"""Run quality control on phenotypes-specific files in the bundle."""
import sys
import tempfile
from pathlib import Path
from zipfile import ZipFile
from logging import Logger, getLogger, StreamHandler

import MySQLdb as mdb

from r_qtl import r_qtl2 as rqtl2
from r_qtl import r_qtl2_qc as rqc
from r_qtl import exceptions as rqe

from uploader.files import sha256_digest_over_file
from scripts.rqtl2.entry import build_main
from scripts.rqtl2.cli_parser import add_bundle_argument
from scripts.cli_parser import init_cli_parser, add_global_data_arguments

def validate(phenobundle: Path, logger: Logger) -> dict:
    """Check that the bundle is generally valid"""
    try:
        rqc.validate_bundle(phenobundle)
    except rqe.RQTLError as rqtlerr:
        # logger.error("Bundle file validation failed!", exc_info=True)
        return {
            "skip": True,
            "logger": logger,
            "phenobundle": phenobundle,
            "errors": (" ".join(rqtlerr.args),)
        }
    return {
        "errors": tuple(),
        "skip": False,
        "phenobundle": phenobundle,
        "logger": logger
    }


def check_for_mandatory_pheno_keys(
        phenobundle: Path,
        logger: Logger,
        **kwargs
) -> dict:
    """Check that the mandatory keys exist for phenotypes."""
    if kwargs.get("skip", False):
        return {
            **kwargs,
            "logger": logger,
            "phenobundle": phenobundle
        }

    _mandatory_keys = ("pheno", "phenocovar")
    _cdata = rqtl2.read_control_file(phenobundle)
    _errors = kwargs.get("errors", tuple()) + tuple(
        f"Expected '{key}' file(s) are not declared in the bundle."
        for key in _mandatory_keys if key not in _cdata.keys())
    return {
        **kwargs,
        "logger": logger,
        "phenobundle": phenobundle,
        "errors": _errors,
        "skip": len(_errors) > 0
    }


def check_for_averages_files(
        phenobundle: Path,
        logger: Logger,
        **kwargs
) -> dict:
    """Check that averages files appear together"""
    if kwargs.get("skip", False):
        return {
            **kwargs,
            "logger": logger,
            "phenobundle": phenobundle
        }

    _together = (("phenose", "phenonum"), ("phenonum", "phenose"))
    _cdata = rqtl2.read_control_file(phenobundle)
    _errors = kwargs.get("errors", tuple()) + tuple(
        f"'{first}' is defined in the control file but there is no "
        f"corresponding '{second}'"
        for first, second in _together
        if ((first in _cdata.keys()) and (second not in _cdata.keys())))
    return {
        **kwargs,
        "logger": logger,
        "phenobundle": phenobundle,
        "errors": _errors,
        "skip": len(_errors) > 0
    }


def extract_bundle(bundle: Path, workdir: Path) -> tuple[Path, tuple[Path, ...]]:
    """Extract the bundle."""
    with ZipFile(bundle) as zfile:
        extractiondir = workdir.joinpath(
            f"{sha256_digest_over_file(bundle)}_phenotype_qc_{bundle.name}")
        return extractiondir, rqtl2.extract(zfile, extractiondir)
    """Run quality control checks on the bundle."""
    results = check_for_averages_files(
        **check_for_mandatory_pheno_keys(
            **validate(phenobundle, logger)))
    errors = results.get("errors", tuple())
    if len(errors) > 0:
        logger.error("We found the following errors:\n%s",
                     "\n".join(f" - {error}" for error in errors))
        return 1
    # TODO: Run QC on actual values
    #       Steps:
    #       - Extract file to specific directory
    extractiondir, *_bundlefiles = extract_bundle(phenobundle, workingdir)
    #       - For every pheno, phenocovar, phenose, phenonum file, undo
    #         transposition where relevant
    #       - Check that `description` and `units` is present in phenocovar for
    #         all phenotypes
    #       - Check all phenotypes in pheno files exist in phenocovar files
    #       - Check all numeric values
    raise NotImplementedError("WIP!")


if __name__ == "__main__":

    def cli_args():
        """Process command-line arguments for `install_phenos`"""
        parser = add_bundle_argument(add_global_data_arguments(init_cli_parser(
            program="PhenotypesQC",
            description=(
                "Perform Quality Control checks on a phenotypes bundle file"))))
        parser.add_argument(
            "--working-dir",
            default=f"{tempfile.gettempdir()}/phenotypes_qc",
            help=("The directory where this script will put its intermediate "
                  "files."),
            type=Path)
        return parser.parse_args()

    _logger = getLogger("phenotypes_qc")
    _logger.addHandler(StreamHandler(stream=sys.stderr))

    main = build_main(
        cli_args(),
        lambda dbconn, args: run_qc(dbconn, args.rqtl2bundle, _logger),
        _logger,
        "DEBUG")
    sys.exit(main())