# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#            http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Library to run HHsearch from Python."""

import glob
import os
import subprocess
from typing import Sequence

from absl import logging

from modelscope.models.science.unifold.msa import parsers
from . import utils


class HHSearch:
    """Python wrapper of the HHsearch binary."""

    def __init__(self,
                 *,
                 binary_path: str,
                 databases: Sequence[str],
                 maxseq: int = 1_000_000):
        """Initializes the Python HHsearch wrapper.

        Args:
            binary_path: The path to the HHsearch executable.
            databases: A sequence of HHsearch database paths. This should be the
                common prefix for the database files (i.e. up to but not including
                _hhm.ffindex etc.)
            maxseq: The maximum number of rows in an input alignment. Note that this
                parameter is only supported in HHBlits version 3.1 and higher.

        Raises:
            RuntimeError: If HHsearch binary not found within the path.
        """
        self.binary_path = binary_path
        self.databases = databases
        self.maxseq = maxseq

        for database_path in self.databases:
            if not glob.glob(database_path + '_*'):
                logging.error('Could not find HHsearch database %s',
                              database_path)
                raise ValueError(
                    f'Could not find HHsearch database {database_path}')

    @property
    def output_format(self) -> str:
        return 'hhr'

    @property
    def input_format(self) -> str:
        return 'a3m'

    def query(self, a3m: str) -> str:
        """Queries the database using HHsearch using a given a3m."""
        with utils.tmpdir_manager() as query_tmp_dir:
            input_path = os.path.join(query_tmp_dir, 'query.a3m')
            hhr_path = os.path.join(query_tmp_dir, 'output.hhr')
            with open(input_path, 'w') as f:
                f.write(a3m)

            db_cmd = []
            for db_path in self.databases:
                db_cmd.append('-d')
                db_cmd.append(db_path)
            cmd = [
                self.binary_path,
                '-i',
                input_path,
                '-o',
                hhr_path,
                '-maxseq',
                str(self.maxseq),
            ] + db_cmd

            logging.info('Launching subprocess "%s"', ' '.join(cmd))
            process = subprocess.Popen(
                cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
            with utils.timing('HHsearch query'):
                stdout, stderr = process.communicate()
                retcode = process.wait()

            if retcode:
                # Stderr is truncated to prevent proto size errors in Beam.
                raise RuntimeError(
                    'HHSearch failed:\nstdout:\n%s\n\nstderr:\n%s\n' %
                    (stdout.decode('utf-8'), stderr[:100_000].decode('utf-8')))

            with open(hhr_path) as f:
                hhr = f.read()
        return hhr

    def get_template_hits(
            self, output_string: str,
            input_sequence: str) -> Sequence[parsers.TemplateHit]:
        """Gets parsed template hits from the raw string output by the tool."""
        del input_sequence  # Used by hmmseach but not needed for hhsearch.
        return parsers.parse_hhr(output_string)