Package org.anchoranalysis.plugin.io.bean.task

Class CopyFiles<T>

Object

AnchorBean<Task<FileWithDirectoryInput,RecordingCounter<T>>>

Task<FileWithDirectoryInput,RecordingCounter<T>>

CopyFiles<T>

Type Parameters:

T - shared-state of naming

public class CopyFiles<T>
extends Task<FileWithDirectoryInput,RecordingCounter<T>>

Copy files to the output-directory, possibly changing the name or performing other operations like compression in the process.

Unusually this task does not use the InputOutputContext for each job, but rather for the experiment as a whole when determining the destination path for files. Similarly the message-log of the experiment is used for non-error messages.

The following outputs are produced:

Output Name	Default?	Description
"copy"	yes	a copied file for each input file.
outputs from the RecordingCounter
	outputs from Task

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
CopyFiles()

Method Summary

Modifier and Type	Method	Description
void	afterAllJobsAreExecuted(RecordingCounter<T> sharedState, InputOutputContext context)	Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
RecordingCounter<T>	beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<FileWithDirectoryInput> inputs, ParametersExperiment parameters)	Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
OutputEnabledMutable	defaultOutputs()	If specified, default rules for determine which outputs are enabled or not.
void	doJobOnInput(InputBound<FileWithDirectoryInput,RecordingCounter<T>> input)	Performs the task on a particular input.
CopyFilesMethod	getMethod()	How the copying occurs from source to destination file.
CopyFilesNaming<T>	getNaming()	How an output name (and path) is selected for an input file.
boolean	hasVeryQuickPerInputExecution()	Is the execution-time of the task per-input expected to be very quick to execute?
InputTypesExpected	inputTypesExpected()	Highest class(es) that will function as a valid input.
void	setMethod(CopyFilesMethod method)	How the copying occurs from source to destination file.
void	setNaming(CopyFilesNaming<T> naming)	How an output name (and path) is selected for an input file.

Methods inherited from class org.anchoranalysis.experiment.bean.task.Task

executeJob, isInputCompatibleWith

Methods inherited from class org.anchoranalysis.bean.AnchorBean

checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString

Methods inherited from class java.lang.Object

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

Constructor Details

CopyFiles

public CopyFiles()

Method Details

hasVeryQuickPerInputExecution

public boolean hasVeryQuickPerInputExecution()

Description copied from class: Task

Is the execution-time of the task per-input expected to be very quick to execute?

Specified by:

hasVeryQuickPerInputExecution in class Task<FileWithDirectoryInput,RecordingCounter<T>>

Returns:

true iff the execution is expected to be very quick, false otherwise.

inputTypesExpected

public InputTypesExpected inputTypesExpected()

Description copied from class: Task

Highest class(es) that will function as a valid input.

This is usually the class of T (or sometimes the absolute base class InputFromManager).

Specified by:

inputTypesExpected in class Task<FileWithDirectoryInput,RecordingCounter<T>>

Returns:

the input-types that a task expects.

beforeAnyJobIsExecuted

public RecordingCounter<T> beforeAnyJobIsExecuted(Outputter outputter,
 ConcurrencyPlan concurrencyPlan,
 List<FileWithDirectoryInput> inputs,
 ParametersExperiment parameters)
                                           throws ExperimentExecutionException

Description copied from class: Task

Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).

Specified by:

beforeAnyJobIsExecuted in class Task<FileWithDirectoryInput,RecordingCounter<T>>

Parameters:

outputter - the output-manager for the experiment (not for an individual job)

concurrencyPlan - available numbers of processors that can call Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>)

inputs - a list of inputs, each will result in at least one call to Task.executeJob(ParametersUnbound).

parameters - the experiment-parameters.

Returns:

the shared-state that is passed to each call to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>) and to Task.afterAllJobsAreExecuted(S, org.anchoranalysis.io.output.outputter.InputOutputContext).

Throws:

ExperimentExecutionException - if a fatal error occurs executing this step of the experiment.

doJobOnInput

public void doJobOnInput(InputBound<FileWithDirectoryInput,RecordingCounter<T>> input)
                  throws JobExecutionException

Description copied from class: Task

Performs the task on a particular input.

Specified by:

doJobOnInput in class Task<FileWithDirectoryInput,RecordingCounter<T>>

Parameters:

input - the input for the job.

Throws:

JobExecutionException - if an error occurs executing a particular job, that is not otherwise suppressed.

afterAllJobsAreExecuted

public void afterAllJobsAreExecuted(RecordingCounter<T> sharedState,
 InputOutputContext context)
                             throws ExperimentExecutionException

Description copied from class: Task

Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).

Specified by:

afterAllJobsAreExecuted in class Task<FileWithDirectoryInput,RecordingCounter<T>>

Parameters:

sharedState - the shared-state

context - IO-context for experiment (not for an individual job)

Throws:

ExperimentExecutionException - if a fatal error occurs executing this step of the experiment.

defaultOutputs

public OutputEnabledMutable defaultOutputs()

Description copied from class: Task

If specified, default rules for determine which outputs are enabled or not.

Overrides:

defaultOutputs in class Task<FileWithDirectoryInput,RecordingCounter<T>>

Returns:

the default rules if they exist.

getMethod

public CopyFilesMethod getMethod()

How the copying occurs from source to destination file.

e.g. with or without compression.

setMethod

public void setMethod(CopyFilesMethod method)

How the copying occurs from source to destination file.

e.g. with or without compression.

getNaming

public CopyFilesNaming<T> getNaming()

How an output name (and path) is selected for an input file.

setNaming

public void setNaming(CopyFilesNaming<T> naming)

How an output name (and path) is selected for an input file.