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

Class RecipeXMLParser

java.lang.Object

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

public class RecipeXMLParser
extends Object

This class define a recipe XML parser.

Since:

3.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
RecipeXMLParser(Configuration conf, Configuration cliConf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)	Public constructor.
RecipeXMLParser(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)	Public constructor.

Method Summary

Modifier and Type	Method	Description
protected Path	getIncludePath(Element element, String source)	Get the path of a file to include.
protected fr.ens.biologie.genomique.kenetre.log.GenericLogger	getLogger()	Get the logger.
protected String	getRootTagName()	Get the root tag name
E	parse(InputStream is)	Parse XML as an input stream.
E	parse(InputStream is, String source)	Parse XML as an input stream.
E	parse(Path path)	Parse XML as an input stream.
protected Recipe	parse(NodeList nList, String source)	Parse a run step XML tag.

Methods inherited from class java.lang.Object

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

Constructor Detail

RecipeXMLParser

public RecipeXMLParser(Configuration conf,
                       fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)

Public constructor.

Parameters:

conf - initial configuration

logger - default logger

RecipeXMLParser

public RecipeXMLParser(Configuration conf,
                       Configuration cliConf,
                       fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)

Public constructor.

Parameters:

conf - initial configuration

cliConf - configuration that will overwrite global configuration of the recipe

logger - default logger

Method Detail

parse

protected Recipe parse(NodeList nList,
                       String source)
                throws Aozan3Exception

Parse a run step XML tag.

Parameters:

nList - node list

source - XML source description

Returns:

a list with step objects

Throws:

Aozan3Exception - if an error occurs while parsing the XML

getLogger

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

Get the logger.

Returns:

the logger

getRootTagName

protected String getRootTagName()

Get the root tag name

Returns:

the root tag name

parse

public E parse(Path path)
        throws Aozan3Exception

Parse XML as an input stream.

Parameters:

path - file path

Returns:

a list of Step

Throws:

Aozan3Exception - if an error occurs while parsing the file

parse

public E parse(InputStream is)
        throws Aozan3Exception

Parse XML as an input stream.

Parameters:

is - input stream

Returns:

a Recipe object

Throws:

Aozan3Exception - if an error occurs while parsing the file

parse

public E parse(InputStream is,
               String source)
        throws Aozan3Exception

Parse XML as an input stream.

Parameters:

is - input stream

source - XML source description

Returns:

a Recipe object

Throws:

Aozan3Exception - if an error occurs while parsing the file

getIncludePath

protected Path getIncludePath(Element element,
                              String source)
                       throws Aozan3Exception

Get the path of a file to include.

Parameters:

element - element to parse

Returns:

a Path object if the element to include exists or null

Throws:

Aozan3Exception - if other attribute than include exists for the tag