Index (Gemma Core 1.30.6 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
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
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(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.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
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
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
appDataHome - Variable in class ubic.gemma.persistence.util.SettingsConfigTest
ArrayDesignDaoTest - Class in ubic.gemma.persistence.service.expression.arrayDesign
ArrayDesignDaoTest() - Constructor for class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest
ArrayDesignMergeServiceTest - Class in ubic.gemma.core.loader.expression.arrayDesign
ArrayDesignMergeServiceTest() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeServiceTest
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
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.
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
AuditEventDaoImplTest - Class in ubic.gemma.model.common.auditAndSecurity
AuditEventDaoImplTest() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEventDaoImplTest
AuditEventDaoTest - Class in ubic.gemma.model.common.auditAndSecurity
AuditEventDaoTest() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEventDaoTest
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
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
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
BaselineDetectionTest - Class in ubic.gemma.core.analysis.expression.diff
BaselineDetectionTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.BaselineDetectionTest
BaseSpringContextTest - Class in ubic.gemma.core.util.test: subclass for tests that need the container and use the database
BaseSpringContextTest() - Constructor for class ubic.gemma.core.util.test.BaseSpringContextTest
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
BioAssayServiceTest - Class in ubic.gemma.model.expression.bioAssay
BioAssayServiceTest() - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayServiceTest
BioMartEnsemblNcbiFetcherTest - Class in ubic.gemma.core.util.biomart: Tests that biomart fetcher works correctly.
BioMartEnsemblNcbiFetcherTest() - Constructor for class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiFetcherTest
BioMartEnsemblNcbiObjectGeneratorTest - Class in ubic.gemma.core.util.biomart: Class to test BioMartEnsemblNcbiObjectGeneration.
BioMartEnsemblNcbiObjectGeneratorTest() - Constructor for class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiObjectGeneratorTest
BioMartEnsemblNcbiParserTest - Class in ubic.gemma.core.util.biomart: Tests the parsing of a BioMart file.
BioMartEnsemblNcbiParserTest() - Constructor for class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiParserTest
BioMaterialServiceTest - Class in ubic.gemma.model.expression.biomaterial
BioMaterialServiceTest() - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterialServiceTest
BioSequencePersistTest - Class in ubic.gemma.model.genome
BioSequencePersistTest() - Constructor for class ubic.gemma.model.genome.BioSequencePersistTest
BioSequenceTest - Class in ubic.gemma.model.genome.biosequence
BioSequenceTest() - Constructor for class ubic.gemma.model.genome.biosequence.BioSequenceTest
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

C

cacheManager() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyService2Test.GeneOntologyService2TestContextConfiguration
CharacteristicDaoImplTest - Class in ubic.gemma.persistence.service.common.description
CharacteristicDaoImplTest() - Constructor for class ubic.gemma.persistence.service.common.description.CharacteristicDaoImplTest
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
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
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.
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
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
ContinuousVariableDiffExTest - Class in ubic.gemma.core.analysis.expression.diff
ContinuousVariableDiffExTest() - Constructor for class ubic.gemma.core.analysis.expression.diff.ContinuousVariableDiffExTest
countRowsInTable(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Count the rows in the given table.
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

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
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
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
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
DOE - ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest.FakeEnum
downloadPath - Variable in class ubic.gemma.persistence.util.SettingsConfigTest

E

EntityUtilsTest - Class in ubic.gemma.persistence.util
EntityUtilsTest() - Constructor for class ubic.gemma.persistence.util.EntityUtilsTest
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
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
ExonArrayDataAddIntegrationTest - Class in ubic.gemma.core.loader.expression: Uses the Affy Power Tools, and full-sized data sets.
ExonArrayDataAddIntegrationTest() - Constructor for class ubic.gemma.core.loader.expression.ExonArrayDataAddIntegrationTest
ExperimentalDesignImportDuplicateValueTest - Class in ubic.gemma.core.loader.expression.simple: Test for import that results in multiple factor values for the same factor on a single biomaterial.
ExperimentalDesignImportDuplicateValueTest() - Constructor for class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImportDuplicateValueTest
ExperimentalDesignImporterTest - Class in ubic.gemma.core.loader.expression.simple
ExperimentalDesignImporterTest() - Constructor for class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterTest
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
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
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
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
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
FactorValueServiceTest - Class in ubic.gemma.model.expression.experiment
FactorValueServiceTest() - Constructor for class ubic.gemma.model.expression.experiment.FactorValueServiceTest
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
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
FastUnitTests() - Constructor for class ubic.gemma.core.util.test.suite.FastUnitTests
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
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

