Class BatchInfoPopulationServiceImpl

    • Constructor Detail

      • BatchInfoPopulationServiceImpl

        public BatchInfoPopulationServiceImpl()
    • Method Detail

      • isBatchFactor

        public static boolean isBatchFactor​(ExperimentalFactor ef)
        Parameters:
        ef - ef
        Returns:
        true if the factor seems to be a 'batch' factor.
      • fillBatchInformation

        @Transactional
        public void fillBatchInformation​(ExpressionExperiment ee,
                                         boolean force)
                                  throws BatchInfoPopulationException
        Description copied from interface: BatchInfoPopulationService
        Attempt to obtain batch information from the data provider and populate it into the given experiment. The method used may vary. For GEO, the default method is to download the raw data files, and look in them for a date. This is not implemented for every possible type of raw data file. For RNA-seq, we look for FASTQ headers under the configured FASTQ_HEADERS_ROOT.
        Specified by:
        fillBatchInformation in interface BatchInfoPopulationService
        Parameters:
        ee - the experiment
        force - whether to force recomputation
        Throws:
        BatchInfoPopulationException - describing the issue with populating batch information