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 Details

    • 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.

    • getAnnotationInformation

      void getAnnotationInformation(Collection<ExpressionExperimentDetailsValueObject> vos)

    • populateEventInformation

      void populateEventInformation(Collection<ExpressionExperimentDetailsValueObject> vos)

    • 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

    • recalculateExperimentBatchInfoAsAdmin

      @Secured({"GROUP_AGENT","RUN_AS_ADMIN"}) void recalculateExperimentBatchInfoAsAdmin(ExpressionExperiment ee)
      Recalculates the batch effect and batch confound information for the given dataset.

      This method is designed to be run as a background task by an agent with elevated privileges.

      See Also:

    • recalculateExperimentBatchInfo

      @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) 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.
      See Also:

    • recalculateExperimentBatchConfound

      @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) @Nullable String recalculateExperimentBatchConfound(ExpressionExperiment ee)
      Recompute the batch confound for ee and persist it; emit a BatchProblemsUpdateEvent only when the value actually changed.
      Returns:
      the new batch-confound summary string when an update was recorded, or null when the existing value already matched the freshly computed one. The non-null return is what lets @AuditedConditional(when = "#result != null", ...) fire the audit row.

    • recalculateExperimentBatchEffect

      @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) @Nullable String recalculateExperimentBatchEffect(ExpressionExperiment ee)
      Recompute the batch effect for ee and persist it; emit a BatchProblemsUpdateEvent only when the effect or its statistics actually changed.
      Returns:
      the new batch-effect summary string when an update was recorded, or null when neither the effect nor its statistics differed from the persisted values. The non-null return drives the @AuditedConditional predicate on the implementation.