Package ubic.gemma.apps

Class ArrayDesignProbeCleanupCLI

java.lang.Object

ubic.gemma.cli.util.AbstractCLI

ubic.gemma.cli.util.AbstractAuthenticatedCLI

ubic.gemma.cli.util.AbstractAutoSeekingCLI<ArrayDesign>

ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

ubic.gemma.apps.ArrayDesignProbeCleanupCLI

All Implemented Interfaces:

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

public class ArrayDesignProbeCleanupCLI
extends ArrayDesignSequenceManipulatingCli

Delete design elements (probes) that are invalid for one reason or another. The impetus for this was to remove probes in the MG-U74 version 1 set, but this is of general use. Probes to be removed are given in a file.

Author:

Paul

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.ArrayDesignSequenceManipulatingCli

arrayDesignReportService, arrayDesignService, auditEventService, auditTrailService, entityLocator

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
ArrayDesignProbeCleanupCLI()

Method Summary

Modifier and Type	Method	Description
protected void	buildArrayDesignOptions(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	processArrayDesignOptions(org.apache.commons.cli.CommandLine commandLine)
protected void	processArrayDesigns(Collection<ArrayDesign> arrayDesignsToProcess)

Methods inherited from class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

buildOptions, doAuthenticatedWork, getCommandGroup, getRelatedDesigns, isSubsumedOrMerged, needToRun, processArrayDesign, processOptions, shouldRun, 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, noNeedToRun, 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

ArrayDesignProbeCleanupCLI

public ArrayDesignProbeCleanupCLI()

Method Details

buildArrayDesignOptions

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

Overrides:

buildArrayDesignOptions in class ArrayDesignSequenceManipulatingCli

processArrayDesignOptions

protected void processArrayDesignOptions(org.apache.commons.cli.CommandLine commandLine)

Overrides:

processArrayDesignOptions in class ArrayDesignSequenceManipulatingCli

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.

processArrayDesigns

protected void processArrayDesigns(Collection<ArrayDesign> arrayDesignsToProcess)

Overrides:

processArrayDesigns in class ArrayDesignSequenceManipulatingCli