Package ubic.gemma.apps

Class AffyDataFromCelCli

java.lang.Object

ubic.gemma.cli.util.AbstractCLI

ubic.gemma.cli.util.AbstractAuthenticatedCLI

ubic.gemma.cli.util.AbstractAutoSeekingCLI<ExpressionExperiment>

ubic.gemma.apps.ExpressionExperimentManipulatingCLI

ubic.gemma.apps.AffyDataFromCelCli

All Implemented Interfaces:

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

public class AffyDataFromCelCli
extends ExpressionExperimentManipulatingCLI

Add (or possibly replace) the data associated with an affymetrix data set, going back to the CEL files. Can handle exon or 3' arrays.

Author:

paul

Nested Class Summary

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

CLI.CommandGroup

Field Summary

Fields inherited from class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

auditEventService, auditTrailService, eeService, entityLocator, entityUrlBuilder

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

FORCE_OPTION

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

ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, log, SUCCESS

Constructor Summary

Constructors

Constructor	Description
AffyDataFromCelCli()

Method Summary

Modifier and Type	Method	Description
protected void	buildExperimentOptions(org.apache.commons.cli.Options options)
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	processBioAssaySets(Collection<BioAssaySet> expressionExperiments)	Process multiple BioAssaySet.
protected void	processExperimentOptions(org.apache.commons.cli.CommandLine commandLine)
protected void	processExpressionExperiment(ExpressionExperiment ee)	Process an ExpressionExperiment.

Methods inherited from class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

addSingleExperimentOption, addSingleExperimentOption, buildOptions, doAuthenticatedWork, formatExperiment, getCommandGroup, isAbortOnError, noNeedToRun, preprocessBioAssaySets, processBioAssaySet, processExpressionExperimentSubSet, processOptions, processOtherBioAssaySet, readChangelogEntryFromConsole, refreshExpressionExperimentFromGemmaWeb, setAbortOnError, setDefaultToAll, setSingleExperimentMode, setUseReferencesIfPossible, toBatchObject, toBatchObject

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

addAutoOption, addAutoOption, addErrorObject, addErrorObject, addErrorObject, addForceOption, addForceOption, addLimitingDateOption, addSuccessObject, addSuccessObject, addWarningObject, addWarningObject, getAutoSeekEventType, getLimitingDate, isAutoSeek, isForce, setForce

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

AffyDataFromCelCli

public AffyDataFromCelCli()

Method Detail

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

buildExperimentOptions

protected void buildExperimentOptions(org.apache.commons.cli.Options options)

Overrides:

buildExperimentOptions in class ExpressionExperimentManipulatingCLI

processExperimentOptions

protected void processExperimentOptions(org.apache.commons.cli.CommandLine commandLine)
                                 throws org.apache.commons.cli.ParseException

Overrides:

processExperimentOptions in class ExpressionExperimentManipulatingCLI

Throws:

org.apache.commons.cli.ParseException

processBioAssaySets

protected void processBioAssaySets(Collection<BioAssaySet> expressionExperiments)

Description copied from class: ExpressionExperimentManipulatingCLI

Process multiple BioAssaySet.

This only called if more than one experiment was found.

Overrides:

processBioAssaySets in class ExpressionExperimentManipulatingCLI

processExpressionExperiment

protected void processExpressionExperiment(ExpressionExperiment ee)

Description copied from class: ExpressionExperimentManipulatingCLI

Process an ExpressionExperiment.

Overrides:

processExpressionExperiment in class ExpressionExperimentManipulatingCLI