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

Class LegacyRecipes

java.lang.Object

fr.ens.biologie.genomique.aozan.aozan3.legacy.LegacyRecipes

public class LegacyRecipes
extends Object

This class define recipes that perform like Aozan 2 steps.

Since:

3.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
LegacyRecipes(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger, Path aozan2ConfFile)

Method Summary

Modifier and Type	Method	Description
Recipe	getDemuxStepRecipe()	Get the demux step recipe.
Recipe	getEndRunStepRecipe()	Get the new run step recipe.
Path	getLockDirectory(Recipe recipe)	Get the path where creating locks of a recipe.
Path	getMainLockPath()	Get the main lock path.
Recipe	getNewRunStepRecipe()	Get the new run step recipe.
Recipe	getQCStepRecipe()	Get the QC step recipe.
String	getRecipeDoneDenyFilename(Recipe recipe)	Get the done filename for a recipe.
SendMail	getSendMail()	Return SendMail object.
Recipe	getSyncStepRecipe()	Get the synchronization step recipe.
Path	getVarPath()	Get the path for var files.
boolean	isAozanEnabled()	Test if Aozan is enabled.
void	logAozanStart()	Log the start of the application.
void	logAozanStop()	Log the end of the application.

Methods inherited from class java.lang.Object

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

Constructor Detail

LegacyRecipes

public LegacyRecipes(Configuration conf,
                     fr.ens.biologie.genomique.kenetre.log.GenericLogger logger,
                     Path aozan2ConfFile)
              throws Aozan3Exception

Throws:

Aozan3Exception

Method Detail

isAozanEnabled

public boolean isAozanEnabled()

Test if Aozan is enabled.

Returns:

true if Aozan is enabled

getVarPath

public Path getVarPath()

Get the path for var files.

Returns:

the path for var files

getMainLockPath

public Path getMainLockPath()

Get the main lock path.

Returns:

the main lock path

getNewRunStepRecipe

public Recipe getNewRunStepRecipe()

Get the new run step recipe.

Returns:

the new run step recipe or null is not enabled

getEndRunStepRecipe

public Recipe getEndRunStepRecipe()

Get the new run step recipe.

Returns:

the new run step recipe or null is not enabled

getSyncStepRecipe

public Recipe getSyncStepRecipe()

Get the synchronization step recipe.

Returns:

the synchronization step recipe or null is not enable

getDemuxStepRecipe

public Recipe getDemuxStepRecipe()

Get the demux step recipe.

Returns:

the demux step recipe or null is not enabled

getQCStepRecipe

public Recipe getQCStepRecipe()

Get the QC step recipe.

Returns:

the QC step recipe or null is not enabled

getLockDirectory

public Path getLockDirectory(Recipe recipe)

Get the path where creating locks of a recipe.

Parameters:

recipe - the recipe

Returns:

the lock directory path of the recipe

getRecipeDoneDenyFilename

public String getRecipeDoneDenyFilename(Recipe recipe)

Get the done filename for a recipe.

Parameters:

recipe - the recipe

Returns:

the done filename

getSendMail

public SendMail getSendMail()

Return SendMail object.

Returns:

the SendMail object

logAozanStart

public void logAozanStart()

Log the start of the application.

logAozanStop

public void logAozanStop()

Log the end of the application.