Class DifferentialExpressionAnalysisCliTest

java.lang.Object
ubic.gemma.core.util.test.BaseTest5
ubic.gemma.apps.DifferentialExpressionAnalysisCliTest
@WithMockUser("bob") @DirtiesContext(classMode=AFTER_EACH_TEST_METHOD) @ContextConfiguration @TestExecutionListeners(value=org.springframework.security.test.context.support.WithSecurityContextTestExecutionListener.class, mergeMode=MERGE_WITH_DEFAULTS) public class DifferentialExpressionAnalysisCliTest extends BaseTest5

  • Constructor Details

    • DifferentialExpressionAnalysisCliTest

      public DifferentialExpressionAnalysisCliTest()

  • Method Details

    • setUp

      @BeforeEach public void setUp() throws IOException
      Throws:
      IOException

    • testAnalysisWithAutomaticallySelectedFactors

      @Test public void testAnalysisWithAutomaticallySelectedFactors() throws IOException
      Throws:
      IOException

    • testAnalysisWithAutomaticallySelectedFactorsWhenBatchFactorIsPresent

      @Test public void testAnalysisWithAutomaticallySelectedFactorsWhenBatchFactorIsPresent() throws IOException
      Throws:
      IOException

    • testAnalysisWithAutomaticallySelectedFactorsWhenDeExcludeFactorIsPresent

      @Test public void testAnalysisWithAutomaticallySelectedFactorsWhenDeExcludeFactorIsPresent() throws IOException
      The DE_Include/DE_Exclude marker is not a biological factor. Counting it took a two-factor design over the automatic selector's limit of two and refused the run outright.
      Throws:
      IOException

    • testAnalysisWithAutomaticallySelectedFactorsWhenDeExcludeAndBatchFactorsArePresent

      @Test public void testAnalysisWithAutomaticallySelectedFactorsWhenDeExcludeAndBatchFactorsArePresent() throws IOException
      GSE13367's shape: two real factors, the DE_Include/DE_Exclude marker and a batch factor.
      Throws:
      IOException

    • testDeExcludeFactorCanStillBeRequestedExplicitly

      @Test public void testDeExcludeFactorCanStillBeRequestedExplicitly() throws IOException
      The marker is still selectable by ID, so a curator can inspect that design deliberately.
      Throws:
      IOException

    • testAnalysisWithAutomaticallySelectedFactorsWithBatchFactorIsPresentAndIncluded

      @Test public void testAnalysisWithAutomaticallySelectedFactorsWithBatchFactorIsPresentAndIncluded() throws IOException
      Throws:
      IOException

    • testSubSetAnalysisWithAutomaticallySelectedFactorsWhenContinuousFactorIsPresent

      @Test public void testSubSetAnalysisWithAutomaticallySelectedFactorsWhenContinuousFactorIsPresent()

    • testSubSetAnalysisWithAutomaticallySelectedFactorsAndContinuousFactor

      @Test public void testSubSetAnalysisWithAutomaticallySelectedFactorsAndContinuousFactor()

    • testAnalysisWithManuallySelectedFactors

      @Test public void testAnalysisWithManuallySelectedFactors()

    • testAnalysisWithManuallySelectedFactorsWhenFactorsAreRepeated

      @Test public void testAnalysisWithManuallySelectedFactorsWhenFactorsAreRepeated()

    • testAnalysisWithManuallySelectedFactorsWithNoInteraction

      @Test public void testAnalysisWithManuallySelectedFactorsWithNoInteraction()

    • testAnalysisWithManuallySelectedFactorsWithInteractionOfContinuousFactor

      @Test public void testAnalysisWithManuallySelectedFactorsWithInteractionOfContinuousFactor()

    • testAnalysisWithManuallySelectedFactorsWhenFactorDoesNotExist

      @Test public void testAnalysisWithManuallySelectedFactorsWhenFactorDoesNotExist()

    • testAnalysisWithManuallySelectedInteraction

      @Test public void testAnalysisWithManuallySelectedInteraction()

    • testAnalysisWithManuallySelectedInteractionWhenInteractionIsRepeated

      @Test public void testAnalysisWithManuallySelectedInteractionWhenInteractionIsRepeated()

    • testAnalysisWithManuallySelectedInteractionOfContinuousFactor

      @Test public void testAnalysisWithManuallySelectedInteractionOfContinuousFactor()

    • testSubSetAnalysisWithManuallySelectedFactors

      @Test public void testSubSetAnalysisWithManuallySelectedFactors()

    • testSubSetAnalysisWithManuallySelectedFactorsAndContinuousFactor

      @Test public void testSubSetAnalysisWithManuallySelectedFactorsAndContinuousFactor()

    • testSubSetAnalysisWithManuallySelectedFactorsWhenSubSetFactorIsSelected

      @Test public void testSubSetAnalysisWithManuallySelectedFactorsWhenSubSetFactorIsSelected()

    • testSubSetAnalysisWithManuallySelectedFactorsAndNoInteraction

      @Test public void testSubSetAnalysisWithManuallySelectedFactorsAndNoInteraction()

    • testRedoAnalysis

      @Test public void testRedoAnalysis()

    • testAnExperimentThatProducedNoAnalysisFails

      @Test public void testAnExperimentThatProducedNoAnalysisFails()
      An experiment that produced no analysis is not a success. GSE74400 (eid 12822) had both its subsets skipped as "design is not valid", printed "Performed 0 differential expression analyses." and exited 0, and a batch runner testing the exit status counted it as done for hours.

    • testARedoThatProducedNoAnalysisFails

      @Test public void testARedoThatProducedNoAnalysisFails()
      Same for a redo: the CLI reports what came back, and nothing coming back is not something to report as done.

    • testDeleteAnalysis

      @Test public void testDeleteAnalysis()

    • testCompleteSubSetFactors

      @Test public void testCompleteSubSetFactors()

    • testCompleteFactors

      @Test public void testCompleteFactors()