.gemma.web.controller.expression.CuratableValueObjectTest
CustomResource() - Constructor for class ubic.gemma.rest.providers.WebApplicationExceptionMapperTest.CustomResource

D

DatabaseEntryDaoImplTest - Class in ubic.gemma.model.common.description
DatabaseEntryDaoImplTest() - Constructor for class ubic.gemma.model.common.description.DatabaseEntryDaoImplTest
DatabaseSearchSourceTest - Class in ubic.gemma.core.search.source
DatabaseSearchSourceTest() - Constructor for class ubic.gemma.core.search.source.DatabaseSearchSourceTest
DatasetCombinerTest - Class in ubic.gemma.core.loader.expression.geo
DatasetCombinerTest() - Constructor for class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest
datasetRestService(ExpressionExperimentService, SearchService) - Method in class ubic.gemma.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration
DatasetsRestTest - Class in ubic.gemma.rest
DatasetsRestTest() - Constructor for class ubic.gemma.rest.DatasetsRestTest
DatasetsWebServiceTest - Class in ubic.gemma.rest
DatasetsWebServiceTest() - Constructor for class ubic.gemma.rest.DatasetsWebServiceTest
dataSource() - Method in class ubic.gemma.core.util.test.BaseDatabaseTest.BaseDatabaseTestContextConfiguration
dataSourceInitializer(DataSource) - Method in class ubic.gemma.core.util.test.BaseDatabaseTest.BaseDatabaseTestContextConfiguration
DataSourceInitializer(DataSource) - Constructor for class ubic.gemma.core.util.test.BaseDatabaseTest.DataSourceInitializer
DataUpdaterTest - Class in ubic.gemma.core.loader.expression
DataUpdaterTest() - Constructor for class ubic.gemma.core.loader.expression.DataUpdaterTest
deleteFromTables(String...) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method for deleting all rows from the specified tables.
DesignElementDataVectorServiceTest - Class in ubic.gemma.model.expression.bioAssayData
DesignElementDataVectorServiceTest() - Constructor for class ubic.gemma.model.expression.bioAssayData.DesignElementDataVectorServiceTest
DetectFactorBaselineTest - Class in ubic.gemma.core.datastructure.matrix
DetectFactorBaselineTest() - Constructor for class ubic.gemma.core.datastructure.matrix.DetectFactorBaselineTest
DifferentialExpressionAnalysisControllerTest - Class in ubic.gemma.web.controller.diff
DifferentialExpressionAnalysisControllerTest() - Constructor for class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisControllerTest
DifferentialExpressionAnalysisDaoTest - Class in ubic.gemma.persistence.service.analysis.expression.diff
DifferentialExpressionAnalysisDaoTest() - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDaoTest
DifferentialExpressionAnalysisHelperServiceTest - Class in ubic.gemma.core.analysis.expression.diff
DifferentialExpressionAnalysisHelperServiceTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperServiceTest
DifferentialExpressionAnalysisServiceTest - Class in ubic.gemma.model.analysis
DifferentialExpressionAnalysisServiceTest() - Constructor for class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest
DifferentialExpressionAnalyzerServiceTest - Class in ubic.gemma.core.analysis.expression.diff
DifferentialExpressionAnalyzerServiceTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest
DifferentialExpressionAnalyzerTest - Class in ubic.gemma.core.analysis.expression.diff
DifferentialExpressionAnalyzerTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerTest
DifferentialExpressionResultDaoTest - Class in ubic.gemma.persistence.service.analysis.expression.diff
DifferentialExpressionResultDaoTest() - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoTest
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
digest() - Static method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors: Creates a DigestRequestPostProcessor that enables easily adding digest based authentication to a request.
digest(String) - Static method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors: Creates a DigestRequestPostProcessor that enables easily adding digest based authentication to a request.
DigestRequestPostProcessor() - Constructor for class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.DigestRequestPostProcessor
DiseaseOntologyTest - Class in ubic.gemma.core.ontology.providers
DiseaseOntologyTest() - Constructor for class ubic.gemma.core.ontology.providers.DiseaseOntologyTest
DOE - ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest.FakeEnum
doesNotExist() - Method in class ubic.gemma.web.util.dwr.AbstractDwrReplyMatchers
downloadPath - Variable in class ubic.gemma.persistence.util.SettingsConfigTest
dwr(Class<?>, String, Object...) - Method in class ubic.gemma.web.util.dwr.MockDwrBatchRequestBuilders: Perform a DWR call.
dwr(Class<?>, String, Object...) - Static method in class ubic.gemma.web.util.dwr.MockDwrRequestBuilders: Perform a DWR call.
dwrBatch(int) - Static method in class ubic.gemma.web.util.dwr.MockDwrRequestBuilders: Perform a batched DWR call.
DwrBatchHandlers - Class in ubic.gemma.web.util.dwr: Handles DWR batches.
DwrBatchHandlers(int) - Constructor for class ubic.gemma.web.util.dwr.DwrBatchHandlers
DwrBatchMatchers - Class in ubic.gemma.web.util.dwr: Match DWR batch results.
DwrBatchMatchers(int) - Constructor for class ubic.gemma.web.util.dwr.DwrBatchMatchers
DwrCallbackHandler<T> - Class in ubic.gemma.web.util.dwr
DwrCallbackHandler(int, int, Consumer<T>) - Constructor for class ubic.gemma.web.util.dwr.DwrCallbackHandler
DwrCallbackMatchers - Class in ubic.gemma.web.util.dwr: Matches successful DWR replies.
DwrCallbackMatchers(int, int) - Constructor for class ubic.gemma.web.util.dwr.DwrCallbackMatchers
DwrException - Class in ubic.gemma.web.util.dwr
DwrException() - Constructor for class ubic.gemma.web.util.dwr.DwrException
DwrExceptionHandler - Class in ubic.gemma.web.util.dwr
DwrExceptionHandler(int, int, Consumer<DwrException>) - Constructor for class ubic.gemma.web.util.dwr.DwrExceptionHandler
DwrExceptionMatchers - Class in ubic.gemma.web.util.dwr: Matches erroneous DWR replies.
DwrExceptionMatchers(int, int) - Constructor for class ubic.gemma.web.util.dwr.DwrExceptionMatchers
DwrRequestBuilder - Class in ubic.gemma.web.util.dwr: Request builder that allows multiple DWR calls to be performed.
DwrRequestBuilder(String, Class<?>, String, int) - Constructor for class ubic.gemma.web.util.dwr.DwrRequestBuilder
dwrStaticPage(String) - Static method in class ubic.gemma.web.util.dwr.MockDwrRequestBuilders: Request the DWR static page.

E

entity() - Method in class ubic.gemma.rest.util.ResponseAssert
entityAs(Class<T>) - 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
EntityDelegatorTest - Class in ubic.gemma.web.remote
EntityDelegatorTest() - Constructor for class ubic.gemma.web.remote.EntityDelegatorTest
EntityUtilsTest - Class in ubic.gemma.persistence.util
EntityUtilsTest() - Constructor for class ubic.gemma.persistence.util.EntityUtilsTest
ErrorPagesTest - Class in ubic.gemma.web.controller
ErrorPagesTest() - Constructor for class ubic.gemma.web.controller.ErrorPagesTest
ErrorsAssert - Class in ubic.gemma.rest.util
ErrorsAssert(Errors) - Constructor for class ubic.gemma.rest.util.ErrorsAssert
ESearchXMLParserTest - Class in ubic.gemma.core.loader.entrez.pubmed
ESearchXMLParserTest() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.ESearchXMLParserTest
EutilFetchTest - Class in ubic.gemma.core.loader.entrez
EutilFetchTest() - Constructor for class ubic.gemma.core.loader.entrez.EutilFetchTest
exception() - Method in class ubic.gemma.web.util.dwr.DwrBatchMatchers
exception() - Static method in class ubic.gemma.web.util.dwr.MockDwrResultMatchers
exception(int) - Method in class ubic.gemma.web.util.dwr.DwrBatchMatchers: Match a DWR exception.
exception(int) - Static method in class ubic.gemma.web.util.dwr.MockDwrResultMatchers: Match a DWR exception.
exceptionResolver() - Method in class ubic.gemma.web.util.BaseWebTest.BaseWebTestContextConfiguration
ExceptionWithMessage(String) - Constructor for exception ubic.gemma.persistence.service.AbstractServiceTest.ExceptionWithMessage
ExceptionWithoutMessage() - Constructor for exception ubic.gemma.persistence.service.AbstractServiceTest.ExceptionWithoutMessage
executeSqlScript(String, boolean) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Execute the given SQL script.
ExecutingTaskTest - Class in ubic.gemma.core.job
ExecutingTaskTest() - Constructor for class ubic.gemma.core.job.ExecutingTaskTest
exist() - Method in class ubic.gemma.web.util.dwr.AbstractDwrReplyMatchers
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
ExperimentalDesignControllerIntegrationTest - Class in ubic.gemma.web.controller.expression.experiment
ExperimentalDesignControllerIntegrationTest() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerIntegrationTest
ExperimentalDesignControllerTest - Class in ubic.gemma.web.controller.expression.experiment
ExperimentalDesignControllerTest() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest
ExperimentalDesignImportDuplicateValueTest - Class in ubic.gemma.core.loader.expression.simple: Test for import that results in multiple factor values for the same factor on a single biomaterial.
ExperimentalDesignImportDuplicateValueTest() - Constructor for class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImportDuplicateValueTest
ExperimentalDesignImporterTest - Class in ubic.gemma.core.loader.expression.simple
ExperimentalDesignImporterTest() - Constructor for class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterTest
ExperimentalDesignWriterTest - Class in ubic.gemma.core.datastructure.matrix
ExperimentalDesignWriterTest() - Constructor for class ubic.gemma.core.datastructure.matrix.ExperimentalDesignWriterTest
ExperimentalFactorDaoTest - Class in ubic.gemma.persistence.service.expression.experiment
ExperimentalFactorDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDaoTest
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 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
ExpressionDataDoubleMatrixUtilTest - Class in ubic.gemma.core.datastructure.matrix
ExpressionDataDoubleMatrixUtilTest() - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
ExpressionDataFileServiceTest - Class in ubic.gemma.core.analysis.service
ExpressionDataFileServiceTest() - Constructor for class ubic.gemma.core.analysis.service.ExpressionDataFileServiceTest
ExpressionDataMatrixColumnSortTest - Class in ubic.gemma.core.datastructure.matrix
ExpressionDataMatrixColumnSortTest() - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSortTest
expressionDataMatrixService - Variable in class ubic.gemma.core.analysis.expression.diff.BaseAnalyzerConfigurationTest
ExpressionDataSVDTest - Class in ubic.gemma.core.analysis.preprocess
ExpressionDataSVDTest() - Constructor for class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest
ExpressionDataTestMatrix - Class in ubic.gemma.core.datastructure.matrix: Creates a sample small test matrix, not persistent.
ExpressionDataTestMatrix() - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataTestMatrix
ExpressionExperimentBatchCorrectionServiceTest - Class in ubic.gemma.core.analysis.preprocess.batcheffects
ExpressionExperimentBatchCorrectionServiceTest() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceTest
ExpressionExperimentBibRefFinderTest - Class in ubic.gemma.core.loader.entrez.pubmed
ExpressionExperimentBibRefFinderTest() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest
ExpressionExperimentControllerTest - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentControllerTest() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentControllerTest
ExpressionExperimentDaoTest - Class in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest
ExpressionExperimentDeleteTest - Class in ubic.gemma.model.expression.experiment
ExpressionExperimentDeleteTest() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentDeleteTest
ExpressionExperimentPlatformSwitchTest - Class in ubic.gemma.core.loader.expression: Switching of platforms that have no composite sequences.
ExpressionExperimentPlatformSwitchTest() - Constructor for class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchTest
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.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration
ExpressionExperimentServiceImplTest - Class in ubic.gemma.model.expression.experiment
ExpressionExperimentServiceImplTest() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceImplTest
ExpressionExperimentServiceIntegrationTest - Class in ubic.gemma.model.expression.experiment
ExpressionExperimentServiceIntegrationTest() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
ExpressionExperimentServiceTest - Class in ubic.gemma.model.expression.experiment
ExpressionExperimentServiceTest() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest
ExpressionExperimentSetServiceTest - Class in ubic.gemma.model.expression.experiment: Tests for methods that perform operations on or with expressionExperiment sets
ExpressionExperimentSetServiceTest() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentSetServiceTest
ExpressionExperimentSetValueObjectHelperTest - Class in ubic.gemma.model.expression.experiment: Tests for methods that create ExpressionExperimentSetValueObjects from expressionExperiment entities
ExpressionExperimentSetValueObjectHelperTest() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObjectHelperTest
ExpressionExperimentSubSetServiceTest - Class in ubic.gemma.model.expression
ExpressionExperimentSubSetServiceTest() - Constructor for class ubic.gemma.model.expression.ExpressionExperimentSubSetServiceTest
externalDatabaseService - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest
ExternalDatabaseServiceTest - Class in ubic.gemma.persistence.service.common.description
ExternalDatabaseServiceTest() - Constructor for class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceTest
ExternalDatabaseUpdaterCliTest - Class in ubic.gemma.core.apps
ExternalDatabaseUpdaterCliTest() - Constructor for class ubic.gemma.core.apps.ExternalDatabaseUpdaterCliTest
ExternalFileGeneLoaderServiceTest - Class in ubic.gemma.core.loader.genome.gene: Test that Gemma can load genes from an external gene file with format : #GeneSymbol GeneName Uniprot ZYX ZYXIN Q15942 ZXDC ZXD FAMILY ZINC FINGER C Q8C8V1
ExternalFileGeneLoaderServiceTest() - Constructor for class ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceTest

F

FactorValueDaoTest - Class in ubic.gemma.persistence.service.expression.experiment
FactorValueDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoTest
FactorValueMigratorCLITest - Class in ubic.gemma.core.apps: Deprecated.
FactorValueMigratorCLITest() - Constructor for class ubic.gemma.core.apps.FactorValueMigratorCLITest: Deprecated.
FactorValueMigratorServiceTest - Class in ubic.gemma.core.apps: Deprecated.
FactorValueMigratorServiceTest() - Constructor for class ubic.gemma.core.apps.FactorValueMigratorServiceTest: Deprecated.
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
FactorValueServiceIntegrationTest - Class in ubic.gemma.model.expression.experiment
FactorValueServiceIntegrationTest() - Constructor for class ubic.gemma.model.expression.experiment.FactorValueServiceIntegrationTest
FactorValueServiceTest - Class in ubic.gemma.model.expression.experiment
FactorValueServiceTest() - Constructor for class ubic.gemma.model.expression.experiment.FactorValueServiceTest
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
factory() - Method in annotation type org.springframework.security.test.context.support.WithSecurityContext: The WithUserDetailsSecurityContextFactory to use to create the SecurityContext.
FastaParserTest - Class in ubic.gemma.core.loader.genome
FastaParserTest() - Constructor for class ubic.gemma.core.loader.genome.FastaParserTest
FastIntegrationTests - Class in ubic.gemma.core.util.test.suite: Fast integration tests.
FastIntegrationTests() - Constructor for class ubic.gemma.core.util.test.suite.FastIntegrationTests
FastTests - Class in ubic.gemma.core.util.test.suite: Test suite that excludes all the slow tests (i.e.
FastTests() - Constructor for class ubic.gemma.core.util.test.suite.FastTests
FastUnitTests - Class in ubic.gemma.core.util.test.suite: Fast unit tests.
FastUnitTests() - Constructor for class ubic.gemma.core.util.test.suite.FastUnitTests
FileUploadUtilTest - Class in ubic.gemma.web.util.upload
FileUploadUtilTest() - Constructor for class ubic.gemma.web.util.upload.FileUploadUtilTest
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
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
findByExperimentAnalyzed() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoTest
FindObsoleteTermsCliTest - Class in ubic.gemma.core.apps
FindObsoleteTermsCliTest() - Constructor for class ubic.gemma.core.apps.FindObsoleteTermsCliTest
FOO - ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest.FakeEnum
formLogin() - Static method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestBuilders: Creates a request (including any necessary CsrfToken) that will submit a form based login to POST "/login".
formLogin(String) - Static method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestBuilders: Creates a request (including any necessary CsrfToken) that will submit a form based login to POST loginProcessingUrl.

