Class ExternalFileGeneLoaderCLI

java.lang.Object
ubic.gemma.cli.util.AbstractCLI
ubic.gemma.cli.util.AbstractAuthenticatedCLI
ubic.gemma.apps.ExternalFileGeneLoaderCLI
All Implemented Interfaces:
org.springframework.beans.factory.Aware, org.springframework.beans.factory.InitializingBean, org.springframework.context.ApplicationContextAware, org.springframework.context.EnvironmentAware, CLI
public class ExternalFileGeneLoaderCLI extends AbstractAuthenticatedCLI
CLI for loading genes from a non NCBI files. A taxon and gene file should be supplied as command line arguments. File should be in tab delimited format containing gene symbol, gene name, uniprot id in that order.
Author:
ldonnison

  • Constructor Details

    • ExternalFileGeneLoaderCLI

      public ExternalFileGeneLoaderCLI()

  • Method Details

    • 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

    • processOptions

      protected void processOptions(org.apache.commons.cli.CommandLine commandLine)
      This method is called at the end of processCommandLine
      Overrides:
      processOptions 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

    • doAuthenticatedWork

      protected void doAuthenticatedWork() throws Exception
      Main entry point to service class which reads a gene file and persists the genes in that file.
      Specified by:
      doAuthenticatedWork in class AbstractAuthenticatedCLI
      Throws:
      Exception