diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/insert_data.py | 4 | ||||
| -rw-r--r-- | scripts/insert_samples.py | 8 | ||||
| -rw-r--r-- | scripts/process_rqtl2_bundle.py | 6 | ||||
| -rw-r--r-- | scripts/qc.py | 2 | ||||
| -rw-r--r-- | scripts/qc_on_rqtl2_bundle.py | 6 | ||||
| -rw-r--r-- | scripts/qcapp_wsgi.py | 4 | ||||
| -rw-r--r-- | scripts/rqtl2/entry.py | 6 | ||||
| -rw-r--r-- | scripts/validate_file.py | 4 | ||||
| -rw-r--r-- | scripts/worker.py | 4 |
9 files changed, 22 insertions, 22 deletions
diff --git a/scripts/insert_data.py b/scripts/insert_data.py index 1465348..4b2e5f3 100644 --- a/scripts/insert_data.py +++ b/scripts/insert_data.py @@ -14,8 +14,8 @@ from MySQLdb.cursors import DictCursor from functional_tools import take from quality_control.file_utils import open_file -from qc_app.db_utils import database_connection -from qc_app.check_connections import check_db, check_redis +from uploader.db_utils import database_connection +from uploader.check_connections import check_db, check_redis # Set up logging stderr_handler = logging.StreamHandler(stream=sys.stderr) diff --git a/scripts/insert_samples.py b/scripts/insert_samples.py index 8431462..87f29dc 100644 --- a/scripts/insert_samples.py +++ b/scripts/insert_samples.py @@ -7,10 +7,10 @@ import argparse import MySQLdb as mdb from redis import Redis -from qc_app.db_utils import database_connection -from qc_app.check_connections import check_db, check_redis -from qc_app.db import species_by_id, population_by_id -from qc_app.samples import ( +from uploader.db_utils import database_connection +from uploader.check_connections import check_db, check_redis +from uploader.db import species_by_id, population_by_id +from uploader.samples import ( save_samples_data, read_samples_file, cross_reference_samples) diff --git a/scripts/process_rqtl2_bundle.py b/scripts/process_rqtl2_bundle.py index 4da3936..a7e169d 100644 --- a/scripts/process_rqtl2_bundle.py +++ b/scripts/process_rqtl2_bundle.py @@ -17,9 +17,9 @@ import r_qtl.errors as rqe import r_qtl.r_qtl2 as rqtl2 import r_qtl.r_qtl2_qc as rqc -from qc_app import jobs -from qc_app.db_utils import database_connection -from qc_app.check_connections import check_db, check_redis +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 from scripts.redis_logger import setup_redis_logger diff --git a/scripts/qc.py b/scripts/qc.py index e8573a9..6de051f 100644 --- a/scripts/qc.py +++ b/scripts/qc.py @@ -11,7 +11,7 @@ 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 qc_app.db_utils import database_connection +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 40809b7..150fbce 100644 --- a/scripts/qc_on_rqtl2_bundle.py +++ b/scripts/qc_on_rqtl2_bundle.py @@ -16,9 +16,9 @@ from redis import Redis from quality_control.errors import InvalidValue from quality_control.checks import decimal_points_error -from qc_app import jobs -from qc_app.db_utils import database_connection -from qc_app.check_connections import check_db, check_redis +from uploader import jobs +from uploader.db_utils import database_connection +from uploader.check_connections import check_db, check_redis from r_qtl import errors as rqe from r_qtl import r_qtl2 as rqtl2 diff --git a/scripts/qcapp_wsgi.py b/scripts/qcapp_wsgi.py index 349c006..fe77031 100644 --- a/scripts/qcapp_wsgi.py +++ b/scripts/qcapp_wsgi.py @@ -5,8 +5,8 @@ from logging import getLogger, StreamHandler from flask import Flask -from qc_app import create_app -from qc_app.check_connections import check_db, check_redis +from uploader import create_app +from uploader.check_connections import check_db, check_redis def setup_logging(appl: Flask) -> Flask: """Setup appropriate logging paradigm depending on environment.""" diff --git a/scripts/rqtl2/entry.py b/scripts/rqtl2/entry.py index 93fc130..b7fb68e 100644 --- a/scripts/rqtl2/entry.py +++ b/scripts/rqtl2/entry.py @@ -6,9 +6,9 @@ from argparse import Namespace from redis import Redis from MySQLdb import Connection -from qc_app import jobs -from qc_app.db_utils import database_connection -from qc_app.check_connections import check_db, check_redis +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 0028795..a40d7e7 100644 --- a/scripts/validate_file.py +++ b/scripts/validate_file.py @@ -12,8 +12,8 @@ from redis.exceptions import ConnectionError # pylint: disable=[redefined-builti from quality_control.utils import make_progress_calculator from quality_control.parsing import FileType, strain_names, collect_errors -from qc_app import jobs -from qc_app.db_utils import database_connection +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 diff --git a/scripts/worker.py b/scripts/worker.py index 0eb9ea5..91b0332 100644 --- a/scripts/worker.py +++ b/scripts/worker.py @@ -11,8 +11,8 @@ from tempfile import TemporaryDirectory from redis import Redis -from qc_app import jobs -from qc_app.check_connections import check_redis +from uploader import jobs +from uploader.check_connections import check_redis def parse_args(): "Parse the command-line arguments" |