All Classes Interface Summary Class Summary Enum Summary Exception Summary Annotation Types Summary
| Class |
Description |
| AbstractArrayDesignProcessingTest |
Base test for tests that need persistent array design with sequences.
|
| AbstractDaoTest |
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| AbstractDaoTest.MyDao |
|
| AbstractDaoTest.MyEntity |
|
| AbstractDwrReplyMatchers |
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| AbstractDwrReplyParser |
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| AbstractFetcherTest |
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| AbstractFileServiceTest |
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| AbstractFilteringVoEnabledDaoTest |
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| AbstractFilteringVoEnabledDaoTest.FakeEnum |
|
| AbstractGeoServiceTest |
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| AbstractServiceTest |
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| AbstractServiceTest.ExceptionWithMessage |
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| AbstractServiceTest.ExceptionWithoutMessage |
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| AclAdviceTest |
Tests of ACL management: adding and removing from objects during CRUD operations.
|
| AclAuthorizationTest |
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| AclCollectionBeforeTest |
Test the AclCollectionEntryVoter.
|
| AclCriteriaUtilsTest |
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| AclQueryUtilsTest |
|
| AclTestUtils |
Methods for checking ACLs.
|
| AffyChipTypeExtractorTest |
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| AffyPowerToolsProbesetSummarizeTest |
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| AffyProbeReaderTest |
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| AffyScanDateExtractorTest |
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| AgilentScanDateExtractorTest |
Tests of parsing various flat file formats used for Agilent slides (and possibly other types)
|
| AllenBrainAtlasServiceTest |
Alan brain Atlas service test.
|
| AllenBrainAtlasTest |
Mark tests that require the Allen Brain Atlas RESTful API.
|
| AllTests |
Test suite consisting of all the tests in the current classpath.
|
| AnalysisResultSetsJerseyTest |
Integration test for the result sets endpoint.
|
| AnalysisResultSetsWebServiceTest |
|
| AnchorTagUtilTest |
|
| AncovaTest |
Tests of ANCOVA: using linear models with mixtures of fixed level and continuous parameters.
|
| AnnotationsWebServiceTest |
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| AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration |
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| ArrayDesignControllerTest |
|
| ArrayDesignDaoTest |
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| ArrayDesignMergeCliTest |
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| ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration |
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| ArrayDesignMergeServiceTest |
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| ArrayDesignReportServiceTest |
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| ArrayDesignSequenceAlignmentandMappingTest |
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| ArrayDesignSequenceProcessorFastacmdTest |
Test exercises the fastacmd - requires executable.
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| ArrayDesignSequenceProcessorTest |
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| ArrayDesignServiceTest |
|
| Assertions |
Entrypoint for custom AssertJ assertions.
|
| Assumptions |
Reusable assumptions for tests.
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| AsyncBeanAutowiringTest |
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| AsyncBeanAutowiringTest.MyService |
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| AsyncBeanAutowiringTest.MyService2 |
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| AsyncBeanAutowiringTest.MyService2Factory |
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| AsyncBeanAutowiringTest.MyServiceFactory |
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| AsyncFactoryTest |
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| AsyncFactoryTest.MyService |
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| AsyncFactoryTest.MyServiceFactory |
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| AsyncSingletonFactoryTest |
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| AsyncSingletonFactoryTest.MyService |
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| AsyncSingletonFactoryTest.MyServiceFactory |
|
| AuditAdviceTest |
Test of adding audit events when objects are created, updated or deleted.
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| AuditControllerTest |
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| AuditEventDaoTest |
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| AuditEventServiceTest |
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| AuditEventTypeTest |
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| AuditTrailDaoTest |
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| AuditTrailServiceImplTest |
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| BaseAnalyzerConfigurationTest |
Other tests can extend this class if they want an expression experiment with complete block design and biological
replicates.
|
| BaseCLIIntegrationTest |
Base class for CLI integration tests.
|
| BaseCodeConfigurerTest |
|
| BaseDatabaseTest |
Minimalist test setup with an in-memory database and transactional test cases.
