Class DeleteExperimentsCli

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.DeleteExperimentsCli

All Implemented Interfaces:

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

public class DeleteExperimentsCli
extends ExpressionExperimentManipulatingCLI

Delete one or more experiments from the system.

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
DeleteExperimentsCli()

Method Summary

Modifier and Type	Method	Description
protected void	buildExperimentOptions(org.apache.commons.cli.Options options)
protected void	doAuthenticatedWork()
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	processExperimentOptions(org.apache.commons.cli.CommandLine commandLine)
protected void	processExpressionExperiment(ExpressionExperiment ee)	Process an ExpressionExperiment.
protected boolean	selectsOwnExperiments(org.apache.commons.cli.CommandLine commandLine)	Whether the given options select what to process by some means other than -all, -e, -eeset, -f or -q.

Methods inherited from class ExpressionExperimentManipulatingCLI

addCellMetadataFileOptions, addDataFileOptions, addDataFileOptions, addDesignFileOptions, addExpressionDataFileOptions, addSingleCellExpressionDataFileOptions, addSingleExperimentAutoOption, addSingleExperimentEnumOption, addSingleExperimentOption, addSingleExperimentOption, buildOptions, formatExperiment, getCellMetadataFileOptionValue, getCommandGroup, getDataFileOptionValue, getDataFileOptionValue, getDesignFileOptionValue, getExpressionDataFileOptionValue, getSingleCellExpressionDataFileOptionValue, isAbortOnError, noNeedToRun, postprocessExpressionExperiments, preprocessExpressionExperiments, processAllExpressionExperiments, processExpressionExperiments, processOptions, readChangelogEntryFromConsole, refreshExpressionExperimentFromGemmaWeb, refreshExpressionExperimentFromGemmaWebSilently, 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

DeleteExperimentsCli

public DeleteExperimentsCli()

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

buildExperimentOptions

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

Overrides:

buildExperimentOptions in class ExpressionExperimentManipulatingCLI

selectsOwnExperiments

protected boolean selectsOwnExperiments(org.apache.commons.cli.CommandLine commandLine)

Description copied from class: ExpressionExperimentManipulatingCLI

Whether the given options select what to process by some means other than -all, -e, -eeset, -f or -q.

If so, giving none of those is not an error. The subclass is then responsible for its own selection, e.g. by overriding ExpressionExperimentManipulatingCLI.doAuthenticatedWork(). This is checked before ExpressionExperimentManipulatingCLI.processExperimentOptions(CommandLine).

Overrides:

selectsOwnExperiments 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

doAuthenticatedWork

protected void doAuthenticatedWork()
                            throws Exception

Overrides:

doAuthenticatedWork in class ExpressionExperimentManipulatingCLI

Throws:

Exception

processExpressionExperiment

protected void processExpressionExperiment(ExpressionExperiment ee)

Description copied from class: ExpressionExperimentManipulatingCLI

Process an ExpressionExperiment.

Overrides:

processExpressionExperiment in class ExpressionExperimentManipulatingCLI