"""Load genotypes from R/qtl2 bundle into the database."""
import sys
import uuid
import logging
import traceback
from pathlib import Path
from zipfile import ZipFile
from argparse import ArgumentParser

import MySQLdb as mdb
from redis import Redis

from r_qtl import r_qtl2 as rqtl2

from quality_control.parsing import take

from qc_app.db_utils import database_connection
from qc_app.check_connections import check_db, check_redis

from scripts.redis_logger import RedisLogger

stderr_handler = logging.StreamHandler(stream=sys.stderr)
logger = logging.getLogger("install_genotypes")
logger.addHandler(stderr_handler)

def insert_markers(dbconn: mdb.Connection,
                   speciesid: int,
                   markers: tuple[str, ...]) -> int:
    """Insert genotype and genotype values into the database."""
    with dbconn.cursor() as cursor:
        cursor.executemany(
            "INSERT INTO Geno(SpeciesId, Name, Marker_Name) "
            "VALUES (%(speciesid)s, %(marker)s, %(marker)s) "
            "ON DUPLICATE KEY UPDATE SpeciesId=SpeciesId",
            tuple({"speciesid": speciesid, "marker": marker}
                  for marker in markers))
        return cursor.rowcount
        # TODO: Install geno data: GenoData
        return cursor.rowcount

def install_genotypes(dbconn: mdb.Connection,
                      speciesid: int,
                      populationid: int,
                      rqtl2bundle: Path) -> int:
    """Load any existing genotypes into the database."""
    count = 0
    with ZipFile(str(rqtl2bundle.absolute()), "r") as zfile:
        try:
            logger.info("Validating bundle")
            rqtl2.validate_bundle(zfile)
            logger.info("Bundle validated successfully.")
            logger.info(("Loading genotypes. This could take a while. "
                         "Please be patient."))

            cdata = rqtl2.control_data(zfile)
            genotypes = rqtl2.file_data(zfile,
                                        "geno",
                                        cdata,
                                        rqtl2.make_process_data_geno(cdata))
            while True:
                batch = tuple(take(genotypes, 5000))
                if len(batch) == 0:
                    logger.info("Loading Genotypes complete!")
                    logger.info(
                        "Total rows processed: %s", count)
                    break

                insert_markers(
                    dbconn,
                    speciesid,
                    tuple(key for key in batch[0].keys() if key != "id"))
                count = count + len(batch)

            if "gmap" in cdata:
                logger.info("Loading genetic mapping info.")
                # TODO: load gmap files
                logger.info("Successfully loaded genetic mapping.")

            if "pmap" in cdata:
                logger.info("Loading physical mapping info.")
                # TODO: load pmap files
                logger.info("Successfully loaded physical mapping.")
        except rqtl2.InvalidFormat as exc:
            logger.error(str(exc))
            logger.info("There are no genotypes to load.")
        except Exception as _exc:
            logger.error("Failing with exception: %s", traceback.format_exc())
            return 3

    return 0

if __name__ == "__main__":

    def cli_args():
        """Process command-line arguments for install_genotypes"""
        parser = ArgumentParser(
            prog="install_genotypes",
            description="Parse genotypes from R/qtl2 bundle into the database.")

        parser.add_argument("databaseuri", help="URL to MariaDB")
        parser.add_argument("redisuri", help="URL to Redis")
        parser.add_argument("jobid",
                            help="Job ID that this belongs to.",
                            type=uuid.UUID)

        parser.add_argument("speciesid",
                            help="Species to which bundle relates.")
        parser.add_argument("populationid",
                            help="Population to group data under")
        parser.add_argument("rqtl2bundle",
                            help="Path to R/qtl2 bundle zip file.",
                            type=Path)

        parser.add_argument("--redisexpiry",
                            help="How long to keep any redis keys around.",
                            type=int,
                            default=86400)

        return parser.parse_args()

    def main():
        """Run `install_genotypes` scripts."""
        args = cli_args()
        check_db(args.databaseuri)
        check_redis(args.redisuri)
        if not args.rqtl2bundle.exists():
            logging.error("File not found: '%s'.", args.rqtl2bundle)
            return 2

        with (Redis.from_url(args.redisuri, decode_responses=True) as rconn,
              database_connection(args.databaseuri) as dbconn):
            formatter = logging.Formatter(
                "%(asctime)s - %(name)s - %(levelname)s: %(message)s")
            job_messagelist = f"{str(args.jobid)}:log-messages"
            rconn.hset(name=str(args.jobid),
                       key="log-messagelist",
                       value=job_messagelist)
            redislogger = RedisLogger(
                rconn, args.jobid, expiry=args.redisexpiry)
            redislogger.setFormatter(formatter)
            logger.addHandler(redislogger)
            logger.setLevel("INFO")
            return install_genotypes(dbconn,
                                     args.speciesid,
                                     args.populationid,
                                     args.rqtl2bundle)

    sys.exit(main())