# Source code for macsypy.model_conf_parser

    #########################################################################
    # MacSyFinder - Detection of macromolecular systems in protein dataset  #
    #               using systems modelling and similarity search.          #
    # Authors: Sophie Abby, Bertrand Neron                                  #
    # Copyright (c) 2014-2022  Institut Pasteur (Paris) and CNRS.           #
    # See the COPYRIGHT file for details                                    #
    #                                                                       #
    # This file is part of MacSyFinder package.                             #
    #                                                                       #
    # MacSyFinder is free software: you can redistribute it and/or modify   #
    # it under the terms of the GNU General Public License as published by  #
    # the Free Software Foundation, either version 3 of the License, or     #
    # (at your option) any later version.                                   #
    #                                                                       #
    # MacSyFinder is distributed in the hope that it will be useful,        #
    # but WITHOUT ANY WARRANTY; without even the implied warranty of        #
    # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the          #
    # GNU General Public License for more details .                         #
    #                                                                       #
    # You should have received a copy of the GNU General Public License     #
    # along with MacSyFinder (COPYING).                                     #
    # If not, see <https://www.gnu.org/licenses/>.                          #
    #########################################################################

    import xml.etree.ElementTree as Et
    import logging
    _log = logging.getLogger(__name__)

    from macsypy.error import MacsypyError

    class ModelConfParser:
        """
        Handle model_conf.xml configuration file.
        """

        def __init__(self, path):
            """

            :param str path: The path to the configuration file
            """
            self._path = path

        def parse(self):
            """
            Parse the xml 'model_conf' file set at the root of a data package

            :return: The specific configuration for a model family
            :rtype: dict with the name of variables as keys and value as values
            """
            model_conf_node = self._get_model_conf_node()
            weights_node = model_conf_node.find("./weights")

            filtering_opt = {}
            weights = {}
            if weights_node:
                weights = self.parse_weights(weights_node)

            filtering_node = model_conf_node.find("./filtering")
            if filtering_node:
                filtering_opt = self.parse_filtering(filtering_node)

            model_conf = {k: v for conf_part in (weights, filtering_opt) for k, v in conf_part.items()}
            return model_conf

        def _get_model_conf_node(self):
            """
            Find the root of the document

            :return: the document root of model_conf
            """
            try:
                tree = Et.parse(self._path)
                model_node = tree.getroot()
            except Exception as err:
                msg = f"unable to parse model configuration '{self._path}' : {err}"
                _log.critical(msg)
                raise MacsypyError(msg) from None
            return model_node

        def parse_weights(self, weights_node):
            """
            Parse the node 'weights' contening the scoring weight configuration

            :param weights_node: the node 'weights'
            :type weights_node: :class"`Et.ElementTree` object
            :return: the configuration option/value about the scores
            :rtype: dict
            """
            elements = {'itself': float,
                        'exchangeable': float,
                        'mandatory': float,
                        'accessory': float,
                        'neutral': float,
                        'out_of_cluster': float,
                        'redundancy_penalty': float}
            weights_conf = self._parse_section(weights_node, elements)
            # rename options as in the other part of MSF
            weights_conf = {(f"{k}_weight"if k != 'redundancy_penalty' else k): v for k, v in weights_conf.items()}
            return weights_conf

        def parse_filtering(self, filtering_node):
            """
            Parse the node 'filtering' containing the filtering options configuration

            :param filtering_node: the node 'filtering'
            :type filtering_node: :class"`Et.ElementTree` object
            :return: the configuration option/value about the filtering
            :rtype: dict
            """
            def parse_cut_ga(value):
                if value.lower() in ('true', 1):
                    return True
                elif value.lower() in ('false', 0):
                    return False
                else:
                    msg = f"cannot parse 'cut_ga' element in '{self._path}' expect True, 1, False, 0 got : '{value}'"
                    _log.critical(msg)
                    raise MacsypyError(msg)

            elements = {'e_value_search': float,
                        'i_evalue_sel': float,
                        'coverage_profile': float,
                        'cut_ga': parse_cut_ga,
                        }
            fiter_conf = self._parse_section(filtering_node, elements)
            # in the general config the cut_ga option is no_cut_ga
            # so rename and convert it
            if 'cut_ga' in fiter_conf:
                cut_ga = fiter_conf['cut_ga']
                del fiter_conf['cut_ga']
                if cut_ga:
                    pass
                    # this is the default
                else:
                    fiter_conf['no_cut_ga'] = True
            return fiter_conf

        def _parse_section(self, section_node, allowed_elements):
            """
            Parse a node containing configurations options and value

            :param section_node:
            :param allowed_elements: The elements allowed in this section
                                     Only these elements are parsed and in the final dictionnary
            :type allowed_elements: a dict with options name as keys and function to parse the element
            :return: dict
            """
            section = {}
            for child in section_node:
                element = child.tag
                if element in allowed_elements:
                    value = child.text
                    try:
                        value = allowed_elements[element](value)
                    except (TypeError, ValueError) as err:
                        msg = f"The model configuration file '{self._path}' cannot be parsed: {err}"
                        _log.critical(msg)
                        raise MacsypyError(msg) from None
                else:
                    _log.warning(f"unknown element '{element}' in '{self._path}' ignore it.")
                    continue
                section[element] = value
            return section