Interface PreprocessorHelperService

All Known Implementing Classes:
PreprocessorHelperServiceImpl
public interface PreprocessorHelperService
Co-bean carrying the processFor* diagnostic steps that PreprocessorServiceImpl.processDiagnostics(ExpressionExperiment) runs as part of the post-load preprocessing pipeline.

Hoisted out of PreprocessorServiceImpl so the methods can carry @AuditedOnError declarations and be intercepted by Spring AOP -- private self-invoked methods on PreprocessorServiceImpl were invisible to the proxy and could not be migrated off the imperative addUpdateEvent(...) pattern in bucket 2e.

See Also:

  • Method Details

    • batchCorrect

      @Nullable Integer batchCorrect(ExpressionExperiment ee) throws PreprocessingException
      If possible, batch-correct the processed data vectors via ComBat. A successful run emits a BatchCorrectionEvent via the @Audited aspect; the note records how many vectors were replaced. When the experiment is not batch-correctable, the method returns without writing a vector or an audit event.

      Hoisted out of PreprocessorServiceImpl (where it lived as private void batchCorrect(ExpressionExperiment) and was self- invoked from process()) so the call passes through a Spring proxy and the audit aspect can fire — bucket 2b of AUDIT_PHASE_C_RECCE.md (inventory #3).

      Returns:
      the number of processed vectors that were replaced by the batch-corrected matrix, or null when the experiment is not batch-correctable (no audit event written in that case). The return value drives the @Audited note via messageSpel; callers may ignore it.
      Throws:
      PreprocessingException

    • processForMeanVarianceRelation

      void processForMeanVarianceRelation(ExpressionExperiment ee) throws PreprocessingException
      Compute and persist the mean-variance scatter used for the heteroscedasticity diagnostic plot. A failure emits a FailedMeanVarianceUpdateEvent via the audit aspect.
      Throws:
      PreprocessingException

    • processForPca

      void processForPca(ExpressionExperiment ee) throws SVDRelatedPreprocessingException
      Run SVD / PCA for diagnostics. A failure emits a FailedPCAAnalysisEvent via the audit aspect.
      Throws:
      SVDRelatedPreprocessingException

    • processForSampleCorrelation

      void processForSampleCorrelation(ExpressionExperiment ee) throws SampleCoexpressionRelatedPreprocessingException
      Compute and persist the sample-sample correlation matrix used for the diagnostic heatmap. A failure emits a FailedSampleCorrelationAnalysisEvent via the audit aspect.
      Throws:
      SampleCoexpressionRelatedPreprocessingException