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
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
GenericValueObjectConverterTest - Class in ubic.gemma.persistence.util
GenericValueObjectConverterTest() - Constructor for class ubic.gemma.persistence.util.GenericValueObjectConverterTest
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
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
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.
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
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
getTestElementCollectionSize() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestExpressionExperimentWithAllDependencies() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Add an expressionExperiment to the database for testing purposes.
getTestExpressionExperimentWithAllDependencies(boolean) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Add an expressionExperiment to the database for testing purposes.
getTestExpressionExperimentWithAllDependencies(ExpressionExperiment) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestExpressionExperimentWithAnalysisAndResults() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Create a test EE with analysis results.
getTestFileBasePath() - Method in class ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest
getTestFileBasePath(String) - Method in class ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest
getTestNonPersistentBioSequence(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestNonPersistentBioSequence(Taxon) - Static method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestNonPersistentGeneProduct(Gene) - Static method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestNonPersistentQuantitationType() - Static method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Note that if you want a 'preferred' qt or other special properties you have to set it yourself.
getTestPersistentArrayDesign(int, boolean) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.
getTestPersistentArrayDesign(int, boolean, boolean) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.
getTestPersistentArrayDesign(int, boolean, boolean, boolean) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.
getTestPersistentArrayDesign(List<String>, Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.
getTestPersistentBasicExpressionExperiment() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBasicExpressionExperiment() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBasicExpressionExperiment(ArrayDesign) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBasicExpressionExperiment(ArrayDesign) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBibliographicReference(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBibliographicReference(String) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBioAssay(ArrayDesign) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
getTestPersistentBioAssay(ArrayDesign) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBioAssay(ArrayDesign, BioMaterial) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
getTestPersistentBioAssay(ArrayDesign, BioMaterial) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
getTestPersistentBioMaterial() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBioMaterial() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBioMaterial(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBioMaterial(Taxon) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBioSequence() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBioSequence() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBioSequence(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBioSequence(Taxon) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBioSequence2GeneProducts(BioSequence) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBioSequence2GeneProducts(BioSequence) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentBlatResult(BioSequence) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBlatResult(BioSequence, Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentBlatResult(BioSequence, Taxon) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentCompleteExpressionExperiment(boolean) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to get a (fairly) complete randomly generated persisted expression experiment.
getTestPersistentCompleteExpressionExperimentWithSequences() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to get a (fairly) complete randomly generated persisted expression experiment.
getTestPersistentCompleteExpressionExperimentWithSequences(ExpressionExperiment) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentContact() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide a Contact that can be used to fill non-nullable associations in test objects.
getTestPersistentContact() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide a Contact that can be used to fill non-nullable associations in test objects.
getTestPersistentDatabaseEntry() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Get a database entry from a fictitious database.
getTestPersistentDatabaseEntry(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentDatabaseEntry(String, String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentDatabaseEntry(String, String) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentDatabaseEntry(String, ExternalDatabase) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
getTestPersistentDatabaseEntry(String, ExternalDatabase) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
getTestPersistentDatabaseEntry(ExternalDatabase) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
getTestPersistentDatabaseEntry(ExternalDatabase) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
getTestPersistentExpressionExperiment() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.
getTestPersistentExpressionExperiment() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.
getTestPersistentExpressionExperiment(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.
getTestPersistentExpressionExperiment(Taxon) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.
getTestPersistentGene() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentGene() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentGene(Taxon) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentGene(Taxon) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentGeneProduct(Gene) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
getTestPersistentGeneProduct(Gene) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
getTestPersistentQuantitationType() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Convenience method to provide a QuantitationType that can be used to fill non-nullable associations in test objects.
getTestPersistentQuantitationType() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper: Convenience method to provide a QuantitationType that can be used to fill non-nullable associations in test objects.
getTestPersistentTaxon() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
GoldenPathQueryTest - Class in ubic.gemma.core.externalDb: These tests require a populated Human database.
GoldenPathQueryTest() - Constructor for class ubic.gemma.core.externalDb.GoldenPathQueryTest
GoldenPathTest - Class in ubic.gemma.core.util.test.category: Test depending on GoldenPath database availability.
GoldenPathTest() - Constructor for class ubic.gemma.core.util.test.category.GoldenPathTest

