diff options
| -rw-r--r-- | qc_app/jobs.py | 1 | ||||
| -rw-r--r-- | qc_app/parse.py | 10 | ||||
| -rw-r--r-- | scripts/insert_data.py | 4 | ||||
| -rw-r--r-- | scripts/worker.py | 1 | ||||
| -rw-r--r-- | tests/qc/test_cells_average.py | 2 | ||||
| -rw-r--r-- | tests/qc/test_cells_standard_error.py | 2 | ||||
| -rw-r--r-- | wsgi.py | 1 |
7 files changed, 14 insertions, 7 deletions
diff --git a/qc_app/jobs.py b/qc_app/jobs.py index 5f351d4..10ba832 100644 --- a/qc_app/jobs.py +++ b/qc_app/jobs.py @@ -7,7 +7,6 @@ from uuid import uuid4 from datetime import timedelta from redis import Redis -from flask import current_app as app def error_filename(job_id, error_dir): "Compute the path of the file where errors will be dumped." diff --git a/qc_app/parse.py b/qc_app/parse.py index 70ef551..ceb8fcf 100644 --- a/qc_app/parse.py +++ b/qc_app/parse.py @@ -10,8 +10,14 @@ from quality_control.errors import InvalidValue, DuplicateHeading from . import jobs parsebp = Blueprint("parse", __name__) -isinvalidvalue = lambda item: isinstance(item, InvalidValue) -isduplicateheading = lambda item: isinstance(item, DuplicateHeading) + +def isinvalidvalue(item): + """Check whether item is of type InvalidValue""" + return isinstance(item, InvalidValue) + +def isduplicateheading(item): + """Check whether item is of type DuplicateHeading""" + return isinstance(item, DuplicateHeading) @parsebp.route("/parse", methods=["GET"]) def parse(): diff --git a/scripts/insert_data.py b/scripts/insert_data.py index e1cc29b..c5879ed 100644 --- a/scripts/insert_data.py +++ b/scripts/insert_data.py @@ -153,13 +153,13 @@ def __xref_params__(dbconn: mdb.Connection, means: list[dict]) -> dict: "ProbeSetId": ids[str(mean["ProbeSetId"])] } for mean in means) -def insert_means( +def insert_means(# pylint: disable=[too-many-locals, too-many-arguments] filepath: str, speciesid: int, platform_id: int, datasetid: int, dbconn: mdb.Connection, rconn: Redis) -> int: # pylint: disable=[unused-argument] "Insert the means/averages data into the database" headings = read_file_headings(filepath) strains = strains_info(dbconn, headings[1:], speciesid) - check_strains(headings[1:], strains), + check_strains(headings[1:], strains) probeset_query = ( "INSERT INTO ProbeSet(ChipId, Name) " "VALUES (%(ChipId)s, %(Name)s) ") diff --git a/scripts/worker.py b/scripts/worker.py index 391f522..13556df 100644 --- a/scripts/worker.py +++ b/scripts/worker.py @@ -35,6 +35,7 @@ def update_stdout_stderr(rconn, job_id, bytes_read, stream: str): rconn.hset(name=job_id, key=stream, value=new_contents) def update_status(rconn, job_id, status): + """Update status of job in redis.""" rconn.hset(name=job_id, key="status", value=status) def run_job(job, rconn): diff --git a/tests/qc/test_cells_average.py b/tests/qc/test_cells_average.py index c2b382a..68fd4ec 100644 --- a/tests/qc/test_cells_average.py +++ b/tests/qc/test_cells_average.py @@ -1,4 +1,4 @@ -import re +"""Test average values.""" from random import randint from hypothesis import given from hypothesis import strategies as st diff --git a/tests/qc/test_cells_standard_error.py b/tests/qc/test_cells_standard_error.py index aa25aa8..90c13cf 100644 --- a/tests/qc/test_cells_standard_error.py +++ b/tests/qc/test_cells_standard_error.py @@ -1,4 +1,4 @@ -import re +"""Test standard error values.""" from random import randint @@ -4,6 +4,7 @@ from qc_app import create_app, instance_path from qc_app.check_connections import check_db, check_redis def check_and_build_app(): + """Setup the application for running.""" # Setup the app appl = create_app(instance_path()) |