G

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
GemmaEndpointTest - Class in ubic.gemma.web.services
GemmaEndpointTest() - Constructor for class ubic.gemma.web.services.GemmaEndpointTest
GemmaOntologyServiceTest - Class in ubic.gemma.core.ontology.providers
GemmaOntologyServiceTest() - Constructor for class ubic.gemma.core.ontology.providers.GemmaOntologyServiceTest
Gene2GeneCoexpressionServiceTest - Class in ubic.gemma.model.association.coexpression
Gene2GeneCoexpressionServiceTest() - Constructor for class ubic.gemma.model.association.coexpression.Gene2GeneCoexpressionServiceTest
gene2GOAssociationService() - 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
GeneCoexpressionTestedInTest - Class in ubic.gemma.model.analysis.expression.coexpression
GeneCoexpressionTestedInTest() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedInTest
GeneDaoTest - Class in ubic.gemma.persistence.service.genome
GeneDaoTest() - Constructor for class ubic.gemma.persistence.service.genome.GeneDaoTest
GeneDiffExMetaAnalysisServiceTest - Class in ubic.gemma.model.analysis
GeneDiffExMetaAnalysisServiceTest() - Constructor for class ubic.gemma.model.analysis.GeneDiffExMetaAnalysisServiceTest
GeneMultifunctionalityPopulationServiceTest - Class in ubic.gemma.core.analysis.service
GeneMultifunctionalityPopulationServiceTest() - Constructor for class ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationServiceTest
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
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.model.genome.gene
GeneSearchTest() - Constructor for class ubic.gemma.model.genome.gene.GeneSearchTest
geneService() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test.GeneOntologyService2TestContextConfiguration
GeneServiceImplTest - Class in ubic.gemma.model.genome.gene
GeneServiceImplTest() - Constructor for class ubic.gemma.model.genome.gene.GeneServiceImplTest
GeneServiceTest - Class in ubic.gemma.model.genome.gene
GeneServiceTest() - Constructor for class ubic.gemma.model.genome.gene.GeneServiceTest
GeneSetServiceTest - Class in ubic.gemma.model.genome.gene
GeneSetServiceTest() - Constructor for class ubic.gemma.model.genome.gene.GeneSetServiceTest
GeneSetValueObjectHelperTest - Class in ubic.gemma.model.genome.gene
GeneSetValueObjectHelperTest() - Constructor for class ubic.gemma.model.genome.gene.GeneSetValueObjectHelperTest
GeneTest - Class in ubic.gemma.model.genome: Tests of 'equals' implementation
GeneTest() - Constructor for class ubic.gemma.model.genome.GeneTest
GeneValueObjectTest - Class in ubic.gemma.model.genome.gene
GeneValueObjectTest() - Constructor for class ubic.gemma.model.genome.gene.GeneValueObjectTest
GenomePersisterTest - Class in ubic.gemma.persistence
GenomePersisterTest() - Constructor for class ubic.gemma.persistence.GenomePersisterTest
GeoBrowserServiceParseTest - Class in ubic.gemma.core.loader.expression.geo.service
GeoBrowserServiceParseTest() - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceParseTest
GeoBrowserServiceTest - Class in ubic.gemma.core.loader.expression.geo.service
GeoBrowserServiceTest() - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceTest
GeoBrowserTest - Class in ubic.gemma.core.loader.expression.geo
GeoBrowserTest() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoBrowserTest
GeoCharacteristicParseTest - Class in ubic.gemma.core.loader.expression.geo
GeoCharacteristicParseTest() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoCharacteristicParseTest
GeoConverterTest - Class in ubic.gemma.core.loader.expression.geo: Unit test for GeoConversion Added extension BaseSpringContextTest as want Taxon Service to be called
GeoConverterTest() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoConverterTest
GeoDatasetServiceTest - Class in ubic.gemma.core.loader.expression.geo.service: Test full procedure of loading GEO data, focus on corner cases.
GeoDatasetServiceTest() - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest
GeoFamilyParserTest - Class in ubic.gemma.core.loader.expression.geo
GeoFamilyParserTest() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest
GeoPlatformServiceTest - Class in ubic.gemma.core.loader.expression.geo.service: Tests of GeoPlatformService
GeoPlatformServiceTest() - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoPlatformServiceTest
GeoPlatformTest - Class in ubic.gemma.core.loader.expression.geo
GeoPlatformTest() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoPlatformTest
geoService - Variable in class ubic.gemma.core.analysis.expression.diff.BaselineDetectionTest
geoService - Variable in class ubic.gemma.model.expression.bioAssayData.DesignElementDataVectorServiceTest
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
getAcl(Securable) - Method in class ubic.gemma.core.security.authorization.acl.AclTestUtils
getAd() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AbstractArrayDesignProcessingTest
getBatch(int) - Static method in class ubic.gemma.web.util.dwr.MockDwrResultHandlers
getCallback(int, Consumer<T>) - Method in class ubic.gemma.web.util.dwr.DwrBatchHandlers
getCallback(int, Consumer<T>) - Static method in class ubic.gemma.web.util.dwr.MockDwrResultHandlers
getCallback(Consumer<T>) - Method in class ubic.gemma.web.util.dwr.DwrBatchHandlers
getCallback(Consumer<T>) - Static method in class ubic.gemma.web.util.dwr.MockDwrResultHandlers
getContext() - Static method in class org.springframework.security.test.context.TestSecurityContextHolder: Gets the SecurityContext from TestSecurityContextHolder.
getCsrfTokenRepository(HttpServletRequest) - Static method in class org.springframework.security.test.web.support.WebTestUtils: Gets the CsrfTokenRepository for the specified HttpServletRequest.
getException(int, Consumer<DwrException>) - Method in class ubic.gemma.web.util.dwr.DwrBatchHandlers
getException(int, Consumer<DwrException>) - Static method in class ubic.gemma.web.util.dwr.MockDwrResultHandlers
getException(Consumer<DwrException>) - Method in class ubic.gemma.web.util.dwr.DwrBatchHandlers
getException(Consumer<DwrException>) - Static method in class ubic.gemma.web.util.dwr.MockDwrResultHandlers
getExperimentalDesign(Collection<FactorValue>) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getExperimentalFactors(ExperimentalDesign) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getFactorValues(ExperimentalFactor) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getFactorValues(ExperimentalFactor, Collection<FactorValue>) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getId() - Method in class ubic.gemma.persistence.service.AbstractDaoTest.MyEntity
getNewTestPersistentCompleteExpressionExperiment() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getReply(MvcResult) - Method in class ubic.gemma.web.util.dwr.AbstractDwrReplyParser
getSecurityContextRepository(HttpServletRequest) - Static method in class org.springframework.security.test.web.support.WebTestUtils: Gets the SecurityContextRepository for the specified HttpServletRequest.
getTaxon(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestCharacteristic(String, String) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestContainerFactory() - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapperTest
getTestContainerFactory() - Method in class ubic.gemma.rest.util.BaseJerseyTest
getTestElementCollectionSize() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestExpressionExperimentWithAllDependencies() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Add an expressionExperiment to the database for testing purposes.
getTestExpressionExperimentWithAllDependencies(boolean) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Add an expressionExperiment to the database for testing purposes.
getTestExpressionExperimentWithAllDependencies(ExpressionExperiment) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestExpressionExperimentWithAnalysisAndResults() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Create a test EE with analysis results.
getTestFileBasePath() - Method in class ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest
getTestFileBasePath(String) - Method in class ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest
getTestNonPersistentBioSequence(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestNonPersistentBioSequence(Taxon) - Static method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestNonPersistentGeneProduct(Gene) - Static method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestNonPersistentQuantitationType() - Static method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Note that if you want a 'preferred' qt or other special properties you have to set it yourself.
getTestPersistentArrayDesign(int, boolean) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.
getTestPersistentArrayDesign(int, boolean, boolean) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.
getTestPersistentArrayDesign(int, boolean, boolean, boolean) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.
getTestPersistentArrayDesign(List<String>, Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.
getTestPersistentBasicExpressionExperiment() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBasicExpressionExperiment() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBasicExpressionExperiment(ArrayDesign) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBasicExpressionExperiment(ArrayDesign) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBibliographicReference(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBibliographicReference(String) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBioAssay(ArrayDesign) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
getTestPersistentBioAssay(ArrayDesign) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBioAssay(ArrayDesign, BioMaterial) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
getTestPersistentBioAssay(ArrayDesign, BioMaterial) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
getTestPersistentBioMaterial() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBioMaterial() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBioMaterial(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBioMaterial(Taxon) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBioSequence() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBioSequence() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBioSequence(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBioSequence(Taxon) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBioSequence2GeneProducts(BioSequence) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBioSequence2GeneProducts(BioSequence) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBlatResult(BioSequence) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBlatResult(BioSequence, Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBlatResult(BioSequence, Taxon) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentCompleteExpressionExperiment(boolean) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to get a (fairly) complete randomly generated persisted expression experiment.
getTestPersistentCompleteExpressionExperimentWithSequences() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to get a (fairly) complete randomly generated persisted expression experiment.
getTestPersistentCompleteExpressionExperimentWithSequences(ExpressionExperiment) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentContact() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide a Contact that can be used to fill non-nullable associations in test objects.
getTestPersistentContact() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide a Contact that can be used to fill non-nullable associations in test objects.
getTestPersistentDatabaseEntry() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Get a database entry from a fictitious database.
getTestPersistentDatabaseEntry(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentDatabaseEntry(String, String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentDatabaseEntry(String, String) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentDatabaseEntry(String, ExternalDatabase) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
getTestPersistentDatabaseEntry(String, ExternalDatabase) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
getTestPersistentDatabaseEntry(ExternalDatabase) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
getTestPersistentDatabaseEntry(ExternalDatabase) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
getTestPersistentExpressionExperiment() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.
getTestPersistentExpressionExperiment() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.
getTestPersistentExpressionExperiment(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.
getTestPersistentExpressionExperiment(Taxon) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.
getTestPersistentGene() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentGene() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentGene(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentGene(Taxon) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentGeneProduct(Gene) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentGeneProduct(Gene) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentQuantitationType() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide a QuantitationType that can be used to fill non-nullable associations in test objects.
getTestPersistentQuantitationType() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide a QuantitationType that can be used to fill non-nullable associations in test objects.
getTestPersistentTaxon() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestStatement(String, String) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
GoldenPathQueryTest - Class in ubic.gemma.core.externalDb: These tests require a populated Human database.
GoldenPathQueryTest() - Constructor for class ubic.gemma.core.externalDb.GoldenPathQueryTest
GoldenPathTest - Class in ubic.gemma.core.util.test.category: Test depending on GoldenPath database availability.
GoldenPathTest() - Constructor for class ubic.gemma.core.util.test.category.GoldenPathTest
GoogleAnalytics4ProviderTest - Class in ubic.gemma.rest.analytics.ga4
GoogleAnalytics4ProviderTest() - Constructor for class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4ProviderTest

H

handle(MvcResult) - Method in class ubic.gemma.web.util.dwr.DwrCallbackHandler
handle(MvcResult) - Method in class ubic.gemma.web.util.dwr.DwrExceptionHandler
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.
hasHeader(String, String) - Method in class ubic.gemma.rest.util.ResponseAssert: Asserts that the response has the given header.
hasLanguage(Locale) - Method in class ubic.gemma.rest.util.ResponseAssert
hasLength(int) - Method in class ubic.gemma.rest.util.ResponseAssert
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.
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
HibernateConfigTest - Class in ubic.gemma.core.util.test
HibernateConfigTest() - Constructor for class ubic.gemma.core.util.test.HibernateConfigTest
HibernateSearchSourceTest - Class in ubic.gemma.core.search.source
HibernateSearchSourceTest() - Constructor for class ubic.gemma.core.search.source.HibernateSearchSourceTest
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
httpBasic(String, String) - Static method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors: Convenience mechanism for setting the Authorization header to use HTTP Basic with the given username and password.
HttpFetcherTest - Class in ubic.gemma.core.loader.util
HttpFetcherTest() - Constructor for class ubic.gemma.core.loader.util.HttpFetcherTest

I

IlluminaProbeReaderTest - Class in ubic.gemma.core.loader.expression.arrayDesign
IlluminaProbeReaderTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReaderTest
indexAsJson() - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapperTest.CustomResource
indexAsString() - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapperTest.CustomResource
IntegrationTest - Interface in ubic.gemma.core.util.test.category: Mark a test as an integration test.
IntegrationTests - Class in ubic.gemma.core.util.test.suite: Integration tests.
IntegrationTests() - Constructor for class ubic.gemma.core.util.test.suite.IntegrationTests
isSingleton() - Method in class ubic.gemma.persistence.util.AsyncBeanAutowiringTest.MyService2Factory
isSingleton() - Method in class ubic.gemma.persistence.util.AsyncBeanAutowiringTest.MyServiceFactory
isSingleton() - Method in class ubic.gemma.persistence.util.AsyncFactoryTest.MyServiceFactory
isSingleton() - Method in class ubic.gemma.persistence.util.AsyncSingletonFactoryTest.MyServiceFactory

J

javaClassName(String) - Method in class ubic.gemma.web.util.dwr.DwrExceptionMatchers
jdbcTemplate - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest: The SimpleJdbcTemplate that this base class manages, available to subclasses.
JOB_LENGTH - Static variable in interface ubic.gemma.web.util.MockLongJobController
JOHN - ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest.FakeEnum

L

LinkAnalysisServiceTest - Class in ubic.gemma.core.analysis.expression.coexpression.links
LinkAnalysisServiceTest() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisServiceTest
ListUtilsTest - Class in ubic.gemma.persistence.util: Tests for extra utilities for List.
ListUtilsTest() - Constructor for class ubic.gemma.persistence.util.ListUtilsTest
log - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest
LoggingIntegrationTest - Class in ubic.gemma.web.logging
LoggingIntegrationTest() - Constructor for class ubic.gemma.web.logging.LoggingIntegrationTest
loginProcessingUrl(String) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestBuilders.FormLoginRequestBuilder: Specifies the URL to POST to.
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.
logout() - Static method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestBuilders: Creates a logout request.
logout(String) - Static method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestBuilders: Creates a logout request (including any necessary CsrfToken) to the specified logoutUrl
logoutUrl(String) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestBuilders.LogoutRequestBuilder: Specifies the logout URL to POST to.
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
LuceneQueryUtilsTest - Class in ubic.gemma.core.search.lucene
LuceneQueryUtilsTest() - Constructor for class ubic.gemma.core.search.lucene.LuceneQueryUtilsTest
luceneRamIndexTest() - Method in class ubic.gemma.core.search.LuceneTest: Searching uses a ram index to deal with queries using logical operators.
LuceneTest - Class in ubic.gemma.core.search
LuceneTest() - Constructor for class ubic.gemma.core.search.LuceneTest

M

mailEngine() - Method in class ubic.gemma.web.util.BaseWebTest.BaseWebTestContextConfiguration
MailEngineTest - Class in ubic.gemma.persistence.util
MailEngineTest() - Constructor for class ubic.gemma.persistence.util.MailEngineTest
ManualAuthenticationProcessingTest - Class in ubic.gemma.core.security.authentication
ManualAuthenticationProcessingTest() - Constructor for class ubic.gemma.core.security.authentication.ManualAuthenticationProcessingTest
manualAuthenticationService() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration
map(K, V, Object...) - Static method in class ubic.gemma.core.util.test.Maps
Maps - Class in ubic.gemma.core.util.test: Extensions for AssertJ's Maps.
Maps() - Constructor for class ubic.gemma.core.util.test.Maps
match(MvcResult) - Method in class org.springframework.security.test.web.servlet.response.SecurityMockMvcResultMatchers.AuthenticatedMatcher
MatrixConversionTest - Class in ubic.gemma.core.datastructure.matrix
MatrixConversionTest() - Constructor for class ubic.gemma.core.datastructure.matrix.MatrixConversionTest
MeanVarianceServiceTest - Class in ubic.gemma.core.analysis.preprocess
MeanVarianceServiceTest() - Constructor for class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceTest
message(String) - Method in class ubic.gemma.web.util.dwr.DwrExceptionMatchers
MessageSourceTest - Class in ubic.gemma.web.util
MessageSourceTest() - Constructor for class ubic.gemma.web.util.MessageSourceTest
messageUtil() - Method in class ubic.gemma.web.util.BaseWebTest.BaseWebTestContextConfiguration
MeterRegistryCliConfigurerTest - Class in ubic.gemma.core.metrics
MeterRegistryCliConfigurerTest() - Constructor for class ubic.gemma.core.metrics.MeterRegistryCliConfigurerTest
MockDwrBatchRequestBuilders - Class in ubic.gemma.web.util.dwr
MockDwrBatchRequestBuilders(String, int) - Constructor for class ubic.gemma.web.util.dwr.MockDwrBatchRequestBuilders
MockDwrRequestBuilders - Class in ubic.gemma.web.util.dwr
MockDwrRequestBuilders() - Constructor for class ubic.gemma.web.util.dwr.MockDwrRequestBuilders
MockDwrResultHandlers - Class in ubic.gemma.web.util.dwr: Handles DWR results.
MockDwrResultHandlers() - Constructor for class ubic.gemma.web.util.dwr.MockDwrResultHandlers
MockDwrResultMatchers - Class in ubic.gemma.web.util.dwr: Match DWR results.
MockDwrResultMatchers() - Constructor for class ubic.gemma.web.util.dwr.MockDwrResultMatchers
mockitoRule - Variable in class ubic.gemma.rest.util.args.FilterArgTest
mockitoRule - Variable in class ubic.gemma.web.logging.SlackAppenderTest
MockLongJobController - Interface in ubic.gemma.web.util: Note: do not use parameterized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.
MockLongJobControllerImpl - Class in ubic.gemma.web.util: Controller that does nothing except wait a while.
MockLongJobControllerImpl() - Constructor for class ubic.gemma.web.util.MockLongJobControllerImpl
mvc - Variable in class ubic.gemma.web.util.BaseSpringWebTest
mvc - Variable in class ubic.gemma.web.util.BaseWebTest
MyDao(SessionFactory) - Constructor for class ubic.gemma.persistence.service.AbstractDaoTest.MyDao
MyEntity() - Constructor for class ubic.gemma.persistence.service.AbstractDaoTest.MyEntity
MyModel() - Constructor for class ubic.gemma.rest.providers.WebApplicationExceptionMapperTest.CustomResource.MyModel
MyService() - Constructor for class ubic.gemma.core.metrics.GenericMeterRegistryConfigurerTest.MyService
MyService() - Constructor for class ubic.gemma.persistence.util.AsyncBeanAutowiringTest.MyService
MyService() - Constructor for class ubic.gemma.persistence.util.AsyncFactoryTest.MyService
MyService() - Constructor for class ubic.gemma.persistence.util.AsyncSingletonFactoryTest.MyService
MyService2() - Constructor for class ubic.gemma.persistence.util.AsyncBeanAutowiringTest.MyService2
MyService2Factory() - Constructor for class ubic.gemma.persistence.util.AsyncBeanAutowiringTest.MyService2Factory
MyService2Impl() - Constructor for class ubic.gemma.core.metrics.GenericMeterRegistryConfigurerTest.MyService2Impl
MyServiceFactory() - Constructor for class ubic.gemma.persistence.util.AsyncBeanAutowiringTest.MyServiceFactory
MyServiceFactory() - Constructor for class ubic.gemma.persistence.util.AsyncFactoryTest.MyServiceFactory
MyServiceFactory() - Constructor for class ubic.gemma.persistence.util.AsyncSingletonFactoryTest.MyServiceFactory

N

NCBIGene2GOAssociationLoaderCLITest - Class in ubic.gemma.core.apps
NCBIGene2GOAssociationLoaderCLITest() - Constructor for class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLITest
NCBIGene2GOAssociationParserTest - Class in ubic.gemma.core.loader.association: Tests multiple both parsing and loading.
NCBIGene2GOAssociationParserTest() - Constructor for class ubic.gemma.core.loader.association.NCBIGene2GOAssociationParserTest
NCBIGeneHistoryParserTest - Class in ubic.gemma.core.loader.genome.gene.ncbi: TODO Document Me
NCBIGeneHistoryParserTest() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneHistoryParserTest
NCBIGeneLoadingTest - Class in ubic.gemma.core.loader.genome.gene.ncbi
NCBIGeneLoadingTest() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneLoadingTest
NCBIGeneParserTest - Class in ubic.gemma.core.loader.genome.gene.ncbi
NCBIGeneParserTest() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneParserTest
newGet(String) - Method in class ubic.gemma.web.util.BaseSpringWebTest
newPost(String) - Method in class ubic.gemma.web.util.BaseSpringWebTest: Convenience methods to make tests simpler

O

OneWayAnovaAnalyzerTest - Class in ubic.gemma.core.analysis.expression.diff: Tests the one way anova analyzer.
OneWayAnovaAnalyzerTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.OneWayAnovaAnalyzerTest
onSetUpInTransaction() - Method in class ubic.gemma.model.genome.BioSequencePersistTest
onTearDownInTransaction() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonLoaderTest
onTearDownInTransaction() - Method in class ubic.gemma.model.genome.BioSequencePersistTest
OntologyCacheTest - Class in ubic.gemma.core.ontology
OntologyCacheTest() - Constructor for class ubic.gemma.core.ontology.OntologyCacheTest
OntologyControllerTest - Class in ubic.gemma.web.controller
OntologyControllerTest() - Constructor for class ubic.gemma.web.controller.OntologyControllerTest
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
OntologySearchSourceTest - Class in ubic.gemma.core.search.source
OntologySearchSourceTest() - Constructor for class ubic.gemma.core.search.source.OntologySearchSourceTest
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
OpenApiTest - Class in ubic.gemma.rest
OpenApiTest() - Constructor for class ubic.gemma.rest.OpenApiTest
org.springframework.security.test.context - package org.springframework.security.test.context
org.springframework.security.test.context.annotation - package org.springframework.security.test.context.annotation
org.springframework.security.test.context.support - package org.springframework.security.test.context.support
org.springframework.security.test.web.servlet.request - package org.springframework.security.test.web.servlet.request
org.springframework.security.test.web.servlet.response - package org.springframework.security.test.web.servlet.response
org.springframework.security.test.web.support - package org.springframework.security.test.web.support
OutlierDetectionServiceTest - Class in ubic.gemma.core.analysis.preprocess: Tests for OutlierDetectionService
OutlierDetectionServiceTest() - Constructor for class ubic.gemma.core.analysis.preprocess.OutlierDetectionServiceTest