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| BaseDatabaseTest.BaseDatabaseTestContextConfiguration |
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| BaseIntegrationTest |
Base class for integration tests.
|
| BaseJerseyIntegrationTest |
Base class for Jersey-based integration tests.
|
| BaseJerseyTest |
Base class for Jersey-based tests that needs a WebApplicationContext for loading and configuring or mocking
Spring components. |
| BaselineDetectionTest |
|
| BaselineSelectionTest |
|
| BaselineTest |
|
| BaseSpringContextTest |
Deprecated.
|
| BaseSpringWebTest |
Deprecated.
|
| BaseWebIntegrationTest |
Base class for web integration tests.
|
| BaseWebTest |
Base class for a Web-based unit test.
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| BaseWebTest.BaseWebTestContextConfiguration |
|
| BatchInfoPopulationServiceIntegrationTest |
Test fetching and loading the batch information from raw files.
|
| BatchInfoPopulationServiceTest |
Unit tests.
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| BibliographicReferenceServiceImplTest |
|
| BibliographicReferenceServiceTest |
This class tests the bibliographic reference data access object.
|
| BibRefControllerTest |
Tests the BibliographicReferenceController
|
| BioAssayServiceTest |
|
| BioMartEnsemblNcbiFetcherTest |
Tests that biomart fetcher works correctly.
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| BioMartEnsemblNcbiObjectGeneratorTest |
Class to test BioMartEnsemblNcbiObjectGeneration.
|
| BioMartEnsemblNcbiParserTest |
Tests the parsing of a BioMart file.
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| BioMaterialDaoTest |
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| BioMaterialServiceTest |
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| BioSequencePersistTest |
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| BioSequenceTest |
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| BlacklistedEntityDaoImplTest |
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| BlacklistedEntityServiceTest |
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| BlacklistTest |
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| BlatAssociationScorerTest |
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| BlatAssociationServiceTest |
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| BlatResultParserTest |
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| BlatResultServiceTest |
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| BlatResultTest |
|
| BootstrappedDataSourceFactoryTest |
|
| BuildInfoTest |
|
| CellLineOntologyTest |
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| CharacteristicDaoImplTest |
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| CharacteristicServiceTest |
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| CharacteristicSortTest |
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| CharacteristicTest |
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| CharacteristicUtilsTest |
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| CharacteristicValueObjectTest |
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| CliTest |
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| CoexpressionDaoTest |
|
| CoexpressionNodeDegreeValueObjectTest |
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| ComBatTest |
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| CompletionGeneratorTest |
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| CompositeSequenceDaoTest |
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| CompositeSequenceGeneMapperServiceTest |
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| CompositeSequenceParserTest |
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| CompositeSequenceServiceTest |
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| ConfigurationCookieTest |
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| ContinuousVariableDiffExTest |
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| ContrastTest |
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| CorsFilterTest |
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| CuratableDaoTest |
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| CuratableValueObjectTest |
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| DatabaseEntryDaoImplTest |
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| DatabaseSearchSourceTest |
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| DatasetCombinerTest |
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| DatasetsRestTest |
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| DatasetsWebServiceTest |
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| DataUpdaterTest |
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| DesignElementDataVectorServiceTest |
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| DetectFactorBaselineTest |
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| DifferentialExpressionAnalysisControllerTest |
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| DifferentialExpressionAnalysisDaoTest |
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| DifferentialExpressionAnalysisHelperServiceTest |
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| DifferentialExpressionAnalysisServiceTest |
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| DifferentialExpressionAnalyzerServiceTest |
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| DifferentialExpressionAnalyzerTest |
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| DifferentialExpressionResultDaoTest |
|
| DiffExMetaAnalyzerServiceTest |
This is a test that requires complex setup: loading several data sets, information on genes, array design
annotations, conducting differential expression, and finally the meta-analysis.
|
| DiffExTest |
Tests added to check various cases of differential expression analysis.
|
| DiffExWithInvalidInteraction2Test |
for bug 3927
|
| DiffExWithInvalidInteractionTest |
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| DiseaseOntologyTest |
|
| DwrBatchHandlers |
Handles DWR batches.
|
| DwrBatchMatchers |
Match DWR batch results.
|
| DwrCallbackHandler<T> |
|
| DwrCallbackMatchers |
Matches successful DWR replies.
