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-rw-r--r--uploader/db/datasets.py4
-rw-r--r--uploader/phenotypes/models.py5
-rw-r--r--uploader/phenotypes/views.py23
-rw-r--r--uploader/publications/models.py4
-rw-r--r--uploader/publications/pubmed.py4
-rw-r--r--uploader/publications/views.py10
-rw-r--r--uploader/samples/views.py8
-rw-r--r--uploader/species/models.py2
8 files changed, 33 insertions, 27 deletions
diff --git a/uploader/db/datasets.py b/uploader/db/datasets.py
index 767ec41..4b263f5 100644
--- a/uploader/db/datasets.py
+++ b/uploader/db/datasets.py
@@ -53,7 +53,7 @@ def probeset_study_by_id(conn: mdb.Connection, studyid) -> Optional[dict]:
_study = cursor.fetchone()
return dict(_study) if bool(_study) else None
-def probeset_create_study(conn: mdb.Connection,#pylint: disable=[too-many-arguments]
+def probeset_create_study(conn: mdb.Connection,#pylint: disable=[too-many-arguments, too-many-positional-arguments]
populationid: int,
platformid: int,
tissueid: int,
@@ -87,7 +87,7 @@ def probeset_create_study(conn: mdb.Connection,#pylint: disable=[too-many-argume
(studyid, studyid))
return {**studydata, "studyid": studyid}
-def probeset_create_dataset(conn: mdb.Connection,#pylint: disable=[too-many-arguments]
+def probeset_create_dataset(conn: mdb.Connection,#pylint: disable=[too-many-arguments, too-many-positional-arguments]
studyid: int,
averageid: int,
datasetname: str,
diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py
index 4a1b2d5..4b8b223 100644
--- a/uploader/phenotypes/models.py
+++ b/uploader/phenotypes/models.py
@@ -92,7 +92,8 @@ def dataset_phenotypes(conn: mdb.Connection,
limit: Optional[int] = None) -> tuple[dict, ...]:
"""Fetch the actual phenotypes."""
_query = (
- "SELECT pheno.*, pxr.Id AS xref_id, pxr.InbredSetId, ist.InbredSetCode FROM Phenotype AS pheno "
+ "SELECT pheno.*, pxr.Id AS xref_id, pxr.InbredSetId, ist.InbredSetCode "
+ "FROM Phenotype AS pheno "
"INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId "
"INNER JOIN PublishFreeze AS pf ON pxr.InbredSetId=pf.InbredSetId "
"INNER JOIN InbredSet AS ist ON pf.InbredSetId=ist.Id "
@@ -218,7 +219,7 @@ def phenotype_by_id(
).values())
}
if bool(_pheno) and len(_pheno.keys()) > 1:
- raise Exception(
+ raise Exception(# pylint: disable=[broad-exception-raised]
"We found more than one phenotype with the same identifier!")
return None
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 04cdc3b..0e626ad 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -385,7 +385,7 @@ def process_phenotypes_individual_files(error_uri):
arcname=filedata["original-name"])
cdata[rqtlkey] = cdata.get(rqtlkey, []) + [filedata["original-name"]]
else:
- # TODO: Check this path: fix any bugs.
+ # T0DO: Check this path: fix any bugs.
_sentfile = request.files[formkey]
if not bool(_sentfile):
flash(f"Expected file ('{formkey}') was not provided.",
@@ -640,12 +640,16 @@ def load_data_to_database(
**kwargs
):# pylint: disable=[unused-argument]
"""Load the data from the given QC job into the database."""
- jobs_db = app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"]
+ _jobs_db = app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"]
with (Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn,
- sqlite3.connection(jobs_db) as conn):
+ sqlite3.connection(_jobs_db) as conn):
+ # T0DO: Maybe break the connection between the jobs here, pass:
+ # - the bundle name (rebuild the full path here.)
+ # - publication details, where separate
+ # - details about the files: e.g. total lines, etc
qc_job = jobs.job(rconn, jobs.jobsnamespace(), request.form["data-qc-job-id"])
_meta = json.loads(qc_job["job-metadata"])
- load_job_id = uuid.uuid4()
+ _load_job_id = uuid.uuid4()
_loglevel = logging.getLevelName(app.logger.getEffectiveLevel()).lower()
command = [
sys.executable,
@@ -653,8 +657,8 @@ def load_data_to_database(
"-m",
"scripts.load_phenotypes_to_db",
app.config["SQL_URI"],
- jobs_db,
- str(load_job_id),
+ _jobs_db,
+ str(_load_job_id),
"--log-level",
_loglevel
]
@@ -674,7 +678,7 @@ def load_data_to_database(
).then(
lambda token: gnlibs_jobs.initialise_job(
conn,
- load_job_id,
+ _load_job_id,
command,
"load-new-phenotypes-data",
extra_meta={
@@ -692,7 +696,7 @@ def load_data_to_database(
).then(
lambda job: gnlibs_jobs.launch_job(
job,
- jobs_db,
+ _jobs_db,
Path(f"{app.config['UPLOAD_FOLDER']}/job_errors"),
worker_manager="gn_libs.jobs.launcher",
loglevel=_loglevel)
@@ -972,6 +976,7 @@ def load_data_success(
job_id: uuid.UUID,
**kwargs
):# pylint: disable=[unused-argument]
+ """Display success page if loading data to database was successful."""
with (database_connection(app.config["SQL_URI"]) as conn,
sqlite3.connection(app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"])
as jobsconn):
@@ -1016,5 +1021,5 @@ def load_data_success(
"FormID": "searchResult"
}),
fragment="")))
- except JobNotFound as jnf:
+ except JobNotFound as _jnf:
return render_template("jobs/job-not-found.html", job_id=job_id)
diff --git a/uploader/publications/models.py b/uploader/publications/models.py
index f37b67d..f83be58 100644
--- a/uploader/publications/models.py
+++ b/uploader/publications/models.py
@@ -30,6 +30,7 @@ def create_new_publications(
conn: Connection,
publications: tuple[dict, ...]
