Package ubic.gemma.core.loader.expression.geo.service

Interface GeoService

All Known Implementing Classes:
GeoServiceImpl
public interface GeoService
Author:
paul

  • Method Details

    • addElements

      ArrayDesign addElements(ArrayDesign targetPlatform)
      For the rare cases (Exon arrays) where we load the platform in two stages.
      Parameters:
      targetPlatform - already persistent array design.
      Returns:
      updated (persistent) array design

    • fetchAndLoad

      Collection<?> fetchAndLoad(String geoAccession, boolean loadPlatformOnly, boolean doSampleMatching, boolean splitIncompatiblePlatforms)
      Load data, no restrictions on superseries or subseries
      Parameters:
      geoAccession - accession
      loadPlatformOnly - load platforms only
      doSampleMatching - do sample matching
      splitIncompatiblePlatforms - split incompatible platforms
      Returns:
      collection

    • fetchAndLoad

      Collection<?> fetchAndLoad(String geoAccession, boolean loadPlatformOnly, boolean doSampleMatching, boolean splitIncompatiblePlatforms, boolean allowSuperSeriesImport, boolean allowSubSeriesImport)
      Parameters:
      geoAccession - accession
      loadPlatformOnly - load platforms only
      doSampleMatching - do sample matching
      splitIncompatiblePlatforms - split incompatible platforms
      allowSuperSeriesImport - Allow loading if the Series is a SuperSeries
      allowSubSeriesImport - Allow loading if the Series is a SubSeries
      Returns:
      collection

    • updateFromGEO

      void updateFromGEO(String geoAccession, GeoService.GeoUpdateConfig geoUpdateConfig)
      Refetch and reprocess the GEO series, updating select information. Currently only implemented for experiments (GSEs)

      All experiments that uses the GEO accession will be updated as per updateFromGEO(ExpressionExperiment, GeoUpdateConfig).

    • updateFromGEO

      void updateFromGEO(ExpressionExperiment expressionExperiment, GeoService.GeoUpdateConfig geoUpdateConfig)
      Refetch and reprocess a given experiment.

    • loadFromSoftFile

      Collection<?> loadFromSoftFile(String accession, String softFile, boolean loadPlatformOnly, boolean doSampleMatching, boolean splitByPlatform)
      Load from a SOFT file. This can be used for testing but maybe there are other situations it is useful.
      Parameters:
      accession - e.g GSE1234
      softFile - the full path to the SOFT file. The file name has to be [accession].soft.gz
      Returns:
      a single experiment.

    • setGeoDomainObjectGenerator

      void setGeoDomainObjectGenerator(GeoDomainObjectGenerator generator)