P

password() - Method in annotation type org.springframework.security.test.context.support.WithMockUser: The password to be used.
password(String) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestBuilders.FormLoginRequestBuilder: The value of the password parameter.
password(String) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.DigestRequestPostProcessor: Configures the password to use
password(String) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.UserRequestPostProcessor: Populates the user's password.
password(String, String) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestBuilders.FormLoginRequestBuilder: Specify both the password parameter name and the password.
passwordParam(String) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestBuilders.FormLoginRequestBuilder: The HTTP parameter to place the password.
PatoOntologyServiceTest - Class in ubic.gemma.core.ontology.providers
PatoOntologyServiceTest() - Constructor for class ubic.gemma.core.ontology.providers.PatoOntologyServiceTest
PersistentDummyObjectHelper - Class in ubic.gemma.core.util.test: Used to generate test data.
PersistentDummyObjectHelper() - Constructor for class ubic.gemma.core.util.test.PersistentDummyObjectHelper
persisterHelper - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest
PersisterTest - Class in ubic.gemma.persistence
PersisterTest() - Constructor for class ubic.gemma.persistence.PersisterTest
pessimisticOperation() - Method in class ubic.gemma.persistence.retry.RetryTest.TestRetryService
pessimisticOperationWithoutRetry() - Method in class ubic.gemma.persistence.retry.RetryTest.TestRetryService
pessimisticOperationWithTransactionalAnnotation() - Method in class ubic.gemma.persistence.retry.RetryTest.TestRetryService
PhenotypeAssociationTest - Class in ubic.gemma.model.association.phenotype: This test will likely fail if the full disease ontology is configured to load; instead we want to load a small 'fake' one.
PhenotypeAssociationTest() - Constructor for class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
PhenotypeImportingTest - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
PhenotypeImportingTest() - Constructor for class ubic.gemma.core.loader.association.phenotype.PhenotypeImportingTest: Deprecated.
platformArgService(ArrayDesignService) - Method in class ubic.gemma.rest.SearchWebServiceTest.SearchWebServiceTestContextConfiguration
PlatformsWebServiceTest - Class in ubic.gemma.rest
PlatformsWebServiceTest() - Constructor for class ubic.gemma.rest.PlatformsWebServiceTest
platformTransactionManager(SessionFactory) - Method in class ubic.gemma.core.util.test.BaseDatabaseTest.BaseDatabaseTestContextConfiguration
PointcutsTest - Class in ubic.gemma.core.security.audit
PointcutsTest() - Constructor for class ubic.gemma.core.security.audit.PointcutsTest
postProcessRequest(MockHttpServletRequest) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.CsrfRequestPostProcessor
postProcessRequest(MockHttpServletRequest) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.DigestRequestPostProcessor
postProcessRequest(MockHttpServletRequest) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.UserRequestPostProcessor
PrincipalTest - Class in ubic.gemma.core.security.principal: Test that we can log users in, etc.
PrincipalTest() - Constructor for class ubic.gemma.core.security.principal.PrincipalTest
ProbeMapperTest - Class in ubic.gemma.core.analysis.sequence: Unaware of the Gemma database but uses the hg19 and mm10 databases (tests will not work with hg38)
ProbeMapperTest() - Constructor for class ubic.gemma.core.analysis.sequence.ProbeMapperTest
ProbeSequenceParserTest - Class in ubic.gemma.core.loader.genome
ProbeSequenceParserTest() - Constructor for class ubic.gemma.core.loader.genome.ProbeSequenceParserTest
ProcessedExpressionDataCreateServiceTest - Class in ubic.gemma.core.analysis.preprocess
ProcessedExpressionDataCreateServiceTest() - Constructor for class ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataCreateServiceTest
ProcessedExpressionDataVectorDaoTest - Class in ubic.gemma.persistence.service.expression.bioAssayData
ProcessedExpressionDataVectorDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoTest
processedExpressionDataVectorService - Variable in class ubic.gemma.core.analysis.expression.diff.BaseAnalyzerConfigurationTest
ProcessedExpressionDataVectorServiceTest - Class in ubic.gemma.model.expression.bioAssayData
ProcessedExpressionDataVectorServiceTest() - Constructor for class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVectorServiceTest
ProgressAppenderTest - Class in ubic.gemma.core.util.progress: For this test to work you should have the appender configured in log4j-test.properties.
ProgressAppenderTest() - Constructor for class ubic.gemma.core.util.progress.ProgressAppenderTest
ProgressDataTest - Class in ubic.gemma.core.util.progress
ProgressDataTest() - Constructor for class ubic.gemma.core.util.progress.ProgressDataTest
PubMedQueryControllerTest - Class in ubic.gemma.web.controller.common.description.bibref
PubMedQueryControllerTest() - Constructor for class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerTest
PubMedSearcherIntegrationTest - Class in ubic.gemma.core.loader.entrez.pubmed: Tests command line.
PubMedSearcherIntegrationTest() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcherIntegrationTest
PubMedSearchTest - Class in ubic.gemma.core.loader.entrez.pubmed
PubMedSearchTest() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedSearchTest
PubMedTest - Class in ubic.gemma.core.util.test.category: Test depending on PubMed availability.
PubMedTest() - Constructor for class ubic.gemma.core.util.test.category.PubMedTest
PubMedXMLFetcherTest - Class in ubic.gemma.core.loader.entrez.pubmed
PubMedXMLFetcherTest() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest
PubMedXMLParserTest - Class in ubic.gemma.core.loader.entrez.pubmed
PubMedXMLParserTest() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest

Q

QuantileNormalizerTest - Class in ubic.gemma.core.analysis.preprocess
QuantileNormalizerTest() - Constructor for class ubic.gemma.core.analysis.preprocess.QuantileNormalizerTest
QuantitationTypeDaoTest - Class in ubic.gemma.persistence.service.common.quantitationtype
QuantitationTypeDaoTest() - Constructor for class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoTest
QuantitationTypeParameterGuesserTest - Class in ubic.gemma.core.loader.expression.geo
QuantitationTypeParameterGuesserTest() - Constructor for class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
QueryUtilsTest - Class in ubic.gemma.persistence.util
QueryUtilsTest() - Constructor for class ubic.gemma.persistence.util.QueryUtilsTest

R

randomCountMatrix(ExpressionExperiment) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils
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
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, 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
randomLog2Matrix(ExpressionExperiment) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils
randomLog2RatiometricMatrix(ExpressionExperiment) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils
randomName() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience shortcut for RandomStringUtils.randomAlphabetic( 10 ) (or something similar to that)
RawAndProcessedExpressionDataVectorDaoTest - Class in ubic.gemma.persistence.service.expression.bioAssayData
RawAndProcessedExpressionDataVectorDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoTest
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
realm(String) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.DigestRequestPostProcessor: Configures the realm to use
removeCacheDirectory() - Static method in class ubic.gemma.core.util.test.HibernateConfigTest
removeGene2CsStatusFileAndDirectory() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilIntegrationTest
removeWithBioAssayDimension() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest
RepeatScanTest - Class in ubic.gemma.core.analysis.sequence
RepeatScanTest() - Constructor for class ubic.gemma.core.analysis.sequence.RepeatScanTest
replyPattern - Variable in class ubic.gemma.web.util.dwr.AbstractDwrReplyParser
resetMocks() - Method in class ubic.gemma.core.ontology.OntologyCacheTest
resetMocks() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceImplTest
resetMocks() - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisControllerTest
resetTestCollectionSize() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Restore to default.
resetTestElementCollectionSize() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
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
retryPolicy - Variable in class ubic.gemma.persistence.retry.RetryTest
RetryTest - Class in ubic.gemma.persistence.retry
RetryTest() - Constructor for class ubic.gemma.persistence.retry.RetryTest
RetryTest.TestRetryDao - Interface in ubic.gemma.persistence.retry
RetryTest.TestRetryService - Class in ubic.gemma.persistence.retry
RNASeqBatchInfoPopulationTest - Class in ubic.gemma.core.analysis.preprocess.batcheffects
RNASeqBatchInfoPopulationTest() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
RNASeqDataAddCliTest - Class in ubic.gemma.core.apps
RNASeqDataAddCliTest() - Constructor for class ubic.gemma.core.apps.RNASeqDataAddCliTest
roles() - Method in annotation type org.springframework.security.test.context.support.WithMockUser: The roles to use.
roles(String...) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.UserRequestPostProcessor: Specify the roles of the user to authenticate as.
RootWebServiceTest - Class in ubic.gemma.rest
RootWebServiceTest() - Constructor for class ubic.gemma.rest.RootWebServiceTest
RssFeedControllerTest - Class in ubic.gemma.web.controller.common.rss
RssFeedControllerTest() - Constructor for class ubic.gemma.web.controller.common.rss.RssFeedControllerTest
rule - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest: This allows the usage of Mock annotation to create mocks.
runAsAdmin() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
runAsAdmin() - Method in interface ubic.gemma.core.util.test.TestAuthenticationUtils
runAsAdmin() - Method in class ubic.gemma.core.util.test.TestAuthenticationUtilsImpl: Elevate to administrative privileges (tests normally run this way, this can be used to set it back if you called runAsUser).
runAsAgent() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
runAsAgent() - Method in interface ubic.gemma.core.util.test.TestAuthenticationUtils
runAsAgent() - Method in class ubic.gemma.core.util.test.TestAuthenticationUtilsImpl
runAsAnonymous() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
runAsAnonymous() - Method in interface ubic.gemma.core.util.test.TestAuthenticationUtils
runAsAnonymous() - Method in class ubic.gemma.core.util.test.TestAuthenticationUtilsImpl
runAsUser(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
runAsUser(String, boolean) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
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.
runJob(TaskCommand) - Method in interface ubic.gemma.web.util.MockLongJobController
runJob(TaskCommand) - Method in class ubic.gemma.web.util.MockLongJobControllerImpl
runSecuredMethodOnSchedule() - Method in class ubic.gemma.web.scheduler.SchedulerSecurityTest
runSecuredMethodOnScheduleMultiGroup() - Method in class ubic.gemma.web.scheduler.SchedulerSecurityTest
runUnauthorizedMethodOnSchedule() - Method in class ubic.gemma.web.scheduler.SchedulerSecurityTest

S

SampleCoexpressionAnalysisServiceTest - Class in ubic.gemma.core.analysis.preprocess
SampleCoexpressionAnalysisServiceTest() - Constructor for class ubic.gemma.core.analysis.preprocess.SampleCoexpressionAnalysisServiceTest
SchedulerSecurityTest - Class in ubic.gemma.web.scheduler: Tests security of methods run by Quartz.
SchedulerSecurityTest() - Constructor for class ubic.gemma.web.scheduler.SchedulerSecurityTest
SDRFFetcherTest - Class in ubic.gemma.core.loader.expression.arrayExpress
SDRFFetcherTest() - Constructor for class ubic.gemma.core.loader.expression.arrayExpress.SDRFFetcherTest
search(StringArrayArg) - Method in class ubic.gemma.rest.util.args.StringArrayArgTest.Api
searchDir - Variable in class ubic.gemma.persistence.util.SettingsConfigTest
searchExpressionExperiment() - Method in class ubic.gemma.core.search.SearchServiceTest
searchExpressionExperiment_whenQueryHasMultipleClauses_thenParseAccordingly() - Method in class ubic.gemma.core.search.SearchServiceTest
searchExpressionExperimentsByUri_whenQueryIsAUri_thenEnsureTheUriIsUsedDirectly() - Method in class ubic.gemma.core.search.SearchServiceTest
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.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration
searchService() - Method in class ubic.gemma.rest.SearchWebServiceTest.SearchWebServiceTestContextConfiguration
SearchServiceIntegrationTest - Class in ubic.gemma.core.search
SearchServiceIntegrationTest() - Constructor for class ubic.gemma.core.search.SearchServiceIntegrationTest
SearchServiceTest - Class in ubic.gemma.core.search
SearchServiceTest() - Constructor for class ubic.gemma.core.search.SearchServiceTest
SearchServiceVoConversionTest - Class in ubic.gemma.core.search: Test conversion to VOs for search results.
SearchServiceVoConversionTest() - Constructor for class ubic.gemma.core.search.SearchServiceVoConversionTest
SearchSettingsTest - Class in ubic.gemma.model.common.search
SearchSettingsTest() - Constructor for class ubic.gemma.model.common.search.SearchSettingsTest
searchWebService() - Method in class ubic.gemma.rest.SearchWebServiceTest.SearchWebServiceTestContextConfiguration
SearchWebServiceTest - Class in ubic.gemma.rest
SearchWebServiceTest() - Constructor for class ubic.gemma.rest.SearchWebServiceTest
SearchWebServiceTest.SearchWebServiceTestContextConfiguration - Class in ubic.gemma.rest
SearchWebServiceTestContextConfiguration() - Constructor for class ubic.gemma.rest.SearchWebServiceTest.SearchWebServiceTestContextConfiguration
SecureValueObjectAuthorizationTest - Class in ubic.gemma.core.security.authorization
SecureValueObjectAuthorizationTest() - Constructor for class ubic.gemma.core.security.authorization.SecureValueObjectAuthorizationTest
securityContext(SecurityContext) - Static method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors: Establish the specified SecurityContext to be used.
SecurityControllerTest - Class in ubic.gemma.web.controller.security
SecurityControllerTest() - Constructor for class ubic.gemma.web.controller.security.SecurityControllerTest
SecurityMockMvcRequestBuilders - Class in org.springframework.security.test.web.servlet.request: Contains Spring Security related MockMvc RequestBuilders.
SecurityMockMvcRequestBuilders.FormLoginRequestBuilder - Class in org.springframework.security.test.web.servlet.request: Creates a form based login request including any necessary CsrfToken.
SecurityMockMvcRequestBuilders.LogoutRequestBuilder - Class in org.springframework.security.test.web.servlet.request: Creates a logout request (including any necessary CsrfToken)
SecurityMockMvcRequestPostProcessors - Class in org.springframework.security.test.web.servlet.request: Contains MockMvc RequestPostProcessor implementations for Spring Security.
SecurityMockMvcRequestPostProcessors.CsrfRequestPostProcessor - Class in org.springframework.security.test.web.servlet.request: Populates a valid CsrfToken into the request.
SecurityMockMvcRequestPostProcessors.DigestRequestPostProcessor - Class in org.springframework.security.test.web.servlet.request
SecurityMockMvcRequestPostProcessors.UserRequestPostProcessor - Class in org.springframework.security.test.web.servlet.request: Creates a UsernamePasswordAuthenticationToken and sets the principal to be a User and associates it to the MockHttpServletRequest.
SecurityMockMvcResultMatchers - Class in org.springframework.security.test.web.servlet.response: Security related MockMvc ResultMatchers.
SecurityMockMvcResultMatchers.AuthenticatedMatcher - Class in org.springframework.security.test.web.servlet.response: A MockMvc ResultMatcher that verifies a specific user is associated to the MvcResult.
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
SecurityTestExecutionListeners - Annotation Type in org.springframework.security.test.context.annotation: There are many times a user may want to use Spring Security's test support (i.e.
SecurityUtilsTest - Class in ubic.gemma.persistence.util
SecurityUtilsTest() - Constructor for class ubic.gemma.persistence.util.SecurityUtilsTest
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
ServiceBasedValueObjectConverterTest - Class in ubic.gemma.persistence.util
ServiceBasedValueObjectConverterTest() - Constructor for class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest
ServiceBasedValueObjectConverterTest.VoConverterTestContextConfiguration - Class in ubic.gemma.persistence.util
ServletUtilsTest - Class in ubic.gemma.rest.util
ServletUtilsTest() - Constructor for class ubic.gemma.rest.util.ServletUtilsTest
sessionFactory - Variable in class ubic.gemma.core.util.test.BaseDatabaseTest
sessionFactory(DataSource) - Method in class ubic.gemma.core.util.test.BaseDatabaseTest.BaseDatabaseTestContextConfiguration
setContext(SecurityContext) - Static method in class org.springframework.security.test.context.TestSecurityContextHolder: Sets the SecurityContext on TestSecurityContextHolder and SecurityContextHolder.
setId(long) - Method in class ubic.gemma.persistence.service.AbstractDaoTest.MyEntity
setPersisterHelper(PersisterHelper) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
setSecurityContextRepository(HttpServletRequest, SecurityContextRepository) - Static method in class org.springframework.security.test.web.support.WebTestUtils: Sets the SecurityContextRepository for the specified HttpServletRequest.
setSeed(long) - Static method in class ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils
setTaxonService(TaxonService) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
setTestCollectionSize(int) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Change the number of elements created in collections (basically controls the size of test data sets).
setTestElementCollectionSize(int) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Override the number of elements made in collections.
setTestRetryDao(RetryTest.TestRetryDao) - Method in class ubic.gemma.persistence.retry.RetryTest.TestRetryService
SettingsConfigTest - Class in ubic.gemma.persistence.util
SettingsConfigTest() - Constructor for class ubic.gemma.persistence.util.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.core.loader.genome.SimpleFastaCmdTest
setUp() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisServiceTest
setUp() - Method in class ubic.gemma.core.analysis.expression.diff.BaseAnalyzerConfigurationTest
setUp() - Method in class ubic.gemma.core.analysis.expression.diff.BaselineDetectionTest
setUp() - Method in class ubic.gemma.core.analysis.expression.diff.ContinuousVariableDiffExTest
setUp() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExWithInvalidInteraction2Test
setUp() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExWithInvalidInteractionTest
setUp() - Method in class ubic.gemma.core.analysis.expression.diff.LowVarianceDataTest
setUp() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysis2Test
setUp() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysis3Test
setUp() - Method in class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionsTest2
setUp() - Method in class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionTest2
setUp() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceTest
setUp() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
setUp() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest
setUp() - Method in class ubic.gemma.core.analysis.preprocess.QuantileNormalizerTest
setUp() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceTest
setUp() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest
setUp() - Method in class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperServiceTest
setUp() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceTest
setUp() - Method in class ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationServiceTest
setUp() - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImplTest
setUp() - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceTest
setUp() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCliTest
setUp() - Method in class ubic.gemma.core.apps.FactorValueMigratorCLITest: Deprecated.
setUp() - Method in class ubic.gemma.core.apps.FactorValueMigratorServiceTest: Deprecated.
setUp() - Method in class ubic.gemma.core.apps.RNASeqDataAddCliTest
setUp() - Method in class ubic.gemma.core.datastructure.matrix.ExperimentalDesignWriterTest
setUp() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixTest
setUp() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
setUp() - Method in class ubic.gemma.core.externalDb.GoldenPathQueryTest
setUp() - Method in class ubic.gemma.core.job.ExecutingTaskTest
setUp() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearchTest
setUp() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest
setUp() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest
setUp() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReaderTest
setUp() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorTest
setUp() - Method in class ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParserTest
setUp() - Method in class ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReaderTest
setUp() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest
setUp() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
setUp() - Method in class ubic.gemma.core.loader.expression.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.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.ontology.OntologyCacheTest
setUp() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest
setUp() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
setUp() - Method in class ubic.gemma.core.security.authentication.UserServiceImplTest
setUp() - Method in class ubic.gemma.core.security.authorization.acl.AclAuthorizationTest
setUp() - Method in class ubic.gemma.core.security.authorization.acl.AclCollectionBeforeTest
setUp() - Method in class ubic.gemma.core.security.authorization.SecureValueObjectAuthorizationTest
setUp() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest
setUp() - Method in class ubic.gemma.core.security.UserGroupServiceTest
setUp() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiFetcherTest
setUp() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiObjectGeneratorTest
setUp() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiParserTest
setUp() - Method in class ubic.gemma.core.util.progress.ProgressAppenderTest
setUp() - Method in class ubic.gemma.core.util.progress.ProgressDataTest
setUp() - Method in class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest
setUp() - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpressionServiceTest
setUp() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
setUp() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventServiceTest
setUp() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailDaoTest
setUp() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest
setUp() - Method in class ubic.gemma.model.common.description.CharacteristicServiceTest
setUp() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
setUp() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayServiceTest
setUp() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialServiceTest
setUp() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
setUp() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetServiceTest
setUp() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObjectHelperTest
setUp() - Method in class ubic.gemma.model.expression.experiment.FactorValueServiceIntegrationTest
setUp() - Method in class ubic.gemma.model.genome.BlatResultTest
setUp() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest
setUp() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest
setUp() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObjectHelperTest
setUp() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest
setUp() - Method in class ubic.gemma.model.genome.GeneTest
setUp() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociationServiceTest
setUp() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultServiceTest
setUp() - Method in class ubic.gemma.persistence.service.AbstractDaoTest
setUp() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest
setUp() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoTest
setUp() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest
setUp() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceTest
setUp() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilTest
setUp() - Method in class ubic.gemma.persistence.util.AclCriteriaUtilsTest
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.AnalysisResultSetsWebServiceTest
setUp() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4ProviderTest
setUp() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest
setUp() - Method in class ubic.gemma.rest.DatasetsRestTest
setUp() - Method in class ubic.gemma.rest.PlatformsWebServiceTest
setUp() - Method in class ubic.gemma.rest.TaxaWebServiceTest
setUp() - Method in class ubic.gemma.rest.util.BaseJerseyTest
setUp() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupControllerTest
setUp() - Method in class ubic.gemma.web.controller.common.description.bibref.BibRefControllerTest
setUp() - Method in class ubic.gemma.web.controller.common.rss.RssFeedControllerTest
setUp() - Method in class ubic.gemma.web.controller.expression.CuratableValueObjectTest
setUp() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerIntegrationTest
setUp() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest
setUp() - Method in class ubic.gemma.web.controller.OntologyControllerTest
setUp() - Method in class ubic.gemma.web.controller.security.SecurityControllerTest
setUp() - Static method in class ubic.gemma.web.logging.LoggingIntegrationTest
setUp() - Method in class ubic.gemma.web.logging.SlackAppenderTest
SetUp() - Method in class ubic.gemma.core.image.aba.AllenBrainAtlasServiceTest
setupArrayDesign() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AbstractArrayDesignProcessingTest
setUpAuthentication() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Setup the authentication for the test.
setUpAuthentication() - Method in class ubic.gemma.rest.util.BaseJerseyIntegrationTest
setupMocks() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceImplTest
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.DatasetsWebServiceTest
setUpMocks() - Method in class ubic.gemma.rest.SearchWebServiceTest
setUpMocks() - Method in class ubic.gemma.web.util.AnchorTagUtilTest
setUpSecurityContextHolderStrategy() - Static method in class ubic.gemma.core.util.test.BaseSpringContextTest
setUpSecurityContextHolderStrategy() - Static method in class ubic.gemma.rest.util.BaseJerseyIntegrationTest
setUpSpec() - Method in class ubic.gemma.rest.OpenApiTest
SignupControllerTest - Class in ubic.gemma.web.controller.common.auditAndSecurity: This test replaces the recaptcha service used by SignupController, so it is annotated with DirtiesContext to invalidate the context once all the tests have completed.
SignupControllerTest() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SignupControllerTest
SimpleExpressionDataLoaderServiceTest - Class in ubic.gemma.core.loader.expression.simple
SimpleExpressionDataLoaderServiceTest() - Constructor for class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceTest
SimpleFastaCmdTest - Class in ubic.gemma.core.loader.genome
SimpleFastaCmdTest() - Constructor for class ubic.gemma.core.loader.genome.SimpleFastaCmdTest
SlackAppenderTest - Class in ubic.gemma.web.logging
SlackAppenderTest() - Constructor for class ubic.gemma.web.logging.SlackAppenderTest
SlowTest - Class in ubic.gemma.core.util.test.category: Used to mark slow tests.
SlowTest() - Constructor for class ubic.gemma.core.util.test.category.SlowTest
SlowTests - Class in ubic.gemma.core.util.test.suite: Run all the slow tests.
SlowTests() - Constructor for class ubic.gemma.core.util.test.suite.SlowTests
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
SpearmanMetricsTest - Class in ubic.gemma.core.analysis.expression.coexpression.links
SpearmanMetricsTest() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetricsTest
SplitExperimentTest - Class in ubic.gemma.core.analysis.preprocess
SplitExperimentTest() - Constructor for class ubic.gemma.core.analysis.preprocess.SplitExperimentTest
StatementTest - Class in ubic.gemma.model.expression.experiment
StatementTest() - Constructor for class ubic.gemma.model.expression.experiment.StatementTest
StopWatchUtilsTest - Class in ubic.gemma.core.util
StopWatchUtilsTest() - Constructor for class ubic.gemma.core.util.StopWatchUtilsTest
stressTest() - Method in class ubic.gemma.persistence.util.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
SubqueryUtilsTest - Class in ubic.gemma.persistence.service
SubqueryUtilsTest() - Constructor for class ubic.gemma.persistence.service.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
SubsettedAnalysisTest - Class in ubic.gemma.core.analysis.expression.diff
SubsettedAnalysisTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysisTest
SupportDetailsTest - Class in ubic.gemma.model.analysis.expression.coexpression
SupportDetailsTest() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.SupportDetailsTest
SVDServiceImplTest - Class in ubic.gemma.core.analysis.preprocess.svd
SVDServiceImplTest() - Constructor for class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImplTest
SwissProtParserTest - Class in ubic.gemma.core.loader.genome.gene
SwissProtParserTest() - Constructor for class ubic.gemma.core.loader.genome.gene.SwissProtParserTest