) -> tuple[dict, ...]:
+ """Create new publications in the database."""
if len(publications) > 0:
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.executemany(
@@ -47,7 +48,8 @@ def create_new_publications(
return tuple({
**row, "publication_id": row["Id"]
} for row in cursor.fetchall())
- return tuple()
+
+ return tuple()
def update_publications(conn: Connection , publications: tuple[dict, ...]) -> tuple[dict, ...]:
diff --git a/uploader/publications/pubmed.py b/uploader/publications/pubmed.py
index e8b0584..2531c4a 100644
--- a/uploader/publications/pubmed.py
+++ b/uploader/publications/pubmed.py
@@ -29,9 +29,7 @@ def __journal__(journal: etree.Element) -> dict:
}
def __author__(author: etree.Element) -> str:
- return "%s %s" % (
- author.find("LastName").text,
- author.find("Initials").text)
+ return f'{author.find("LastName").text} {author.find("Initials").text}'
def __pages__(pagination: etree.Element) -> str:
diff --git a/uploader/publications/views.py b/uploader/publications/views.py
index e7aa412..a88f754 100644
--- a/uploader/publications/views.py
+++ b/uploader/publications/views.py
@@ -27,21 +27,21 @@ pubbp = Blueprint("publications", __name__)
@require_login
def index():
"""Index page for publications."""
- with database_connection(app.config["SQL_URI"]) as conn:
- return render_template("publications/index.html")
+ return render_template("publications/index.html")
@pubbp.route("/list", methods=["GET"])
@require_login
def list_publications():
+ """Fetch publications that fulfill a specific search, or all of them, if
+ there is no search term."""
# request breakdown:
# https://datatables.net/manual/server-side
_page = int(request.args.get("draw"))
_length = int(request.args.get("length") or '-1')
_start = int(request.args.get("start") or '0')
_search = request.args["search[value]"]
- with (database_connection(app.config["SQL_URI"]) as conn,
- conn.cursor(cursorclass=DictCursor) as cursor):
+ with database_connection(app.config["SQL_URI"]) as conn:
_publications, _current_rows, _totalfiltered, _totalrows = fetch_publications(
conn,
_search,
@@ -73,7 +73,7 @@ def view_publication(publication_id: int):
@require_login
def create_publication():
"""Create a new publication."""
- if(request.method == "GET"):
+ if request.method == "GET":
return render_template("publications/create-publication.html")
form = request.form
authors = form.get("publication-authors").encode("utf8")
diff --git a/uploader/samples/views.py b/uploader/samples/views.py
index c0adb88..4705a96 100644
--- a/uploader/samples/views.py
+++ b/uploader/samples/views.py
@@ -96,7 +96,7 @@ def list_samples(species: dict, population: dict, **kwargs):# pylint: disable=[u
activelink="list-samples")
-def build_sample_upload_job(# pylint: disable=[too-many-arguments]
+def build_sample_upload_job(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
speciesid: int,
populationid: int,
samplesfile: Path,
@@ -159,7 +159,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma
"alert-error")
return samples_uploads_page
- firstlineheading = (request.form.get("first_line_heading") == "on")
+ firstlineheading = request.form.get("first_line_heading") == "on"
separator = request.form.get("separator", ",")
if separator == "other":
@@ -172,7 +172,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma
redisuri = app.config["REDIS_URL"]
with Redis.from_url(redisuri, decode_responses=True) as rconn:
- #TODO: Add a QC step here — what do we check?
+ #T0DO: Add a QC step here — what do we check?
# 1. Does any sample in the uploaded file exist within the database?
# If yes, what is/are its/their species and population?
# 2. If yes 1. above, provide error with notes on which species and
@@ -251,7 +251,7 @@ def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs):
@require_login
@with_population(species_redirect_uri="species.populations.samples.index",
redirect_uri="species.populations.samples.select_population")
-def upload_failure(species: dict, population: dict, job_id: uuid.UUID, **kwargs):
+def upload_failure(species: dict, population: dict, job_id: uuid.UUID, **kwargs):# pylint: disable=[unused-argument]
"""Display the errors of the samples upload failure."""
job = with_redis_connection(lambda rconn: jobs.job(
rconn, jobs.jobsnamespace(), job_id))
diff --git a/uploader/species/models.py b/uploader/species/models.py
index db53d48..acfa51e 100644
--- a/uploader/species/models.py
+++ b/uploader/species/models.py
@@ -92,7 +92,7 @@ def save_species(conn: mdb.Connection,
}
-def update_species(# pylint: disable=[too-many-arguments]
+def update_species(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
conn: mdb.Connection,
species_id: int,
common_name: str,
generated by cgit v1.2.3 (git 2.47.1) at 2025-07-19 15:18:37 +0000