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

Class GeoDomainObjectGenerator

java.lang.Object
ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
All Implemented Interfaces:
SourceDomainObjectGenerator
Direct Known Subclasses:
GeoDomainObjectGeneratorLocal
public class GeoDomainObjectGenerator extends Object implements SourceDomainObjectGenerator
Handle fetching and parsing GEO files.
Author:
pavlidis

  • Field Details

    • log

      protected static org.apache.commons.logging.Log log

  • Constructor Details

    • GeoDomainObjectGenerator

      public GeoDomainObjectGenerator()

    • GeoDomainObjectGenerator

      protected GeoDomainObjectGenerator(DatasetFetcher datasetFetcher, SeriesFetcher seriesFetcher, Fetcher platformFetcher)

  • Method Details

    • generate

      public Collection<? extends GeoData> generate(String geoAccession)
      Description copied from interface: SourceDomainObjectGenerator
      Combines the necessary data fetching and parsing steps to get a collection of source domain objects.
      Specified by:
      generate in interface SourceDomainObjectGenerator
      Parameters:
      geoAccession - , either a GPL, GDS or GSE value.
      Returns:
      If processPlatformsOnly is true, a collection of GeoPlatforms. Otherwise a Collection of series (just one). If the accession is a GPL then processPlatformsOnly is set to true and any sample data is ignored.

    • getProjectedAccessions

      @Nullable public Collection<DatabaseEntry> getProjectedAccessions(String geoAccession)
      Determine the set of external accession values that will be generated during parsing. This can be used to pre-empty time-consuming fetch and download of data we already have.
      Parameters:
      geoAccession - geo accession
      Returns:
      database entries

    • processDataSet

      public void processDataSet(GeoSeries series, String dataSetAccession, GeoFamilyParser parser)
      Process a data set and add it to the series

    • setNcbiApiKey

      public void setNcbiApiKey(String ncbiApiKey)
      Set the NCBI API key to use.

      This is only used to resolve GEO datasets from series, so it is not critical for the good functioning of this class, but it is preferable to set it.

    • setDoSampleMatching

      public void setDoSampleMatching(boolean doSampleMatching)

    • setProcessPlatformsOnly

      public void setProcessPlatformsOnly(boolean b)