T

TableMaintenanceUtilIntegrationTest - Class in ubic.gemma.persistence.service
TableMaintenanceUtilIntegrationTest() - Constructor for class ubic.gemma.persistence.service.TableMaintenanceUtilIntegrationTest
TableMaintenanceUtilTest - Class in ubic.gemma.persistence.service
TableMaintenanceUtilTest() - Constructor for class ubic.gemma.persistence.service.TableMaintenanceUtilTest
TaskRunningTest - Class in ubic.gemma.web.controller: Test of long job control.
TaskRunningTest() - Constructor for class ubic.gemma.web.controller.TaskRunningTest
TaskUtilsTest - Class in ubic.gemma.core.job
TaskUtilsTest() - Constructor for class ubic.gemma.core.job.TaskUtilsTest
TaxaWebServiceTest - Class in ubic.gemma.rest
TaxaWebServiceTest() - Constructor for class ubic.gemma.rest.TaxaWebServiceTest
taxonArgService(TaxonService) - Method in class ubic.gemma.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration
taxonArgService(TaxonService) - Method in class ubic.gemma.rest.SearchWebServiceTest.SearchWebServiceTestContextConfiguration
TaxonArgServiceTest - Class in ubic.gemma.rest.util.args
TaxonArgServiceTest() - Constructor for class ubic.gemma.rest.util.args.TaxonArgServiceTest
TaxonLoaderTest - Class in ubic.gemma.core.loader.genome.taxon
TaxonLoaderTest() - Constructor for class ubic.gemma.core.loader.genome.taxon.TaxonLoaderTest
TaxonParserTest - Class in ubic.gemma.core.loader.genome.taxon
TaxonParserTest() - Constructor for class ubic.gemma.core.loader.genome.taxon.TaxonParserTest
taxonService - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest
taxonService() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration
taxonService() - Method in class ubic.gemma.rest.SearchWebServiceTest.SearchWebServiceTestContextConfiguration
TaxonServiceImplTest - Class in ubic.gemma.model.genome
TaxonServiceImplTest() - Constructor for class ubic.gemma.model.genome.TaxonServiceImplTest
TaxonUtilityTest - Class in ubic.gemma.core.util
TaxonUtilityTest() - Constructor for class ubic.gemma.core.util.TaxonUtilityTest
TaxonValueObjectTest - Class in ubic.gemma.model.genome
TaxonValueObjectTest() - Constructor for class ubic.gemma.model.genome.TaxonValueObjectTest
teardown() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceTest
teardown() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysis2Test
teardown() - Method in class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionsTest2
teardown() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceTest
teardown() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
teardown() - Method in class ubic.gemma.core.analysis.preprocess.SplitExperimentTest
tearDown() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisServiceTest
tearDown() - Method in class ubic.gemma.core.analysis.expression.diff.BaseAnalyzerConfigurationTest
tearDown() - Method in class ubic.gemma.core.analysis.expression.diff.BaselineDetectionTest
tearDown() - Method in class ubic.gemma.core.analysis.expression.diff.ContinuousVariableDiffExTest
tearDown() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest
tearDown() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExTest
tearDown() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExWithInvalidInteraction2Test
tearDown() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExWithInvalidInteractionTest
tearDown() - Method in class ubic.gemma.core.analysis.preprocess.QuantileNormalizerTest
tearDown() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImplTest
tearDown() - Method in class ubic.gemma.core.analysis.preprocess.VectorMergingServiceTest
tearDown() - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceTest
tearDown() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceTest
tearDown() - Method in class ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationServiceTest
tearDown() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCliTest
tearDown() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCliTest
tearDown() - Method in class ubic.gemma.core.apps.FactorValueMigratorServiceTest: Deprecated.
tearDown() - Method in class ubic.gemma.core.apps.RNASeqDataAddCliTest
tearDown() - Method in class ubic.gemma.core.datastructure.matrix.ExperimentalDesignWriterTest
tearDown() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixTest
tearDown() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest
tearDown() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest
tearDown() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AbstractArrayDesignProcessingTest
tearDown() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReaderTest
tearDown() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentandMappingTest
tearDown() - Method in class ubic.gemma.core.loader.expression.DataUpdaterTest
tearDown() - Method in class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchTest
tearDown() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest
tearDown() - Method in class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterTest
tearDown() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneLoadingTest
tearDown() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonParserTest
tearDown() - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcherTest
tearDown() - Method in class ubic.gemma.core.loader.util.HttpFetcherTest
tearDown() - Method in class ubic.gemma.core.ontology.OntologyServiceTest
tearDown() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest
tearDown() - Method in class ubic.gemma.core.search.SearchServiceTest
tearDown() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
tearDown() - Method in class ubic.gemma.core.search.source.DatabaseSearchSourceTest
tearDown() - Method in class ubic.gemma.core.search.source.OntologySearchSourceTest
tearDown() - Method in class ubic.gemma.core.security.audit.PointcutsTest
tearDown() - Method in class ubic.gemma.core.util.progress.ProgressDataTest
tearDown() - Method in class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest
tearDown() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
tearDown() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest
tearDown() - Method in class ubic.gemma.model.expression.bioAssayData.DesignElementDataVectorServiceTest
tearDown() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
tearDown() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest
tearDown() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetServiceTest
tearDown() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObjectHelperTest
tearDown() - Method in class ubic.gemma.model.expression.experiment.FactorValueServiceIntegrationTest
tearDown() - Method in class ubic.gemma.model.expression.experiment.FactorValueServiceTest
tearDown() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest
tearDown() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest
tearDown() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest
tearDown() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociationServiceTest
tearDown() - Method in class ubic.gemma.persistence.retry.RetryTest
tearDown() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest
tearDown() - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceTest
tearDown() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoTest
tearDown() - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityServiceTest
tearDown() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilTest
tearDown() - Method in class ubic.gemma.persistence.util.AclCriteriaUtilsTest
tearDown() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest
tearDown() - Method in class ubic.gemma.persistence.util.MailEngineTest
tearDown() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest
tearDown() - Method in class ubic.gemma.rest.AnalysisResultSetsJerseyTest
tearDown() - Method in class ubic.gemma.rest.AnalysisResultSetsWebServiceTest
tearDown() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4ProviderTest
tearDown() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest
tearDown() - Method in class ubic.gemma.rest.DatasetsRestTest
tearDown() - Method in class ubic.gemma.rest.DatasetsWebServiceTest
tearDown() - Method in class ubic.gemma.rest.PlatformsWebServiceTest
tearDown() - Method in class ubic.gemma.rest.SearchWebServiceTest
tearDown() - Method in class ubic.gemma.rest.TaxaWebServiceTest
tearDown() - Method in class ubic.gemma.rest.util.args.TaxonArgServiceTest
tearDown() - Method in class ubic.gemma.rest.util.BaseJerseyTest
tearDown() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupControllerTest
tearDown() - Method in class ubic.gemma.web.controller.expression.CuratableValueObjectTest
tearDown() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerIntegrationTest
tearDown() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest
tearDown() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentControllerTest
tearDown() - Method in class ubic.gemma.web.controller.OntologyControllerTest
tearDown() - Method in class ubic.gemma.web.util.upload.FileUploadUtilTest
tearDownSecurityContext() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Clear the SecurityContextHolder so that subsequent tests don't inherit authentication.
tearDownSecurityContext() - Method in class ubic.gemma.rest.util.BaseJerseyIntegrationTest: Clear the SecurityContextHolder so that subsequent tests don't inherit authentication.
tesAsUser() - Method in class ubic.gemma.persistence.util.AclCriteriaUtilsTest
test() - Method in class ubic.gemma.core.analysis.expression.diff.ContinuousVariableDiffExTest
test() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExWithInvalidInteraction2Test
test() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExWithInvalidInteractionTest: This should automatically drop the interaction.
test() - Method in class ubic.gemma.core.analysis.expression.diff.LowVarianceDataTest
test() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysis2Test
test() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysis3Test
test() - Method in class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionsTest2
test() - Method in class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionTest2
test() - Method in class ubic.gemma.core.analysis.preprocess.SampleCoexpressionAnalysisServiceTest
test() - Method in class ubic.gemma.core.analysis.preprocess.VectorMergingServiceTest
test() - Method in class ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationServiceTest
test() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCliTest
test() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCliTest
test() - Method in class ubic.gemma.core.apps.FindObsoleteTermsCliTest
test() - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLITest
test() - Method in class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchTest: for bug 3451
test() - Method in class ubic.gemma.core.loader.expression.geo.GeoTermReplacementTest
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.metrics.MeterRegistryCliConfigurerTest
test() - Method in class ubic.gemma.core.ontology.providers.DiseaseOntologyTest
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.search.SearchResultSetTest
test() - Method in class ubic.gemma.core.search.source.HibernateSearchSourceTest
test() - Method in class ubic.gemma.core.search.source.OntologySearchSourceTest
test() - Method in class ubic.gemma.core.util.BuildInfoTest
test() - Method in class ubic.gemma.core.util.StrictBeanDefinitionValidatorTest
test() - Method in class ubic.gemma.core.util.test.HibernateConfigTest
test() - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedInTest
test() - Method in class ubic.gemma.model.analysis.expression.coexpression.SupportDetailsTest
test() - Method in class ubic.gemma.model.analysis.GeneDiffExMetaAnalysisServiceTest
test() - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventTypeTest
test() - Method in class ubic.gemma.model.expression.experiment.FactorValueUtilsTest
test() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest
test() - Method in class ubic.gemma.persistence.service.SubqueryUtilsTest
test() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilTest
test() - Method in class ubic.gemma.persistence.util.AclCriteriaUtilsTest
test() - Method in class ubic.gemma.persistence.util.FiltersTest
test() - Method in class ubic.gemma.persistence.util.MailEngineTest
test() - Method in class ubic.gemma.persistence.util.QueryUtilsTest
test() - Method in class ubic.gemma.persistence.util.SettingsConfigTest
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() - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisControllerTest
test() - Method in class ubic.gemma.web.controller.ErrorPagesTest
test() - Method in class ubic.gemma.web.logging.SlackAppenderTest
test() - Method in class ubic.gemma.web.remote.EntityDelegatorTest
test() - Method in class ubic.gemma.web.util.MessageSourceTest
test_quotedTerms() - Method in class ubic.gemma.core.search.source.DatabaseSearchSourceTest
test_whenQueryContainsAsterisk_thenSubstituteForPercent() - Method in class ubic.gemma.core.search.source.DatabaseSearchSourceTest
test_whenQueryContainsLikePatterns_thenEscape() - Method in class ubic.gemma.core.search.source.DatabaseSearchSourceTest
test_whenQueryContainsQuote_thenStripThem() - Method in class ubic.gemma.core.search.source.DatabaseSearchSourceTest
test_whenTaxonIsNameIsUsedInQuery_thenAddTaxonToSearchSettings() - Method in class ubic.gemma.core.search.SearchServiceTest
test1() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBatTest
test2WithMissingValues() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBatTest
test3() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBatTest: Based on GSE13712
test3NoCovariate() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBatTest
test4() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBatTest
test5C() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
test5NonParametric() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBatTest
testa() - Method in class ubic.gemma.model.analysis.expression.coexpression.CoexpressionNodeDegreeValueObjectTest
testAbsCall() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testAclCollectionEntryVoter() - Method in class ubic.gemma.core.security.authorization.acl.AclCollectionBeforeTest
testAclCollectionEntryVoterOK() - Method in class ubic.gemma.core.security.authorization.acl.AclCollectionBeforeTest
testAddAclJoinParameters() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest
testAddAffyExonArrayDataExpressionExperiment() - Method in class ubic.gemma.core.loader.expression.ExonArrayDataAddIntegrationTest
testAddAffyExonHuman() - Method in class ubic.gemma.core.loader.expression.ExonArrayDataAddIntegrationTest
testAddAffyExonRat() - Method in class ubic.gemma.core.loader.expression.ExonArrayDataAddIntegrationTest
testAddCharacteristicToFactorValue() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerIntegrationTest
testAddData() - Method in class ubic.gemma.core.loader.expression.DataUpdaterTest
testAddDoesNotNeedsAttentionEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest
testAddEventWhenTransactionIsRolledBack() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest
testAddEventWhenTransactionIsRolledBack2() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest
testAddExceptionEventOnTransientEntity() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest
testAddingExperimentOfWrongTaxonUpdate() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetServiceTest
testAddingExperimentOfWrongTaxonUpdateDatabaseEntityMembers() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetServiceTest
testAddNeedsAttentionEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest
testAddOKEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest
testAddStatementToFactorValue() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerIntegrationTest
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.model.common.auditAndSecurity.AuditTrailServiceImplTest
testAddUpdateEvent() - Method in class ubic.gemma.web.remote.AuditControllerTest
testAddUpdateEventAuditableAuditEventTypeString() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest
testAddUpdateEventAuditableString() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest
testAddUpdateEventOnTransientEntity() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest
testAddWhenMaxResultsIsReached() - Method in class ubic.gemma.core.search.SearchResultSetTest
testAll() - Method in class ubic.gemma.rest.DatasetsRestTest
testAll() - Method in class ubic.gemma.rest.PlatformsWebServiceTest
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
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
testAnalysisAcl() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest
testAnalyze() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceTest
testAnalyzeAndDelete() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest
testAnalyzeAndDeleteSpecificAnalysis() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest: Test for bug 2026, not a subsetted analysis.
testAnalyzeAndDeleteSpecificAnalysisWithSubset() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest: Tests running with a subset factor, then deleting.
testAnalyzeWithSubsetWhenOneIsNotUsableAndWithInteractionInTheOther() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest: Test inspired by bug 2605
testAncovaContinuousCovariate() - Method in class ubic.gemma.core.analysis.expression.diff.AncovaTest
testAncovaCovariate() - Method in class ubic.gemma.core.analysis.expression.diff.AncovaTest
testAncovaTriLevel() - Method in class ubic.gemma.core.analysis.expression.diff.AncovaTest
testAncovaTwoway() - Method in class ubic.gemma.core.analysis.expression.diff.AncovaTest
testAncovaWithInteraction() - Method in class ubic.gemma.core.analysis.expression.diff.AncovaTest
TestAnnotatedVo() - Constructor for class ubic.gemma.core.util.StrictBeanDefinitionValidatorTest.TestAnnotatedVo
testareaCall() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testArrayDesignAcls() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest
testArrayDesignAclsUser() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest
testAsAdmin() - Method in class ubic.gemma.persistence.util.AclCriteriaUtilsTest
testAsAdmin() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest
testAsAnonymous() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest
testAsRegularGoId() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest
testAssignSequencesToDesignElements() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorTest
testAssignSequencesToDesignElementsMissingSequence() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorTest
testAsUser() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest
testAttemptAuthentication() - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationProcessingTest
testAttemptAuthenticationNonexistentUser() - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationProcessingTest
testAttemptAuthenticationWrongPassword() - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationProcessingTest
testAttributesToRetrieveFromBioMart() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiFetcherTest
testAuditCreateAndDeleteExpressionExperiment() - Method in class ubic.gemma.core.security.audit.AuditAdviceTest
testAuditFindOrCreateConcurrentTorture() - Method in class ubic.gemma.core.security.audit.AuditAdviceTest
TestAuthenticationUtils - 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
testAutowiredBean() - Method in class ubic.gemma.persistence.util.AsyncBeanAutowiringTest
testAutowiredList() - Method in class ubic.gemma.persistence.util.AsyncBeanAutowiringTest
testAutowiredListOfFactories() - Method in class ubic.gemma.persistence.util.AsyncBeanAutowiringTest
testAutowiredMap() - Method in class ubic.gemma.persistence.util.AsyncBeanAutowiringTest
testbackground() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testbackgroundB() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testBadRatio() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
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
testBash() - Method in class ubic.gemma.core.util.CompletionGeneratorTest
testBashCompletions() - Method in class ubic.gemma.core.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
testBatchCall() - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisControllerTest
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
testBatchLoadingByIds() - Method in class ubic.gemma.persistence.service.AbstractDaoTest
testBatchM() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchMixedHeaders() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest: See https://github.com/PavlidisLab/GemmaCuration/issues/64
testBatchMixedHeadersSinglePlatform() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchMixedHeadersSinglePlatformSingleton() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchO() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchP() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchParameterList() - Method in class ubic.gemma.persistence.util.QueryUtilsTest
testBatchQ() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBinFromRangeA() - Method in class ubic.gemma.core.analysis.sequence.SequenceBinUtilsTest
testBinFromRangeB() - Method in class ubic.gemma.core.analysis.sequence.SequenceBinUtilsTest
testBinFromRangeC() - Method in class ubic.gemma.core.analysis.sequence.SequenceBinUtilsTest
testBinFromRangeD() - Method in class ubic.gemma.core.analysis.sequence.SequenceBinUtilsTest
testbkdst() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testBlacklist() - Method in class ubic.gemma.model.expression.BlacklistTest
testBlacklistedConversion() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
testBlacklistedExperimentAsNonAdmin() - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityServiceTest
testBlacklistExperiment() - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityServiceTest
testBlacklistPlatformProperlyCascadeThroughAllExperiments() - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityServiceTest
testBlankMeasurementId() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4ProviderTest
testBrowse() - Method in class ubic.gemma.model.common.description.CharacteristicServiceTest
testBrowseWithInvalidField() - Method in class ubic.gemma.model.common.description.CharacteristicServiceTest
testBulkAdd() - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedInTest
testCacheConfigurations() - Method in class ubic.gemma.core.util.test.HibernateConfigTest
testCacheInvalidationWhenACharacteristicIsDeleted() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testCancelledRun() - Method in class ubic.gemma.web.controller.TaskRunningTest
testCascadeCreateCompositeSequences() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testCascadingCreateOnUpdate() - Method in class ubic.gemma.core.security.audit.AuditAdviceTest
testCascadingCreateWithAssociatedAuditable() - Method in class ubic.gemma.core.security.audit.AuditAdviceTest
testCELnameregex() - Method in class ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarizeTest
testChangePassword() - Method in class ubic.gemma.core.security.principal.PrincipalTest
testCheckBiologicalReplicates() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperServiceTest
testClearNeedsAttention() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest
testClearNeedsAttentionFlag() - Method in class ubic.gemma.model.expression.experiment.FactorValueServiceTest
testClearNeedsAttentionFlagThatAlreadyNeedsAttention() - Method in class ubic.gemma.model.expression.experiment.FactorValueServiceTest
testClearNeedsAttentionFlagWhenANeedsAttentionEventWasResolved() - Method in class ubic.gemma.model.expression.experiment.FactorValueServiceTest
testCollectionWithNullElement() - Method in class ubic.gemma.persistence.util.FilterTest
testCollectionWithSubclass() - Method in class ubic.gemma.persistence.util.FilterTest
testColumnMapping() - Method in class ubic.gemma.core.datastructure.matrix.MatrixConversionTest
testComBatOnEE() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceTest
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.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest
testCompareToNull() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest
testCompareToOrdering() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest
testCompareToTaxon() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest
testCompareToValue() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest
testCompareToValueUri() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest
testComplexClause() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest
testComputeDevRankForExpressionExperimentB() - Method in class ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataCreateServiceTest
testComputeDevRankForExpressionExperimentMultiArrayWithGaps() - Method in class ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataCreateServiceTest: Three platforms, one sample was not run on GPL81.
testComputeSpecificityA() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest
testComputeSpecificityB() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest
testComputeSpecificityC() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest
testComputeSpecificityD() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest
testConfigurationCookieA() - Method in class ubic.gemma.web.util.ConfigurationCookieTest
testConfigurationCookieB() - Method in class ubic.gemma.web.util.ConfigurationCookieTest
testConfigurationCookieC() - Method in class ubic.gemma.web.util.ConfigurationCookieTest
testConfigurationCookieD() - Method in class ubic.gemma.web.util.ConfigurationCookieTest
testConfigurationCookieE() - Method in class ubic.gemma.web.util.ConfigurationCookieTest
testConjunction() - Method in class ubic.gemma.rest.util.args.FilterArgTest
