ubic.gemma.core.apps

Class ReplaceDataCli

java.lang.Object

ubic.gemma.core.util.AbstractCLI

ubic.gemma.core.util.AbstractSpringAwareCLI

ubic.gemma.core.util.AbstractCLIContextCLI

ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI

ubic.gemma.core.apps.ReplaceDataCli

All Implemented Interfaces:

CLI

public class ReplaceDataCli
extends ExpressionExperimentManipulatingCLI

Replace data in an existing data set. This is only to be used in special cases where AffyDataFromCelCli or RNASeqDataAddCli are not appropriate (that is, for any other types of platforms) and the data imported from GEO (from the SOFT) is not usable. For example, sometimes the submitted provides data that are filtered and normalized in some weird way, and we can get better data from either the supplementary files in GEO or from an external source (e.g. the authors). It is assumed that the quantitation type is the same (you can edit the QT details through the web interface). Again, don't use this this except as a last resort.

Author:

Paul

Field Summary

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

auditEventService, auditTrailService

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

AUTO_OPTION_NAME, autoSeek, autoSeekEventType, FAILURE, FAILURE_FROM_ERROR_OBJECTS, FOOTER, HEADER, host, log, mDate, numThreads, port, SUCCESS, THREADS_OPTION

Constructor Summary

Constructors

Constructor and Description
ReplaceDataCli()

Method Summary

Modifier and Type	Method and 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 grup.
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.
protected void	processOptions(org.apache.commons.cli.CommandLine commandLine) Process command line options.

Methods inherited from class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI

findGeneByOfficialSymbol, getEeService, getExpressionExperiments, getGeneService, getTaxon, getTaxonService, setTaxon, suppressAllOption

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

locateArrayDesign, readListFileToStrings, setTaxonByName

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

executeBatchTasks, getBean, getBean, getPersisterHelper, noNeedToRun, processStandardOptions, requireLogin

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

addAutoOption, addDateOption, addErrorObject, addErrorObject, addErrorObject, addHostAndPortOptions, addSuccessObject, addSuccessObject, addThreadsOption, buildStandardOptions, executeCommand, getDoubleOptionValue, getDoubleOptionValue, getFileNameOptionValue, getFileNameOptionValue, getIntegerOptionValue, getIntegerOptionValue, getLimitingDate, printHelp, resetLogging

Methods inherited from class java.lang.Object

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

Constructor Detail

ReplaceDataCli

public ReplaceDataCli()

Method Detail

getCommandGroup

public GemmaCLI.CommandGroup getCommandGroup()

Description copied from interface: CLI

Obtain the command grup.

Specified by:

getCommandGroup in interface CLI

Overrides:

getCommandGroup in class ExpressionExperimentManipulatingCLI

Returns:

the command group for this CLI

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 ExpressionExperimentManipulatingCLI

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 ExpressionExperimentManipulatingCLI

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, this will not be available as a shortcut command.

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)

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 AbstractSpringAwareCLI