|
| DwrException |
|
| DwrExceptionHandler |
|
| DwrExceptionMatchers |
Matches erroneous DWR replies.
|
| DwrRequestBuilder |
Request builder that allows multiple DWR calls to be performed.
|
| EntityDelegatorTest |
|
| EntityUtilsTest |
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| ErrorPagesTest |
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| ErrorsAssert |
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| ESearchXMLParserTest |
|
| EutilFetchTest |
|
| ExecutingTaskTest |
|
| ExonArrayDataAddIntegrationTest |
Uses the Affy Power Tools, and full-sized data sets.
|
| ExperimentalDesignControllerIntegrationTest |
|
| ExperimentalDesignControllerTest |
|
| ExperimentalDesignImportDuplicateValueTest |
Test for import that results in multiple factor values for the same factor on a single biomaterial.
|
| ExperimentalDesignImporterTest |
|
| ExperimentalDesignWriterTest |
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| ExperimentalFactorDaoTest |
|
| ExpressionAnalysisResultSetDaoTest |
|
| ExpressionAnalysisResultSetServiceTest |
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. |
| ExpressionDataDoubleMatrixTest |
|
| ExpressionDataDoubleMatrixUtilTest |
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| ExpressionDataFileServiceTest |
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| ExpressionDataMatrixColumnSortTest |
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| ExpressionDataSVDTest |
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| ExpressionDataTestMatrix |
Creates a sample small test matrix, not persistent.
|
| ExpressionExperimentBatchCorrectionServiceTest |
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| ExpressionExperimentBatchInformationServiceTest |
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| ExpressionExperimentBibRefFinderTest |
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| ExpressionExperimentControllerTest |
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| ExpressionExperimentDaoTest |
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| ExpressionExperimentDeleteTest |
|
| ExpressionExperimentPlatformSwitchTest |
Switching of platforms that have no composite sequences.
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| ExpressionExperimentReportServiceTest |
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| ExpressionExperimentServiceImplTest |
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| ExpressionExperimentServiceIntegrationTest |
|
| ExpressionExperimentServiceTest |
|
| ExpressionExperimentSetServiceTest |
Tests for methods that perform operations on or with expressionExperiment sets
|
| ExpressionExperimentSetValueObjectHelperTest |
Tests for methods that create ExpressionExperimentSetValueObjects from expressionExperiment entities
|
| ExpressionExperimentSubSetServiceTest |
|
| ExternalDatabaseServiceTest |
|
| ExternalDatabaseUpdaterCliTest |
|
| ExternalFileGeneLoaderServiceTest |
Test that Gemma can load genes from an external gene file with format : #GeneSymbol GeneName Uniprot ZYX ZYXIN Q15942
ZXDC ZXD FAMILY ZINC FINGER C Q8C8V1
|
| FactorValueDaoTest |
|
| FactorValueMigratorCLITest |
Deprecated. |
| FactorValueMigratorServiceTest |
Deprecated. |
| FactorValueOntologyServiceTest |
|
| FactorValueOntologyUtilsTest |
|
| FactorValueServiceIntegrationTest |
|
| FactorValueServiceTest |
|
| FactorValueTest |
|
| FactorValueUtilsTest |
|
| FactorValueValueObjectSerializerTest |
|
| FastaParserTest |
|
| FastIntegrationTests |
Fast integration tests.
|
| FastTests |
Test suite that excludes all the slow tests (i.e.
|
| FastUnitTests |
Fast unit tests.
|
| FileUploadUtilTest |
|
| FilterArgTest |
|
| FilteringVoEnabledServiceIntegrationTest |
Test all possible filterable properties for filtering and sorting results.
|
| FilterQueryUtilsTest |
|
| FiltersTest |
|
| FilterTest |
|
| FindObsoleteTermsCliTest |
|
| GemmaAndExperimentalFactorOntologyTest |
This test covers cases where inference is done across two distinct OntologyService. |
| GemmaEndpointTest |
|
| GemmaOntologyServiceTest |
|
| GemmaRestApiClientTest |
|
| Gene2GeneCoexpressionServiceTest |
|
| GeneArgServiceTest |
|
| GeneCoexpressionTestedInTest |
|
| GeneDaoTest |
|
| GeneDiffExMetaAnalysisServiceTest |
|
| GeneMultifunctionalityPopulationServiceTest |
|
| GeneOntologySearchSourceTest |
|
| GeneOntologyService2Test |
Additional tests with updated ontology file, fixing problems getting aspects.
