Class MakeExperimentsPublicCli

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.MakeExperimentsPublicCli

All Implemented Interfaces:

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

public class MakeExperimentsPublicCli
extends ExpressionExperimentManipulatingCLI

Make data sets public. You must be the owner of the experiment to do this.

Author:

paul

Nested Class Summary

Nested classes/interfaces inherited from interface CLI

CLI.CommandGroup

Field Summary

Fields inherited from class ExpressionExperimentManipulatingCLI

auditEventService, auditTrailService, eeService, entityLocator, entityUrlBuilder

Fields inherited from class AbstractAutoSeekingCLI

FORCE_OPTION

Fields inherited from class AbstractCLI

ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, log, SUCCESS

Constructor Summary

Constructors

Constructor	Description
MakeExperimentsPublicCli()

Method Summary

Modifier and Type	Method	Description
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	processExpressionExperiment(ExpressionExperiment ee)	Process an ExpressionExperiment.

Methods inherited from class ExpressionExperimentManipulatingCLI

addCellMetadataFileOptions, addDataFileOptions, addDataFileOptions, addDesignFileOptions, addExpressionDataFileOptions, addSingleCellExpressionDataFileOptions, addSingleExperimentAutoOption, addSingleExperimentEnumOption, addSingleExperimentOption, addSingleExperimentOption, buildExperimentOptions, buildOptions, doAuthenticatedWork, formatExperiment, getCellMetadataFileOptionValue, getCommandGroup, getDataFileOptionValue, getDataFileOptionValue, getDesignFileOptionValue, getExpressionDataFileOptionValue, getSingleCellExpressionDataFileOptionValue, isAbortOnError, noNeedToRun, postprocessExpressionExperiments, preprocessExpressionExperiments, processAllExpressionExperiments, processExperimentOptions, processExpressionExperiments, processOptions, readChangelogEntryFromConsole, refreshExpressionExperimentFromGemmaWeb, refreshExpressionExperimentFromGemmaWebSilently, selectsOwnExperiments, setAbortOnError, setAllIsLazy, setDefaultToAll, setExplicitEEsOnly, setSingleExperimentMode, setUseReferencesIfPossible, toBatchObject

Methods inherited from class AbstractAutoSeekingCLI

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

Methods inherited from class AbstractAuthenticatedCLI

afterPropertiesSet, doWork, setAuthenticateAnonymously, setEnvironment, setRequireLogin

Methods inherited from class AbstractCLI

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

Methods inherited from class Object

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

Constructor Details

MakeExperimentsPublicCli

public MakeExperimentsPublicCli()

Method Details

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

processExpressionExperiment

protected void processExpressionExperiment(ExpressionExperiment ee)

Description copied from class: ExpressionExperimentManipulatingCLI

Process an ExpressionExperiment.

Overrides:

processExpressionExperiment in class ExpressionExperimentManipulatingCLI