# -*- coding: utf-8 -*-
# (c) The James Hutton Institute 2017-2019
# (c) University of Strathclyde 2019-2020
# Author: Leighton Pritchard
#
# Contact:
# leighton.pritchard@strath.ac.uk
#
# Leighton Pritchard,
# Strathclyde Institute for Pharmacy and Biomedical Sciences,
# Cathedral Street,
# Glasgow,
# G4 0RE
# Scotland,
# UK
#
# The MIT License
#
# Copyright (c) 2017-2019 The James Hutton Institute
# Copyright (c) 2019-2020 University of Strathclyde
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
"""Module providing command-line parser definitions."""

import sys

from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter, Namespace
from typing import List, Optional

from pyani.scripts.parsers import (
    download_parser,
    index_parser,
    createdb_parser,
    anim_parser,
    anib_parser,
    aniblastall_parser,
    fastani_parser,
    report_parser,
    plot_parser,
    classify_parser,
    scheduling_parser,
    common_parser,
    run_common_parser,
    listdeps_parser,
)


# Process command-line
def parse_cmdline(argv: Optional[List] = None) -> Namespace:
    """Parse command-line arguments for script.

    :param argv:  Namespace, command-line arguments

    The script offers a single main parser, with subcommands for the actions:

    - download
        download all available NCBI assemblies below the passed taxonomy ID
    - index
        index genome sequence files in a subdirectory, for analysis
    - createdb
        generate SQLite database for data and analysis results
    - anim
        conduct ANIm analysis
    - anib
        conduct ANIb analysis
    - aniblastall
        conduct ANIblastall analysis
    - fastani
        conduct fastANI analysis
    - report
        generate output describing analyses, genomes, and results
    - plot
        generate graphical output describing results
    - classify
        produce graph-based classification of genomes on the basis of ANI analysis
    """
    # Main parent parser
    parser_main = ArgumentParser(
        prog="pyani.py", formatter_class=ArgumentDefaultsHelpFormatter
    )
    subparsers = parser_main.add_subparsers(
        title="subcommands", description="valid subcommands", help="additional help"
    )
        parser_main.add_argument(
        "--version", action="version", version="%(prog)s 0.3.0-alpha"
    )
    parser_main.add_argument(
        "--citation", action="store_true", dest="citation", default=False, help="Display pyani citation"
    )

    # Parsers common to multiple subcommand parsers
    parser_common = common_parser.build()
    parser_scheduler = scheduling_parser.build()
    parser_run_common = run_common_parser.build()

    # Add subcommand parsers
    download_parser.build(subparsers, parents=[parser_common])
    index_parser.build(subparsers, parents=[parser_common])
    createdb_parser.build(subparsers, parents=[parser_common])
    anim_parser.build(
        subparsers, parents=[parser_common, parser_scheduler, parser_run_common]
    )
    anib_parser.build(
        subparsers, parents=[parser_common, parser_scheduler, parser_run_common]
    )
    aniblastall_parser.build(
        subparsers, parents=[parser_common, parser_scheduler, parser_run_common]
    )
    fastani_parser.build(
        subparsers, parents=[parser_common, parser_scheduler, parser_run_common]
    )
    report_parser.build(subparsers, parents=[parser_common])
    plot_parser.build(subparsers, parents=[parser_common])
    classify_parser.build(subparsers, parents=[parser_common])
    listdeps_parser.build(subparsers, parents=[parser_common])

    # Parse arguments
    # The list comprehension is to allow PosixPaths to be defined and passed in testing
    if argv is None:
        argv = sys.argv[1:]
    return parser_main.parse_args([str(_) for _ in argv])

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