|
| GeneOntologyService2Test.GeneOntologyService2TestContextConfiguration |
|
| GeneOntologyServiceTest |
|
| GeneOntologyUtilsTest |
|
| GenericMeterRegistryConfigurerTest |
|
| GenericMeterRegistryConfigurerTest.MyService |
|
| GenericMeterRegistryConfigurerTest.MyService2 |
|
| GenericMeterRegistryConfigurerTest.MyService2Impl |
|
| GenericScanFileDateExtractorTest |
|
| GeneSearchTest |
|
| GeneServiceImplTest |
|
| GeneServiceTest |
|
| GeneSetServiceTest |
|
| GeneSetValueObjectHelperTest |
|
| GeneTest |
Tests of 'equals' implementation
|
| GeneValueObjectTest |
|
| GeneWebServiceTest |
|
| GenomePersisterTest |
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| GeoBrowserServiceParseTest |
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| GeoBrowserServiceTest |
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| GeoBrowserTest |
|
| GeoCharacteristicParseTest |
|
| GeoConverterTest |
Unit test for GeoConversion Added extension BaseSpringContextTest as want Taxon Service to be called
|
| GeoDatasetServiceTest |
Test full procedure of loading GEO data, focus on corner cases.
|
| GeoFamilyParserTest |
|
| GeoPlatformServiceTest |
Tests of GeoPlatformService
|
| GeoPlatformTest |
|
| GeoTermReplacementTest |
Test replacements for GEO terms.
|
| GeoTest |
Test depending on GEO availability.
|
| GoldenPathQueryTest |
These tests require a populated Human database.
|
| GoldenPathTest |
Test depending on GoldenPath database availability. |
| GoogleAnalytics4ProviderTest |
|
| HibernateConfigTest |
|
| HibernateSearchSourceTest |
|
| HomePageControllerTest |
|
| HomologeneServiceTest |
Tests the homologeneService but only access methods that don't require a DB connection (using the gemma db).
|
| HttpFetcherTest |
|
| IlluminaProbeReaderTest |
|
| IntegrationTest |
Mark a test as an integration test.
|
| IntegrationTests |
Integration tests.
|
| LazyInitByDefaultPostProcessorTest |
|
| LinkAnalysisServiceTest |
|
| ListUtilsTest |
Tests for extra utilities for List. |
| LoggingIntegrationTest |
|
| LowVarianceDataTest |
Test based on GSE19480, see bug 3177
|
| LuceneQueryUtilsTest |
|
| LuceneTest |
|
| MailEngineTest |
|
| ManualAuthenticationProcessingTest |
|
| ManualAuthenticationServiceBasedSecurityContextFactoryTest |
|
| Maps |
Extensions for AssertJ's Maps.
|
| MarkCLIsAsPrototypesTest |
Test various behaviours of CLIs when injected as bean.
|
| MatrixConversionTest |
|
| MeanVarianceServiceTest |
|
| MessageSourceTest |
|
| MeterRegistryCliConfigurerTest |
|
| MissingBuildInfoTest |
|
| MockDwrBatchRequestBuilders |
|
| MockDwrRequestBuilders |
|
| MockDwrResultHandlers |
Handles DWR results.
|
| MockDwrResultMatchers |
Match DWR results.
|
| MockLongJobController |
Controller that does nothing except wait a while.
|
| NCBIGene2GOAssociationLoaderCLITest |
|
| NCBIGene2GOAssociationParserTest |
Tests multiple both parsing and loading.
|
| NCBIGeneHistoryParserTest |
TODO Document Me
|
| NCBIGeneLoadingTest |
|
| NCBIGeneParserTest |
|
| OneWayAnovaAnalyzerTest |
Tests the one way anova analyzer.
|
| OntologyCacheTest |
|
| OntologyControllerTest |
|
| OntologyLoadingTest |
This test does not use the test profile as it aims to verify that all the ontologies we use in production are working
properly.
