diff options
Diffstat (limited to 'scripts/qc_on_rqtl2_bundle.py')
| -rw-r--r-- | scripts/qc_on_rqtl2_bundle.py | 6 |
1 files changed, 3 insertions, 3 deletions
diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py index fc95d13..0207938 100644 --- a/scripts/qc_on_rqtl2_bundle.py +++ b/scripts/qc_on_rqtl2_bundle.py @@ -12,12 +12,12 @@ from typing import Union, Sequence, Callable, Iterator import MySQLdb as mdb from redis import Redis +from gn_libs.mysqldb import database_connection from quality_control.errors import InvalidValue from quality_control.checks import decimal_points_error from uploader import jobs -from uploader.db_utils import database_connection from uploader.check_connections import check_db, check_redis from r_qtl import r_qtl2 as rqtl2 @@ -191,7 +191,7 @@ def check_pheno_samples( return allerrors -def qc_pheno_errors(# pylint: disable=[too-many-arguments] +def qc_pheno_errors(# pylint: disable=[too-many-arguments, too-many-positional-arguments] rconn, fqjobid, dburi, speciesid, zfile, logger) -> bool: """Check for errors in `pheno` file(s).""" cdata = rqtl2.control_data(zfile) @@ -260,7 +260,7 @@ def run_qc(rconn: Redis, if qc_missing_files(rconn, fqjobid, zfile, logger): return 1 - def with_zipfile(# pylint: disable=[too-many-arguments] + def with_zipfile(# pylint: disable=[too-many-arguments,too-many-positional-arguments] rconn, fqjobid, dbconn, speciesid, filename, logger, func ): with ZipFile(filename, "r") as zfile: |