Package fr.ens.biologie.genomique.aozan.aozan3.recipe

Class Recipe

java.lang.Object

fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe

public class Recipe
extends Object

This class define a recipe.

Since:

3.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
Recipe(String recipeName, String description, Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)	Public constructor.

Method Summary

Modifier and Type	Method	Description
void	addDataProvider(RunDataProvider dataProvider)	Set an existing data provider
void	addDataProvider(String providerName, String storageName, boolean inProgress, Configuration conf)	Add a data provider.
void	addStep(Step step)	Add a step.
void	addSteps(Collection<Step> steps)	Add steps.
void	addStorage(String name, DataStorage storage)	Add a storage.
Set<RunId>	availableRuns()	Get available runs.
Set<RunId>	availableRuns(Collection<RunId> excludedRunIds)	Get available runs.
void	execute()	Use the recipe to process run provided by the run data provider
boolean	execute(String runId)	Execute the recipe for a run.
Set<RunId>	execute(List<String> runIds)	Execute a list of run Ids.
List<String>	getAvalaibleRuns()	Get the list of available runs.
Configuration	getConfiguration()	Get the configuration.
String	getDescription()	Get the recipe name
fr.ens.biologie.genomique.kenetre.log.GenericLogger	getLogger()	Get the logger.
String	getName()	Get the recipe name
DataStorageRegistry	getStorages()	Get storages
void	init()	Initialize the steps of the recipe

Methods inherited from class java.lang.Object

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

Constructor Detail

Recipe

public Recipe(String recipeName,
              String description,
              Configuration conf,
              fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
       throws Aozan3Exception

Public constructor.

Parameters:

recipeName - recipe name

description - description of the recipe

conf - configuration

logger - logger

Throws:

Aozan3Exception - if an error occurs while initializing the email sending

Method Detail

getName

public String getName()

Get the recipe name

Returns:

the name of the recipe

getDescription

public String getDescription()

Get the recipe name

Returns:

the name of the recipe

getLogger

public fr.ens.biologie.genomique.kenetre.log.GenericLogger getLogger()

Get the logger.

Returns:

the logger

getConfiguration

public Configuration getConfiguration()

Get the configuration.

Returns:

a copy of the configuration of the recipe

getStorages

public DataStorageRegistry getStorages()

Get storages

Returns:

the storage registry

addStorage

public void addStorage(String name,
                       DataStorage storage)

Add a storage.

Parameters:

name - name of the storage

storage - storage to add

addDataProvider

public void addDataProvider(String providerName,
                            String storageName,
                            boolean inProgress,
                            Configuration conf)
                     throws Aozan3Exception

Add a data provider.

Parameters:

providerName - provider name

storageName - storage used by the provider

inProgress - true if in progress data must be used

conf - provider configuration

Throws:

Aozan3Exception - if an error occurs while setting the provider

addDataProvider

public void addDataProvider(RunDataProvider dataProvider)

Set an existing data provider

Parameters:

dataProvider - provider to set

addSteps

public void addSteps(Collection<Step> steps)

Add steps.

Parameters:

steps - a collection of step to add

addStep

public void addStep(Step step)

Add a step.

Parameters:

step - the step to add

init

public void init()
          throws Aozan3Exception

Initialize the steps of the recipe

Throws:

Aozan3Exception - if an error occurs while initializing the steps

execute

public void execute()
             throws Aozan3Exception

Use the recipe to process run provided by the run data provider

Throws:

Aozan3Exception - if an error occurs while executing the recipe

execute

public boolean execute(String runId)
                throws Aozan3Exception

Execute the recipe for a run.

Parameters:

runId - the run identifier

Throws:

Aozan3Exception - if an error occurs while executing the recipe

execute

public Set<RunId> execute(List<String> runIds)
                   throws Aozan3Exception

Execute a list of run Ids.

Parameters:

runIds - a list of run ids

Throws:

Aozan3Exception - if an error occurs while executing the recipe

availableRuns

public Set<RunId> availableRuns()
                         throws Aozan3Exception

Get available runs.

Returns:

a set with available runs.

Throws:

Aozan3Exception - if an error occurs while getting the available runs

availableRuns

public Set<RunId> availableRuns(Collection<RunId> excludedRunIds)
                         throws Aozan3Exception

Get available runs.

Parameters:

excludedRunIds - run ids to exclude from the result

Returns:

a set with available runs.

Throws:

Aozan3Exception - if an error occurs while getting the available runs

getAvalaibleRuns

public List<String> getAvalaibleRuns()
                              throws Aozan3Exception

Get the list of available runs.

Returns:

a list with available runs

Throws:

Aozan3Exception - if an error occurs while getting the available runs