All Classes Interface Summary Class 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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| AbstractFetcherTest |
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| AbstractGeoServiceTest |
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| AbstractTsvFileServiceTest |
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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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| 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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| 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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| AuditAdviceTest |
Test of adding audit events when objects are created, updated or deleted.
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| AuditControllerTest |
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| AuditEventDaoImplTest |
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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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| BaseCliTest.BaseCliTestContextConfiguration |
Basic context configuration
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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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| BaseSpringContextTest |
subclass for tests that need the container and use the database
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| BaseSpringWebTest |
Class to extend for tests of controllers et al. that need a spring context.
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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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| BioMaterialServiceTest |
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| BioSequencePersistTest |
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| BioSequenceTest |
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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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| CharacteristicDaoImplTest |
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| CharacteristicServiceTest |
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| CharacteristicSortTest |
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| CharacteristicValueObjectTest |
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| CliTest |
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| CoexpressionNodeDegreeValueObjectTest |
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| ComBatTest |
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| CompassSearchSourceTest |
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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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| 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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| DifferentialExpressionAnalysisHelperServiceTest |
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| DifferentialExpressionAnalysisServiceTest |
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| DifferentialExpressionAnalyzerServiceTest |
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| DifferentialExpressionAnalyzerTest |
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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.
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| DiffExTest |
Tests added to check various cases of differential expression analysis.
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| DiffExWithInvalidInteraction2Test |
for bug 3927
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| DiffExWithInvalidInteractionTest |
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| EntityUtilsTest |
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| EntityUtilsTest.Bar |
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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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| ExperimentalDesignControllerTest |
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| ExperimentalDesignImportDuplicateValueTest |
Test for import that results in multiple factor values for the same factor on a single biomaterial.
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| ExperimentalDesignImporterTest |
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| ExperimentalDesignWriterTest |
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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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| 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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| ExpressionExperimentDeleteTest |
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| ExpressionExperimentPlatformSwitchTest |
Switching of platforms that have no composite sequences.
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| ExpressionExperimentServiceImplTest |
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| ExpressionExperimentServiceTest |
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| ExpressionExperimentSetServiceTest |
Tests for methods that perform operations on or with expressionExperiment sets
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| ExpressionExperimentSetValueObjectHelperTest |
Tests for methods that create ExpressionExperimentSetValueObjects from expressionExperiment entities
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| ExpressionExperimentSubSetServiceTest |
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| ExternalDatabaseDaoTest |
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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
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| FactorValueServiceTest |
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| FastaParserTest |
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| FastTests |
Test suite that excludes all the slow tests (i.e. marked with SlowTest). |
| FileUploadUtilTest |
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| FilterArgTest |
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| GemmaEndpointTest |
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| Gene2GeneCoexpressionServiceTest |
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| GeneCoexpressionTestedInTest |
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| GeneDiffExMetaAnalysisServiceTest |
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| GeneMultifunctionalityPopulationServiceTest |
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| GeneOntologyServiceTest |
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| GeneOntologyServiceTest2 |
Additional tests with updated ontology file, fixing problems getting aspects.
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| GenericScanFileDateExtractorTest |
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| GeneSearchTest |
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| GeneServiceImplTest |
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| 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
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| GeoDatasetServiceTest |
Test full procedure of loading GEO data, focus on corner cases.
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| GeoFamilyParserTest |
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| GeoPlatformServiceTest |
Tests of GeoPlatformService
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| GeoPlatformTest |
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| GeoTest |
Test depending on GEO availability.
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| GoldenPathQueryTest |
These tests require a populated Human database.
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| GoldenPathTest |
Test depending on GoldenPath database availability. |
| HomologeneServiceTest |
Tests the homologeneService but only access methods that don't require a DB connection (using the gemma db).
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| HttpFetcherTest |
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| IlluminaProbeReaderTest |
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| IntegrationTests |
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| LinkAnalysisServiceTest |
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| ListUtilsTest |
Tests for extra utilities for List. |
| LowVarianceDataTest |
Test based on GSE19480, see bug 3177
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| LuceneTest |
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| ManualAuthenticationProcessingTest |
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| MatrixConversionTest |
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| MeanVarianceServiceTest |
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| MockLongJobController |
Note: do not use parameterized collections as parameters for ajax methods in this class!
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| 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.
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| NCBIGeneHistoryParserTest |
TODO Document Me
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| NCBIGeneLoadingTest |
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| NCBIGeneParserTest |
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| ObjectFilterQueryUtilsTest |
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| ObjectFilterTest |
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| OneWayAnovaAnalyzerTest |
Tests the one way anova analyzer.
