# Source code for macsypy.profile

    #########################################################################
    # MacSyFinder - Detection of macromolecular systems in protein dataset  #
    #               using systems modelling and similarity search.          #
    # Authors: Sophie Abby, Bertrand Neron                                  #
    # Copyright (c) 2014-2023  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/>.                          #
    #########################################################################

    """
    Manage HMM profiles and hmmsearch execution
    """

    import os
    import logging
    _log = logging.getLogger(__name__)

    from subprocess import Popen
    from threading import Lock

    from .report import GembaseHMMReport, GeneralHMMReport, OrderedHMMReport
    from .error import MacsypyError

    class ProfileFactory:
        """
        Build and store all Profile objects. Profiles must not be instanciated directly.
        The profile_factory must be used. The profile_factory ensures there is only one instance
        of profile for a given name.
        To get a profile, use the method get_profile. If the profile is already cached, this instance is returned.
        Otherwise a new profile is built, stored in the profile_factory and then returned.

        """

        def __init__(self, cfg):
            self._profiles = {}
            self.cfg = cfg

        def get_profile(self, gene, model_location):
            """
            :param gene: the gene associated to this profile
            :type gene: :class:`macsypy.gene.Gene` or :class:`macsypy.gene.Homolog` or :class:`macsypy.gene.Analog` object
            :param model_location: The where to get the profile
            :type model_location: :class:`macsypy.registries.ModelLocation` object.
            :return: the profile corresponding to the name.
                     If the profile already exists, return it. Otherwise build it, store it and return it.
            :rtype: :class:`macsypy.profile.Profile` object
            """
            key = (model_location.name, gene.name)
            if key in self._profiles:
                profile = self._profiles[key]
            else:
                try:
                    path = model_location.get_profile(gene.name)
                except KeyError:
                    raise MacsypyError(f"'{model_location.name}/{gene.name}': No such profile")
                profile = Profile(gene, self.cfg, path)
                self._profiles[key] = profile
            return profile

    class Profile:
        """
        Handle a HMM protein profile
        """

        def __init__(self, gene, cfg, path):
            """

            :param gene: the gene corresponding to this profile
            :type gene: :class:`macsypy.secretion.Gene` object
            :param cfg: the configuration
            :type cfg: :class:`macsypy.config.Config` object
            :param path: the path to the hmm profile.
            :type path: string
            """
            self.gene = gene
            self.path = path
            self.len, self.ga_threshold = self._profile_features()
            self.cfg = cfg
            self.hmm_raw_output = None
            self._report = None
            self._lock = Lock()

        def __len__(self):
            """
            :return: the length of the HMM protein profile
            :rtype: int
            """
            return self.len

        def _profile_features(self):
            """
            Parse the HMM profile to extract the length and the presence of GA bit threshold

            :return: the length, presence of ga bit threshold
            :rtype: tuple(int length, bool ga_threshold)
            """
            length = None
            ga_threshold = False
            with open(self.path) as hmm_file:
                for line in hmm_file:
                    if line.startswith('LENG'):
                        length = int(line.split()[1])
                    elif line.startswith('GA'):
                        try:
                            header, thld_1, thld_2 = line.split()
                        except ValueError:
                            _log.warning(f"{self.gene.name} GA score is not well formatted. expected: "
                                         f"'GA float float' got '{line.rstrip()}'.")
                            _log.warning(f"GA score will not used for gene '{self.gene.name}'.")
                            continue
                        if thld_2.endswith(';'):
                            thld_2 = thld_2[:-1]
                        try:
                            thld_1 = float(thld_1)
                            thld_2 = float(thld_2)
                            ga_threshold = True
                        except ValueError:
                            _log.warning(f"{self.gene.name} GA score is not well formatted "
                                         f"expected 2 floats got '{thld_1}' '{thld_2}'.")
                            _log.warning(f"GA score will not used for gene '{self.gene.name}'.")
                            continue
                    elif line.startswith('STATS LOCAL'):
                        break
            return length, ga_threshold

        def __str__(self):
            """
            Print the name of the corresponding gene and the path to the HMM profile.
            """
            return f"{self.gene.name} : {self.path}"

        def execute(self, cpu=1):
            """
            Launch the Hmmer search (hmmsearch executable) with this profile

            :param int cpu: the number of cpu to use for hmmsearch (must be >= 1)
            :return: an object storing information on the results of the HMM search (HMMReport)
            :rtype:  :class:`macsypy.report.HMMReport` object
            """
            with self._lock:
                # the results of HMM is cached
                # so HMMsearch is executed only once per run
                # if this method is called several times,
                # the first call induce the execution of HMMsearch and generate a report
                # the other calls return directly this report
                if self._report is not None:
                    return self._report
                hmmer_dir = os.path.join(self.cfg.working_dir(), self.cfg.hmmer_dir())
                if not os.path.exists(hmmer_dir):
                    os.mkdir(hmmer_dir)
                output_path = os.path.join(hmmer_dir,  self.gene.name + self.cfg.res_search_suffix())
                err_path = os.path.join(hmmer_dir,
                                        self.gene.name + os.path.splitext(self.cfg.res_search_suffix())[0] + ".err")

                with open(err_path, 'w') as err_file:
                    if not self.cfg.cut_ga():
                        hmmer_threshold = f"-E {self.cfg.e_value_search():f}"
                    elif self.cfg.cut_ga() and self.ga_threshold:
                        hmmer_threshold = "--cut_ga"
                    else:
                        # cut_ga is True set but there is not self.ga_threshold:
                        hmmer_threshold = f"-E {self.cfg.e_value_search():f}"
                        _log.warning(f"GA bit thresholds unavailable on profile {self.gene.name}. "
                                     f"Switch to e-value threshold ({hmmer_threshold})")

                    command = f'"{self.cfg.hmmer()}" --cpu {cpu} -o "{output_path}" {hmmer_threshold} ' \
                              f'"{self.path}" "{self.cfg.sequence_db()}" '
                    _log.debug(f"{self.gene.name} Hmmer command line : {command}")
                    try:
                        hmmer = Popen(command,
                                      shell=True,
                                      stdout=None,
                                      stdin=None,
                                      stderr=err_file,
                                      close_fds=False,
                                      )
                    except Exception as err:
                        msg = f"Hmmer execution failed: command = {command} : {err}"
                        _log.critical(msg, exc_info=True)
                        raise err
                    hmmer.wait()

                if hmmer.returncode != 0:
                    if hmmer.returncode == -15:
                        msg = f"The Hmmer execution was aborted: command = {command} : " \
                              f"return code = {hmmer.returncode:d} check {err_path}"
                        _log.critical(msg)
                        return
                    else:
                        msg = f"an error occurred during Hmmer execution: command = {command} : " \
                              f"return code = {hmmer.returncode:d} check {err_path}"
                        _log.debug(msg, exc_info=True)
                        _log.critical(msg)
                        raise RuntimeError(msg)
                self.hmm_raw_output = output_path
                db_type = self.cfg.db_type()
                if db_type == 'gembase':
                    report = GembaseHMMReport(self.gene, output_path, self.cfg)
                elif db_type == 'ordered_replicon':
                    report = OrderedHMMReport(self.gene, output_path, self.cfg)
                else:
                    report = GeneralHMMReport(self.gene, output_path, self.cfg)
                self._report = report
                return report