Package ubic.gemma.apps

Class ExpressionExperimentVectorsManipulatingCli<T extends ubic.gemma.model.expression.bioAssayData.DataVector>

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<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:

CellLevelMetadataWriterCli, DetectQuantitationTypeCli, ListQuantitationTypesCli, ProcessedDataDeleterCli, RawDataDeleterCli, RawExpressionDataWriterCli, SingleCellDataAggregatorCli, SingleCellDataDeleterCli, SingleCellDataUpdaterCli, SingleCellDataWriterCli

public abstract class ExpressionExperimentVectorsManipulatingCli<T extends ubic.gemma.model.expression.bioAssayData.DataVector>
extends ExpressionExperimentManipulatingCLI

Base class for CLI tools that manipulate expression experiment vectors.

Author:

poirigui

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

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

Method Summary

Modifier and Type	Method	Description
protected final void	addErrorObject(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.common.quantitationtype.QuantitationType qt, Exception exception)
protected final void	addErrorObject(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.common.quantitationtype.QuantitationType qt, String message)
protected final void	addErrorObject(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.common.quantitationtype.QuantitationType qt, String message, Throwable throwable)
protected final void	addSuccessObject(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.common.quantitationtype.QuantitationType qt, String message)
protected final void	buildExperimentOptions(org.apache.commons.cli.Options options)
protected void	buildExperimentVectorsOptions(org.apache.commons.cli.Options options)
protected final void	processExperimentOptions(org.apache.commons.cli.CommandLine commandLine)
protected void	processExperimentVectorsOptions(org.apache.commons.cli.CommandLine commandLine)
protected void	processExpressionExperiment(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment)	Process an ExpressionExperiment.
protected void	processExpressionExperimentVectors(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.common.quantitationtype.QuantitationType qt)	Process a set of vectors identified by a QuantitationType.
protected void	processExpressionExperimentVectors(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.common.quantitationtype.QuantitationType qt, Class<? extends T> vectorType)
protected void	setDefaultToPreferredQuantitationType()	Use the preferred QT if no identifier is provided, otherwise process all the QTs.

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, 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, 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 Details

ExpressionExperimentVectorsManipulatingCli

protected ExpressionExperimentVectorsManipulatingCli(Class<T> dataVectorType)

Method Details

setDefaultToPreferredQuantitationType

protected void setDefaultToPreferredQuantitationType()

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

When this is set, an -allQts option will be added to process all QTs.

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(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment)
                                    throws Exception

Description copied from class: ExpressionExperimentManipulatingCLI

Process an ExpressionExperiment.

Overrides:

processExpressionExperiment in class ExpressionExperimentManipulatingCLI

Throws:

Exception

processExpressionExperimentVectors

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

Throws:

Exception

processExpressionExperimentVectors

protected void processExpressionExperimentVectors(ubic.gemma.model.expression.experiment.ExpressionExperiment ee,
 ubic.gemma.model.common.quantitationtype.QuantitationType qt)
                                           throws Exception

Process a set of vectors identified by a QuantitationType.

Throws:

Exception

addSuccessObject

protected final void addSuccessObject(ubic.gemma.model.expression.experiment.ExpressionExperiment ee,
 ubic.gemma.model.common.quantitationtype.QuantitationType qt,
 String message)

addErrorObject

protected final void addErrorObject(ubic.gemma.model.expression.experiment.ExpressionExperiment ee,
 ubic.gemma.model.common.quantitationtype.QuantitationType qt,
 String message)

addErrorObject

protected final void addErrorObject(ubic.gemma.model.expression.experiment.ExpressionExperiment ee,
 ubic.gemma.model.common.quantitationtype.QuantitationType qt,
 String message,
 Throwable throwable)

addErrorObject

protected final void addErrorObject(ubic.gemma.model.expression.experiment.ExpressionExperiment ee,
 ubic.gemma.model.common.quantitationtype.QuantitationType qt,
 Exception exception)