"""
Copyright 2023 Kat Holt
Copyright 2023 Ryan Wick (rrwick@gmail.com)
https://github.com/katholt/Kleborate/

This file is part of Kleborate. Kleborate 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. Kleborate 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 Kleborate. If
not, see <https://www.gnu.org/licenses/>.
"""

import os
import pathlib
import shutil
import sys

from ...shared.mlst import mlst


def description():
    return 'chromosomal MLST for Escherichia coli using the Pasteur scheme'


def prerequisite_modules():
    return []


def get_headers():
    full_headers = ['ST',
                    'dinB', 'icdA', 'pabB', 'polB', 'putP', 'trpA', 'trpB', 'uidA']
    stdout_headers = ['ST']
    return full_headers, stdout_headers


def add_cli_options(parser):
    module_name = os.path.basename(__file__)[:-3]
    group = parser.add_argument_group(f'{module_name} module')
    group.add_argument('--escherichia_mlst_pasteur_min_identity', type=float, default=90.0,
                       help='Minimum alignment percent identity for Escherchia-Pasteur MLST')
    group.add_argument('--escherichia_mlst_pasteur_min_coverage', type=float, default=80.0,
                       help='Minimum alignment percent coverage for Escherchia-Pasteur MLST')
    group.add_argument('--escherichia_mlst_pasteur_required_exact_matches', type=int, default=4,
                       help='At least this many exact matches are required to call an ST')
    return group


def check_cli_options(args):
    if args.escherichia_mlst_pasteur_min_identity <= 50.0 or \
            args.escherichia_mlst_pasteur_min_identity >= 100.0:
        sys.exit('Error: --escherichia_mlst_pasteur_min_identity must be between 50.0 and 100.0')
    if args.escherichia_mlst_pasteur_min_coverage <= 50.0 or \
            args.escherichia_mlst_pasteur_min_coverage >= 100.0:
        sys.exit('Error: --escherichia_mlst_pasteur_min_coverage must be between 50.0 and 100.0')
    if args.escherichia_mlst_pasteur_required_exact_matches < 0:
        sys.exit('Error: --escherichia_mlst_pasteur_required_exact_matches must be a positive '
                 'integer')


def check_external_programs():
    if not shutil.which('minimap2'):
        sys.exit('Error: could not find minimap2')
    return ['minimap2']


def data_dir():
    return pathlib.Path(__file__).parents[0] / 'data'


def get_results(assembly, minimap2_index, args, previous_results):
    genes = ['dinB', 'icdA', 'pabB', 'polB', 'putP', 'trpA', 'trpB', 'uidA']
    profiles = data_dir() / 'profiles.tsv'
    alleles = {gene: data_dir() / f'{gene}.fasta' for gene in genes}

    st, _, alleles = \
        mlst(assembly, minimap2_index, profiles, alleles, genes, None,
             args.escherichia_mlst_pasteur_min_identity, args.escherichia_mlst_pasteur_min_coverage,
             args.escherichia_mlst_pasteur_required_exact_matches)

    return {'ST': st,
            'dinB': alleles['dinB'], 'icdA': alleles['icdA'], 'pabB': alleles['pabB'],
            'polB': alleles['polB'], 'putP': alleles['putP'], 'trpA': alleles['trpA'],
            'trpB': alleles['trpB'], 'uidA': alleles['uidA']}