testConjunctionOfDisjunctions() - Method in class ubic.gemma.rest.util.args.FilterArgTest
testConstructExpressionDataDoubleMatrix() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixTest: Tests the construction of an ExpressionDataDoubleMatrix
testConstructExpressionDataDoubleMatrixWithGeoValues() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixTest: This is a self-contained test.
testContinuousFactor() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest
testConvertAlreadyConvertedCollection() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
testConvertArrayDesign() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
testConvertArrayDesignCollection() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
testConvertBibliographicReference() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
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
testConvertCompositeSequence() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
testConvertCompositeSequenceCollection() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
testConvertDataDoubles() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertDataIntegers() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertEntitiesFromIds() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest
testConvertEntityFromId() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest
testConvertExpressionExperiment() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
testConvertGenePix() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertGeneSet() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
testConvertGSE106() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertGSE18Stress() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertGSE2122SAGE() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertGSE29014() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertGSE2982() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertGSE360() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertGSE3791() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertGSE404() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertGSE4229IMAGE() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertGse59() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertGSE60() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertGSE8134() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertMultiSeriesPerSample() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testConvertMultiTaxonDatasetGSE7540() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
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.model.expression.experiment.ExpressionExperimentSetValueObjectHelperTest
testConvertToLightValueObject() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObjectHelperTest: Tests loading 'light' value objects - VOs without EEIds
testConvertToLightValueObject() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObjectHelperTest
testConvertToValueObject() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObjectHelperTest: Tests loading value objects with EEIds.
testConvertToValueObject() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObjectHelperTest
testConvertUninitializedResult() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
testConvertUnknownType() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest
testConvertWithLotsOfPlatforms() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testCopyUploadedFileStreamClosed() - Method in class ubic.gemma.web.util.upload.FileUploadUtilTest
testCopyUploadFileWhenFileContainsDirectory() - Method in class ubic.gemma.web.util.upload.FileUploadUtilTest
testCorrel() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetricsTest: Value from R; this has ties.
testCorrelB() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetricsTest: This tests the same values as testCorrelWithMissing, different method than testCorrelC
testCorrelC() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetricsTest: Without missing values, fast method (same data as testCorrelB)
testCorrelFromRanks() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetricsTest
testCorrelWithMissing() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetricsTest: See testCorrelB for the same numbers tested a different way (with no missing values)
testCountAll() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testCountByValueLike() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest
testCountByValueUriIn() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest
testCountConversion() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testCountData() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExTest: Test differential expression analysis on RNA-seq data.
testCounts() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testCountsWhenPlatformIsMicroarrayThenReportAsLinear() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testCountsWhenPlatformIsNotSequencing() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testCountsWhenValueIsNegativeTreatAsLogbaseUnknown() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testCreate() - Method in class ubic.gemma.model.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
testCreateDatabaseEntry() - Method in class ubic.gemma.model.common.description.DatabaseEntryDaoImplTest
testCreateExperimentalFactor() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerIntegrationTest
testCreateFactorValueCharacteristic() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest
testCreateFactorValueWithBlankCategory() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest
testCreateFactorValueWithBlankValue() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest
testCreateInvalidAnalysis() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDaoTest
testCreateLoadAndRemove() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest: Test of cascade create
testCreateProcessedDataVectors() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoTest
testCreateProcessedDataVectorsFromLog2Data() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoTest
testCreateProcessedDataVectorsFromLog2RatiometricData() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoTest
testCreateStatement() - Method in class ubic.gemma.model.expression.experiment.FactorValueServiceTest
testCreateStatementWithDetachedFactorValue() - Method in class ubic.gemma.model.expression.experiment.FactorValueServiceTest
testCreateUserGroup() - Method in class ubic.gemma.core.security.UserGroupServiceTest: Tests creating a UserGroup
testCrud() - Method in class ubic.gemma.core.security.audit.PointcutsTest
testCrudDelete() - Method in class ubic.gemma.core.security.audit.PointcutsTest
testCrudRead() - Method in class ubic.gemma.core.security.audit.PointcutsTest
testCrudSave() - Method in class ubic.gemma.core.security.audit.PointcutsTest
testCtd() - Method in class ubic.gemma.core.loader.association.phenotype.PhenotypeImportingTest: Deprecated.
testCuratableValueObjectCreation() - Method in class ubic.gemma.web.controller.expression.CuratableValueObjectTest
testCuratableValueObjectInteraction() - Method in class ubic.gemma.web.controller.expression.CuratableValueObjectTest
testDatesToBatchA() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceTest
testDatesToBatchB() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceTest
testDatesToBatchC() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceTest
testDatesToBatchD() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceTest
testDatesToBatchE() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceTest
testDefaultNoArgConstructor() - Method in class ubic.gemma.model.genome.TaxonValueObjectTest
testDelete() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testDelete() - Method in class ubic.gemma.model.expression.experiment.FactorValueServiceIntegrationTest
testDelete() - Method in class ubic.gemma.web.controller.common.description.bibref.BibRefControllerTest
testDeleteAll() - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDaoImplTest
testDeleteExperimentalFactor() - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDaoTest
testDeleteExperimentalFactorUsedByASample() - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDaoTest
testDeleteOfNonExistingEntry() - Method in class ubic.gemma.web.controller.common.description.bibref.BibRefControllerTest
testDeleteUserGroup() - Method in class ubic.gemma.core.security.UserGroupServiceTest: Test for deleting a user group
testDetermineAnalysisA() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerTest
testDetermineAnalysisB() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerTest
testDiffExAnalysisControllerTestPage() - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisControllerTest
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.CharacteristicDaoImplTest
testDisjunction() - Method in class ubic.gemma.rest.util.args.FilterArgTest
testDisplayForm() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerTest
testDuplicateAcesNotAddedOnPrivateExpressionExperiment() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest
testEditArrayDesignDisallowed() - Method in class ubic.gemma.core.security.authorization.acl.AclAuthorizationTest
testEigenvalues() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest
testEmptyArray() - Method in class ubic.gemma.rest.util.args.StringArrayArgTest
testEmptyBase64EncodedArray() - Method in class ubic.gemma.rest.util.args.StringArrayArgTest
testEmptyFilter() - Method in class ubic.gemma.rest.util.args.FilterArgTest
testEmptyPath() - Method in class ubic.gemma.persistence.service.SubqueryUtilsTest
testEmptySortArg() - Method in class ubic.gemma.rest.util.args.SortArgTest
testEmptySubClause() - Method in class ubic.gemma.persistence.util.FiltersTest
testEnglishAnalyzer() - Method in class ubic.gemma.core.search.LuceneTest
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
testEntityDelegatorWithNullId() - Method in class ubic.gemma.web.remote.EntityDelegatorTest
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
testEqualsA() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest
testEqualsA() - Method in class ubic.gemma.model.genome.GeneTest
testEqualsB() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest
testEqualsB() - Method in class ubic.gemma.model.genome.GeneTest
testEqualsC() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest
testEqualsC() - Method in class ubic.gemma.model.genome.GeneTest
testEqualsD() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest
testEqualsD() - Method in class ubic.gemma.model.genome.GeneTest
testEqualsE() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest
testEqualsE() - Method in class ubic.gemma.model.genome.GeneTest
testEqualsF() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest
testEqualsG() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObjectTest
testEqualsID() - Method in class ubic.gemma.model.genome.biosequence.BioSequenceTest
testEqualsName() - Method in class ubic.gemma.model.genome.biosequence.BioSequenceTest
testEqualsSeq() - Method in class ubic.gemma.model.genome.biosequence.BioSequenceTest
testEqualsTaxon() - Method in class ubic.gemma.model.genome.biosequence.BioSequenceTest
testEscapeTsv() - Method in class ubic.gemma.core.analysis.service.AbstractFileServiceTest
testExceptionTranslation() - Method in class ubic.gemma.persistence.service.AbstractDaoIntegrationTest
testExistsByExpressionExperimentAndVectorType() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoTest
testExonArrayInfo() - Method in class ubic.gemma.core.loader.expression.geo.GeoPlatformTest
testExpressionExperimentAcls() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest
testExpressionExperimentFindAll() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceImplTest
testExternalDatabaseWithRelatedDatabases() - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceTest: This test applies to fixtures found in init-entities.sql.
testExtractAgilent() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractorTest
testExtractAgilent2() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractorTest
testExtractDnf() - Method in class ubic.gemma.core.search.lucene.LuceneQueryUtilsTest
testExtractDnfWithNestedAndInSubClause() - Method in class ubic.gemma.core.search.lucene.LuceneQueryUtilsTest
testExtractDnfWithNestedOrInClause() - Method in class ubic.gemma.core.search.lucene.LuceneQueryUtilsTest
testExtractDnfWithQuotedSpaces() - Method in class ubic.gemma.core.search.lucene.LuceneQueryUtilsTest
testExtractDnfWithUris() - Method in class ubic.gemma.core.search.lucene.LuceneQueryUtilsTest
testExtractGenePix() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest
testExtractGenePixB() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest
testExtractGeneSpring() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest
testExtractGpr() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest
testExtractGPR() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractorTest
testExtractImagene() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest
testExtractInputStreamGCOS() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractorTest
testExtractInputStreamGCOS() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractorTest
testExtractInputStreamV3() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractorTest
testExtractInputStreamV3() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractorTest
testExtractInputStreamV4() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractorTest
testExtractInputStreamV4() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractorTest
testExtractInputStreamVx() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractorTest
testExtractInputStreamVx() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractorTest
testExtractLongDate() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest
testExtractTerms() - Method in class ubic.gemma.core.search.lucene.LuceneQueryUtilsTest
testFactorValueStatementsNotListedInOldStyleCharacteristics() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoTest
testFailedRun() - Method in class ubic.gemma.web.controller.TaskRunningTest
testFetch() - Method in class ubic.gemma.core.loader.entrez.EutilFetchTest
testFetch() - Method in class ubic.gemma.core.loader.expression.arrayExpress.SDRFFetcherTest
testFetch() - Method in class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcherTest: Test method for 'ubic.gemma.core.loader.expression.geo.RawDataFetcher.fetch(String)'.
testFetch() - Method in class ubic.gemma.core.loader.util.HttpFetcherTest
testFetch() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventDaoTest
testFetchAndLoadGPL101Short() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoPlatformServiceTest
testFetchAndLoadGSE1133() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest
testFetchAndLoadGSE12135EXON() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest
testFetchAndLoadGSE13657() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest
testFetchAndLoadGSE16035() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest
testFetchAndLoadGSE18162() - Method in class ubic.gemma.core.analysis.expression.diff.BaselineDetectionTest
testFetchAndLoadGSE18707() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest
testFetchAndLoadGSE37646RNASEQ() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest
testFetchAndLoadGSE5949() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest
testFetchAndLoadGSE8294() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testFetchAndLoadGSE9048() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest
testFetchAndLoadMultiChipPerSeriesShort() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest
testFetchAndLoadWithIdentifiers() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorTest
testFetchAndLoadWithSequences() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorTest
testFetchNothingThere() - Method in class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcherTest
testFileIncorrectFormatIllegalArgumentExceptionException() - Method in class ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceTest
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
testFilterByAllCharacteristics() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testFilterByGeeqQualityScore() - Method in class ubic.gemma.rest.DatasetsRestTest
testFilterByGeeqScore() - Method in class ubic.gemma.model.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.
testFilterBySuitabilityScoreAsAdmin() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testFilterBySuitabilityScoreAsNonAdmin() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testFilteringByAllFilterableProperties() - Method in class ubic.gemma.persistence.service.FilteringVoEnabledServiceIntegrationTest
testFilterVosByNumberOfCharacteristics() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceTest
testFilterVosByNumberOfResults() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceTest
testfind() - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceTest
testFind() - Method in class ubic.gemma.model.expression.ExpressionExperimentSubSetServiceTest
testFind() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoTest
testFind() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoTest
testFindAll() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest
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
testFindBibliographicReference() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testFindBioAssayDimensionsLong() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayServiceTest: Tests HQL
testFindBioMaterial() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialServiceTest: Test method for BioMaterialDaoImpl.find(ubic.gemma.model.expression.biomaterial.BioMaterial) .
testFindBioMaterialByAccessionOnly() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialServiceTest
testFindBioMaterialByNameOnly() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialServiceTest
testFindBioSequence() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociationServiceTest
testFindBlatResultByBioSequence() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultServiceTest
testFindByAccession() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayServiceTest
testFindByAccession() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testFindByAccessionNcbi() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest
testFindByAccessionNcbiWithSource() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest
testFindByAccessionNoSource() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest
testFindByAccessionOther() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest
testFindByExternalId() - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImplTest
testFindByExternalIdentString() - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceTest
testFindByFactor() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testFindByFactor() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDaoTest
testFindByFactors() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDaoTest
testFindByFactorValue() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testFindByFactorValueId() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testFindByGene() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest
testFindByGene() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoTest
testFindByGene() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest
testFindByGeneAndExperimentAnalyzed() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoTest
testFindByGeneAndPlatform() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest
testFindByGeneSlice() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest
testFindByGoId() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest
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.model.analysis.DifferentialExpressionAnalysisServiceTest
testFindByInvestigations() - Method in class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest
testFindByName() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest
testFindByNameExact() - Method in class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest
testFindByNameRecent() - Method in class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest
testFindByNcbiId() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest
testFindByNcbiId() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest
testFindByOfficialName() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest
testFindByOfficialSymbol() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest
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.model.genome.gene.GeneServiceImplTest
testFindByQt() - Method in class ubic.gemma.model.expression.bioAssayData.DesignElementDataVectorServiceTest
testFindCandidateGenes() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testFindCoexpressionRelationships() - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpressionServiceTest
testFindDatabaseEntry() - Method in class ubic.gemma.model.common.description.DatabaseEntryDaoImplTest
testFindEvenThoughHaveSameSymbol() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest
testFindEvidenceByFilters() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testFindEvidenceByGeneId() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testFindExperimentsByUris() - Method in class ubic.gemma.model.common.description.CharacteristicServiceTest
testFindExperimentsByUris() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest
testFindExperimentsByUrisAsAdmin() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest
testFindExperimentsByUrisAsAnonymous() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest
testFindExperimentsByUrisAsAnonymousUser() - Method in class ubic.gemma.model.common.description.CharacteristicServiceTest
testFindExperimentsByUrisAsProxies() - Method in class ubic.gemma.model.common.description.CharacteristicServiceTest
testFindExperimentsByUrisAsUser() - Method in class ubic.gemma.model.common.description.CharacteristicServiceTest
testFindGDSGrouping() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest
testFindGene() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociationServiceTest
testFindGenesWithEvidence() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testFindGenesWithPhenotype() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testFindGSE13() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest
testFindGSE267() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest
testFindGSE3193() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest
testFindGSE469() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest
testFindGSE493() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest
testFindGSE611() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest
testFindGSE88() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest
testFindGSE91() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest
testFindGSECorrespondence() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest
testFindInResultSets() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoTest
testFindOrCreate() - Method in class ubic.gemma.model.genome.TaxonServiceImplTest: Test method for TaxonService.findOrCreate(Taxon) )}.
testFindPhenotypesForBibliographicReference() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testFindTerm() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest
testFindTermInexact() - Method in class ubic.gemma.core.ontology.OntologyServiceTest
testFindTermWithEmptyQuery() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest
testFindTermWithMultipleTerms() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest
testFindWithExternalReference() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testFindWithExternalReferenceNotFound() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testFish() - Method in class ubic.gemma.core.util.CompletionGeneratorTest
testFishCompletions() - Method in class ubic.gemma.core.util.CompletionGeneratorTest
testForcedBaseline() - Method in class ubic.gemma.core.analysis.expression.diff.BaselineSelectionTest
testFormAclJoinClauseAsAdmin() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest
testFormAclJoinClauseAsNonAdminIncludesAoiEntriesInnerJointure() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest
testFormatNumber() - Method in class ubic.gemma.core.analysis.service.AbstractFileServiceTest
testFormNativeAclJoinClause() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest
testFormNativeAclJoinClauseAsAnonymous() - Method in class ubic.gemma.persistence.util.AclQueryUtilsTest
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
testFromClasspath() - 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
testGemmaOntologyUnavailable() - Method in class ubic.gemma.web.controller.OntologyControllerTest
testGeneLoader() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneLoadingTest
testGeneralSearch4Brain() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest: Tests that general search terms are resolved to their proper ontology terms and objects tagged with those terms are found, -- requires LARQ index.
testGenerate() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiObjectGeneratorTest: Tests that given a taxon biomart file a BioMartEnsembleNcbi can be returned and that the genes are correctly mapped.
testGenerateArrayDesignGeneMappingEvent() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceTest
testGenerateArrayDesignSequenceAnalysisEvent() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceTest
testGenerateArrayDesignSequenceUpdateEvent() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceTest
testGenerateName() - Method in class ubic.gemma.core.analysis.preprocess.SplitExperimentTest
