Package ubic.gemma.apps

Class ArrayDesignSequenceManipulatingCli

java.lang.Object

ubic.gemma.cli.util.AbstractCLI

ubic.gemma.cli.util.AbstractAuthenticatedCLI

ubic.gemma.cli.util.AbstractAutoSeekingCLI<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:

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

public abstract class ArrayDesignSequenceManipulatingCli
extends AbstractAutoSeekingCLI<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 ArrayDesignReportService	arrayDesignReportService
protected ArrayDesignService	arrayDesignService
protected AuditEventService	auditEventService
protected 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	buildArrayDesignOptions(org.apache.commons.cli.Options options)
protected final void	buildOptions(org.apache.commons.cli.Options options)	Build option implementation.
protected final void	doAuthenticatedWork()
CLI.CommandGroup	getCommandGroup()	Obtain the command group for this CLI.
protected Collection<ArrayDesign>	getRelatedDesigns(ArrayDesign design)	Mergees or subsumees of the platform.
protected boolean	isSubsumedOrMerged(ArrayDesign arrayDesign)
protected boolean	needToRun(Date skipIfLastRunLaterThan, ArrayDesign arrayDesign, Class<? extends ArrayDesignAnalysisEvent> eventClass)
protected void	processArrayDesign(ArrayDesign arrayDesign)
protected void	processArrayDesignOptions(org.apache.commons.cli.CommandLine commandLine)
protected void	processArrayDesigns(Collection<ArrayDesign> arrayDesigns)
protected final void	processOptions(org.apache.commons.cli.CommandLine commandLine)	Process command line options.
protected boolean	shouldRun(Date skipIfLastRunLaterThan, ArrayDesign design, Class<? extends ArrayDesignAnalysisEvent> cls)
protected Serializable	toBatchObject(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, 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, 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 Details

arrayDesignReportService

@Autowired
protected ArrayDesignReportService arrayDesignReportService

arrayDesignService

@Autowired
protected ArrayDesignService arrayDesignService

auditTrailService

@Autowired
protected AuditTrailService auditTrailService

auditEventService

@Autowired
protected AuditEventService auditEventService

entityLocator

@Autowired
protected EntityLocator entityLocator

Constructor Details

ArrayDesignSequenceManipulatingCli

protected ArrayDesignSequenceManipulatingCli()

Method Details

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

buildOptions

protected final 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

buildArrayDesignOptions

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

processOptions

@OverridingMethodsMustInvokeSuper
protected final 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<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.

processArrayDesignOptions

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

Throws:

org.apache.commons.cli.ParseException

doAuthenticatedWork

protected final void doAuthenticatedWork()
                                  throws Exception

Specified by:

doAuthenticatedWork in class AbstractAuthenticatedCLI

Throws:

Exception

processArrayDesigns

protected void processArrayDesigns(Collection<ArrayDesign> arrayDesigns)

processArrayDesign

protected void processArrayDesign(ArrayDesign arrayDesign)

toBatchObject

protected Serializable toBatchObject(@Nullable
 ArrayDesign object)

Description copied from class: AbstractAutoSeekingCLI

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

Specified by:

toBatchObject in class AbstractAutoSeekingCLI<ArrayDesign>

isSubsumedOrMerged

protected boolean isSubsumedOrMerged(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,
 ArrayDesign design,
 Class<? extends ArrayDesignAnalysisEvent> cls)

getRelatedDesigns

protected Collection<ArrayDesign> getRelatedDesigns(ArrayDesign design)

Mergees or subsumees of the platform.

Parameters:

design - a platform

Returns:

related platforms

needToRun

protected boolean needToRun(@Nullable
 Date skipIfLastRunLaterThan,
 ArrayDesign arrayDesign,
 Class<? extends 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.