Class RawExpressionDataWriterCli

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<RawExpressionDataVector>

ubic.gemma.apps.RawExpressionDataWriterCli

All Implemented Interfaces:

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

public class RawExpressionDataWriterCli
extends ExpressionExperimentVectorsManipulatingCli<RawExpressionDataVector>

Nested Class Summary

Nested classes/interfaces inherited from class ExpressionExperimentManipulatingCLI

ExpressionExperimentManipulatingCLI.ExpressionDataFileResult

Nested classes/interfaces inherited from interface CLI

CLI.CommandGroup

Field Summary

Fields inherited from class ExpressionExperimentManipulatingCLI

auditEventService, auditTrailService, eeService, entityLocator, entityUrlBuilder, OUTPUT_DIR_OPTION, OUTPUT_FILE_OPTION, STANDARD_LOCATION_OPTION, STANDARD_OUTPUT_OPTION

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
RawExpressionDataWriterCli()

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	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 ExpressionExperimentVectorsManipulatingCli

buildExperimentOptions, processExperimentOptions, processExpressionExperiment, setQuantitationTypeIdentifierRequired, setUsePreferredQuantitationType

Methods inherited from class ExpressionExperimentManipulatingCLI

addExpressionDataFileOptions, addSingleExperimentOption, addSingleExperimentOption, buildOptions, doAuthenticatedWork, formatExperiment, getCommandGroup, getExpressionDataFileResult, isAbortOnError, noNeedToRun, preprocessExpressionExperiments, processExpressionExperiments, processOptions, readChangelogEntryFromConsole, refreshExpressionExperimentFromGemmaWeb, setAbortOnError, setDefaultToAll, 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, setEnvironment, setRequireLogin

Methods inherited from class 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 Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

RawExpressionDataWriterCli

public RawExpressionDataWriterCli()

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

buildExperimentVectorsOptions

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

Overrides:

buildExperimentVectorsOptions in class ExpressionExperimentVectorsManipulatingCli<RawExpressionDataVector>

processExperimentVectorsOptions

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

Overrides:

processExperimentVectorsOptions in class ExpressionExperimentVectorsManipulatingCli<RawExpressionDataVector>

Throws:

org.apache.commons.cli.ParseException

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<RawExpressionDataVector>