Package ubic.gemma.core.apps

Class ArrayDesignSequenceManipulatingCli

java.lang.Object

ubic.gemma.core.util.AbstractCLI

ubic.gemma.core.util.AbstractAuthenticatedCLI

ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli

All Implemented Interfaces:

CLI

Direct Known Subclasses:

AffyProbeCollapseCli, ArrayDesignAnnotationFileCli, ArrayDesignAuditTrailCleanupCli, ArrayDesignBioSequenceDetachCli, ArrayDesignBlatCli, ArrayDesignMapSummaryCli, ArrayDesignMergeCli, ArrayDesignProbeCleanupCLI, ArrayDesignProbeMapperCli, ArrayDesignProbeRenamerCli, ArrayDesignRepeatScanCli, ArrayDesignSequenceAssociationCli, ArrayDesignSubsumptionTesterCli, BioSequenceCleanupCli

public abstract class ArrayDesignSequenceManipulatingCli
extends AbstractAuthenticatedCLI

Aggregates functionality useful when writing CLIs that need to get an array design from the database and do something with it.

Author:

pavlidis

Field Summary

Fields

Modifier and Type	Field	Description
protected ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService	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
ArrayDesignSequenceManipulatingCli()

Method Summary

Modifier and Type	Method	Description
protected void	buildOptions(org.apache.commons.cli.Options options)	Build option implementation.
protected ubic.gemma.core.analysis.report.ArrayDesignReportService	getArrayDesignReportService()
protected ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService	getArrayDesignService()
protected Collection<ubic.gemma.model.expression.arrayDesign.ArrayDesign>	getArrayDesignsToProcess()
GemmaCLI.CommandGroup	getCommandGroup()	Obtain the command group for this CLI.
protected boolean	isSubsumedOrMerged(ubic.gemma.model.expression.arrayDesign.ArrayDesign arrayDesign)
protected ubic.gemma.model.expression.arrayDesign.ArrayDesign	locateArrayDesign(String name)
protected void	processOptions(org.apache.commons.cli.CommandLine commandLine)	Process command line options.
protected boolean	shouldRun(Date skipIfLastRunLaterThan, ubic.gemma.model.expression.arrayDesign.ArrayDesign design, Class<? extends ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignAnalysisEvent> cls)

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, doWork, 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

Methods inherited from interface ubic.gemma.core.util.CLI

getCommandName, getShortDesc

Field Detail

auditTrailService

@Autowired
protected ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService auditTrailService

Constructor Detail

ArrayDesignSequenceManipulatingCli

public ArrayDesignSequenceManipulatingCli()

Method Detail

getCommandGroup

public GemmaCLI.CommandGroup getCommandGroup()

Description copied from interface: CLI

Obtain the command group for this CLI.

getArrayDesignsToProcess

protected Collection<ubic.gemma.model.expression.arrayDesign.ArrayDesign> getArrayDesignsToProcess()

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.

Specified by:

buildOptions in class AbstractCLI

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().

Specified by:

processOptions in class AbstractCLI

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.

getArrayDesignReportService

protected ubic.gemma.core.analysis.report.ArrayDesignReportService getArrayDesignReportService()

getArrayDesignService

protected ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService getArrayDesignService()

isSubsumedOrMerged

protected boolean isSubsumedOrMerged(ubic.gemma.model.expression.arrayDesign.ArrayDesign arrayDesign)

Parameters:

arrayDesign - the array design to check

Returns:

true if the sequences on the given array design would be equivalently treated by analyzing another array design. In the case of subsumption, this only works if the array design has been either analyzed for subsuming status. (the analysis is not done as part of this call).

shouldRun

protected boolean shouldRun(Date skipIfLastRunLaterThan,
                            ubic.gemma.model.expression.arrayDesign.ArrayDesign design,
                            Class<? extends ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignAnalysisEvent> cls)

locateArrayDesign

protected ubic.gemma.model.expression.arrayDesign.ArrayDesign locateArrayDesign(String name)

Parameters:

name - of the array design to find.

Returns:

an array design, if found. Bails otherwise with an error exit code