testGeneratePublicWeeklyReport() - Method in class ubic.gemma.core.analysis.report.WhatsNewServiceTest
testGenerateTaskId() - Method in class ubic.gemma.core.job.TaskUtilsTest: Test method for TaskUtils.generateTaskId().
testGeneUriSearch() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest: Tests that gene uris get handled correctly
testGeneValueObjectWithoutTaxon() - Method in class ubic.gemma.model.genome.gene.GeneValueObjectTest
testGeoEmptyMINiML() - Method in class ubic.gemma.core.loader.expression.geo.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
testGetAnnotationsById() - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtilsTest
testGetAnnotationsByLevel() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest
testGetAnnotationsUsageFrequency() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest
testGetAnnotationsUsageFrequencyWithFilters() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest
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
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
testGetBatches() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest: Test of creating batch factor.
testGetBean() - Method in class ubic.gemma.persistence.util.AsyncFactoryTest
testGetBean() - Method in class ubic.gemma.persistence.util.AsyncSingletonFactoryTest
testGetBeanAndGetBeanAsync() - Method in class ubic.gemma.persistence.util.AsyncSingletonFactoryTest
testGetBeanAsync() - Method in class ubic.gemma.persistence.util.AsyncFactoryTest
testGetBeanAsync() - Method in class ubic.gemma.persistence.util.AsyncSingletonFactoryTest
testGetBeanAsyncThenCancel() - Method in class ubic.gemma.persistence.util.AsyncFactoryTest
testGetBeanAsyncThenCancel() - Method in class ubic.gemma.persistence.util.AsyncSingletonFactoryTest
testGetBeanAsyncThenWait() - Method in class ubic.gemma.persistence.util.AsyncFactoryTest
testGetBeanThenCancel() - Method in class ubic.gemma.persistence.util.AsyncSingletonFactoryTest
testGetBioMartFieldsPerRow() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiParserTest
testGetBioMartTaxonName() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiFetcherTest
testGetBioMaterialCount() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testGetBioMaterialLink() - Method in class ubic.gemma.web.util.AnchorTagUtilTest
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.model.genome.gene.GeneServiceTest
testGetByTaxon() - Method in class ubic.gemma.model.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
testGetChildren() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest
testGetChildrenPartOf() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest
testGetCompositeSequencesByGeneId() - Method in class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperServiceTest: Tests finding the composite sequences for a given gene id.
testGetCompositeSequencesForArrayDesign() - Method in class ubic.gemma.core.security.authorization.acl.AclAuthorizationTest
testGetCount() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayServiceTest
testGetDatasetAnnotations() - Method in class ubic.gemma.rest.DatasetsWebServiceTest
testGetDatasetProcessedExpression() - Method in class ubic.gemma.rest.DatasetsWebServiceTest
testGetDatasetProcessedExpressionWhenNoProcessedVectorsExist() - Method in class ubic.gemma.rest.DatasetsWebServiceTest
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.rest.AnalysisResultSetsJerseyTest
testGetDatasets() - 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
testGetDatasetsOrderedByGeeqScore() - Method in class ubic.gemma.rest.DatasetsWebServiceTest
testGetDatasetsPlatformsUsageStatistics() - 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
testGetDesignElementDataVectorCount() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testGetDesignElementDataVectorsByQt() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testGetDetails() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceTest
testGetEnsemblNcibidata() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiFetcherTest
testGetEntitiesWithEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest
testGetExperimentalFactors() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerIntegrationTest
testGetExperimentalFactorValues() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerIntegrationTest
testGetExpressionExperimentLink() - Method in class ubic.gemma.web.util.AnchorTagUtilTest
testGetExpressionExperimentsById() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testGetFields() - Method in class ubic.gemma.core.search.SearchServiceTest
testGetFilter() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest: EE service has a few extensions for supporting various filtering strategies in the frontend, so we need to test them here.
testGetFilter() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest
testGetFilterableProperties() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testGetFilterableProperties() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest
testGetFilterableProperties() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest
testGetFilterablePropertyType() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testGetFilters() - Method in class ubic.gemma.rest.util.args.TaxonArgServiceTest
testGetFiltersWithCategories() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceTest
testGetFiltersWithInferredAnnotations() - Method in class ubic.gemma.model.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
testGetGene() - Method in class ubic.gemma.core.image.aba.AllenBrainAtlasServiceTest
testGetGenes() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest
testGetGenesForCompositeSequence() - Method in class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperServiceTest: Tests finding all genes for a given composite sequence.
testGetGeoRecordGSE93825() - Method in class ubic.gemma.core.loader.expression.geo.GeoBrowserTest
testGetGeoRecords() - Method in class ubic.gemma.core.loader.expression.geo.GeoBrowserTest: Exercises getting details
testGetGeoRecordsB() - Method in class ubic.gemma.core.loader.expression.geo.GeoBrowserTest
testGetGeoRecordsBySearchTerm() - Method in class ubic.gemma.core.loader.expression.geo.GeoBrowserTest
testGetHomologues() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceTest
testGetHomologues2() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceTest
testGetIdMap() - Method in class ubic.gemma.persistence.util.EntityUtilsTest
testGetInfo() - Method in class ubic.gemma.web.controller.security.SecurityControllerTest: Experiment has to be public.
testGetLabelFromTermUri() - Method in class ubic.gemma.core.search.source.OntologySearchSourceTest
testGetLastEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventDaoTest
testGetLastEvents() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventDaoTest
testGetLatestExperiments() - Method in class ubic.gemma.web.controller.common.rss.RssFeedControllerTest
testGetMetadata() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceTest
testGetMicroRnaByTaxon() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest
testGetMissingTerm() - Method in class ubic.gemma.web.controller.OntologyControllerTest
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
testGetObo() - Method in class ubic.gemma.web.controller.OntologyControllerTest
testGetOriginalPlatformUsageFrequency() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest
testGetParents() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest
testGetParents() - Method in class ubic.gemma.model.common.description.CharacteristicServiceTest
testGetParents() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest
testGetParentsPartOf() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest
testGetPerTaxonCount() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testGetPerTaxonCount() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest
testGetPlatforms() - Method in class ubic.gemma.rest.AnalysisResultSetsJerseyTest
testGetPreferredQuantitationType() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testGetProcessedDataMatrices() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVectorServiceTest: Test method for ProcessedExpressionDataVectorDaoImpl.getProcessedDataArrays(java.util.Collection, java.util.Collection) .
testGetProcessedVectors() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoTest
testGetQuantitationTypeCount() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testGetQuantitationTypes() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testGetRawExpressionDataVectors() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testGetRecentGeoRecords() - Method in class ubic.gemma.core.loader.expression.geo.GeoBrowserTest
testGetRecentRecords() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceTest
testGetResultSets() - Method in class ubic.gemma.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
testGetSort() - Method in class ubic.gemma.rest.util.args.SortArgTest
testGetSortWhenFieldDoesNotExistThenRaiseMalformedArgumentException() - Method in class ubic.gemma.rest.util.args.SortArgTest
testGetTaxaMultipleTaxonForArray() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest: Test retrieving multiple taxa for an arraydesign where hibernate query is not restricted to return just 1 taxon.
testGetTaxaOneTaxonForArray() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testGetTaxon() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testGetTechnologyTypeUsageFrequency() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest
testGetTerm() - Method in class ubic.gemma.web.controller.OntologyControllerTest
testGetTermForId() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest
testGetTgfvoAsHtml() - Method in class ubic.gemma.web.controller.OntologyControllerTest
testGetTgfvoAsRdf() - Method in class ubic.gemma.web.controller.OntologyControllerTest
testGetU() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest
testGetUri() - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtilsTest
testGPL6096ExonArray() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testGSE14285OneBatch() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testGSE156689NoBatchinfo() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testGSE35930() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExTest: Test where probes have constant values.
testGSE44903() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testGSE465() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest
testGSE8872() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testGuessQuantitationTypeParameters() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testHandleAddEventAuditableAuditEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailDaoTest
testHandleGetNewSinceDate() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventServiceTest
testHandleGetUpdatedSinceDate() - Method in class ubic.gemma.model.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
testHelper - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest
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
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
testIndex() - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisControllerTest
testIndexOfCaseInsensitiveStringElements() - Method in class ubic.gemma.persistence.util.ListUtilsTest
testIndexOfElements() - Method in class ubic.gemma.persistence.util.ListUtilsTest
testInferenceInGemma() - Method in class ubic.gemma.core.ontology.GemmaAndExperimentalFactorOntologyTest
testInferredLogbaseDifferFromQuantitations() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testInfoMatchContentOfOpenApiConfiguration() - Method in class ubic.gemma.rest.OpenApiTest
testInitializeAllOntologies() - Method in class ubic.gemma.core.ontology.OntologyLoadingTest
testInjectBeanDirectly() - Method in class ubic.gemma.persistence.util.AsyncBeanAutowiringTest
testInjectViaBeanFactory() - Method in class ubic.gemma.persistence.util.AsyncBeanAutowiringTest
testInjectViaServiceFactory() - Method in class ubic.gemma.persistence.util.AsyncBeanAutowiringTest
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
testInvalidSubsetFactor() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysisTest
testIsAdmin() - Method in class ubic.gemma.persistence.util.SecurityUtilsTest
testIsAutomaticallyGenerated() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetServiceTest
testIsBaselineA() - Method in class ubic.gemma.core.datastructure.matrix.DetectFactorBaselineTest
testIsBaselineB() - Method in class ubic.gemma.core.datastructure.matrix.DetectFactorBaselineTest
testIsFreeText() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsTest
testIsFreeTextCategory() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsTest
testIsHuman() - Method in class ubic.gemma.core.util.TaxonUtilityTest
testIsLog10Ratiometric() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testIsMouse() - Method in class ubic.gemma.core.util.TaxonUtilityTest
testIsNotBaselineA() - Method in class ubic.gemma.core.datastructure.matrix.DetectFactorBaselineTest
testIsRat() - Method in class ubic.gemma.core.util.TaxonUtilityTest
testIsUserLoggedIn() - Method in class ubic.gemma.persistence.util.SecurityUtilsTest
testIsWildcard() - Method in class ubic.gemma.core.search.lucene.LuceneQueryUtilsTest
testJsEngine() - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisControllerTest
testJsonRepresentation() - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapperTest
testLike() - Method in class ubic.gemma.persistence.util.FilterTest
testLikeRestrictionClause() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest
testLikeWithInvalidPropertyType() - Method in class ubic.gemma.persistence.util.FilterTest
testLimitArgIs5000ForGetDatasetsAnnotations() - Method in class ubic.gemma.rest.OpenApiTest
testLinearConversion() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
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
testloadAllNeurocartaPhenotypes() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testLoadAllPhenotypeUris() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testLoadAllValueObjects() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testLoadAllValueObjects() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testLoadAllValueObjectsOneTaxon() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest: Test to ensure that if one taxon is present on an array only 1 string is returned with taxon name
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.
testLoadAnalyzeSaveAndCoexpSearch() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisServiceTest
testLoadB() - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceTest
testLoadBlacklistedValueObjects() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testLoadByIds() - Method in class ubic.gemma.persistence.service.AbstractDaoTest
testLoadCommandConsoleFormat() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceIntegrationTest
testLoadCompositeSequences() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testLoadDuplicatedRow() - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceTest
testLoadEvidenceWithExternalDatabaseName() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
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.model.genome.gene.GeneServiceTest
testLoadGSE28383ExonArray() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest
testLoadGSE30521ExonArray() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest
testLoadIds() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoTest
testLoadInputStream() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonLoaderTest
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
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
testLoadStatistics() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testLoadStatusSummariesLimit() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentControllerTest
testLoadTree() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testLoadUpdateDeleteEvidence() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testLoadValueObject() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest
testLoadValueObject() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest
testLoadValueObject() - Method in class ubic.gemma.model.genome.TaxonServiceImplTest
testLoadValueObjectLite() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest
testLoadValueObjects() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest
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.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testLoadValueObjectsByCharacteristic() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testLoadValueObjectsByFactorValueCharacteristic() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testLoadValueObjectsByIds() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testLoadValueObjectsBySampleUsedCharacteristic() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testLoadValueObjectsWithPagination() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceTest
testLoadValueObjetsByArrayDesign() - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceTest
testLoadWithEmptyCollection() - Method in class ubic.gemma.model.common.description.DatabaseEntryDaoImplTest
testLocateGene() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest
testLocateGeneOnWrongStrand() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest
testLocatePrimaryReference() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest
testLocatePrimaryReferenceInvalidGSE() - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinderTest
testLog10Conversion() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testLog2Ratiometric() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testLog2ShouldDoNothing() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testLoggingInProgressUpdateCallbackDoesNotResultInLoggingRecursion() - Method in class ubic.gemma.core.util.progress.ProgressAppenderTest
testLogin() - Method in class ubic.gemma.core.security.principal.PrincipalTest
testLoginNonexistentUser() - Method in class ubic.gemma.core.security.principal.PrincipalTest
testLoginWrongPassword() - Method in class ubic.gemma.core.security.principal.PrincipalTest
testLookupByMaximalSubset() - Method in class ubic.gemma.core.ontology.OntologyCacheTest
testLookupByMaximalSubsetWhenMinSubsetSizeIsSet() - Method in class ubic.gemma.core.ontology.OntologyCacheTest
testMain() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcherIntegrationTest: Test method for AbstractCLI.executeCommand(String[]).
testMakeEEGroupReadWrite() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest
testMakeExpressionExperimentPrivate() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest
testMakePrivateWithoutPermission() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest
testMakeTitle() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testMarkAsNeedsAttention() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest
testMarkAsNeedsAttentionWhenFactorValueIsAlreadyMarked() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest
testMas5() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testMas6() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testMaskPwd() - Method in class ubic.gemma.core.apps.CliTest
testMatrixConversion() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixTest
testMatrixReconstruct() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest
testMatrixReconstructB() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest
testMeasuredRegion() - Method in class ubic.gemma.core.util.StopWatchUtilsTest
testMeasuredRegionWhhenStopWatchIsAlreadyStarted() - Method in class ubic.gemma.core.util.StopWatchUtilsTest
testMeasuredRegionWhhenStopWatchIsStopped() - Method in class ubic.gemma.core.util.StopWatchUtilsTest
testMeasuredRegionWithInnerRegion() - Method in class ubic.gemma.core.util.StopWatchUtilsTest
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
testMergingHighlightWhenReplacingAResult() - Method in class ubic.gemma.core.search.SearchResultSetTest
testMergingHighlightWhenRetainingAnExistingResult() - Method in class ubic.gemma.core.search.SearchResultSetTest
testMessageDefinedInGemmaCore() - Method in class ubic.gemma.web.util.MessageSourceTest
testMigrateFactorValues() - Method in class ubic.gemma.core.apps.FactorValueMigratorCLITest: Deprecated.
testMigrationThatReuseObject() - Method in class ubic.gemma.core.apps.FactorValueMigratorServiceTest: Deprecated.
testMigrationThatReusesExistingStatement() - Method in class ubic.gemma.core.apps.FactorValueMigratorServiceTest: Deprecated.
testMigrationWithFreeTextSubject() - Method in class ubic.gemma.core.apps.FactorValueMigratorServiceTest: Deprecated.
testMINiMLParse() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceParseTest
testMissingEndpoint() - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisControllerTest
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
testMultipleCalls() - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisControllerTest
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
testNcbiId() - Method in class ubic.gemma.rest.util.args.GeneArgServiceTest
testNeedsAttentionIsResetWhenFVIsSaved() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest
testNestedSubquery() - Method in class ubic.gemma.persistence.util.FilterQueryUtilsTest
testNestedSubquery() - Method in class ubic.gemma.persistence.util.FilterTest
testNormalize() - Method in class ubic.gemma.core.analysis.preprocess.QuantileNormalizerTest
testNormalizeByValue() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest
testNotEqualsID() - Method in class ubic.gemma.model.genome.biosequence.BioSequenceTest
testNumBioSequencesById() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testNumBlatResultsById() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testNumCompositeSequencesArrayDesign() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testNumExperiments() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest
testNumExperiments() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest
testNumGenesById() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testOneSampleTtest() - Method in class ubic.gemma.core.analysis.expression.diff.TTestAnalyzerTest
testOneWayAnova() - Method in class ubic.gemma.core.analysis.expression.diff.OneWayAnovaAnalyzerTest: Tests the OneWayAnova method.
testOnewayAnovaB() - Method in class ubic.gemma.core.analysis.expression.diff.OneWayAnovaAnalyzerTest
testOnSubmit() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerTest
testOnSubmitAlreadyExists() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerTest
testOnSubmitInvalidValue() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerTest
testOnSubmitNotFound() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerTest
testOpenApiEndpoint() - Method in class ubic.gemma.rest.AnalysisResultSetsJerseyTest
testOrderByExperimentalDesignB() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSortTest
testOrderOfExecutionFailure() - Method in class ubic.gemma.core.job.ExecutingTaskTest
testOrderOfExecutionSuccess() - Method in class ubic.gemma.core.job.ExecutingTaskTest
testPadToNextPowerOfTwo() - Method in class ubic.gemma.persistence.util.ListUtilsTest
testPaired() - Method in class ubic.gemma.core.apps.RNASeqDataAddCliTest
testParametersAnnotatedWithExplode() - Method in class ubic.gemma.rest.util.args.StringArrayArgTest
testParents() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test
testParse() - Method in class ubic.gemma.core.loader.entrez.pubmed.ESearchXMLParserTest
testParse() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest
testParse() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceParseTest
testParse() - Method in class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImportDuplicateValueTest
testParse() - Method in class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterTest
testParse() - Method in class ubic.gemma.core.loader.genome.gene.SwissProtParserTest
testParse2() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceParseTest
testParse3() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceParseTest
testParseA() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneHistoryParserTest
testParseAndLoad() - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationParserTest
testParseB() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneHistoryParserTest
testParseBigA() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest
testParseBigBPlatformOnly() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest
testParseBook() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest
testParseBookArticle() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest
testParseBoolean() - Method in class ubic.gemma.persistence.util.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
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.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
testParseFailedDryRun() - Method in class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterTest
testParseGene2Accession() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneParserTest
testParseGeneInfo() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneParserTest
testParseGenePix() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest
testParseGEOSampleCharacteristic() - Method in class ubic.gemma.core.loader.expression.geo.GeoCharacteristicParseTest
testParseGSE18707() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testParseGSE29014() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest
testParseGse432() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest
testParseGSE44625() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testParseHeaders() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testParseInputStream() - Method in class ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParserTest
