Package ubic.gemma.apps

Class ExpressionExperimentVectorsManipulatingCli<T extends DataVector>

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<T>

All Implemented Interfaces:

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

Direct Known Subclasses:

ListQuantitationTypesCli, ProcessedDataDeleterCli, RawDataDeleterCli, RawExpressionDataWriterCli, SingleCellDataAggregateDeleterCli, SingleCellDataAggregatorCli, SingleCellDataDeleterCli, SingleCellDataWriterCli

public abstract class ExpressionExperimentVectorsManipulatingCli<T extends DataVector>
extends ExpressionExperimentManipulatingCLI

Base class for CLI tools that manipulate expression experiment vectors.

Author:

poirigui

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

Modifier	Constructor	Description
protected	ExpressionExperimentVectorsManipulatingCli(Class<T> dataVectorType)

Method Summary

Modifier and Type	Method	Description
protected void	buildExperimentOptions(org.apache.commons.cli.Options options)
protected void	buildExperimentVectorsOptions(org.apache.commons.cli.Options options)
protected void	processExperimentOptions(org.apache.commons.cli.CommandLine commandLine)
protected void	processExperimentVectorsOptions(org.apache.commons.cli.CommandLine commandLine)
protected void	processExpressionExperiment(ExpressionExperiment expressionExperiment)	Process an ExpressionExperiment.
protected abstract void	processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt)	Process a set of vectors identified by a QuantitationType.
protected void	setQuantitationTypeIdentifierRequired()	Makes it so that the quantitation type identifier is required.
protected void	setUsePreferredQuantitationType()	Use the preferred QT if no identifier is provided, otherwise process all the QTs.

Methods inherited from class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

addSingleExperimentOption, addSingleExperimentOption, buildOptions, doAuthenticatedWork, formatExperiment, getCommandGroup, isAbortOnError, noNeedToRun, preprocessBioAssaySets, processBioAssaySet, processBioAssaySets, 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, getCommandName, 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 Detail

ExpressionExperimentVectorsManipulatingCli

protected ExpressionExperimentVectorsManipulatingCli(Class<T> dataVectorType)

Method Detail

setQuantitationTypeIdentifierRequired

protected void setQuantitationTypeIdentifierRequired()

Makes it so that the quantitation type identifier is required.

This is incompatible with setUsePreferredQuantitationType().

setUsePreferredQuantitationType

protected void setUsePreferredQuantitationType()

Use the preferred QT if no identifier is provided, otherwise process all the QTs.

This is incompatible with setQuantitationTypeIdentifierRequired().

buildExperimentOptions

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

Overrides:

buildExperimentOptions in class ExpressionExperimentManipulatingCLI

buildExperimentVectorsOptions

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

processExperimentOptions

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

Overrides:

processExperimentOptions in class ExpressionExperimentManipulatingCLI

Throws:

org.apache.commons.cli.ParseException

processExperimentVectorsOptions

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

Throws:

org.apache.commons.cli.ParseException

processExpressionExperiment

protected void processExpressionExperiment(ExpressionExperiment expressionExperiment)

Description copied from class: ExpressionExperimentManipulatingCLI

Process an ExpressionExperiment.

Overrides:

processExpressionExperiment in class ExpressionExperimentManipulatingCLI

processExpressionExperimentVectors

protected abstract void processExpressionExperimentVectors(ExpressionExperiment ee,
                                                           QuantitationType qt)

Process a set of vectors identified by a QuantitationType.