H

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
initialize(OntologyService, InputStream) - Static method in class ubic.gemma.core.ontology.OntologyTestUtils: Initialize an ontology, cancelling any pending initialization.
IntegrationTests - Class in ubic.gemma.core.util.test.suite
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

jdbcTemplate - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest: The SimpleJdbcTemplate that this base class manages, available to subclasses.
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
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
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

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

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

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
OntologySearchSourceTest - Class in ubic.gemma.core.search.source
OntologySearchSourceTest() - Constructor for class ubic.gemma.core.search.source.OntologySearchSourceTest
OntologyServiceFactoryTest - Class in ubic.gemma.core.ontology.providers
OntologyServiceFactoryTest() - Constructor for class ubic.gemma.core.ontology.providers.OntologyServiceFactoryTest
OntologyServiceIntegrationTest - Class in ubic.gemma.core.ontology
OntologyServiceIntegrationTest() - Constructor for class ubic.gemma.core.ontology.OntologyServiceIntegrationTest
OntologyServiceTest - Class in ubic.gemma.core.ontology
OntologyServiceTest() - Constructor for class ubic.gemma.core.ontology.OntologyServiceTest
OntologyTestUtils - Class in ubic.gemma.core.ontology: Utilities for testing ontologies.
OntologyTestUtils() - Constructor for class ubic.gemma.core.ontology.OntologyTestUtils
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.
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
PubMedSearchTest - Class in ubic.gemma.core.loader.entrez.pubmed
PubMedSearchTest() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedSearchTest
PubMedTest - Class in ubic.gemma.core.util.test.category: Test depending on PubMed availability.
PubMedTest() - Constructor for class ubic.gemma.core.util.test.category.PubMedTest
PubMedXMLFetcherTest - Class in ubic.gemma.core.loader.entrez.pubmed
PubMedXMLFetcherTest() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcherTest
PubMedXMLParserTest - Class in ubic.gemma.core.loader.entrez.pubmed
PubMedXMLParserTest() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParserTest

Q

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

R

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
removeGene2CsStatusFileAndDirectory() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilIntegrationTest
RepeatScanTest - Class in ubic.gemma.core.analysis.sequence
RepeatScanTest() - Constructor for class ubic.gemma.core.analysis.sequence.RepeatScanTest
resetMocks() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceImplTest
resetTestCollectionSize() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: Restore to default.
resetTestElementCollectionSize() - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
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
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.
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.

