Package ubic.gemma.core.analysis.report

Interface ExpressionExperimentReportService

  • All Known Implementing Classes:
    ExpressionExperimentReportServiceImpl
    public interface ExpressionExperimentReportService
    Methods for reading and creating reports on ExpressinExperiments. Reports are typically updated either on demand or after an analysis; and retrieval is usually from the web interface.
    Author:
    paul

    • Method Detail

      • evictFromCache

        void evictFromCache​(Long id)
        Invalidate the cached 'report' for the experiment with the given id. If it is not cached nothing happens.
        Parameters:
        id - the id of the entity to evict

      • generateSummary

        ExpressionExperimentDetailsValueObject generateSummary​(Long id)
        Generate a value object that contain summary information about links, biomaterials, and datavectors
        Parameters:
        id - the id of the ee to generate summary for
        Returns:
        details VO

      • generateSummaryObjects

        @Secured("GROUP_AGENT")
Collection<ExpressionExperimentDetailsValueObject> generateSummaryObjects()
        Generates reports on ALL experiments, including 'private' ones. This should only be run by administrators as it takes a while to run.

      • populateReportInformation

        void populateReportInformation​(Collection<ExpressionExperimentDetailsValueObject> vos)
        Fills in link analysis and differential expression analysis summaries, and other info from the report.
        Parameters:
        vos - value objects

      • retrieveSummaryObjects

        Collection<ExpressionExperimentDetailsValueObject> retrieveSummaryObjects​(Collection<Long> ids)
        retrieves a collection of cached value objects containing summary information
        Parameters:
        ids - the ids of ees for which the summary objects should be retrieved.
        Returns:
        a collection of cached value objects

      • recalculateExperimentBatchInfo

        @Secured("GROUP_AGENT")
void recalculateExperimentBatchInfo​(ExpressionExperiment ee)
        Recalculates the batch effect and batch confound information for the given dataset.
        Parameters:
        ee - the experiment to recalculate the batch properties for.