Package ubic.gemma.apps

Class SingleCellDataWriterCli

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<SingleCellExpressionDataVector>

ubic.gemma.apps.SingleCellDataWriterCli

All Implemented Interfaces:

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

public class SingleCellDataWriterCli
extends ExpressionExperimentVectorsManipulatingCli<SingleCellExpressionDataVector>

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
SingleCellDataWriterCli()

Method Summary

Modifier and Type	Method	Description
protected void	buildExperimentVectorsOptions(org.apache.commons.cli.Options options)
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	processBioAssaySets(Collection<BioAssaySet> expressionExperiments)	Process multiple BioAssaySet.
protected void	processExperimentVectorsOptions(org.apache.commons.cli.CommandLine commandLine)
protected void	processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt)	Process a set of vectors identified by a QuantitationType.

Methods inherited from class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli

buildExperimentOptions, processExperimentOptions, processExpressionExperiment, setQuantitationTypeIdentifierRequired, setUsePreferredQuantitationType

Methods inherited from class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

addSingleExperimentOption, addSingleExperimentOption, buildOptions, doAuthenticatedWork, formatExperiment, getCommandGroup, isAbortOnError, noNeedToRun, preprocessBioAssaySets, processBioAssaySet, processExpressionExperimentSubSet, processOptions, processOtherBioAssaySet, readChangelogEntryFromConsole, refreshExpressionExperimentFromGemmaWeb, setAbortOnError, setDefaultToAll, setSingleExperimentMode, setUseReferencesIfPossible, toBatchObject, 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, createBatchTaskExecutorService, 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, 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 Detail

SingleCellDataWriterCli

public SingleCellDataWriterCli()

Method Detail

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

buildExperimentVectorsOptions

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

Overrides:

buildExperimentVectorsOptions in class ExpressionExperimentVectorsManipulatingCli<SingleCellExpressionDataVector>

processExperimentVectorsOptions

protected void processExperimentVectorsOptions(org.apache.commons.cli.CommandLine commandLine)
                                        throws org.apache.commons.cli.ParseException

Overrides:

processExperimentVectorsOptions in class ExpressionExperimentVectorsManipulatingCli<SingleCellExpressionDataVector>

Throws:

org.apache.commons.cli.ParseException

processBioAssaySets

protected void processBioAssaySets(Collection<BioAssaySet> expressionExperiments)

Description copied from class: ExpressionExperimentManipulatingCLI

Process multiple BioAssaySet.

This only called if more than one experiment was found.

Overrides:

processBioAssaySets in class ExpressionExperimentManipulatingCLI

processExpressionExperimentVectors

protected void processExpressionExperimentVectors(ExpressionExperiment ee,
                                                  QuantitationType qt)

Description copied from class: ExpressionExperimentVectorsManipulatingCli

Process a set of vectors identified by a QuantitationType.

Specified by:

processExpressionExperimentVectors in class ExpressionExperimentVectorsManipulatingCli<SingleCellExpressionDataVector>