Class GeoSingleCellDataDownloaderCli

java.lang.Object
ubic.gemma.cli.util.AbstractCLI
ubic.gemma.apps.GeoSingleCellDataDownloaderCli
All Implemented Interfaces:
org.springframework.beans.factory.Aware, org.springframework.context.ApplicationContextAware, CLI
public class GeoSingleCellDataDownloaderCli extends AbstractCLI
Download single-cell data from GEO supplementary material.

Also support downloading data from CELLxGENE that are linked to GEO series.

Author:
poirigui

  • Constructor Details

    • GeoSingleCellDataDownloaderCli

      public GeoSingleCellDataDownloaderCli()

  • Method Details

    • getCommandName

      @Nullable public String getCommandName()
      Description copied from interface: CLI
      A short memorable name for the command that can be used to locate this class.
      Specified by:
      getCommandName in interface CLI
      Overrides:
      getCommandName in class AbstractCLI
      Returns:
      name; if null or blank, this will not be available as a shortcut command.

    • getShortDesc

      @Nullable public String getShortDesc()
      Description copied from interface: CLI
      Obtain a short description for this command explaining what it does.
      Specified by:
      getShortDesc in interface CLI
      Overrides:
      getShortDesc in class AbstractCLI

    • getCommandGroup

      public CLI.CommandGroup getCommandGroup()
      Description copied from interface: CLI
      Obtain the command group for this CLI.
      Specified by:
      getCommandGroup in interface CLI
      Overrides:
      getCommandGroup in class AbstractCLI

    • buildOptions

      protected void buildOptions(org.apache.commons.cli.Options options)
      Description copied from class: AbstractCLI
      Build option implementation.

      Implement this method to add options to your command line, using the OptionBuilder.

      This is called right after AbstractCLI.buildStandardOptions(Options) so the options will be added after standard options.

      Overrides:
      buildOptions in class AbstractCLI

    • processOptions

      protected void processOptions(org.apache.commons.cli.CommandLine commandLine) throws org.apache.commons.cli.ParseException
      Description copied from class: AbstractCLI
      Process command line options.

      Implement this to provide processing of options. It is called after AbstractCLI.buildOptions(Options) and right before AbstractCLI.doWork().

      Overrides:
      processOptions in class AbstractCLI
      Throws:
      org.apache.commons.cli.ParseException - in case of unrecoverable failure (i.e. missing option or invalid value), an exception can be raised and will result in an exit code of AbstractCLI.FAILURE.

    • doWork

      protected void doWork() throws Exception
      Description copied from class: AbstractCLI
      Command line implementation.

      This is called after AbstractCLI.buildOptions(Options) and AbstractCLI.processOptions(CommandLine). so the implementation can assume that all its arguments have already been initialized and any setup behaviour have been performed.

      Specified by:
      doWork in class AbstractCLI
      Throws:
      Exception - in case of unrecoverable failure, an exception is thrown and will result in a AbstractCLI.FAILURE exit code, otherwise use AbstractCLI.addErrorObject(Serializable, String, Throwable) to indicate an error and resume processing