Package ubic.gemma.apps

Class ListQuantitationTypesCli

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.ExpressionExperimentVectorsManipulatingCli<DataVector>

ubic.gemma.apps.ListQuantitationTypesCli

All Implemented Interfaces:

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

public class ListQuantitationTypesCli
extends ExpressionExperimentVectorsManipulatingCli<DataVector>

Author:

poirigui

Nested Class Summary

Nested classes/interfaces inherited from class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

ExpressionExperimentManipulatingCLI.ExpressionDataFileResult

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, OUTPUT_DIR_OPTION, OUTPUT_FILE_OPTION, STANDARD_LOCATION_OPTION, STANDARD_OUTPUT_OPTION

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
ListQuantitationTypesCli()

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 expressionExperiment)	Process an ExpressionExperiment.
protected void	processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt)	Process a set of vectors identified by a QuantitationType.

Methods inherited from class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli

addErrorObject, addErrorObject, addErrorObject, addSuccessObject, buildExperimentOptions, buildExperimentVectorsOptions, processExperimentOptions, processExperimentVectorsOptions, processExpressionExperimentVectors, setQuantitationTypeIdentifierRequired, setUsePreferredQuantitationType

Methods inherited from class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

addExpressionDataFileOptions, addExpressionDataFileOptions, addSingleExperimentEnumOption, addSingleExperimentOption, addSingleExperimentOption, buildOptions, doAuthenticatedWork, formatExperiment, getCommandGroup, getExpressionDataFileResult, getExpressionDataFileResult, isAbortOnError, noNeedToRun, preprocessExpressionExperiments, processExpressionExperiments, processOptions, readChangelogEntryFromConsole, refreshExpressionExperimentFromGemmaWeb, setAbortOnError, setDefaultToAll, setSingleExperimentMode, setUseReferencesIfPossible, 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, 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, getBatchTaskProgressReporter, 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 Details

ListQuantitationTypesCli

public ListQuantitationTypesCli()

Method Details

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

processExpressionExperiment

protected void processExpressionExperiment(ExpressionExperiment expressionExperiment)
                                    throws Exception

Description copied from class: ExpressionExperimentManipulatingCLI

Process an ExpressionExperiment.

Overrides:

processExpressionExperiment in class ExpressionExperimentVectorsManipulatingCli<DataVector>

Throws:

Exception

processExpressionExperimentVectors

protected void processExpressionExperimentVectors(ExpressionExperiment ee,
 QuantitationType qt)

Description copied from class: ExpressionExperimentVectorsManipulatingCli

Process a set of vectors identified by a QuantitationType.

Overrides:

processExpressionExperimentVectors in class ExpressionExperimentVectorsManipulatingCli<DataVector>