Package ubic.gemma.apps

Class NcbiGeneLoaderCLI

java.lang.Object

ubic.gemma.cli.util.AbstractCLI

ubic.gemma.cli.util.AbstractAuthenticatedCLI

ubic.gemma.apps.NcbiGeneLoaderCLI

All Implemented Interfaces:

org.springframework.beans.factory.Aware, org.springframework.beans.factory.InitializingBean, org.springframework.context.ApplicationContextAware, org.springframework.context.EnvironmentAware, CLI

public class NcbiGeneLoaderCLI
extends AbstractAuthenticatedCLI

Command line interface to gene parsing and loading

Author:

joseph

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.cli.util.CLI

CLI.CommandGroup

Field Summary

Fields inherited from class ubic.gemma.cli.util.AbstractCLI

ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, log, SUCCESS

Constructor Summary

Constructors

Constructor	Description
NcbiGeneLoaderCLI()

Method Summary

Modifier and Type	Method	Description
protected void	buildOptions(org.apache.commons.cli.Options options)	Build option implementation.
protected void	doAuthenticatedWork()
CLI.CommandGroup	getCommandGroup()	Obtain the command group for this CLI.
String	getCommandName()	A short memorable name for the command that can be used to locate this class.
NcbiGeneLoader	getLoader()
String	getShortDesc()	Obtain a short description for this command explaining what it does.
protected void	processOptions(org.apache.commons.cli.CommandLine commandLine)	Process command line options.

Methods inherited from class ubic.gemma.cli.util.AbstractAuthenticatedCLI

afterPropertiesSet, createBatchTaskExecutorService, doWork, setEnvironment, setRequireLogin

Methods inherited from class ubic.gemma.cli.util.AbstractCLI

abort, addBatchOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, addWarningObject, addWarningObject, allowPositionalArguments, awaitBatchExecutorService, executeCommand, getApplicationContext, getBatchTaskExecutor, getCliContext, getCommandAliases, getHelpFooter, getNumThreads, getOptions, getUsage, promptConfirmationOrAbort, setAllowPositionalArguments, setApplicationContext, setEstimatedMaxTasks, setReportFrequencyMillis

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

NcbiGeneLoaderCLI

public NcbiGeneLoaderCLI()

Method Detail

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

getLoader

public NcbiGeneLoader getLoader()

Returns:

Returns the loader

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.

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

Specified by:

doAuthenticatedWork in class AbstractAuthenticatedCLI

Throws:

Exception

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

processOptions

protected void processOptions(org.apache.commons.cli.CommandLine commandLine)

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