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"""Load pheno from R/qtl2 bundle into the database."""
import sys
import logging
# import traceback
from pathlib import Path
import MySQLdb as mdb
from scripts.rqtl2.entry import build_main
from scripts.cli_parser import init_cli_parser
from scripts.rqtl2.cli_parser import add_common_arguments
stderr_handler = logging.StreamHandler(stream=sys.stderr)
logger = logging.getLogger("install_phenos")
logger.addHandler(stderr_handler)
def install_pheno_files(_dbconn: mdb.Connection,
_speciesid: int,
_populationid: int,
_platformid: int,
_studyid: int,
_datasetid: int,
_rqtl2bundle: Path) -> int:
"""Load data in `pheno` files and other related files into the database."""
logger.debug("WE ARE HERE!!!")
return 5
if __name__ == "__main__":
def cli_args():
"""Process command-line arguments for install_genotypes"""
parser = init_cli_parser(
"install_genotypes",
"Parse genotypes from R/qtl2 bundle into the database.")
parser.add_argument(
"platformid",
help="The platform from which the data was generated.")
parser.add_argument("studyid",
help="The study to which the data belongs.")
parser = add_common_arguments(parser)
return parser.parse_args()
main = build_main(
cli_args,
lambda dbconn, args: install_pheno_files(dbconn,
args.speciesid,
args.populationid,
args.platformid,
args.studyid,
args.datasetid,
args.rqtl2bundle),
logger,
"DEBUG")
sys.exit(main())
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