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.
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| AbstractDaoIntegrationTest |
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| AbstractDaoTest |
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| AbstractDaoTest.MyDao |
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| AbstractDaoTest.MyEntity |
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| 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 |
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| 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.
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| AclAuthorizationTest |
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| AclCollectionBeforeTest |
Test the AclCollectionEntryVoter.
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| AclCriteriaUtilsTest |
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| AclQueryUtilsTest |
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| AclTestUtils |
Methods for checking ACLs.
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| 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)
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| AllenBrainAtlasServiceTest |
Alan brain Atlas service test.
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| AllenBrainAtlasTest |
Mark tests that require the Allen Brain Atlas RESTful API.
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| AllTests |
Test suite consisting of all the tests in the current classpath.
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| AnalysisResultSetsJerseyTest |
Integration test for the result sets endpoint.
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| AnalysisResultSetsWebServiceTest |
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| AnchorTagUtilTest |
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| AncovaTest |
Tests of ANCOVA: using linear models with mixtures of fixed level and continuous parameters.
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| AnnotationsWebServiceTest |
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| AnnotationsWebServiceTest.AnnotationsWebServiceContextConfiguration |
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| ArrayDesignControllerTest |
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| 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 |
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| Assertions |
Entrypoint for custom AssertJ assertions.
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| 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 |
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| 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.
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| BaseCliTest |
Minimal setup
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| BaseDatabaseTest |
Minimalist test setup with an in-memory database and transactional test cases.
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| BaseDatabaseTest.BaseDatabaseTestContextConfiguration |
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| BaseDatabaseTest.DataSourceInitializer |
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| BaseJerseyIntegrationTest |
Base class for Jersey-based integration tests.
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| BaseJerseyTest |
Base class for Jersey-based tests that needs a WebApplicationContext for loading and configuring or mocking
Spring components. |
| BaselineDetectionTest |
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| BaselineSelectionTest |
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| BaseSpringContextTest |
subclass for tests that need the container and use the database
|
| BaseSpringWebTest |
Class to extend for tests of controllers et al.
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| BaseWebTest |
Base class for a Web-based unit test.
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| BaseWebTest.BaseWebTestContextConfiguration |
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| BatchInfoPopulationServiceIntegrationTest |
Test fetching and loading the batch information from raw files.
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| BatchInfoPopulationServiceTest |
Unit tests.
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| BibliographicReferenceServiceImplTest |
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| BibliographicReferenceServiceTest |
This class tests the bibliographic reference data access object.
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| BibRefControllerTest |
Tests the BibliographicReferenceController
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| BioAssayServiceTest |
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| BioMartEnsemblNcbiFetcherTest |
Tests that biomart fetcher works correctly.
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| BioMartEnsemblNcbiObjectGeneratorTest |
Class to test BioMartEnsemblNcbiObjectGeneration.
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| 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 |
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| BuildInfoTest |
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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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| 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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| 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 |
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| 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
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| DiffExWithInvalidInteractionTest |
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| DiseaseOntologyTest |
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| DwrBatchHandlers |
Handles DWR batches.
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| DwrBatchMatchers |
Match DWR batch results.
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| DwrCallbackHandler<T> |
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| DwrCallbackMatchers |
Matches successful DWR replies.
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| DwrException |
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| DwrExceptionHandler |
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| DwrExceptionMatchers |
Matches erroneous DWR replies.
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| DwrRequestBuilder |
Request builder that allows multiple DWR calls to be performed.
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| EntityDelegatorTest |
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| EntityUtilsTest |
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| ErrorPagesTest |
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| ErrorsAssert |
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| ESearchXMLParserTest |
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| EutilFetchTest |
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| ExecutingTaskTest |
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| ExonArrayDataAddIntegrationTest |
Uses the Affy Power Tools, and full-sized data sets.
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| ExperimentalDesignControllerIntegrationTest |
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| ExperimentalDesignControllerTest |
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| ExperimentalDesignImportDuplicateValueTest |
Test for import that results in multiple factor values for the same factor on a single biomaterial.
|
| ExperimentalDesignImporterTest |
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| ExperimentalDesignWriterTest |
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| ExperimentalFactorDaoTest |
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| ExpressionAnalysisResultSetDaoTest |
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| 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 |
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| 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.
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| ExpressionExperimentBatchCorrectionServiceTest |
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| ExpressionExperimentBibRefFinderTest |
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| ExpressionExperimentControllerTest |
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| ExpressionExperimentDaoTest |
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| ExpressionExperimentDeleteTest |
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| ExpressionExperimentPlatformSwitchTest |
Switching of platforms that have no composite sequences.
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| ExpressionExperimentReportServiceTest |
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| ExpressionExperimentServiceImplTest |
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| ExpressionExperimentServiceIntegrationTest |
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| ExpressionExperimentServiceTest |
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| ExpressionExperimentSetServiceTest |
Tests for methods that perform operations on or with expressionExperiment sets
|
| ExpressionExperimentSetValueObjectHelperTest |
Tests for methods that create ExpressionExperimentSetValueObjects from expressionExperiment entities
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| ExpressionExperimentSubSetServiceTest |
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| ExternalDatabaseServiceTest |
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| ExternalDatabaseUpdaterCliTest |
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| 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 |
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| FactorValueServiceIntegrationTest |
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| FactorValueServiceTest |
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| FactorValueUtilsTest |
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| FactorValueValueObjectSerializerTest |
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| FastaParserTest |
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| FastIntegrationTests |
Fast integration tests.
|
| FastTests |
Test suite that excludes all the slow tests (i.e.
|
| FastUnitTests |
Fast unit tests.
