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

Class ConfigurationXMLParser

java.lang.Object
fr.ens.biologie.genomique.aozan.aozan3.recipe.ConfigurationXMLParser
public class ConfigurationXMLParser extends Object
This class define a XML parser for configuration.
Since:
3.0
Author:
Laurent Jourdren

  • Constructor Details

    • ConfigurationXMLParser

      public ConfigurationXMLParser(String rootTagName, String sectionName, Configuration parentConfiguration, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
      Constructor.
      Parameters:
      rootTagName - root tag name
      sectionName - name of the section in the recipe file
      parentConfiguration - parent configuration
      logger - logger to use

  • Method Details

    • parse

      protected Configuration 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 Configuration 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 Configuration 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 Configuration 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