Package ubic.gemma.apps

Class SingleCellDataTransformCli

java.lang.Object

ubic.gemma.cli.util.AbstractCLI

ubic.gemma.apps.SingleCellDataTransformCli

All Implemented Interfaces:

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

public class SingleCellDataTransformCli
extends AbstractCLI

Transform various single-cell formats.

Author:

poirigui

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
SingleCellDataTransformCli()

Method Summary

Modifier and Type	Method	Description
protected void	buildOptions(org.apache.commons.cli.Options options)	Build option implementation.
protected void	doWork()	Command line implementation.
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.
protected String	getHelpFooter()	Include a detailed help footer in the --help menu.
String	getShortDesc()	Obtain a short description for this command explaining what it does.
protected String	getUsage()	Adjust usage to reflect the transformation-specific options.
protected void	processOptions(org.apache.commons.cli.CommandLine commandLine)	Process command line options.

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

abort, addBatchOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, addWarningObject, addWarningObject, allowPositionalArguments, awaitBatchExecutorService, createBatchTaskExecutorService, executeCommand, getApplicationContext, getBatchTaskExecutor, getCliContext, getCommandAliases, getNumThreads, getOptions, 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

SingleCellDataTransformCli

public SingleCellDataTransformCli()

Method Detail

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(java.io.Serializable, java.lang.String, java.lang.Throwable) to indicate an error and resume processing

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

getUsage

protected String getUsage()

Adjust usage to reflect the transformation-specific options.

Overrides:

getUsage in class AbstractCLI

getHelpFooter

@Nullable
protected String getHelpFooter()

Description copied from class: AbstractCLI

Include a detailed help footer in the --help menu.

Overrides:

getHelpFooter in class AbstractCLI

See Also:

HelpUtils.printHelp(PrintWriter, String, Options, String, String)