Package org.anchoranalysis.experiment.bean.io

Class InputOutputExperiment<T extends InputFromManager,S>

Object

org.anchoranalysis.bean.AnchorBean<Experiment>

org.anchoranalysis.experiment.bean.Experiment

org.anchoranalysis.experiment.bean.io.OutputExperiment

org.anchoranalysis.experiment.bean.io.InputOutputExperiment<T,S>

Type Parameters:

T - input-object type

S - shared-state for job

All Implemented Interfaces:

AssociateXMLUponLoad, ReplaceInputManager<T>, ReplaceOutputManager, ReplaceTask<T,S>

public class InputOutputExperiment<T extends InputFromManager,S>
extends OutputExperiment
implements ReplaceInputManager<T>, ReplaceOutputManager, ReplaceTask<T,S>

An experiment that uses both an InputManager to specify inputs and a OutputManager to specify outputting.

The following outputs are produced:

Output Name	Default?	Description
"logExperiment"	yes	A textual log file for non-job-specific messages, one for the entire experiment.
"logJob"	yes	A textual log file for job-specific messages, one for each job.

Author:

Owen Feehan

Field Summary

Fields inherited from class org.anchoranalysis.experiment.bean.io.OutputExperiment

OUTPUT_EXECUTION_TIME

Constructor Summary

Constructors

Constructor	Description
InputOutputExperiment()

Method Summary

Modifier and Type	Method	Description
protected MultiLevelOutputEnabled	defaultOutputs()	If specified, default rules for determine which outputs are enabled or not.
protected Optional<TaskStatistics>	executeExperimentWithParameters(ParametersExperiment parameters)	Executes the experiment for parameters.
InputManager<T>	getInput()	The input-manager to specify where/which/how necessary inputs for the experiment occur.
LoggingDestination	getLogTask()	Where log messages that do pertain to a specific job (input) appear.
String	getMessageNoInputs()	A message written to the logger if no inputs exist for the experiment, and it thus ends early.
JobProcessor<T,S>	getTaskProcessor()	What task is associated with the experiment, and how it is processed.
void	replaceInputManager(InputManager<T> inputManager)	Replace the existing @{link InputManager} associated with this class.
void	replaceOutputManager(OutputManager output)	Replace the currently-assigned OutputManager with another.
void	replaceTask(Task<T,S> taskToReplace)	Replace the currently-assigned Task with another.
void	setInput(InputManager<T> input)	The input-manager to specify where/which/how necessary inputs for the experiment occur.
void	setLogTask(LoggingDestination logTask)	Where log messages that do pertain to a specific job (input) appear.
void	setMessageNoInputs(String messageNoInputs)	A message written to the logger if no inputs exist for the experiment, and it thus ends early.
void	setTaskProcessor(JobProcessor<T,S> taskProcessor)	What task is associated with the experiment, and how it is processed.
boolean	useDetailedLogging()	Whether to log in more or less detail.

Methods inherited from class org.anchoranalysis.experiment.bean.io.OutputExperiment

executeExperiment, getExperimentIdentifier, getLogExperiment, getOutput, isForceDetailedLogging, setExperimentIdentifier, setForceDetailedLogging, setLogExperiment, setOutput

Methods inherited from class org.anchoranalysis.experiment.bean.Experiment

associateXML, getXMLConfiguration

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

InputOutputExperiment

public InputOutputExperiment()

Method Details

useDetailedLogging

public boolean useDetailedLogging()

Description copied from class: Experiment

Whether to log in more or less detail.

It's appropriate to perform more detailed logging for a lengthier experiment, but something quick and simple is preferable for a short job, which may only be outputted to the console.

Overrides:

useDetailedLogging in class OutputExperiment

Returns:

true iff detailed logging should be employed.

replaceInputManager

public void replaceInputManager(InputManager<T> inputManager) throws OperationFailedException

Description copied from interface: ReplaceInputManager

Replace the existing @{link InputManager} associated with this class.

Specified by:

replaceInputManager in interface ReplaceInputManager<T extends InputFromManager>

Parameters:

inputManager - the new input-manager that is assigned.

Throws:

OperationFailedException - if the assignment cannot complete successfully.

replaceOutputManager

public void replaceOutputManager(OutputManager output) throws OperationFailedException

Description copied from interface: ReplaceOutputManager

Replace the currently-assigned OutputManager with another.

Specified by:

replaceOutputManager in interface ReplaceOutputManager

Parameters:

output - the task to replace.

Throws:

OperationFailedException - if the task cannot be successfully replaced.

replaceTask

public void replaceTask(Task<T,S> taskToReplace) throws OperationFailedException

Description copied from interface: ReplaceTask

Replace the currently-assigned Task with another.

Specified by:

replaceTask in interface ReplaceTask<T extends InputFromManager,S>

Parameters:

taskToReplace - the task to replace.

Throws:

OperationFailedException - if the task cannot be successfully replaced.

executeExperimentWithParameters

protected Optional<TaskStatistics> executeExperimentWithParameters(ParametersExperiment parameters) throws ExperimentExecutionException

Description copied from class: OutputExperiment

Executes the experiment for parameters.

Specified by:

executeExperimentWithParameters in class OutputExperiment

Parameters:

parameters - a combination of run-time and bean-time specified elements used in the experiment.

Returns:

statistics of the tasks, if they exist.

Throws:

ExperimentExecutionException - if anything occurs stop the experiment finishing its execution

defaultOutputs

protected MultiLevelOutputEnabled defaultOutputs()

Description copied from class: OutputExperiment

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

Specified by:

defaultOutputs in class OutputExperiment

Returns:

the default rules if they exist.

getInput

public InputManager<T> getInput()

The input-manager to specify where/which/how necessary inputs for the experiment occur.

setInput

public void setInput(InputManager<T> input)

The input-manager to specify where/which/how necessary inputs for the experiment occur.

getTaskProcessor

public JobProcessor<T,S> getTaskProcessor()

What task is associated with the experiment, and how it is processed.

e.g. how the task processes the inputs in the form of jobs (sequentially, parallel, how many processors? etc.)

setTaskProcessor

public void setTaskProcessor(JobProcessor<T,S> taskProcessor)

What task is associated with the experiment, and how it is processed.

e.g. how the task processes the inputs in the form of jobs (sequentially, parallel, how many processors? etc.)

getLogTask

public LoggingDestination getLogTask()

Where log messages that do pertain to a specific job (input) appear.

This is in contrast to logExperiment where non-job specific log messages appear.

setLogTask

public void setLogTask(LoggingDestination logTask)

Where log messages that do pertain to a specific job (input) appear.

This is in contrast to logExperiment where non-job specific log messages appear.

getMessageNoInputs

public String getMessageNoInputs()

A message written to the logger if no inputs exist for the experiment, and it thus ends early.

setMessageNoInputs

public void setMessageNoInputs(String messageNoInputs)

A message written to the logger if no inputs exist for the experiment, and it thus ends early.