diff options
Diffstat (limited to 'scripts/rqtl2/install_phenos.py')
| -rw-r--r-- | scripts/rqtl2/install_phenos.py | 12 |
1 files changed, 8 insertions, 4 deletions
diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py index a6e9fb2..11ac8a4 100644 --- a/scripts/rqtl2/install_phenos.py +++ b/scripts/rqtl2/install_phenos.py @@ -6,6 +6,7 @@ from zipfile import ZipFile from functools import reduce from logging import Logger, getLogger +from redis import Redis import MySQLdb as mdb from MySQLdb.cursors import DictCursor @@ -18,7 +19,7 @@ from r_qtl import r_qtl2_qc as rqc from functional_tools import take -__MODULE__ = "scripts.rqtl2.install_phenos" +logger = getLogger(__name__) def insert_probesets(dbconn: mdb.Connection, platformid: int, @@ -95,10 +96,13 @@ def cross_reference_probeset_data(dbconn: mdb.Connection, } for row in dataids)) return cursor.rowcount -def install_pheno_files(#pylint: disable=[too-many-arguments, too-many-locals] +def install_pheno_files(#pylint: disable=[too-many-locals] + rconn: Redis,#pylint: disable=[unused-argument] dbconn: mdb.Connection, + fullyqualifiedjobid: str,#pylint: disable=[unused-argument] args: argparse.Namespace, - logger: Logger = getLogger()) -> int: + logger: Logger = logger # pylint: disable=[redefined-outer-name] +) -> int: """Load data in `pheno` files and other related files into the database.""" (speciesid, platformid, datasetid, rqtl2bundle) = ( args.speciesid, args.platformid, args.datasetid, args.rqtl2bundle) @@ -156,5 +160,5 @@ if __name__ == "__main__": return parser.parse_args() - main = build_main(cli_args(), install_pheno_files, __MODULE__) + main = build_main(cli_args(), install_pheno_files, logger) sys.exit(main()) |