import sys
import uuid
import logging
import argparse
from pathlib import Path

from gn_libs import jobs, mysqldb, sqlite3

logging.basicConfig(
    format="%(asctime)s — %(filename)s:%(lineno)s — %(levelname)s: %(message)s")
logger = logging.getLogger(__name__)


def check_ids():
    """Verify that all the `UniqueIdentifier` values are valid."""
    logger.info("Checking the 'UniqueIdentifier' values.")
    pass


def check_for_mandatory_fields():
    """Verify that mandatory fields have values."""
    pass


def compute_differences():
    """Compute differences between data in DB and edited data."""
    logger.info("Computing differences.")
    pass


def update_descriptions():
    """Update descriptions in the database"""
    logger.info("Updating descriptions")
    # Compute differences between db data and uploaded file
    # Only run query for changed descriptions
    pass


def link_publications():
    """Link phenotypes to relevant publications."""
    logger.info("Linking phenotypes to publications.")
    # Create publication if PubMed_ID doesn't exist in db
    pass


def update_values():
    """Update the phenotype values."""
    logger.info("Updating phenotypes values.")
    # Compute differences between db data and uploaded file
    # Only run query for changed data
    pass


def parse_args():
    parser = argparse.ArgumentParser(
        prog="Phenotypes Bulk-Edit Processor",
        description="Process the bulk-edits to phenotype data and descriptions.")
    parser.add_argument("db_uri", type=str, help="MariaDB/MySQL connection URL")
    parser.add_argument(
        "jobs_db_path", type=Path, help="Path to jobs' SQLite database.")
    parser.add_argument("job_id", type=uuid.UUID, help="ID of the running job")
    parser.add_argument(
        "--log-level",
        type=str,
        help="Determines what is logged out.",
        choices=("debug", "info", "warning", "error", "critical"),
        default="info")
    return parser.parse_args()


def run(conn, job):
    """Process the data and update it."""
    check_ids()
    check_for_mandatory_fields()
    # stop running here if any errors are found.
    compute_differences()
    update_descriptions()
    link_publications()
    update_values()
    return 0


def main():
    """Entry-point for this script."""
    args = parse_args()
    logger.setLevel(args.log_level.upper())
    logger.debug("Arguments: %s", args)

    with (mysqldb.database_connection(args.db_uri) as conn,
          sqlite3.connection(args.jobs_db_path) as jobs_conn):
        return run(conn, jobs.job(jobs_conn, args.job_id))


if __name__ == "__main__":
    sys.exit(main())