Class NoSubSetAnalysisIsNotSuccessTest

java.lang.Object
ubic.gemma.core.util.test.BaseTest5
ubic.gemma.core.analysis.expression.diff.NoSubSetAnalysisIsNotSuccessTest
@ContextConfiguration public class NoSubSetAnalysisIsNotSuccessTest extends BaseTest5
Producing no analysis at all is a failure of the experiment, not a quiet empty result.

What went wrong

A subset can leave the per-subset loop without raising anything — it is DE_Exclude, it has no samples left, or fixFactorsForSubset finds nothing it can model and the loop logs "Experimental design is not valid for subset: ...; skipping". The old guard fired only when the result was empty AND at least one subset had thrown, so an experiment whose subsets were all skipped returned an empty collection. GSE74400 (eid 12822) did exactly that: the CLI printed "Performed 0 differential expression analyses." through addSuccessObject and exited 0, and a batch runner testing the exit status counted it as done.

This is a different question from -ignoreFailingSubsets, which is about carrying on when SOME subsets succeed, so the exception is raised whatever that flag says.

Author:
paul

  • Constructor Details

    • NoSubSetAnalysisIsNotSuccessTest

      public NoSubSetAnalysisIsNotSuccessTest()

  • Method Details

    • testEverySubsetSkippedIsAFailure

      @Test public void testEverySubsetSkippedIsAFailure()
      The rule. Every subset skipped as "design is not valid" is not a quiet empty result.

    • testIgnoreFailingSubsetsDoesNotSuppressIt

      @Test public void testIgnoreFailingSubsetsDoesNotSuppressIt()
      -ignoreFailingSubsets is about carrying on when SOME subsets succeed; it does not make "none of them did" a success. GSE74400 would have run with it set.

    • testASubsetThatCanBeModelledStillRuns

      @Test public void testASubsetThatCanBeModelledStillRuns()
      Positive control off the same fixture: let treatment vary within each arm and both subsets are analyzed, so an analyzer that had simply become unable to analyze anything could not pass the two tests above.