Package ubic.gemma.apps

Class LinkAnalysisCli

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.LinkAnalysisCli

All Implemented Interfaces:

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

public class LinkAnalysisCli
extends ExpressionExperimentManipulatingCLI

Commandline tool to conduct link (coexpression) analysis.

Author:

xiangwan, paul (refactoring), vaneet

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
LinkAnalysisCli()

Method Summary

Modifier and Type	Method	Description
protected void	buildExperimentOptions(org.apache.commons.cli.Options options)
protected void	doAuthenticatedWork()
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 Collection<ubic.gemma.model.expression.experiment.ExpressionExperiment>	preprocessExpressionExperiments(Collection<ubic.gemma.model.expression.experiment.ExpressionExperiment> expressionExperiments)	Preprocess the set of ExpressionExperiment before invoking ExpressionExperimentManipulatingCLI.processExpressionExperiments(Collection) or ExpressionExperimentManipulatingCLI.processExpressionExperiment(ExpressionExperiment).
protected void	processExperimentOptions(org.apache.commons.cli.CommandLine commandLine)
protected void	processExpressionExperiment(ubic.gemma.model.expression.experiment.ExpressionExperiment ee)	Process an ExpressionExperiment.

Methods inherited from class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

addExpressionDataFileOptions, addExpressionDataFileOptions, addSingleExperimentAutoOption, addSingleExperimentEnumOption, addSingleExperimentOption, addSingleExperimentOption, buildOptions, formatExperiment, getCommandGroup, getExpressionDataFileResult, getExpressionDataFileResult, isAbortOnError, noNeedToRun, postprocessExpressionExperiments, 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, 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

LinkAnalysisCli

public LinkAnalysisCli()

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.

getShortDesc

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

buildExperimentOptions

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

Overrides:

buildExperimentOptions in class ExpressionExperimentManipulatingCLI

processExperimentOptions

protected 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

doAuthenticatedWork

protected void doAuthenticatedWork()
                            throws Exception

Overrides:

doAuthenticatedWork in class ExpressionExperimentManipulatingCLI

Throws:

Exception

preprocessExpressionExperiments

protected Collection<ubic.gemma.model.expression.experiment.ExpressionExperiment> preprocessExpressionExperiments(Collection<ubic.gemma.model.expression.experiment.ExpressionExperiment> expressionExperiments)

Description copied from class: ExpressionExperimentManipulatingCLI

Preprocess the set of ExpressionExperiment before invoking ExpressionExperimentManipulatingCLI.processExpressionExperiments(Collection) or ExpressionExperimentManipulatingCLI.processExpressionExperiment(ExpressionExperiment).

This can be an opportunity to filter or modify the set of experiments.

Overrides:

preprocessExpressionExperiments in class ExpressionExperimentManipulatingCLI

processExpressionExperiment

protected void processExpressionExperiment(ubic.gemma.model.expression.experiment.ExpressionExperiment ee)

Description copied from class: ExpressionExperimentManipulatingCLI

Process an ExpressionExperiment.

Overrides:

processExpressionExperiment in class ExpressionExperimentManipulatingCLI