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| FileUploadUtilTest |
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| FilterArgTest |
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| FilteringVoEnabledServiceIntegrationTest |
Test all possible filterable properties for filtering and sorting results.
|
| FilterQueryUtilsTest |
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| FiltersTest |
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| FilterTest |
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| FindObsoleteTermsCliTest |
|
| GemmaAndExperimentalFactorOntologyTest |
This test covers cases where inference is done across two distinct OntologyService. |
| GemmaEndpointTest |
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| GemmaOntologyServiceTest |
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| Gene2GeneCoexpressionServiceTest |
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| GeneArgServiceTest |
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| GeneCoexpressionTestedInTest |
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| GeneDaoTest |
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| GeneDiffExMetaAnalysisServiceTest |
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| GeneMultifunctionalityPopulationServiceTest |
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| GeneOntologyService2Test |
Additional tests with updated ontology file, fixing problems getting aspects.
|
| GeneOntologyService2Test.GeneOntologyService2TestContextConfiguration |
|
| GeneOntologyServiceTest |
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| GenericMeterRegistryConfigurerTest |
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| GenericMeterRegistryConfigurerTest.MyService |
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| GenericMeterRegistryConfigurerTest.MyService2 |
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| GenericMeterRegistryConfigurerTest.MyService2Impl |
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| GenericScanFileDateExtractorTest |
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| GeneSearchTest |
|
| GeneServiceImplTest |
|
| GeneServiceTest |
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| GeneSetServiceTest |
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| GeneSetValueObjectHelperTest |
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| GeneTest |
Tests of 'equals' implementation
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| GeneValueObjectTest |
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| GenomePersisterTest |
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| GeoBrowserServiceParseTest |
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| GeoBrowserServiceTest |
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| GeoBrowserTest |
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| GeoCharacteristicParseTest |
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| 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 |
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| GeoPlatformServiceTest |
Tests of GeoPlatformService
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| GeoPlatformTest |
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| 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 |
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| HibernateConfigTest |
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| HibernateSearchSourceTest |
|
| HomologeneServiceTest |
Tests the homologeneService but only access methods that don't require a DB connection (using the gemma db).
|
| HttpFetcherTest |
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| IlluminaProbeReaderTest |
|
| IntegrationTest |
Mark a test as an integration test.
|
| IntegrationTests |
Integration tests.
|
| LinkAnalysisServiceTest |
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| ListUtilsTest |
Tests for extra utilities for List. |
| LoggingIntegrationTest |
|
| LowVarianceDataTest |
Test based on GSE19480, see bug 3177
|
| LuceneQueryUtilsTest |
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| LuceneTest |
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| MailEngineTest |
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| ManualAuthenticationProcessingTest |
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| Maps |
Extensions for AssertJ's Maps.
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| MatrixConversionTest |
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| MeanVarianceServiceTest |
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| MessageSourceTest |
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| MeterRegistryCliConfigurerTest |
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| MockDwrBatchRequestBuilders |
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| MockDwrRequestBuilders |
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| MockDwrResultHandlers |
Handles DWR results.
|
| MockDwrResultMatchers |
Match DWR results.
|
| MockLongJobController |
Note: do not use parameterized collections as parameters for ajax methods in this class! Type information is lost
during proxy creation so DWR can't figure out what type of collection the method should take.
|
| MockLongJobControllerImpl |
Controller that does nothing except wait a while.
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| NCBIGene2GOAssociationLoaderCLITest |
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| NCBIGene2GOAssociationParserTest |
Tests multiple both parsing and loading.
|
| NCBIGeneHistoryParserTest |
TODO Document Me
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| NCBIGeneLoadingTest |
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| NCBIGeneParserTest |
|
| OneWayAnovaAnalyzerTest |
Tests the one way anova analyzer.
|
| OntologyCacheTest |
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| OntologyControllerTest |
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| 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.
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| OntologySearchSourceTest |
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| OntologyServiceFactoryTest |
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| OntologyServiceTest |
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| OpenApiTest |
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| OutlierDetectionServiceTest |
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| PatoOntologyServiceTest |
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| 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 |
|
| 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 |
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| ProcessedExpressionDataCreateServiceTest |
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| ProcessedExpressionDataVectorDaoTest |
|
| ProcessedExpressionDataVectorServiceTest |
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| ProgressAppenderTest |
For this test to work you should have the appender configured in log4j-test.properties.
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| ProgressDataTest |
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| PubMedQueryControllerTest |
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| PubMedSearcherIntegrationTest |
Tests command line.
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| PubMedSearchTest |
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| PubMedTest |
Test depending on PubMed availability.
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| PubMedXMLFetcherTest |
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| PubMedXMLParserTest |
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| QuantileNormalizerTest |
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| QuantitationTypeDaoTest |
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| QuantitationTypeParameterGuesserTest |
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| QueryUtilsTest |
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| RandomExpressionDataMatrixUtils |
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| RawAndProcessedExpressionDataVectorDaoTest |
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| RawAndProcessedExpressionDataVectorServiceTest |
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| RawDataFetcherTest |
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| RawExpressionDataVectorDaoTest |
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| 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.
|
| SDRFFetcherTest |
|
| SearchResultSetTest |
|
| SearchResultTest |
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| SearchServiceIntegrationTest |
|
| SearchServiceTest |
|
| SearchServiceVoConversionTest |
Test conversion to VOs for search results.
|
| SearchSettingsTest |
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| SearchWebServiceTest |
|
| SearchWebServiceTest.SearchWebServiceTestContextConfiguration |
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| 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 |
|
| ServletUtilsTest |
|
| 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 |
|
| StatementTest |
|
| 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 |
|
| TaxonUtilityTest |
|
| TaxonValueObjectTest |
|
| TestAuthenticationUtils |
|
| TestAuthenticationUtilsImpl |
Utilities for manipulating the SecurityContextHolder in a test envirnoment.
|
| 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 |
|