Package ubic.gemma.apps

Class SingleCellSparsityMetricsUpdaterCli

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.SingleCellSparsityMetricsUpdaterCli

All Implemented Interfaces:

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

public class SingleCellSparsityMetricsUpdaterCli
extends ExpressionExperimentManipulatingCLI

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
SingleCellSparsityMetricsUpdaterCli()

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.

Methods inherited from class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

addExpressionDataFileOptions, addExpressionDataFileOptions, addSingleExperimentEnumOption, addSingleExperimentOption, addSingleExperimentOption, buildExperimentOptions, buildOptions, doAuthenticatedWork, formatExperiment, getCommandGroup, getExpressionDataFileResult, getExpressionDataFileResult, isAbortOnError, noNeedToRun, preprocessExpressionExperiments, processExperimentOptions, 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

SingleCellSparsityMetricsUpdaterCli

public SingleCellSparsityMetricsUpdaterCli()

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)

Description copied from class: ExpressionExperimentManipulatingCLI

Process an ExpressionExperiment.

Overrides:

processExpressionExperiment in class ExpressionExperimentManipulatingCLI