S

SampleCoexpressionAnalysisServiceTest - Class in ubic.gemma.core.analysis.preprocess
SampleCoexpressionAnalysisServiceTest() - Constructor for class ubic.gemma.core.analysis.preprocess.SampleCoexpressionAnalysisServiceTest
SDRFFetcherTest - Class in ubic.gemma.core.loader.expression.arrayExpress
SDRFFetcherTest() - Constructor for class ubic.gemma.core.loader.expression.arrayExpress.SDRFFetcherTest
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
SearchResultTest - Class in ubic.gemma.core.search: Tests for SearchResult.
SearchResultTest() - Constructor for class ubic.gemma.core.search.SearchResultTest
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
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.
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
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.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.GeoBrowserTest
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.ontology.providers.GeneOntologyService2Test
setUp() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest
setUp() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest
setUp() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
setUp() - Method in class ubic.gemma.core.security.authentication.UserServiceImplTest
setUp() - Method in class ubic.gemma.core.security.authorization.acl.AclAuthorizationTest
setUp() - Method in class ubic.gemma.core.security.authorization.acl.AclCollectionBeforeTest
setUp() - Method in class ubic.gemma.core.security.authorization.SecureValueObjectAuthorizationTest
setUp() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest
setUp() - Method in class ubic.gemma.core.security.UserGroupServiceTest
setUp() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiFetcherTest
setUp() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiObjectGeneratorTest
setUp() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiParserTest
setUp() - Method in class ubic.gemma.core.util.progress.ProgressAppenderTest
setUp() - Method in class ubic.gemma.core.util.progress.ProgressDataTest
setUp() - Method in class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest
setUp() - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpressionServiceTest
setUp() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
setUp() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventDaoImplTest
setUp() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailDaoTest
setUp() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailServiceImplTest
setUp() - Method in class ubic.gemma.model.common.description.CharacteristicServiceTest
setUp() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
setUp() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayServiceTest
setUp() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialServiceTest
setUp() - Method in class ubic.gemma.model.expression.experiment.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.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.GenericValueObjectConverterTest
setUp() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest
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.
setupMocks() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceImplTest
setUpSecurityContextHolderStrategy() - Static method in class ubic.gemma.core.util.test.BaseSpringContextTest
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
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
SpearmanMetricsTest - Class in ubic.gemma.core.analysis.expression.coexpression.links
SpearmanMetricsTest() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetricsTest
SplitExperimentTest - Class in ubic.gemma.core.analysis.preprocess
SplitExperimentTest() - Constructor for class ubic.gemma.core.analysis.preprocess.SplitExperimentTest
SpringContextTest - Interface in ubic.gemma.core.util.test.category: Mark tests requiring a full Spring context to run.
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
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
TaskUtilsTest - Class in ubic.gemma.core.job
TaskUtilsTest() - Constructor for class ubic.gemma.core.job.TaskUtilsTest
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
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.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.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.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
tearDownSecurityContext() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest: 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.loader.expression.ExpressionExperimentPlatformSwitchTest: for bug 3451
test() - Method in class ubic.gemma.core.metrics.GenericMeterRegistryConfigurerTest.MyService
test() - Method in interface ubic.gemma.core.metrics.GenericMeterRegistryConfigurerTest.MyService2
test() - Method in class ubic.gemma.core.metrics.GenericMeterRegistryConfigurerTest.MyService2Impl
test() - Method in class ubic.gemma.core.ontology.OntologyServiceIntegrationTest
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.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.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.GenericValueObjectConverterTest
test() - Method in class ubic.gemma.persistence.util.MailEngineTest
test() - Method in class ubic.gemma.persistence.util.SettingsConfigTest
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
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
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
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
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
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
testBatchA() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchB() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchC() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchD() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchDX() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchE() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchF() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchG() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchH() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchI() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchJ() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchK() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchL() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchM() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchMixedHeaders() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest: See https://github.com/PavlidisLab/GemmaCuration/issues/64
testBatchMixedHeadersSinglePlatform() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchMixedHeadersSinglePlatformSingleton() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchO() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchP() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testBatchQ() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
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
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
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
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
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
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.
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.GenericValueObjectConverterTest
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.GenericValueObjectConverterTest
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
testConvertFromSubClass() - Method in class ubic.gemma.persistence.util.GenericValueObjectConverterTest
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
testConvertNull() - Method in class ubic.gemma.persistence.util.GenericValueObjectConverterTest
testConvertNullEntity() - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverterTest
testConvertPhenotypeAssociation() - Method in class ubic.gemma.core.search.SearchServiceVoConversionTest
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
testConvertToSuperClass() - Method in class ubic.gemma.persistence.util.GenericValueObjectConverterTest
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
testConvertUnsupportedType() - Method in class ubic.gemma.persistence.util.GenericValueObjectConverterTest
testConvertWithLotsOfPlatforms() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
