Package ubic.gemma.apps

Class SingleCellCellTypeFactorCreatorCli

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.SingleCellCellTypeFactorCreatorCli

All Implemented Interfaces:

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

public class SingleCellCellTypeFactorCreatorCli
extends ExpressionExperimentManipulatingCLI

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
SingleCellCellTypeFactorCreatorCli()

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.
protected void	processExpressionExperiment(ExpressionExperiment expressionExperiment)	Process an ExpressionExperiment.

Methods inherited from class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

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

SingleCellCellTypeFactorCreatorCli

public SingleCellCellTypeFactorCreatorCli()

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.

buildExperimentOptions

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

Overrides:

buildExperimentOptions in class ExpressionExperimentManipulatingCLI

processExpressionExperiment

protected void processExpressionExperiment(ExpressionExperiment expressionExperiment)
                                    throws Exception

Description copied from class: ExpressionExperimentManipulatingCLI

Process an ExpressionExperiment.

Overrides:

processExpressionExperiment in class ExpressionExperimentManipulatingCLI

Throws:

Exception