Package ubic.gemma.apps

Class DetectQuantitationTypeCli

java.lang.Object

ubic.gemma.cli.util.AbstractCLI

ubic.gemma.cli.util.AbstractAuthenticatedCLI

ubic.gemma.cli.util.AbstractAutoSeekingCLI<ubic.gemma.model.expression.experiment.ExpressionExperiment>

ubic.gemma.apps.ExpressionExperimentManipulatingCLI

ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli<ubic.gemma.model.expression.bioAssayData.DataVector>

ubic.gemma.apps.DetectQuantitationTypeCli

All Implemented Interfaces:

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

public class DetectQuantitationTypeCli
extends ExpressionExperimentVectorsManipulatingCli<ubic.gemma.model.expression.bioAssayData.DataVector>

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.cli.util.CLI

CLI.CommandGroup

Field Summary

Fields

Modifier and Type	Field	Description
ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService	singleCellExpressionExperimentService

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
DetectQuantitationTypeCli()

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	processExpressionExperimentVectors(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.common.quantitationtype.QuantitationType qt, Class<? extends ubic.gemma.model.expression.bioAssayData.DataVector> vectorType)

Methods inherited from class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli

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

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, 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, getUsage, promptConfirmationOrAbort, setAllowPositionalArguments, setApplicationContext, setEstimatedMaxTasks, setReportFrequencyMillis

Methods inherited from class java.lang.Object

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

Field Details

singleCellExpressionExperimentService

@Autowired
public ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService singleCellExpressionExperimentService

Constructor Details

DetectQuantitationTypeCli

public DetectQuantitationTypeCli()

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

processExpressionExperimentVectors

protected void processExpressionExperimentVectors(ubic.gemma.model.expression.experiment.ExpressionExperiment ee,
 ubic.gemma.model.common.quantitationtype.QuantitationType qt,
 Class<? extends ubic.gemma.model.expression.bioAssayData.DataVector> vectorType)
                                           throws Exception

Overrides:

processExpressionExperimentVectors in class ExpressionExperimentVectorsManipulatingCli<ubic.gemma.model.expression.bioAssayData.DataVector>

Throws:

Exception