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
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
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.
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.FactorValueServiceTest
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
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
testDisableInference() - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactoryTest
testDisableLoadHomologene() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceTest
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
testEmptyPath() - Method in class ubic.gemma.persistence.service.SubqueryUtilsTest
testEmptySubClause() - Method in class ubic.gemma.persistence.util.FiltersTest
testEnglishAnalyzer() - Method in class ubic.gemma.core.search.LuceneTest
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
testEquality() - Method in class ubic.gemma.persistence.util.FiltersTest
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
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
testFactorValueStatementsNotListedInCharacteristics() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoTest
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
testFilterByAllCharacteristics() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
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.ProcessedExpressionDataVectorDaoTest
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
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
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.expression.designElement.CompositeSequenceDaoTest
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
testFindByInvestigation() - Method in class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest
testFindByInvestigations() - Method in class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest
testFindByName() - Method in class ubic.gemma.model.genome.gene.GeneSetServiceTest
testFindByNameExact() - Method in class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest
testFindByNameRecent() - Method in class ubic.gemma.model.analysis.DifferentialExpressionAnalysisServiceTest
testFindByNcbiId() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest
testFindByNcbiId() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest
testFindByOfficialName() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest
testFindByOfficialSymbol() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest
testFindByOfficialSymbolInexact() - Method in class ubic.gemma.model.genome.gene.GeneServiceImplTest
testFindByQt() - Method in class ubic.gemma.model.expression.bioAssayData.DesignElementDataVectorServiceTest
testFindCandidateGenes() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testFindCoexpressionRelationships() - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpressionServiceTest
testFindDatabaseEntry() - Method in class ubic.gemma.model.common.description.DatabaseEntryDaoImplTest
testFindEvenThoughHaveSameSymbol() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest
testFindEvidenceByFilters() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testFindEvidenceByGeneId() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
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
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
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
testFromSettings() - Method in class ubic.gemma.core.util.BuildInfoTest
testgcrma() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testGDS186() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest
testGeneLoader() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneLoadingTest
testGeneralSearch4Brain() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest: Tests that general search terms are resolved to their proper ontology terms and objects tagged with those terms are found, -- requires LARQ index.
testGenerate() - Method in class ubic.gemma.core.util.biomart.BioMartEnsemblNcbiObjectGeneratorTest: Tests that given a taxon biomart file a BioMartEnsembleNcbi can be returned and that the genes are correctly mapped.
testGenerateArrayDesignGeneMappingEvent() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceTest
testGenerateArrayDesignSequenceAnalysisEvent() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceTest
testGenerateArrayDesignSequenceUpdateEvent() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceTest
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
testGetAllChildren() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest
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
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
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
testGetByGeneAlias() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest
testGetByTaxon() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
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
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
testGetExpressionExperimentsById() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
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
testGetFilterablePropertyType() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentServiceIntegrationTest
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
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
testGetMetadata() - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceTest
testGetMicroRnaByTaxon() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest
testGetMultiple() - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmdTest
testGetMultipleAcc() - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmdTest
testGetMultipleAccSomeNotFound() - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmdTest
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
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
testGetQuantitationTypesForArrayDesign() - 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
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
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
testGetTermForId() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceTest
testGetU() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest
testGPL6096ExonArray() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testGSE14285OneBatch() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testGSE156689NoBatchinfo() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.RNASeqBatchInfoPopulationTest
testGSE35930() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExTest: Test where probes have constant values.
testGSE44903() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testGSE465() - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombinerTest
testGSE8872() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testGuessQuantitationTypeParameters() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testHandleAddEventAuditableAuditEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailDaoTest
testHandleGetNewSinceDate() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventDaoImplTest
testHandleGetUpdatedSinceDate() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventDaoImplTest
testHandleGetUser() - Method in class ubic.gemma.core.security.authentication.UserServiceImplTest
testHandleRemoveUser() - Method in class ubic.gemma.core.security.authentication.UserServiceImplTest
testHandleSaveUser() - Method in class ubic.gemma.core.security.authentication.UserServiceImplTest
testHelper - Variable in class ubic.gemma.core.util.test.BaseSpringContextTest
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
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
testIndexOfCaseInsensitiveStringElements() - Method in class ubic.gemma.persistence.util.ListUtilsTest
testIndexOfElements() - Method in class ubic.gemma.persistence.util.ListUtilsTest
testInferredLogbaseDifferFromQuantitations() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtilTest
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
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
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
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
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
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
testLoadByCollection() - Method in class ubic.gemma.persistence.service.AbstractDaoTest
