From 03b2ee98a1a2da648684e5a1a02c7f8c5b45ddd8 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 24 Sep 2024 10:31:48 -0500
Subject: typing: Fix type errors

---
 uploader/datautils.py             | 4 ++--
 uploader/expression_data/views.py | 5 +++--
 uploader/genotypes/models.py      | 4 ++--
 uploader/platforms/models.py      | 2 +-
 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,))
-- 
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