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-rw-r--r--uploader/datautils.py4
-rw-r--r--uploader/expression_data/views.py5
-rw-r--r--uploader/genotypes/models.py4
-rw-r--r--uploader/platforms/models.py2
4 files changed, 8 insertions, 7 deletions
diff --git a/uploader/datautils.py b/uploader/datautils.py
index 2ee079d..46a55c4 100644
--- a/uploader/datautils.py
+++ b/uploader/datautils.py
@@ -1,7 +1,7 @@
"""Generic data utilities: Rename module."""
import math
-from typing import Sequence
from functools import reduce
+from typing import Union, Sequence
def enumerate_sequence(seq: Sequence[dict], start:int = 1) -> Sequence[dict]:
"""Enumerate sequence beginning at 1"""
@@ -28,7 +28,7 @@ def order_by_family(items: tuple[dict, ...],
key=lambda item: item[0][0])
-def safe_int(val: str) -> int:
+def safe_int(val: Union[str, int, float]) -> int:
"""
Convert val into an integer: if val cannot be converted, return a zero.
"""
diff --git a/uploader/expression_data/views.py b/uploader/expression_data/views.py
index 88c4528..bbe6538 100644
--- a/uploader/expression_data/views.py
+++ b/uploader/expression_data/views.py
@@ -168,7 +168,8 @@ def upload_file(species_id: int, population_id: int):
flash(error, "alert-danger error-expr-data")
return redirect(url_for("species.populations.expression-data.upload_file"))
- filename = secure_filename(request.files["qc_text_file"].filename)
+ filename = secure_filename(
+ request.files["qc_text_file"].filename)# type: ignore[arg-type]
if not os.path.exists(upload_dir):
os.mkdir(upload_dir)
@@ -236,7 +237,7 @@ def parse_file(species_id: int, population_id: int):
job = jobs.launch_job(
jobs.build_file_verification_job(
rconn, app.config["SQL_URI"], redisurl,
- species_id, filepath, filetype,
+ species_id, filepath, filetype,# type: ignore[arg-type]
app.config["JOBS_TTL_SECONDS"]),
redisurl,
f"{app.config['UPLOAD_FOLDER']}/job_errors")
diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py
index 1fe5929..db8cc3e 100644
--- a/uploader/genotypes/models.py
+++ b/uploader/genotypes/models.py
@@ -32,7 +32,7 @@ def genotype_markers(
) -> tuple[dict, ...]:
"""Retrieve markers from the database."""
_query = "SELECT * FROM Geno WHERE SpeciesId=%s"
- if bool(limit) and limit > 0:
+ if bool(limit) and limit > 0:# type: ignore[operator]
_query = _query + f" LIMIT {limit} OFFSET {offset}"
with conn.cursor(cursorclass=DictCursor) as cursor:
@@ -59,7 +59,7 @@ def genotype_dataset(
_params = (species_id, population_id)
if bool(dataset_id):
_query = _query + " AND gf.Id=%s"
- _params = _params + (dataset_id,)
+ _params = _params + (dataset_id,)# type: ignore[assignment]
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(_query, _params)
diff --git a/uploader/platforms/models.py b/uploader/platforms/models.py
index adad0b2..4b690bb 100644
--- a/uploader/platforms/models.py
+++ b/uploader/platforms/models.py
@@ -13,7 +13,7 @@ def platforms_by_species(
"""Retrieve platforms by the species"""
_query = ("SELECT * FROM GeneChip WHERE SpeciesId=%s "
"ORDER BY GeneChipName ASC")
- if bool(limit) and limit > 0:
+ if bool(limit) and limit > 0:# type: ignore[operator]
_query = f"{_query} LIMIT {limit} OFFSET {offset}"
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(_query, (speciesid,))