Package ubic.gemma.apps

Class CellLevelMetadataWriterCli

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.CellLevelMetadataWriterCli

All Implemented Interfaces:

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

public class CellLevelMetadataWriterCli
extends ExpressionExperimentVectorsManipulatingCli<SingleCellExpressionDataVector>

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
CellLevelMetadataWriterCli()

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.
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

addErrorObject, addErrorObject, addErrorObject, addSuccessObject, buildExperimentOptions, processExperimentOptions, processExpressionExperiment, processExpressionExperimentVectors, setDefaultToPreferredQuantitationType

Methods inherited from class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

addExpressionDataFileOptions, addExpressionDataFileOptions, addSingleExperimentAutoOption, addSingleExperimentEnumOption, addSingleExperimentOption, addSingleExperimentOption, buildOptions, doAuthenticatedWork, formatExperiment, getCommandGroup, getExpressionDataFileResult, getExpressionDataFileResult, isAbortOnError, noNeedToRun, postprocessExpressionExperiments, preprocessExpressionExperiments, processAllExpressionExperiments, processExpressionExperiments, processOptions, readChangelogEntryFromConsole, refreshExpressionExperimentFromGemmaWeb, 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

CellLevelMetadataWriterCli

public CellLevelMetadataWriterCli()

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.

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

processExpressionExperimentVectors

protected void processExpressionExperimentVectors(ExpressionExperiment ee,
 QuantitationType qt)
                                           throws IOException

Description copied from class: ExpressionExperimentVectorsManipulatingCli

Process a set of vectors identified by a QuantitationType.

Overrides:

processExpressionExperimentVectors in class ExpressionExperimentVectorsManipulatingCli<SingleCellExpressionDataVector>

Throws:

IOException