Package ubic.gemma.apps

Class ArrayDesignBioSequenceDetachCli

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.ArrayDesignBioSequenceDetachCli

All Implemented Interfaces:

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

public class ArrayDesignBioSequenceDetachCli
extends ArrayDesignSequenceManipulatingCli

Remove all associations that this array design has with BioSequences. This is needed for cases where the original import has associated the probes with the wrong sequences. A common case is for GEO data sets where the actual oligonucleotide is not given. Instead the submitter provides Genbank accessions, which are misleading. This method can be used to clear those until the "right" sequences can be identified and filled in. Note that this does not remove the BioSequences, it just nulls the BiologicalCharacteristics of the CompositeSequences.

Author:

pavlidis

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
ArrayDesignBioSequenceDetachCli()

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.
String	getShortDesc()	Obtain a short description for this command explaining what it does.
protected void	processArrayDesignOptions(org.apache.commons.cli.CommandLine commandLine)
protected void	processArrayDesigns(Collection<ArrayDesign> arrayDesigns)

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, 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

ArrayDesignBioSequenceDetachCli

public ArrayDesignBioSequenceDetachCli()

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

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)
                                  throws org.apache.commons.cli.ParseException

Overrides:

processArrayDesignOptions in class ArrayDesignSequenceManipulatingCli

Throws:

org.apache.commons.cli.ParseException

processArrayDesigns

protected void processArrayDesigns(Collection<ArrayDesign> arrayDesigns)

Overrides:

processArrayDesigns in class ArrayDesignSequenceManipulatingCli