Package ubic.gemma.cli.util

Class AbstractAutoSeekingCLI<T extends Auditable>

java.lang.Object

ubic.gemma.cli.util.AbstractCLI

ubic.gemma.cli.util.AbstractAuthenticatedCLI

ubic.gemma.cli.util.AbstractAutoSeekingCLI<T>

Type Parameters:

T - the type of entity being seeked

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:

ArrayDesignSequenceManipulatingCli, ExpressionExperimentManipulatingCLI

public abstract class AbstractAutoSeekingCLI<T extends Auditable>
extends AbstractAuthenticatedCLI

Provide auto-seeking capabilities to a CLI.

This allows CLIs to process entities that lack certain AuditEvent or that haven't been updated since a certain date.

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 static String	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	AbstractAutoSeekingCLI(Class<T> entityClass)

Method Summary

Modifier and Type	Method	Description
protected void	addAutoOption(org.apache.commons.cli.Options options)	Add the -auto option.
protected void	addAutoOption(org.apache.commons.cli.Options options, Class<? extends AuditEventType> autoSeekEventType)	Add the -auto option for a specific AuditEventType.
protected void	addErrorObject(T errorObject, Exception exception)
protected void	addErrorObject(T errorObject, String message)
protected void	addErrorObject(T errorObject, String message, Throwable throwable)
protected void	addForceOption(org.apache.commons.cli.Options options)
protected void	addForceOption(org.apache.commons.cli.Options options, String description)
protected void	addLimitingDateOption(org.apache.commons.cli.Options options)	Add the -mdate option.
protected void	addSuccessObject(T successObject)
protected void	addSuccessObject(T successObject, String message)
protected void	addWarningObject(T warningObject, String message)
protected void	addWarningObject(T warningObject, String message, Throwable throwable)
protected Class<? extends AuditEventType>	getAutoSeekEventType()	Indicate the event to be used for auto-seeking.
protected Date	getLimitingDate()	Obtain the limiting date (i.e. starting date at which entities should be processed).
protected boolean	isAutoSeek()	Indicate if auto-seek is enabled.
protected boolean	isForce()	Check if forcing is enabled.
protected boolean	noNeedToRun(T auditable, Class<? extends AuditEventType> eventClass)	Check if the given auditable can be skipped.
protected void	processOptions(org.apache.commons.cli.CommandLine commandLine)	Process command line options.
protected void	setForce()	Enable the forcing mode.
protected abstract Serializable	toBatchObject(T object)	Convert the given object to a serializable object for batch processing.

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, buildOptions, executeCommand, getApplicationContext, getBatchTaskExecutor, getCliContext, getCommandAliases, getCommandGroup, 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

FORCE_OPTION

protected static final String FORCE_OPTION

See Also:

Constant Field Values

Constructor Detail

AbstractAutoSeekingCLI

protected AbstractAutoSeekingCLI(Class<T> entityClass)

Method Detail

addAutoOption

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

Add the -auto option.

The auto option value can be retrieved with isAutoSeek().

addAutoOption

protected void addAutoOption(org.apache.commons.cli.Options options,
                             Class<? extends AuditEventType> autoSeekEventType)

Add the -auto option for a specific AuditEventType.

The event type can be retrieved with getAutoSeekEventType().

addLimitingDateOption

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

Add the -mdate option.

The limiting date can be retrieved with getLimitingDate().

addForceOption

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

addForceOption

protected void addForceOption(org.apache.commons.cli.Options options,
                              String description)

isAutoSeek

protected boolean isAutoSeek()

Indicate if auto-seek is enabled.

getAutoSeekEventType

protected Class<? extends AuditEventType> getAutoSeekEventType()

Indicate the event to be used for auto-seeking.

getLimitingDate

@Nullable
protected Date getLimitingDate()

Obtain the limiting date (i.e. starting date at which entities should be processed).

isForce

protected boolean isForce()

Check if forcing is enabled.

setForce

protected void setForce()

Enable the forcing mode.

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 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.

addSuccessObject

protected final void addSuccessObject(T successObject,
                                      String message)

addSuccessObject

protected final void addSuccessObject(T successObject)

addWarningObject

protected final void addWarningObject(@Nullable
                                      T warningObject,
                                      String message)

addWarningObject

protected final void addWarningObject(@Nullable
                                      T warningObject,
                                      String message,
                                      Throwable throwable)

addErrorObject

protected final void addErrorObject(@Nullable
                                    T errorObject,
                                    String message,
                                    Throwable throwable)

addErrorObject

protected final void addErrorObject(@Nullable
                                    T errorObject,
                                    String message)

addErrorObject

protected final void addErrorObject(@Nullable
                                    T errorObject,
                                    Exception exception)

toBatchObject

protected abstract Serializable toBatchObject(@Nullable
                                              T object)

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

noNeedToRun

protected boolean noNeedToRun(T auditable,
                              @Nullable
                              Class<? extends AuditEventType> eventClass)

Check if the given auditable can be skipped.

Parameters:

auditable - auditable

eventClass - can be null

Returns:

boolean