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| OntologyControllerTest |
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| OntologyServiceTest |
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| OutlierDetectionServiceTest |
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| PersistentDummyObjectHelper |
Used to generate test data.
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| PersisterTest |
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| PhenotypeAssociationTest |
This test will likely fail if the full disease ontology is configured to load; instead we want to load a small 'fake'
one.
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| PhenotypeImportingTest |
Minimal test of PhenotypeProcessingUtil - part of Phenocarta
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| PlatformsWebServiceTest |
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| PointcutsTest |
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| PrincipalTest |
Test that we can log users in, etc.
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| ProbeMapperTest |
Unaware of the Gemma database but uses the hg19 and mm10 databases (tests will not work with hg38)
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| ProbeSequenceParserTest |
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| ProcessedExpressionDataCreateServiceTest |
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| 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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| RawDataFetcherTest |
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| RepeatScanTest |
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| RestapidocsIndexRewriteFilterTest |
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| RetryTest |
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| RetryTest.TestRetryDao |
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| RetryTest.TestRetryService |
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| RNASeqBatchInfoPopulationTest |
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| RootWebServiceTest |
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| RssFeedControllerTest |
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| SampleCoexpressionAnalysisServiceTest |
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| SchedulerSecurityTest |
Tests security of methods run by Quartz.
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| SDRFFetcherTest |
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| SearchResultTest |
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| SearchServiceIntegrationTest |
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| SearchServiceTest |
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| SearchServiceVoConversionTest |
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| SearchSettingsTest |
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| SearchWebServiceTest |
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| SearchWebServiceTest.SearchWebServiceTestContextConfiguration |
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| SecureValueObjectAuthorizationTest |
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| SecurityControllerTest |
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| SecurityServiceTest |
Tests the SecurityService: making objects public or private and testing the permissions.
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| SequenceBinUtilsTest |
Test values are from hg18 all_est.
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| SequenceManipulationTest |
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| ServletUtilsTest |
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| SignupControllerTest |
Tortures the signup system by starting many threads and signing up many users, while at the same time creating a lot
of expression experiments.
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| SimpleExpressionDataLoaderServiceTest |
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| SimpleFastaCmdTest |
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| SlackAppenderTest |
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| SlowTest |
Used to mark slow tests.
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| SortArgTest |
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| SortValueObjectTest |
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| SpearmanMetricsTest |
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| SplitExperimentTest |
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| SpringContextTest |
Mark tests requiring a full Spring context to run.
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| StopWatchUtilsTest |
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| StringArrayArgTest |
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| StringArrayArgTest.Api |
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| SubsettedAnalysis2Test |
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| SubsettedAnalysis3Test |
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| SubsettedAnalysisTest |
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| SupportDetailsTest |
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| SVDServiceImplTest |
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| SwissProtParserTest |
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| TableMaintenanceUtilIntegrationTest |
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| TableMaintenanceUtilTest |
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| TaskRunningTest |
Test of long job control.
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| TaskUtilsTest |
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| TaxaWebServiceTest |
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| TaxonLoaderTest |
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| TaxonParserTest |
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| TaxonServiceImplTest |
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| TaxonUtilityTest |
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| TestAuthenticationUtils |
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| TestAuthenticationUtilsImpl |
Utilities for manipulating the SecurityContextHolder in a test envirnoment.
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| TestUtils |
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| TTestAnalyzerTest |
See test/data/stat-tests/README.txt for R code.
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| TwoChannelMissingValuesTest |
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| TwoWayAnovaWithInteractionsAnalyzerTest |
Tests the two way anova analyzer with interactions.
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| TwoWayAnovaWithInteractionsTest2 |
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| TwoWayAnovaWithInteractionTest2 |
Test based on GSE8441
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| TwoWayAnovaWithoutInteractionsAnalyzerTest |
Tests the two way anova analyzer.
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| UnitTests |
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| UserGroupServiceTest |
Tests the Group facilities of the UserManager..
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| UserServiceImplTest |
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| VectorMergingServiceTest |
Tests loading, platform switch, vector merge, and complex deletion (in teardown)
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| WebApplicationExceptionMapperTest |
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| WebApplicationExceptionMapperTest.CustomResource |
This is a very simplisitc example that produces two representation for the same resource.
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| WebApplicationExceptionMapperTest.CustomResource.MyModel |
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