|
| OntologySearchSourceTest |
|
| OntologyServiceFactoryTest |
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| OntologyServiceTest |
|
| OpenApiTest |
|
| OutlierDetectionServiceTest |
|
| PatoOntologyServiceTest |
|
| PersistentDummyObjectHelper |
Used to generate test data.
|
| PersisterTest |
|
| PhenotypeAssociationTest |
This test will likely fail if the full disease ontology is configured to load; instead we want to load a small 'fake'
one.
|
| PhenotypeImportingTest |
Deprecated. |
| PlatformsWebServiceTest |
|
| PointcutsTest |
|
| PrincipalComponentAnalysisDaoImplTest |
|
| PrincipalTest |
Test that we can log users in, etc.
|
| ProbeMapperTest |
Unaware of the Gemma database but uses the hg19 and mm10 databases (tests will not work with hg38)
|
| ProbeSequenceParserTest |
|
| ProcessedExpressionDataCreateServiceTest |
|
| ProcessedExpressionDataVectorDaoTest |
|
| ProcessedExpressionDataVectorServiceTest |
|
| ProgressAppenderTest |
For this test to work you should have the appender configured in log4j-test.properties.
|
| ProgressDataTest |
|
| PubMedQueryControllerTest |
|
| PubMedSearcherIntegrationTest |
Tests command line.
|
| PubMedSearchTest |
|
| PubMedTest |
Test depending on PubMed availability.
|
| PubMedXMLFetcherTest |
|
| PubMedXMLParserTest |
|
| QuantileNormalizerTest |
|
| QuantitationTypeDaoTest |
|
| QuantitationTypeParameterGuesserTest |
|
| QueryUtilsTest |
|
| RandomExpressionDataMatrixUtils |
|
| RawAndProcessedExpressionDataVectorDaoTest |
|
| RawAndProcessedExpressionDataVectorServiceTest |
|
| RawDataFetcherTest |
|
| RawExpressionDataVectorDaoTest |
|
| RepeatScanTest |
|
| ResponseAssert |
Assertions for jax-rs Response.
|
| RestapidocsIndexRewriteFilterTest |
|
| RetryTest |
|
| RetryTest.TestRetryDao |
|
| RetryTest.TestRetryService |
|
| RNASeqBatchInfoPopulationTest |
|
| RNASeqDataAddCliTest |
|
| RootWebServiceTest |
|
| RssFeedControllerTest |
|
| SampleCoexpressionAnalysisServiceTest |
|
| SchedulerSecurityTest |
Tests security of methods run by Quartz.
|
| SchedulerSecurityTest.TestSecureJob |
|
| SDRFFetcherTest |
|
| SearchResultSetTest |
|
| SearchResultTest |
|
| SearchServiceIntegrationTest |
|
| SearchServiceTest |
|
| SearchServiceVoConversionTest |
Test conversion to VOs for search results.
|
| SearchSettingsTest |
|
| SearchWebServiceTest |
|
| SearchWebServiceTest.SearchWebServiceTestContextConfiguration |
|
| SecureValueObjectAuthorizationTest |
|
| SecurityControllerTest |
|
| SecurityMockMvcRequestBuilders |
|
| SecurityMockMvcRequestBuilders.FormLoginRequestBuilder |
Creates a form based login request including any necessary CsrfToken.
|
| SecurityMockMvcRequestBuilders.LogoutRequestBuilder |
Creates a logout request (including any necessary CsrfToken)
|
| SecurityMockMvcRequestPostProcessors |
|
| SecurityMockMvcRequestPostProcessors.CsrfRequestPostProcessor |
Populates a valid CsrfToken into the request.
|
| SecurityMockMvcRequestPostProcessors.DigestRequestPostProcessor |
|
| SecurityMockMvcRequestPostProcessors.UserRequestPostProcessor |
Creates a UsernamePasswordAuthenticationToken and sets the principal to be
a User and associates it to the MockHttpServletRequest. |
| SecurityMockMvcResultMatchers |
|
| SecurityMockMvcResultMatchers.AuthenticatedMatcher |
|
| SecurityServiceTest |
Tests the SecurityService: making objects public or private and testing the permissions.
