allow backfilling of counts and rpkm without triggering preprocessing #771
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Ideally we would just compare the log2cpm with the new one and trigger post-processing if they differ. I'll write some unit tests for the CLI. |
arteymix
reviewed
Jul 24, 2023
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I'll write unit tests instead of adding an integration test because it's impractical to check if the preprocessing service has been interacted with. |
This is needed to write unit tests for DataUpdater.
arteymix
reviewed
Jul 25, 2023
| verify( expressionExperimentService, times( 2 ) ).addRawVectors( same( ee ), any() ); | ||
| dataUpdater.addCountData( ee, ad, countMatrix, rpkmMatrix, 30, false, false, true ); | ||
| verify( expressionExperimentService ).replaceRawVectors( same( ee ), any() ); | ||
| verifyNoMoreInteractions( preprocessorService ); |
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@ppavlidis I've added the unit test here. It checks that the preprocessor service is only invoked once.
I'll add a test to see how differing library sizes are handled. Let me know if you want other cases covered.
arteymix
reviewed
Jul 25, 2023
| ba.setSequencePairedReads( isPairedReads ); | ||
| } | ||
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| if ( ba.getSequenceReadCount() != null && ba.getSequenceReadCount() != librarySize && requireExistingLibrarySizesMatch ) { |
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We need a test case for this specific condition.
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To address curation issue 362.
By using the the
noLog2cpmoption for RNASeqDataAddCli should allow us to backfill counts and rpkm for old data sets in a minimally-invasive way.Needs testing.
TODO