diff options
Diffstat (limited to 'scripts/rqtl2/install_genotypes.py')
| -rw-r--r-- | scripts/rqtl2/install_genotypes.py | 80 |
1 files changed, 18 insertions, 62 deletions
diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py index a1609a0..354bff0 100644 --- a/scripts/rqtl2/install_genotypes.py +++ b/scripts/rqtl2/install_genotypes.py @@ -1,26 +1,22 @@ """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 functools import reduce -from typing import Union, Iterator -from argparse import ArgumentParser +from typing import Iterator, Optional import MySQLdb as mdb -from redis import Redis from MySQLdb.cursors import DictCursor 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 +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_genotypes") @@ -29,7 +25,7 @@ logger.addHandler(stderr_handler) def insert_markers(dbconn: mdb.Connection, speciesid: int, markers: tuple[str, ...], - pmapdata: Union[Iterator[dict], None]) -> int: + pmapdata: Optional[Iterator[dict]]) -> int: """Insert genotype and genotype values into the database.""" mdata = reduce(#type: ignore[var-annotated] lambda acc, row: ({#type: ignore[arg-type, return-value] @@ -129,7 +125,7 @@ def cross_reference_genotypes(dbconn: mdb.Connection, speciesid: int, datasetid: int, dataids: tuple[dict, ...], - gmapdata: Union[Iterator[dict], None]) -> int: + gmapdata: Optional[Iterator[dict]]) -> int: """Cross-reference the data to the relevant dataset.""" _rows, markers, mdata = reduce(#type: ignore[var-annotated] lambda acc, row: (#type: ignore[return-value,arg-type] @@ -221,59 +217,19 @@ 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("datasetid", - help="The dataset to which the data belongs.") - 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) + parser = add_common_arguments(init_cli_parser( + "install_genotypes", + "Parse genotypes from R/qtl2 bundle into the database.")) 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.datasetid, - args.rqtl2bundle) - + main = build_main( + cli_args, + lambda dbconn, args: install_genotypes(dbconn, + args.speciesid, + args.populationid, + args.datasetid, + args.rqtl2bundle), + logger, + "INFO") sys.exit(main()) |