"""Implements the command-line interface for the qc application"""
import os
import sys
import argparse

import magic

from quality_control.errors import ParseError
from quality_control.parsing import (
    FileType,
    parse_file,
    strain_names,
    parse_errors,
    parse_strains)


def is_file_mime(filepath, mimetype):
    """Check that `filepath` has a mimetype of `mimetype` or `text/plain`"""
    return magic.from_file(filepath, mime=True) in ("text/plain", mimetype)

def cli_argument_parser():
    """Create the parser for the CLI arguments"""
    parser = argparse.ArgumentParser(
        prog="qc", description = (
            "Command-Line Interface program for quality control of data files"))
    parser.add_argument(
        "filetype",
        help="The type of file to check",
        choices=("average", "standard-error"))
    parser.add_argument(
        "filepath",
        help=(
            "The path to the file to be checked."
            "If an absolute path is not provided, then the file will be relative to"
            f"\t'{os.getcwd()}'"))
    default_strains_file = os.path.join(
        os.path.dirname(__file__), "strains.csv")
    parser.add_argument(
        "-s", "--strainsfile",
        help=(
            "Path to the file containing allowable strains/samples. "
            f"[default '{default_strains_file}']"),
        default=default_strains_file)

    parser.add_argument(
        "-v", "--verbose",
        help="Controls whether to show extra output",
        default=False, action="store_true")
    return parser

def check(filepath, filetype, strains, verbose=False):
    """Check the file and print out results"""
    try:
        for line_num, line in enumerate(parse_file(
                filepath, filetype, strains), start=1):
            if verbose:
                print(f"Checked line: {line_num}")

        print(f"Successfully checked the file. No errors found.")
    except ParseError as pe:
        print("line\terrors")
        for line_num, error in enumerate(
                parse_errors(filepath, filetype, strains,
                             pe.args[0]["line_number"]),
                start = pe.args[0]["line_number"] + 1):
            print(f"{line_num}\t{' '.join(error['message'])}")
            

def main():
    """Entry point function"""
    argparser = cli_argument_parser()
    args = argparser.parse_args()
    if not os.path.exists(args.filepath):
        print("The file '{args.filepath}' does not exist.", file=sys.stderr)
        return 1

    if not os.path.exists(args.strainsfile):
        print("The file '{args.strainsfile}' does not exist.", file=sys.stderr)
        return 2

    if not is_file_mime(args.filepath, "text/tab-separated-values"):
        print(
            f"The file '{args.filepath}' MUST be a tab-separated file.",
            file=sys.stderr)
        return 3

    if not is_file_mime(args.strainsfile, "text/csv"):
        print(
            f"The file '{args.strainsfile}' MUST be a tab-separated file.",
            file=sys.stderr)
        return 4

    if args.verbose:
        print(f"Parsing the strain names from '{args.strainsfile}'")

    strains = strain_names(parse_strains(os.path.realpath(args.strainsfile)))

    filepath = os.path.realpath(args.filepath)
    if args.verbose:
        print(f"Checking '{filepath}' for errors")

    check(
        filepath, (
            FileType.AVERAGE if args.filetype == "average"
            else FileType.STANDARD_ERROR), strains)

if __name__ == "__main__":
    main()