diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/insert_data.py | 2 | ||||
| -rw-r--r-- | scripts/insert_samples.py | 2 | ||||
| -rw-r--r-- | scripts/process_rqtl2_bundle.py | 2 | ||||
| -rw-r--r-- | scripts/qc.py | 4 | ||||
| -rw-r--r-- | scripts/qc_on_rqtl2_bundle.py | 2 | ||||
| -rw-r--r-- | scripts/rqtl2/entry.py | 2 | ||||
| -rw-r--r-- | scripts/validate_file.py | 2 |
7 files changed, 8 insertions, 8 deletions
diff --git a/scripts/insert_data.py b/scripts/insert_data.py index 4b2e5f3..67038f8 100644 --- a/scripts/insert_data.py +++ b/scripts/insert_data.py @@ -10,11 +10,11 @@ from typing import Tuple, Iterator import MySQLdb as mdb from redis import Redis from MySQLdb.cursors import DictCursor +from gn_libs.mysqldb import database_connection from functional_tools import take from quality_control.file_utils import open_file -from uploader.db_utils import database_connection from uploader.check_connections import check_db, check_redis # Set up logging diff --git a/scripts/insert_samples.py b/scripts/insert_samples.py index e3577b6..1b0a052 100644 --- a/scripts/insert_samples.py +++ b/scripts/insert_samples.py @@ -6,8 +6,8 @@ import argparse import MySQLdb as mdb from redis import Redis +from gn_libs.mysqldb import database_connection -from uploader.db_utils import database_connection from uploader.check_connections import check_db, check_redis from uploader.species.models import species_by_id from uploader.population.models import population_by_id diff --git a/scripts/process_rqtl2_bundle.py b/scripts/process_rqtl2_bundle.py index ade9862..4efc3e0 100644 --- a/scripts/process_rqtl2_bundle.py +++ b/scripts/process_rqtl2_bundle.py @@ -11,6 +11,7 @@ from logging import Logger, getLogger, StreamHandler import MySQLdb as mdb from redis import Redis +from gn_libs.mysqldb import database_connection from functional_tools import take @@ -19,7 +20,6 @@ import r_qtl.r_qtl2_qc as rqc import r_qtl.exceptions as rqe from uploader import jobs -from uploader.db_utils import database_connection from uploader.check_connections import check_db, check_redis from scripts.cli_parser import init_cli_parser diff --git a/scripts/qc.py b/scripts/qc.py index 6de051f..b00f4c1 100644 --- a/scripts/qc.py +++ b/scripts/qc.py @@ -5,14 +5,14 @@ import mimetypes from typing import Union, Callable from argparse import ArgumentParser +from gn_libs.mysqldb import database_connection + from functional_tools import take from quality_control.utils import make_progress_calculator from quality_control.errors import InvalidValue, DuplicateHeading from quality_control.parsing import FileType, strain_names, collect_errors -from uploader.db_utils import database_connection - from .cli_parser import init_cli_parser diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py index fc95d13..9f9248c 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 diff --git a/scripts/rqtl2/entry.py b/scripts/rqtl2/entry.py index bc4cd9f..b45e1dc 100644 --- a/scripts/rqtl2/entry.py +++ b/scripts/rqtl2/entry.py @@ -5,9 +5,9 @@ from argparse import Namespace from redis import Redis from MySQLdb import Connection +from gn_libs.mysqldb import database_connection from uploader import jobs -from uploader.db_utils import database_connection from uploader.check_connections import check_db, check_redis from scripts.redis_logger import setup_redis_logger diff --git a/scripts/validate_file.py b/scripts/validate_file.py index a40d7e7..52e55ec 100644 --- a/scripts/validate_file.py +++ b/scripts/validate_file.py @@ -8,12 +8,12 @@ from zipfile import ZipFile, is_zipfile import jsonpickle from redis import Redis from redis.exceptions import ConnectionError # pylint: disable=[redefined-builtin] +from gn_libs.mysqldb import database_connection from quality_control.utils import make_progress_calculator from quality_control.parsing import FileType, strain_names, collect_errors from uploader import jobs -from uploader.db_utils import database_connection from .cli_parser import init_cli_parser from .qc import add_file_validation_arguments |