Package ubic.gemma.core.analysis.preprocess.batcheffects

Class BatchInfoPopulationServiceImpl

java.lang.Object
ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceImpl
All Implemented Interfaces:
BatchInfoPopulationService
@Service public class BatchInfoPopulationServiceImpl extends Object implements BatchInfoPopulationService
Retrieve batch information from the data source, if possible, and populate it into experiments.
Author:
paul

  • Constructor Details

    • BatchInfoPopulationServiceImpl

      public BatchInfoPopulationServiceImpl()

  • Method Details

    • 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

    • setFastqHeadersDir

      public void setFastqHeadersDir(Path fastqHeadersDir)
      Description copied from interface: BatchInfoPopulationService
      Set the path to use to resolve FASTQ headers.

      Exposed for testing, do not use in production code.

      Specified by:
      setFastqHeadersDir in interface BatchInfoPopulationService