testParseInputStream() - Method in class ubic.gemma.core.loader.genome.FastaParserTest
testParseInputStream() - Method in class ubic.gemma.core.loader.genome.ProbeSequenceParserTest
testParseInputStream() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonParserTest
testParseInputStreamAffyTarget() - Method in class ubic.gemma.core.loader.genome.FastaParserTest
testParseInputStreamNoheader() - Method in class ubic.gemma.core.loader.genome.BlatResultParserTest
testParseInputStreamWheader() - Method in class ubic.gemma.core.loader.genome.BlatResultParserTest
testParseInteger() - Method in class ubic.gemma.persistence.util.FilterTest
testParseInvalidCollection() - Method in class ubic.gemma.persistence.util.FilterTest
testParseInvalidOperator() - Method in class ubic.gemma.rest.util.args.FilterArgTest
testParseMasked() - Method in class ubic.gemma.core.loader.genome.FastaParserTest
testParseMesh() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest
testParseMixtureOfDateAndDateTime() - Method in class ubic.gemma.persistence.util.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
testParseOneValidLineHuman() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiParserTest
testParseOneValidLineNonHuman() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiParserTest
testParseRetracted() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest
testParseSAGE() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParserTest
testParseStandardDate() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest
testParseStandardDateWithGap() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractorTest
testParseString() - Method in class ubic.gemma.persistence.util.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
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.util.biomart.BioMartEnsemblNcbiParserTest
testParseValidFileMouse() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiParserTest
testParseWhereExtraValue() - Method in class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterTest
testPercent() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testPercent() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testPercent1() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testPersistBioSequence() - Method in class ubic.gemma.model.genome.BioSequencePersistTest
testPersistGene() - Method in class ubic.gemma.persistence.GenomePersisterTest
testPersistGeneProduct() - Method in class ubic.gemma.persistence.GenomePersisterTest
testPersistNewArrayDesign() - Method in class ubic.gemma.persistence.PersisterTest
testPersistStatement() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoTest
testPixels() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testPlatformDatasets() - Method in class ubic.gemma.rest.PlatformsWebServiceTest
testPlatformElements() - Method in class ubic.gemma.rest.PlatformsWebServiceTest
testPlatformSwitchingWithExpressionData() - Method in class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchTest
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
testPrepareDatabaseQuery() - Method in class ubic.gemma.core.search.lucene.LuceneQueryUtilsTest
testPrepareDatabaseQueryForInexactMatch() - Method in class ubic.gemma.core.search.lucene.LuceneQueryUtilsTest
testPrepareDatabaseQueryWithUri() - Method in class ubic.gemma.core.search.lucene.LuceneQueryUtilsTest
testPrepareTermUriQuery() - Method in class ubic.gemma.core.search.lucene.LuceneQueryUtilsTest
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
testProcessArrayDesign() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentandMappingTest
testProcessArrayDesignWithFastaCmdFetch() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorFastacmdTest
testProcessBlatResults() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperTest
testProgressData() - Method in class ubic.gemma.core.util.progress.ProgressDataTest
testProgressLogging() - Method in class ubic.gemma.core.util.progress.ProgressAppenderTest
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
testQueryEst() - Method in class ubic.gemma.core.externalDb.GoldenPathQueryTest
testQueryMrna() - Method in class ubic.gemma.core.externalDb.GoldenPathQueryTest
testQueryNoResult() - Method in class ubic.gemma.core.externalDb.GoldenPathQueryTest
testRandomCountMatrix() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testRandomLinearMatrix() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testRandomLog2Matrix() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testRandomRatiometricLog2Matrix() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testRandomSuspiciousLog2Matrix() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testRatio() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testReadInputStream() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReaderTest
testReadInputStream() - Method in class ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReaderTest: Class under test for Map read(InputStream)
testReadInputStreamNew() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReaderTest
testReadReport() - Method in class ubic.gemma.web.services.GemmaEndpointTest
testRecalculateBatchInfo() - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceTest
testRecalculateBatchInfoWithMissingDesign() - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceTest
testRecalculateExperimentBatchInfo() - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceTest
testRedirection() - Method in class ubic.gemma.rest.AnalysisResultSetsJerseyTest
testRemove() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDeleteTest
testRemove() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoTest
testRemove() - Method in class ubic.gemma.persistence.service.genome.GeneDaoTest
testRemoveByCompositeSequence() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoTest
testRemoveDetachedStatementFromDetachedFactorValue() - Method in class ubic.gemma.model.expression.experiment.FactorValueServiceTest
testRemoveExperimentWithSharedBioMaterial() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest
testRemoveMultipleAcesFromPrivateExpressionExperiment() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest
testRemoveStatement() - Method in class ubic.gemma.model.expression.experiment.FactorValueServiceTest
testRemoveUnrelatedStatementRaisesAnException() - Method in class ubic.gemma.model.expression.experiment.FactorValueServiceTest
testRemoveUsersFromGroupDisallowed() - Method in class ubic.gemma.web.controller.security.SecurityControllerTest
testRemoveWithDummyGeneProducts() - Method in class ubic.gemma.persistence.service.genome.GeneDaoTest
testReorder() - Method in class ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataCreateServiceTest
testRepeatedMeasuredRegion() - Method in class ubic.gemma.core.util.StopWatchUtilsTest
testReplaceRawVectors() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceImplTest
testReplaceRawVectorsWithoutPreferredQt() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceImplTest
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
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
testRetrieveByHTTP() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest
testRetrieveByHTTP2() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest
testRetrieveByHTTPBookshelf() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest
testRetrieveByHTTPNotFound() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest
testRetry() - Method in class ubic.gemma.persistence.retry.RetryTest
testRetryableMethod() - Method in class ubic.gemma.core.security.audit.PointcutsTest
testRetryNonTransactionalOperation() - Method in class ubic.gemma.persistence.retry.RetryTest
TestRetryService() - Constructor for class ubic.gemma.persistence.retry.RetryTest.TestRetryService
testRetryTransactionalOperation() - Method in class ubic.gemma.persistence.retry.RetryTest
testRetryWhenNoExceptionIsRaised() - Method in class ubic.gemma.persistence.retry.RetryTest
testRetryWithNonRetryableException() - Method in class ubic.gemma.persistence.retry.RetryTest
testRetryWithRetryableExceptionInCause() - Method in class ubic.gemma.persistence.retry.RetryTest
testrma() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testRootLogger() - Method in class ubic.gemma.web.logging.LoggingIntegrationTest
testRunAsAdmin() - Method in class ubic.gemma.persistence.util.SecurityUtilsTest
testSampleMINiMLParse() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceParseTest
testSaveStatement() - Method in class ubic.gemma.model.expression.experiment.FactorValueServiceTest
testSaveWithTransientEntity() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
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
testSearchByArrayDesign() - Method in class ubic.gemma.rest.SearchWebServiceTest
testSearchByBibRefIdProblems() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest
testSearchByBibRefIdProblemsB() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest
testSearchByTaxon() - Method in class ubic.gemma.rest.SearchWebServiceTest
testSearchEverything() - Method in class ubic.gemma.rest.SearchWebServiceTest
testSearchExpressionExperiment() - Method in class ubic.gemma.core.search.source.HibernateSearchSourceTest
testSearchExpressionExperimentByStatementObject() - Method in class ubic.gemma.core.search.source.HibernateSearchSourceTest
testSearchExpressionExperimentWithBooleanQuery() - Method in class ubic.gemma.core.search.source.OntologySearchSourceTest
testSearchGeneByUri() - Method in class ubic.gemma.core.search.source.DatabaseSearchSourceTest
testSearchGeneByUriInexact() - Method in class ubic.gemma.core.search.source.DatabaseSearchSourceTest
testSearchGenes() - Method in class ubic.gemma.model.genome.gene.GeneSearchTest
testSearchOntologyForPhenotypes() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testSearchTaxonDatasets() - Method in class ubic.gemma.rest.AnnotationsWebServiceTest
testSearchWhenQueryIsEmpty() - Method in class ubic.gemma.rest.SearchWebServiceTest
testSearchWhenQueryIsMissing() - Method in class ubic.gemma.rest.SearchWebServiceTest
testSearchWhenUnknownPlatformIsProvided() - Method in class ubic.gemma.rest.SearchWebServiceTest
testSearchWhenUnknownTaxonIsProvided() - Method in class ubic.gemma.rest.SearchWebServiceTest
testSearchWhenUnsupportedResultTypeIsProvided() - Method in class ubic.gemma.rest.SearchWebServiceTest
testSearchWithInvalidQuery() - Method in class ubic.gemma.rest.SearchWebServiceTest
testSearchWithInvalidQuerySyntax() - Method in class ubic.gemma.core.search.source.HibernateSearchSourceTest
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
testSecurityContext() - Static method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors: Creates a RequestPostProcessor that can be used to ensure that the resulting request is ran with the user in the TestSecurityContextHolder.
TestSecurityContextHolder - Class in org.springframework.security.test.context: The TestSecurityContextHolder is very similar to SecurityContextHolder, but is necessary for testing.
testSecurityContextManagement() - Method in class ubic.gemma.core.job.ExecutingTaskTest
testSendMessageWithVelocityTemplate() - Method in class ubic.gemma.persistence.util.MailEngineTest
testSerializeEWAHCompressedBitmap() - Method in class ubic.gemma.model.analysis.expression.coexpression.SupportDetailsTest
testServiceCreateCountData() - Method in class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceTest
testServiceCreateExistingEe() - Method in class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceTest
testServiceCreateOneColor() - Method in class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceTest
testServiceCreateTwoColor() - Method in class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceTest
testSetDescription() - Method in class ubic.gemma.core.util.progress.ProgressDataTest
testSetDone() - Method in class ubic.gemma.core.util.progress.ProgressDataTest
testSetOwner() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest
testSetPercent() - Method in class ubic.gemma.core.util.progress.ProgressDataTest
testSetPrincipalSID() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest
testSetQueryWhenQueryContainsBlankThenTrimAccordingly() - Method in class ubic.gemma.model.common.search.SearchSettingsTest
testSetQueryWhenQueryIsATermUri() - Method in class ubic.gemma.model.common.search.SearchSettingsTest
testSetQueryWhenQueryIsATermUriWithTrailingBlanks() - Method in class ubic.gemma.model.common.search.SearchSettingsTest
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
testSettingsWithDifferentHighlighterAreEqual() - Method in class ubic.gemma.model.common.search.SearchSettingsTest
testShow() - Method in class ubic.gemma.web.controller.common.description.bibref.BibRefControllerTest
testShowAllArrayDesigns() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerTest
testShowAllForExperiments() - Method in class ubic.gemma.web.controller.common.description.bibref.BibRefControllerTest
testShowExperimentalDesign() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerIntegrationTest
testShowExperimentalDesignByExperimentId() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerIntegrationTest
testShowExperimentalDesignByExperimentShortName() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerIntegrationTest
testSignup() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest
testSignup() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupControllerTest
testSignupWhenRecaptchaIsDisabled() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupControllerTest
testSignupWithPasswordDosentMatch() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupControllerTest
testSignupWithRecaptchaIsInvalid() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupControllerTest
testSimpleAuditFindOrCreate() - Method in class ubic.gemma.core.security.audit.AuditAdviceTest
testSimpleEquality() - Method in class ubic.gemma.rest.util.args.FilterArgTest
testSingleTaxonOnArrayWithNoOrganismColumn() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testSome() - Method in class ubic.gemma.rest.DatasetsRestTest
testSomeById() - 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
testSortCharacteristics() - Method in class ubic.gemma.core.ontology.CharacteristicSortTest
testSortingByAllFilterableProperties() - Method in class ubic.gemma.persistence.service.FilteringVoEnabledServiceIntegrationTest
testSpeedA() - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedInTest
testSpeedB() - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedInTest
testSplitByPlatform() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testSplitGSE123753ByCollectionOfMaterial() - Method in class ubic.gemma.core.analysis.preprocess.SplitExperimentTest
testSplitGSE17183ByOrganismPart() - Method in class ubic.gemma.core.analysis.preprocess.SplitExperimentTest
testStringCannotContainSpace() - Method in class ubic.gemma.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
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.service.SubqueryUtilsTest
testSubqueryWithMultipleJointures() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest
testSubqueryWithRootAlias() - Method in class ubic.gemma.persistence.service.SubqueryUtilsTest
testSubstantiaNigraInUberon() - Method in class ubic.gemma.core.ontology.providers.UberonOntologyTest
testSuccessfulRun() - Method in class ubic.gemma.web.controller.TaskRunningTest
testSummarizeRequest() - Method in class ubic.gemma.rest.util.ServletUtilsTest
testSummarizeRequestWithPrincipal() - Method in class ubic.gemma.rest.util.ServletUtilsTest
testSummarizeRequestWithQueryString() - Method in class ubic.gemma.rest.util.ServletUtilsTest
testsvd() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImplTest
testsvdGapped() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImplTest
testTaxonByCommonName() - Method in class ubic.gemma.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
testTaxonDatasetsByNcbiId() - 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
testTermLackingLabelIsIgnored() - Method in class ubic.gemma.core.ontology.OntologyServiceTest
testTextRepresentation() - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapperTest
testThatChebiDoesNotHaveInferenceEnabled() - Method in class ubic.gemma.core.ontology.OntologyLoadingTest
testThatJerseyServerRuntimeLoggerDoesNotUseTheSlackAppender() - Method in class ubic.gemma.web.logging.LoggingIntegrationTest
testThatTGEMODoesNotProcessImports() - Method in class ubic.gemma.core.ontology.OntologyLoadingTest
testThaw() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testThaw() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest
testThaw() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoTest
testThaw() - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoTest
testThaw() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest
testThawBioAssays() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest
testThawCollection() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceTest
testThawForFrontEnd() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest
testThawTransientEntity() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest
testThawWithoutVectors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest
testTimedMethod() - Method in class ubic.gemma.core.metrics.GenericMeterRegistryConfigurerTest
testTimedMethodAtInterfaceLevel() - Method in class ubic.gemma.core.metrics.GenericMeterRegistryConfigurerTest
testToggleUsability() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceTest
testToOriginalString() - Method in class ubic.gemma.persistence.util.FilterTest
testToOriginalStringWhenOriginalPropertyIsNull() - Method in class ubic.gemma.persistence.util.FilterTest
testTortureQuantitationTypes() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testTransactionalService() - Method in class ubic.gemma.core.security.audit.PointcutsTest
testTTestWithExpressionExperiment() - Method in class ubic.gemma.core.analysis.expression.diff.TTestAnalyzerTest: Tests the t-test with an ExpressionExperiment.
testTwoWayAnova() - Method in class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionsAnalyzerTest
testTwoWayAnova() - Method in class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithoutInteractionsAnalyzerTest: Tests the TwoWayAnova method.
testUMatrixAsExpressionData() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest
testUMatrixAsExpressionDataUnnormalized() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest
testUncategorized() - Method in class ubic.gemma.model.common.description.CharacteristicUtilsTest
testUndefinedProperty() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest
testUndefinedTestPage() - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisControllerTest: This error is produced via HttpServletResponse.sendError(int) and thus is not intercepted by Spring's error handler.
testUnmappedRoute() - Method in class ubic.gemma.rest.AnalysisResultSetsJerseyTest
testUnpaired() - Method in class ubic.gemma.core.apps.RNASeqDataAddCliTest
testUnsupportedResultTypeInCollectionRaisesIllegalArgumentException() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
testUnsupportedResultTypeRaisesIllegalArgumentException() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
testUpdate() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetServiceTest
testUpdate() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest: Test adding a new member via a cascade.
testUpdateAcl() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest
testUpdateBioSequence() - Method in class ubic.gemma.persistence.GenomePersisterTest
testUpdateEE2CAsUser() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilIntegrationTest
testUpdateExpressionExperiment2ArrayDesignEntries() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilIntegrationTest
testUpdateExpressionExperiment2CharacteristicEntries() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilIntegrationTest
testUpdateExternalDatabaseDontCascadeToRelatedDatabases() - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceTest
testUpdateFactorValueCharacteristic() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerTest
testUpdateFactorValueStatement() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerIntegrationTest
testUpdateGroups() - Method in class ubic.gemma.core.security.authentication.UserManagerTest
testUpdatePermissions() - Method in class ubic.gemma.web.controller.security.SecurityControllerTest
testUpdatePubMed() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentControllerTest
testUpdatePubMedAsAnonymousUser() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentControllerTest
testUpdateReleaseDetails() - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceTest
testUpdateSubsumingStatus() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testUpdateSubsumingStatusTrue() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testUpdateUser() - Method in class ubic.gemma.core.security.authentication.UserManagerTest
testUpdateUserGroup() - Method in class ubic.gemma.core.security.UserGroupServiceTest: Tests updating the UserGroup
testUpdateWhenTableIsFresh() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilTest
testUpdateWithTransientEntity() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
testURIChildSearch() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest: Test we find EE tagged with a child term that matches the given uri.
testURISearch() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest: Does the search engine correctly match the spinal cord URI and find objects directly tagged with that URI
testUseBuiltSubClause() - Method in class ubic.gemma.persistence.util.FiltersTest
testUserAddSelvesToAdmin() - Method in class ubic.gemma.core.security.UserGroupServiceTest
testUserCanEdit() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest
testUserCanRead() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest
TestUtils - Class in ubic.gemma.core.loader.util
TestUtils() - Constructor for class ubic.gemma.core.loader.util.TestUtils
testValueOf() - Method in class ubic.gemma.rest.util.args.SortArgTest
testVarianceFractions() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest
testWarnLogsShouldNotBeAppended() - Method in class ubic.gemma.web.logging.SlackAppenderTest
testWhenClassUsesSimpleName() - Method in class ubic.gemma.web.remote.EntityDelegatorTest
testWhenPairednessIsUnknown() - Method in class ubic.gemma.core.apps.RNASeqDataAddCliTest
testWhenSlackApiRaisesException() - Method in class ubic.gemma.web.logging.SlackAppenderTest
testWhenSlackFailsToClose() - Method in class ubic.gemma.web.logging.SlackAppenderTest
testWhenTermIsNotFoundGenerateLabelFromUri() - Method in class ubic.gemma.core.search.source.OntologySearchSourceTest
testWhenUserIsAgent() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilIntegrationTest
testWhenUserIsAnonymous() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilIntegrationTest
testWinnow() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest
testWithDifferentPath() - Method in class ubic.gemma.rest.servlet.RestapidocsIndexRewriteFilterTest
testWithImageNoGenbank() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testWithImages() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testWithoutTrailingSlash() - Method in class ubic.gemma.rest.servlet.RestapidocsIndexRewriteFilterTest
testWithQuery() - Method in class ubic.gemma.rest.servlet.RestapidocsIndexRewriteFilterTest
testWithStacktrace() - Method in class ubic.gemma.web.logging.SlackAppenderTest
testWithSubset() - Method in class ubic.gemma.core.analysis.expression.diff.SubsettedAnalysisTest
testWrapperToPrimitiveConversion() - Method in class ubic.gemma.persistence.util.FilterTest
testWrite() - Method in class ubic.gemma.core.analysis.service.AbstractFileServiceTest
testWrite() - Method in class ubic.gemma.core.datastructure.matrix.ExperimentalDesignWriterTest
testWritePValuesHistogram() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceTest
testWriteToFile() - Method in class ubic.gemma.core.analysis.service.AbstractFileServiceTest
testWriteToRdf() - Method in class ubic.gemma.core.ontology.FactorValueOntologyServiceTest
testZtransformed() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testZTransformedByMedian() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
testZtransformedInLogSpace() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
TTestAnalyzerTest - Class in ubic.gemma.core.analysis.expression.diff: See test/data/stat-tests/README.txt for R code.
TTestAnalyzerTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.TTestAnalyzerTest
TwoChannelMissingValuesTest - Class in ubic.gemma.core.analysis.preprocess
TwoChannelMissingValuesTest() - Constructor for class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesTest
TwoWayAnovaWithInteractionsAnalyzerTest - Class in ubic.gemma.core.analysis.expression.diff: Tests the two way anova analyzer with interactions.
TwoWayAnovaWithInteractionsAnalyzerTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionsAnalyzerTest
TwoWayAnovaWithInteractionsTest2 - Class in ubic.gemma.core.analysis.expression.diff
TwoWayAnovaWithInteractionsTest2() - Constructor for class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionsTest2
TwoWayAnovaWithInteractionTest2 - Class in ubic.gemma.core.analysis.expression.diff: Test based on GSE8441
TwoWayAnovaWithInteractionTest2() - Constructor for class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithInteractionTest2
TwoWayAnovaWithoutInteractionsAnalyzerTest - Class in ubic.gemma.core.analysis.expression.diff: Tests the two way anova analyzer.
TwoWayAnovaWithoutInteractionsAnalyzerTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.TwoWayAnovaWithoutInteractionsAnalyzerTest

