Package ubic.gemma.core.apps

Class ExternalFileGeneLoaderCLI

java.lang.Object

ubic.gemma.core.util.AbstractCLI

ubic.gemma.core.util.AbstractAuthenticatedCLI

ubic.gemma.core.apps.ExternalFileGeneLoaderCLI

All Implemented Interfaces:

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

Field Summary

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

ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, log, SUCCESS

Constructor Summary

Constructors

Constructor	Description
ExternalFileGeneLoaderCLI()

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.
GemmaCLI.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.
String	getShortDesc()	Obtain a short description for this command explaining what it does.
void	processGeneList()	Main entry point to service class which reads a gene file and persists the genes in that file.
protected void	processOptions(org.apache.commons.cli.CommandLine commandLine)	This method is called at the end of processCommandLine
protected boolean	requireLogin()	Indicate if the command requires authentication.

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

createBatchTaskExecutorService, getGemmaRestApiClient, processStandardOptions

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

addAutoOption, addAutoOption, addBatchOption, addDateOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, allowPositionalArguments, buildStandardOptions, executeBatchTasks, executeCommand, getAutoSeekEventType, getBatchTaskExecutor, getBean, getBean, getLimitingDate, getNumThreads, getOptions, isAutoSeek, promptConfirmationOrAbort, setAllowPositionalArguments

Methods inherited from class java.lang.Object

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

Constructor Detail

ExternalFileGeneLoaderCLI

public ExternalFileGeneLoaderCLI()

Method Detail

getShortDesc

public String getShortDesc()

Description copied from interface: CLI

Obtain a short description for this command explaining what it does.

processOptions

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

This method is called at the end of processCommandLine

Specified by:

processOptions in class AbstractCLI

getCommandName

public String getCommandName()

Description copied from interface: CLI

A short memorable name for the command that can be used to locate this class.

Returns:

name; if null or blank, this will not be available as a shortcut command.

requireLogin

protected boolean requireLogin()

Description copied from class: AbstractAuthenticatedCLI

Indicate if the command requires authentication.

Override this to return true to make authentication required.

Overrides:

requireLogin in class AbstractAuthenticatedCLI

Returns:

true if login is required, otherwise false

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.

Specified by:

buildOptions in class AbstractCLI

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.

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.lang.Object, java.lang.String, java.lang.Throwable) to indicate an error and resume processing

processGeneList

public void processGeneList()

Main entry point to service class which reads a gene file and persists the genes in that file.

getCommandGroup

public GemmaCLI.CommandGroup getCommandGroup()

Description copied from interface: CLI

Obtain the command group for this CLI.