|
| SecurityTestExecutionListeners |
There are many times a user may want to use Spring Security's test support
(i.e.
|
| SecurityUtilsTest |
|
| SequenceBinUtilsTest |
Test values are from hg18 all_est.
|
| SequenceManipulationTest |
|
| ServiceBasedValueObjectConverterTest |
|
| ServiceBasedValueObjectConverterTest.VoConverterTestContextConfiguration |
|
| SettingsConfigTest |
|
| SignupControllerTest |
This test replaces the recaptcha service used by SignupController, so it is annotated with DirtiesContext
to invalidate the context once all the tests have completed. |
| SimpleExpressionDataLoaderServiceTest |
|
| SimpleFastaCmdTest |
|
| SlackAppenderTest |
|
| SlowTest |
Used to mark slow tests.
|
| SlowTests |
Run all the slow tests.
|
| SortArgTest |
|
| SortValueObjectTest |
|
| SpearmanMetricsTest |
|
| SplitExperimentTest |
|
| SpringContextUtilsTest |
|
| StatementTest |
|
| StaticCacheKeyLockTest |
|
| StopWatchUtilsTest |
|
| StrictBeanDefinitionValidatorTest |
|
| StrictBeanDefinitionValidatorTest.TestAnnotatedVo |
|
| StrictBeanDefinitionValidatorTest.TestImplicitValueObject |
|
| StringArrayArgTest |
|
| StringArrayArgTest.Api |
|
| SubqueryUtilsTest |
|
| SubsettedAnalysis2Test |
|
| SubsettedAnalysis3Test |
|
| SubsettedAnalysisTest |
|
| SupportDetailsTest |
|
| SVDServiceImplTest |
|
| SwissProtParserTest |
|
| TableMaintenanceUtilIntegrationTest |
|
| TableMaintenanceUtilTest |
|
| TaskRunningTest |
Test of long job control.
|
| TaskUtilsTest |
|
| TaxaWebServiceTest |
|
| TaxonArgServiceTest |
|
| TaxonLoaderTest |
|
| TaxonParserTest |
|
| TaxonServiceImplTest |
|
| TaxonUtilsTest |
|
| TestAuthenticationUtils |
|
| TestAuthenticationUtilsImpl |
Utilities for manipulating the SecurityContextHolder in a test envirnoment.
|
| TestCli |
|
| TestPropertyPlaceholderConfigurer |
Minimalistic placeholder configurer for usage in tests.
|
| TestSecurityContextHolder |
|
| TestUtils |
|
| TTestAnalyzerTest |
See test/data/stat-tests/README.txt for R code.
|
| TwoChannelMissingValuesTest |
|
| TwoWayAnovaWithInteractionsAnalyzerTest |
Tests the two way anova analyzer with interactions.
|
| TwoWayAnovaWithInteractionsTest2 |
|
| TwoWayAnovaWithInteractionTest2 |
Test based on GSE8441
|
| TwoWayAnovaWithoutInteractionsAnalyzerTest |
Tests the two way anova analyzer.
|
| UberonOntologyTest |
|
| UnitTests |
Unit tests.
|
| UserGroupServiceTest |
Tests the Group facilities of the UserManager..
|
| UserManagerTest |
|
| UserServiceImplTest |
|
| VectorMergingServiceTest |
Tests loading, platform switch, vector merge, and complex deletion (in teardown)
|
| WebApplicationExceptionMapperTest |
|
| WebApplicationExceptionMapperTest.CustomResource |
This is a very simplisitc example that produces two representation for the same resource.
|
| WebApplicationExceptionMapperTest.CustomResource.MyModel |
|
| WebTestUtils |
A utility class for testing spring security
|
| WhatsNewServiceTest |
|
| WithMockUser |
|
| WithSecurityContext |
An annotation to determine what SecurityContext to use.
|
| WithSecurityContextFactory<A extends Annotation> |
An API that works with WithUserTestExcecutionListener for creating a
SecurityContext that is populated in the TestSecurityContextHolder. |
| WithSecurityContextTestExecutionListener |
|
| WithUserDetails |
|