Package ubic.gemma.apps

Class 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 Detail

      • MINIMAL

        public static final GeoRetrieveConfig MINIMAL
        Preset when seeking records.

    • Constructor Detail

      • GeoGrabberCli

        public GeoGrabberCli()

    • Method Detail

      • 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

      • 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.