testLoadCommandConsoleFormat() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceIntegrationTest
testLoadCompositeSequences() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignServiceTest
testLoadDuplicatedRow() - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceTest
testLoadEvidenceWithExternalDatabaseName() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
testLoadGeneFileNotFoundIOException() - Method in class ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceTest
testLoadGenes() - Method in class ubic.gemma.model.genome.gene.GeneServiceTest
testLoadGSE28383ExonArray() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest
testLoadGSE30521ExonArray() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoDatasetServiceTest
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
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
testLookupByEnumeration() - Method in class ubic.gemma.core.ontology.OntologyCacheTest
testLookupByMaximalSubset() - Method in class ubic.gemma.core.ontology.OntologyCacheTest
testMakeEEGroupReadWrite() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest
testMakeExpressionExperimentPrivate() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest
testMakePrivateWithoutPermission() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest
testMakeTitle() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testMas5() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testMas6() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
testMatrixConversion() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixTest
testMatrixReconstruct() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest
testMatrixReconstructB() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest
testMeasuredRegion() - Method in class ubic.gemma.core.util.StopWatchUtilsTest
testMeasuredRegionWhhenStopWatchIsAlreadyStarted() - Method in class ubic.gemma.core.util.StopWatchUtilsTest
testMeasuredRegionWhhenStopWatchIsStopped() - Method in class ubic.gemma.core.util.StopWatchUtilsTest
testMeasuredRegionWithInnerRegion() - Method in class ubic.gemma.core.util.StopWatchUtilsTest
testMerge() - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeServiceTest
testMINiMLParse() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceParseTest
testMissingValue() - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesTest
testMissingValueGSE11017() - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesTest: Was giving all missing values.
testMissingValueGSE523() - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesTest
testMissingValueGSE56() - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesTest: GSE56 is corrupt: there is no Channel 1 signal value in the data file.
testMkdirAlreadyExists() - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcherTest
testMkdirMakeSubdirs() - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcherTest
testMkdirMakeTemp() - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcherTest
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
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
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
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
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
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
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
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
testParseUnsupportedType() - Method in class ubic.gemma.persistence.util.FilterTest
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
testPixels() - Method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesserTest
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
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
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
testRemove() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDeleteTest
testRemove() - Method in class ubic.gemma.persistence.service.genome.GeneDaoTest
testRemoveByCompositeSequence() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoTest
testRemoveMultipleAcesFromPrivateExpressionExperiment() - Method in class ubic.gemma.core.security.authorization.SecurityServiceTest
testRemoveWithStatement() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest
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
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
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
testRunAsAdmin() - Method in class ubic.gemma.persistence.util.SecurityUtilsTest
testSampleMINiMLParse() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceParseTest
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
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
testSearchByBibRefIdProblems() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest
testSearchByBibRefIdProblemsB() - Method in class ubic.gemma.core.search.SearchServiceIntegrationTest
testSearchExpressionExperiment() - Method in class ubic.gemma.core.search.source.HibernateSearchSourceTest
testSearchGenes() - Method in class ubic.gemma.model.genome.gene.GeneSearchTest
testSearchOntologyForPhenotypes() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationTest
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
testSetQueryWhenQueryIsNull() - Method in class ubic.gemma.model.common.search.SearchSettingsTest
testSetResultObject() - Method in class ubic.gemma.core.search.SearchResultTest
testSetResultObjectWithDifferentId() - Method in class ubic.gemma.core.search.SearchResultTest
testSetResultObjectWithNullId() - Method in class ubic.gemma.core.search.SearchResultTest
testSetTermUriWhenUriIsBlank() - Method in class ubic.gemma.model.common.search.SearchSettingsTest
testSetTermUriWhenUriIsNull() - Method in class ubic.gemma.model.common.search.SearchSettingsTest
testSettingsWithDifferentHighlighterAreEqual() - Method in class ubic.gemma.model.common.search.SearchSettingsTest
testSignup() - Method in class ubic.gemma.core.security.authorization.acl.AclAdviceTest
testSimpleAuditFindOrCreate() - Method in class ubic.gemma.core.security.audit.AuditAdviceTest
testSingleTaxonOnArrayWithNoOrganismColumn() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
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
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.OntologyServiceIntegrationTest
testsvd() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImplTest
testsvdGapped() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImplTest
testTaxonNotFoundIllegalArgumentExceptionException() - Method in class ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceTest
testTaxonPropertyResolutionInGetFilter() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoTest
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.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
testUndefinedProperty() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDaoTest
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
testUpdateExpressionExperiment2CharacteristicEntries() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilIntegrationTest
testUpdateExternalDatabaseDontCascadeToRelatedDatabases() - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceTest
testUpdateGroups() - Method in class ubic.gemma.core.security.authentication.UserManagerTest
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
testVarianceFractions() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataSVDTest
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
testWithImageNoGenbank() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
testWithImages() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterTest
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
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

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.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.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.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
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
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
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

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

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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.

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