Package ubic.gemma.core.apps

Class ArrayDesignBioSequenceDetachCli

java.lang.Object

ubic.gemma.core.util.AbstractCLI

ubic.gemma.core.util.AbstractAuthenticatedCLI

ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli

ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli

All Implemented Interfaces:

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

Field Summary

Fields inherited from class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli

auditTrailService

Fields inherited from class ubic.gemma.core.util.AbstractCLI

ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, FOOTER, HEADER, log, SUCCESS

Constructor Summary

Constructors

Constructor	Description
ArrayDesignBioSequenceDetachCli()

Method Summary

Modifier and Type	Method	Description
protected void	buildOptions(org.apache.commons.cli.Options options)	Build option implementation.
protected void	doWork()	Command line implementation.
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	processOptions(org.apache.commons.cli.CommandLine commandLine)	Process command line options.

Methods inherited from class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli

getArrayDesignReportService, getArrayDesignService, getArrayDesignsToProcess, getCommandGroup, isSubsumedOrMerged, locateArrayDesign, shouldRun

Methods inherited from class ubic.gemma.core.util.AbstractAuthenticatedCLI

executeBatchTasks, processStandardOptions, requireLogin

Methods inherited from class ubic.gemma.core.util.AbstractCLI

addAutoOption, addAutoOption, addBatchOption, addDateOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, allowPositionalArguments, buildStandardOptions, executeCommand, getAutoSeekEventType, getBean, getBean, getLimitingDate, getNumThreads, getOptions, isAutoSeek, promptConfirmationOrAbort, setAllowPositionalArguments

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ArrayDesignBioSequenceDetachCli

public ArrayDesignBioSequenceDetachCli()

Method Detail

getCommandName

public String getCommandName()

Description copied from interface: CLI

A short memorable name for the command that can be used to locate this class.

Returns:

name; if null or blank, this will not be available as a shortcut command.

buildOptions

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

Description copied from class: AbstractCLI

Build option implementation.

Implement this method to add options to your command line, using the OptionBuilder.

This is called right after AbstractCLI.buildStandardOptions(Options) so the options will be added after standard options.

Overrides:

buildOptions in class ArrayDesignSequenceManipulatingCli

processOptions

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

Description copied from class: AbstractCLI

Process command line options.

Implement this to provide processing of options. It is called after AbstractCLI.buildOptions(Options) and right before AbstractCLI.doWork().

Overrides:

processOptions in class ArrayDesignSequenceManipulatingCli

Throws:

org.apache.commons.cli.ParseException - in case of unrecoverable failure (i.e. missing option or invalid value), an exception can be raised and will result in an exit code of AbstractCLI.FAILURE.

doWork

protected void doWork()
               throws Exception

Description copied from class: AbstractCLI

Command line implementation.

This is called after AbstractCLI.buildOptions(Options) and AbstractCLI.processOptions(CommandLine), so the implementation can assume that all its arguments have already been initialized.

Specified by:

doWork in class AbstractCLI

Throws:

Exception - in case of unrecoverable failure, an exception is thrown and will result in a AbstractCLI.FAILURE exit code, otherwise use AbstractCLI.addErrorObject(java.lang.Object, java.lang.String, java.lang.Throwable) to indicate an error and resume processing

getShortDesc

public String getShortDesc()

Description copied from interface: CLI

Obtain a short description for this command explaining what it does.