Package ca.corefacility.bioinformatics.irida.service

Interface AnalysisExecutionScheduledTask

    • Method Detail

      • prepareAnalyses

        java.util.Set<java.util.concurrent.Future<AnalysisSubmission>> prepareAnalyses()
        Cycle through new AnalysisSubmissions and prepare them for execution.
        Returns:
        A Set of Future AnalysisSubmissions reflecting the changes in this submission along each of the stages.

      • executeAnalyses

        java.util.Set<java.util.concurrent.Future<AnalysisSubmission>> executeAnalyses()
        Cycle through any outstanding AnalysisSubmissions and execute them.
        Returns:
        A Set of Future AnalysisSubmissions reflecting the changes in this submission along each of the stages.

      • monitorRunningAnalyses

        java.util.Set<java.util.concurrent.Future<AnalysisSubmission>> monitorRunningAnalyses()
        Cycle through any AnalysisSubmissions currently running and mark as complete any completed analyses.
        Returns:
        A Set of Future AnalysisSubmissions reflecting the changes in this submission along each of the stages.

      • transferAnalysesResults

        java.util.Set<java.util.concurrent.Future<AnalysisSubmission>> transferAnalysesResults()
        Cycle through any completed AnalysisSubmissions and transfer the results to IRIDA.
        Returns:
        A Set of Future AnalysisSubmissions reflecting the changes in this submission along each of the stages.

      • cleanupAnalysisSubmissions

        java.util.Set<java.util.concurrent.Future<AnalysisSubmission>> cleanupAnalysisSubmissions()
        Cycle through any completed or errored AnalysisSubmissions and delete intermediate files in the execution manager.
        Returns:
        A Set of Future AnalysisSubmissions for all the analyses that were cleaned.