Class GeoLibraryStrategyTest

java.lang.Object
ubic.gemma.core.loader.expression.geo.GeoLibraryStrategyTest
public class GeoLibraryStrategyTest extends Object
The library-strategy vocabulary, and the one case where GEO's declared value is not believed.
Author:
gembro

  • Constructor Details

    • GeoLibraryStrategyTest

      public GeoLibraryStrategyTest()

  • Method Details

    • testEverySpellingResolves

      @Test public void testEverySpellingResolves()
      🛑 Every constant must round-trip from GEO's own spelling. An unlisted value is FATAL in GeoFamilyParser — deliberately, since folding it into OTHER would admit a chromatin or genomic assay as expression — so a constant nothing can parse into is a constant that never fires.

    • testSpellingIsCaseAndWhitespaceInsensitive

      @Test public void testSpellingIsCaseAndWhitespaceInsensitive()

    • testTheSpellingsAlreadySeenInProd

      @Test public void testTheSpellingsAlreadySeenInProd()
      The spellings that were already in the corpus before the vocabulary was completed.

    • testAnUnknownSpellingIsNotGuessedAt

      @Test public void testAnUnknownSpellingIsNotGuessedAt()

    • testRibosomeProfilingSubmittedAsOther

      @Test public void testRibosomeProfilingSubmittedAsOther()
      🛑 The GSE288755 case: titled … Ribo-seq replicate #1, declared OTHER.

    • testADeclaredStrategyIsNotSecondGuessed

      @Test public void testADeclaredStrategyIsNotSecondGuessed()
      A DECLARED strategy is believed, whatever the sample happens to be called.

    • testRelatedButDifferentAssaysAreLeftAsOther

      @Test public void testRelatedButDifferentAssaysAreLeftAsOther()
      ...and the detector stays narrow. These ride alongside ribosome profiling in the same series and are their own methods; calling them RIBO_SEQ would trade one wrong label for another.

    • testANonTranscriptomicSampleIsNotPromoted

      @Test public void testANonTranscriptomicSampleIsNotPromoted()
      A non-transcriptomic source is never reinterpreted, however it is named.