Package ubic.gemma.apps

Class ArrayDesignSequenceManipulatingCli

java.lang.Object

ubic.gemma.cli.util.AbstractCLI

ubic.gemma.cli.util.AbstractAuthenticatedCLI

ubic.gemma.cli.util.AbstractAutoSeekingCLI<ubic.gemma.model.expression.arrayDesign.ArrayDesign>

ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

All Implemented Interfaces:

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

Direct Known Subclasses:

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

public abstract class ArrayDesignSequenceManipulatingCli
extends AbstractAutoSeekingCLI<ubic.gemma.model.expression.arrayDesign.ArrayDesign>

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

Author:

pavlidis

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.cli.util.CLI

CLI.CommandGroup

Field Summary

Fields

Modifier and Type	Field	Description
protected ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService	auditEventService
protected ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService	auditTrailService
protected EntityLocator	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

Modifier	Constructor	Description
protected	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()
CLI.CommandGroup	getCommandGroup()	Obtain the command group for this CLI.
protected boolean	isSubsumedOrMerged(ubic.gemma.model.expression.arrayDesign.ArrayDesign arrayDesign)
protected boolean	needToRun(Date skipIfLastRunLaterThan, ubic.gemma.model.expression.arrayDesign.ArrayDesign arrayDesign, Class<? extends ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignAnalysisEvent> eventClass)
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)
protected Serializable	toBatchObject(ubic.gemma.model.expression.arrayDesign.ArrayDesign object)	Convert the given object to a serializable object for batch processing.

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, createBatchTaskExecutorService, doAuthenticatedWork, doWork, 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, getCliContext, getCommandAliases, getCommandName, 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

Field Detail

auditTrailService

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

auditEventService

@Autowired
protected ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService auditEventService

entityLocator

@Autowired
protected EntityLocator entityLocator

Constructor Detail

ArrayDesignSequenceManipulatingCli

protected ArrayDesignSequenceManipulatingCli()

Method Detail

getCommandGroup

public CLI.CommandGroup getCommandGroup()

Description copied from interface: CLI

Obtain the command group for this CLI.

Specified by:

getCommandGroup in interface CLI

Overrides:

getCommandGroup in class AbstractCLI

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.

Overrides:

buildOptions in class AbstractCLI

processOptions

@OverridingMethodsMustInvokeSuper
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 AbstractAutoSeekingCLI<ubic.gemma.model.expression.arrayDesign.ArrayDesign>

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()

toBatchObject

protected Serializable toBatchObject(@Nullable
                                     ubic.gemma.model.expression.arrayDesign.ArrayDesign object)

Description copied from class: AbstractAutoSeekingCLI

Convert the given object to a serializable object for batch processing.

Specified by:

toBatchObject in class AbstractAutoSeekingCLI<ubic.gemma.model.expression.arrayDesign.ArrayDesign>

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)

needToRun

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

Parameters:

eventClass - e.g., ArrayDesignSequenceAnalysisEvent.class

Returns:

true if skipIfLastRunLaterThan is null, or there is no record of a previous analysis, or if the last analysis was run before skipIfLastRunLaterThan. false otherwise.