U

UberonOntologyTest - Class in ubic.gemma.core.ontology.providers
UberonOntologyTest() - Constructor for class ubic.gemma.core.ontology.providers.UberonOntologyTest
ubic.gemma.core.analysis.expression.coexpression.links - package ubic.gemma.core.analysis.expression.coexpression.links
ubic.gemma.core.analysis.expression.diff - package ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess - package ubic.gemma.core.analysis.preprocess
ubic.gemma.core.analysis.preprocess.batcheffects - package ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.preprocess.svd - package ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.report - package ubic.gemma.core.analysis.report
ubic.gemma.core.analysis.sequence - package ubic.gemma.core.analysis.sequence
ubic.gemma.core.analysis.service - package ubic.gemma.core.analysis.service
ubic.gemma.core.annotation.reference - package ubic.gemma.core.annotation.reference
ubic.gemma.core.apps - package ubic.gemma.core.apps
ubic.gemma.core.datastructure.matrix - package ubic.gemma.core.datastructure.matrix
ubic.gemma.core.externalDb - package ubic.gemma.core.externalDb
ubic.gemma.core.image.aba - package ubic.gemma.core.image.aba
ubic.gemma.core.job - package ubic.gemma.core.job
ubic.gemma.core.loader.association - package ubic.gemma.core.loader.association
ubic.gemma.core.loader.association.phenotype - package ubic.gemma.core.loader.association.phenotype
ubic.gemma.core.loader.entrez - package ubic.gemma.core.loader.entrez
ubic.gemma.core.loader.entrez.pubmed - package ubic.gemma.core.loader.entrez.pubmed
ubic.gemma.core.loader.expression - package ubic.gemma.core.loader.expression
ubic.gemma.core.loader.expression.arrayDesign - package ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.expression.arrayExpress - package ubic.gemma.core.loader.expression.arrayExpress
ubic.gemma.core.loader.expression.geo - package ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.expression.geo.fetcher - package ubic.gemma.core.loader.expression.geo.fetcher
ubic.gemma.core.loader.expression.geo.service - package ubic.gemma.core.loader.expression.geo.service
ubic.gemma.core.loader.expression.simple - package ubic.gemma.core.loader.expression.simple
ubic.gemma.core.loader.genome - package ubic.gemma.core.loader.genome
ubic.gemma.core.loader.genome.gene - package ubic.gemma.core.loader.genome.gene
ubic.gemma.core.loader.genome.gene.ncbi - package ubic.gemma.core.loader.genome.gene.ncbi
ubic.gemma.core.loader.genome.gene.ncbi.homology - package ubic.gemma.core.loader.genome.gene.ncbi.homology
ubic.gemma.core.loader.genome.taxon - package ubic.gemma.core.loader.genome.taxon
ubic.gemma.core.loader.util - package ubic.gemma.core.loader.util
ubic.gemma.core.loader.util.fetcher - package ubic.gemma.core.loader.util.fetcher
ubic.gemma.core.metrics - package ubic.gemma.core.metrics
ubic.gemma.core.ontology - package ubic.gemma.core.ontology
ubic.gemma.core.ontology.providers - package ubic.gemma.core.ontology.providers
ubic.gemma.core.search - package ubic.gemma.core.search
ubic.gemma.core.search.lucene - package ubic.gemma.core.search.lucene
ubic.gemma.core.search.source - package ubic.gemma.core.search.source
ubic.gemma.core.security - package ubic.gemma.core.security
ubic.gemma.core.security.audit - package ubic.gemma.core.security.audit
ubic.gemma.core.security.authentication - package ubic.gemma.core.security.authentication
ubic.gemma.core.security.authorization - package ubic.gemma.core.security.authorization
ubic.gemma.core.security.authorization.acl - package ubic.gemma.core.security.authorization.acl
ubic.gemma.core.security.principal - package ubic.gemma.core.security.principal
ubic.gemma.core.util - package ubic.gemma.core.util
ubic.gemma.core.util.biomart - package ubic.gemma.core.util.biomart
ubic.gemma.core.util.progress - package ubic.gemma.core.util.progress
ubic.gemma.core.util.test - package ubic.gemma.core.util.test
ubic.gemma.core.util.test.category - package ubic.gemma.core.util.test.category
ubic.gemma.core.util.test.suite - package ubic.gemma.core.util.test.suite
ubic.gemma.model.analysis - package ubic.gemma.model.analysis
ubic.gemma.model.analysis.expression.coexpression - package ubic.gemma.model.analysis.expression.coexpression
ubic.gemma.model.association.coexpression - package ubic.gemma.model.association.coexpression
ubic.gemma.model.association.phenotype - package ubic.gemma.model.association.phenotype
ubic.gemma.model.common.auditAndSecurity - package ubic.gemma.model.common.auditAndSecurity
ubic.gemma.model.common.auditAndSecurity.eventType - package ubic.gemma.model.common.auditAndSecurity.eventType
ubic.gemma.model.common.description - package ubic.gemma.model.common.description
ubic.gemma.model.common.search - package ubic.gemma.model.common.search
ubic.gemma.model.expression - package ubic.gemma.model.expression
ubic.gemma.model.expression.arrayDesign - package ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.bioAssay - package ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.bioAssayData - package ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.biomaterial - package ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.experiment - package ubic.gemma.model.expression.experiment
ubic.gemma.model.genome - package ubic.gemma.model.genome
ubic.gemma.model.genome.biosequence - package ubic.gemma.model.genome.biosequence
ubic.gemma.model.genome.gene - package ubic.gemma.model.genome.gene
ubic.gemma.model.genome.gene.phenotype.valueObject - package ubic.gemma.model.genome.gene.phenotype.valueObject
ubic.gemma.model.genome.sequenceAnalysis - package ubic.gemma.model.genome.sequenceAnalysis
ubic.gemma.persistence - package ubic.gemma.persistence
ubic.gemma.persistence.retry - package ubic.gemma.persistence.retry
ubic.gemma.persistence.service - package ubic.gemma.persistence.service
ubic.gemma.persistence.service.analysis.expression.diff - package ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.common.auditAndSecurity - package ubic.gemma.persistence.service.common.auditAndSecurity
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.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.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.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
ubic.gemma.web.controller - package ubic.gemma.web.controller
ubic.gemma.web.controller.common.auditAndSecurity - package ubic.gemma.web.controller.common.auditAndSecurity
ubic.gemma.web.controller.common.description.bibref - package ubic.gemma.web.controller.common.description.bibref
ubic.gemma.web.controller.common.rss - package ubic.gemma.web.controller.common.rss
ubic.gemma.web.controller.diff - package ubic.gemma.web.controller.diff
ubic.gemma.web.controller.expression - package ubic.gemma.web.controller.expression
ubic.gemma.web.controller.expression.arrayDesign - package ubic.gemma.web.controller.expression.arrayDesign
ubic.gemma.web.controller.expression.experiment - package ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.controller.security - package ubic.gemma.web.controller.security
ubic.gemma.web.logging - package ubic.gemma.web.logging
ubic.gemma.web.remote - package ubic.gemma.web.remote
ubic.gemma.web.scheduler - package ubic.gemma.web.scheduler
ubic.gemma.web.services - package ubic.gemma.web.services
ubic.gemma.web.util - package ubic.gemma.web.util
ubic.gemma.web.util.dwr - package ubic.gemma.web.util.dwr: Utilities for testing DWR endpoints.
ubic.gemma.web.util.upload - package ubic.gemma.web.util.upload
unauthenticated() - Static method in class org.springframework.security.test.web.servlet.response.SecurityMockMvcResultMatchers: ResultMatcher that verifies that no user is authenticated.
UnitTests - Class in ubic.gemma.core.util.test.suite: Unit tests.
UnitTests() - Constructor for class ubic.gemma.core.util.test.suite.UnitTests
update(MutableAcl) - Method in class ubic.gemma.core.security.authorization.acl.AclTestUtils
useInvalidToken() - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.CsrfRequestPostProcessor: Populates an invalid token value on the request.
user(String) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestBuilders.FormLoginRequestBuilder: The value of the username parameter.
user(String) - Static method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors: Establish a SecurityContext that has a UsernamePasswordAuthenticationToken for the Authentication.getPrincipal() and a User for the UsernamePasswordAuthenticationToken.getPrincipal().
user(String, String) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestBuilders.FormLoginRequestBuilder: Specify both the password parameter name and the password.
user(UserDetails) - Static method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors: Establish a SecurityContext that has a UsernamePasswordAuthenticationToken for the Authentication.getPrincipal() and a custom UserDetails for the UsernamePasswordAuthenticationToken.getPrincipal().
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
username() - Method in annotation type org.springframework.security.test.context.support.WithMockUser: The username to be used.
userParameter(String) - Method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestBuilders.FormLoginRequestBuilder: The HTTP parameter to place the username.
UserServiceImplTest - Class in ubic.gemma.core.security.authentication
UserServiceImplTest() - Constructor for class ubic.gemma.core.security.authentication.UserServiceImplTest

V

value() - Method in annotation type org.springframework.security.test.context.support.WithMockUser: Convenience mechanism for specifying the username.
value() - Method in annotation type org.springframework.security.test.context.support.WithUserDetails: The username to look up in the UserDetailsService
value(Object) - Method in class ubic.gemma.web.util.dwr.DwrCallbackMatchers
value(Matcher<T>) - Method in class ubic.gemma.web.util.dwr.DwrCallbackMatchers
valueOf(String) - Static method in enum ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest.FakeEnum: Returns the enum constant of this type with the specified name.
values() - Static method in enum ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest.FakeEnum: Returns an array containing the constants of this enum type, in the order they are declared.
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
VoConverterTestContextConfiguration() - Constructor for class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest.VoConverterTestContextConfiguration

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
WebTestUtils - Class in org.springframework.security.test.web.support: A utility class for testing spring security
WhatsNewServiceTest - Class in ubic.gemma.core.analysis.report
WhatsNewServiceTest() - Constructor for class ubic.gemma.core.analysis.report.WhatsNewServiceTest
withAuthentication(Authentication) - Method in class org.springframework.security.test.web.servlet.response.SecurityMockMvcResultMatchers.AuthenticatedMatcher: Specifies the expected Authentication
withAuthenticationName(String) - Method in class org.springframework.security.test.web.servlet.response.SecurityMockMvcResultMatchers.AuthenticatedMatcher: Specifies the expected Principal.getName()
withAuthenticationPrincipal(Object) - Method in class org.springframework.security.test.web.servlet.response.SecurityMockMvcResultMatchers.AuthenticatedMatcher: Specifies the expected principal
withAuthorities(Collection<GrantedAuthority>) - Method in class org.springframework.security.test.web.servlet.response.SecurityMockMvcResultMatchers.AuthenticatedMatcher: Specifies the Authentication.getAuthorities()
WithMockUser - Annotation Type in org.springframework.security.test.context.support: When used with WithSecurityContextTestExecutionListener this annotation can be added to a test method to emulate running with a mocked user.
withRoles(String...) - Method in class org.springframework.security.test.web.servlet.response.SecurityMockMvcResultMatchers.AuthenticatedMatcher: Specifies the Authentication.getAuthorities()
withSecurityContext(SecurityContext) - Method in class org.springframework.security.test.web.servlet.response.SecurityMockMvcResultMatchers.AuthenticatedMatcher: Specifies the expected SecurityContext
WithSecurityContext - Annotation Type in org.springframework.security.test.context.support: An annotation to determine what SecurityContext to use.
WithSecurityContextFactory<A extends Annotation> - Interface in org.springframework.security.test.context.support: An API that works with WithUserTestExcecutionListener for creating a SecurityContext that is populated in the TestSecurityContextHolder.
WithSecurityContextTestExecutionListener - Class in org.springframework.security.test.context.support: A TestExecutionListener that will find annotations that are annotated with WithSecurityContext on a test method or at the class level.
WithSecurityContextTestExecutionListener() - Constructor for class org.springframework.security.test.context.support.WithSecurityContextTestExecutionListener
WithUserDetails - Annotation Type in org.springframework.security.test.context.support: When used with WithSecurityContextTestExecutionListener this annotation can be added to a test method to emulate running with a UserDetails returned from the UserDetailsService.
withUsername(String) - Method in class org.springframework.security.test.web.servlet.response.SecurityMockMvcResultMatchers.AuthenticatedMatcher: Specifies the expected username
work() - Method in interface ubic.gemma.persistence.retry.RetryTest.TestRetryDao

X

x509(String) - Static method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors: Finds an X509Cetificate using a resoureName and populates it on the request.
x509(X509Certificate...) - Static method in class org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors: Populates the provided X509Certificate instances on the request.

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