Package ubic.gemma.apps

Class GeoGrabberCli

java.lang.Object
ubic.gemma.cli.util.AbstractCLI
ubic.gemma.cli.util.AbstractAuthenticatedCLI
ubic.gemma.apps.GeoGrabberCli
All Implemented Interfaces:
org.springframework.beans.factory.Aware, org.springframework.beans.factory.InitializingBean, org.springframework.context.ApplicationContextAware, org.springframework.context.EnvironmentAware, CLI
public class GeoGrabberCli extends AbstractAuthenticatedCLI implements org.springframework.beans.factory.InitializingBean
Scans GEO for experiments that are not in Gemma, subject to some filtering criteria, outputs to a file for further screening. See #160
Author:
paul

  • Field Details

    • MINIMAL

      public static final GeoRetrieveConfig MINIMAL
      Preset when seeking records.

  • Constructor Details

    • GeoGrabberCli

      public GeoGrabberCli()

  • Method Details

    • afterPropertiesSet

      public void afterPropertiesSet()
      Specified by:
      afterPropertiesSet in interface org.springframework.beans.factory.InitializingBean
      Overrides:
      afterPropertiesSet in class AbstractAuthenticatedCLI

    • getCommandName

      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

      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.

    • doAuthenticatedWork

      protected void doAuthenticatedWork() throws Exception
      Specified by:
      doAuthenticatedWork in class AbstractAuthenticatedCLI
      Throws:
      Exception