diff options
Diffstat (limited to 'scripts/rqtl2')
| -rw-r--r-- | scripts/rqtl2/entry.py | 3 | ||||
| -rw-r--r-- | scripts/rqtl2/install_genotypes.py | 8 | ||||
| -rw-r--r-- | scripts/rqtl2/install_phenos.py | 8 |
3 files changed, 9 insertions, 10 deletions
diff --git a/scripts/rqtl2/entry.py b/scripts/rqtl2/entry.py index e2d70a6..eccc19d 100644 --- a/scripts/rqtl2/entry.py +++ b/scripts/rqtl2/entry.py @@ -11,13 +11,12 @@ from qc_app.check_connections import check_db, check_redis from scripts.redis_logger import setup_redis_logger -def build_main(cli_args: Callable[[], Namespace], +def build_main(args: Namespace, run_fn: Callable[[Connection, Namespace], int], logger: Logger, loglevel: str = "INFO") -> Callable[[],int]: """Build a function to be used as an entry-point for scripts.""" def main(): - args = cli_args() check_db(args.databaseuri) check_redis(args.redisuri) if not args.rqtl2bundle.exists(): diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py index 77e7163..733ccf9 100644 --- a/scripts/rqtl2/install_genotypes.py +++ b/scripts/rqtl2/install_genotypes.py @@ -15,8 +15,8 @@ from r_qtl import r_qtl2 as rqtl2 from functional_tools import take from scripts.rqtl2.entry import build_main -from scripts.cli_parser import init_cli_parser from scripts.rqtl2.cli_parser import add_common_arguments +from scripts.cli_parser import init_cli_parser, add_global_data_arguments stderr_handler = logging.StreamHandler(stream=sys.stderr) logger = logging.getLogger("install_genotypes") @@ -217,14 +217,14 @@ if __name__ == "__main__": def cli_args(): """Process command-line arguments for install_genotypes""" - parser = add_common_arguments(init_cli_parser( + parser = add_common_arguments(add_global_data_arguments(init_cli_parser( "install_genotypes", - "Parse genotypes from R/qtl2 bundle into the database.")) + "Parse genotypes from R/qtl2 bundle into the database."))) return parser.parse_args() main = build_main( - cli_args, + cli_args(), lambda dbconn, args: install_genotypes(dbconn, args.speciesid, args.populationid, diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py index 5c25866..21b5f00 100644 --- a/scripts/rqtl2/install_phenos.py +++ b/scripts/rqtl2/install_phenos.py @@ -10,8 +10,8 @@ import MySQLdb as mdb from MySQLdb.cursors import DictCursor from scripts.rqtl2.entry import build_main -from scripts.cli_parser import init_cli_parser from scripts.rqtl2.cli_parser import add_common_arguments +from scripts.cli_parser import init_cli_parser, add_global_data_arguments from r_qtl import r_qtl2 as rqtl2 @@ -143,9 +143,9 @@ if __name__ == "__main__": def cli_args(): """Process command-line arguments for `install_phenos`""" - parser = init_cli_parser( + parser = add_global_data_arguments(init_cli_parser( "install_genotypes", - "Parse genotypes from R/qtl2 bundle into the database.") + "Parse genotypes from R/qtl2 bundle into the database.")) parser.add_argument( "platformid", @@ -156,7 +156,7 @@ if __name__ == "__main__": return parser.parse_args() main = build_main( - cli_args, + cli_args(), lambda dbconn, args: install_pheno_files(dbconn, args.speciesid, args.platformid, |