From f461e4f29a8f32ec954cf858fb21de936f3b325b Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 7 Oct 2024 15:54:33 -0500
Subject: linting: Fix minor linting issues.

---
 uploader/input_validation.py |  2 --
 uploader/phenotypes/views.py |  4 ++--
 uploader/population/views.py |  1 -
 uploader/samples/views.py    | 17 ++++++-----------
 4 files changed, 8 insertions(+), 16 deletions(-)

diff --git a/uploader/input_validation.py b/uploader/input_validation.py
index b84fca6..3b5d4dd 100644
--- a/uploader/input_validation.py
+++ b/uploader/input_validation.py
@@ -4,8 +4,6 @@ import json
 import base64
 from typing import Any
 
-from flask import request
-
 def is_empty_string(value: str) -> bool:
     """Check whether as string is empty"""
     return (isinstance(value, str) and value.strip() == "")
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index c7bc965..312179e 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -236,7 +236,7 @@ def view_phenotype(# pylint: disable=[unused-argument]
 @with_population(
     species_redirect_uri="species.populations.phenotypes.index",
     redirect_uri="species.populations.phenotypes.select_population")
-def create_dataset(species: dict, population: dict, **kwargs):
+def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument]
     """Create a new phenotype dataset."""
     with (database_connection(app.config["SQL_URI"]) as conn,
           conn.cursor(cursorclass=DictCursor) as cursor):
@@ -267,7 +267,7 @@ def create_dataset(species: dict, population: dict, **kwargs):
 
         dataset_shortname = (
             form["dataset-shortname"] or form["dataset-name"]).strip()
-        pheno_dataset = save_new_dataset(
+        _pheno_dataset = save_new_dataset(
             cursor,
             population["Id"],
             form["dataset-name"].strip(),
diff --git a/uploader/population/views.py b/uploader/population/views.py
index b101d94..36201ba 100644
--- a/uploader/population/views.py
+++ b/uploader/population/views.py
@@ -1,5 +1,4 @@
 """Views dealing with populations/inbredsets"""
-import re
 import json
 import base64
 
diff --git a/uploader/samples/views.py b/uploader/samples/views.py
index 9ba1df8..b8ec4d4 100644
--- a/uploader/samples/views.py
+++ b/uploader/samples/views.py
@@ -3,11 +3,8 @@ import os
 import sys
 import uuid
 from pathlib import Path
-from typing import Iterator
 
-import MySQLdb as mdb
 from redis import Redis
-from MySQLdb.cursors import DictCursor
 from flask import (flash,
                    request,
                    url_for,
@@ -20,11 +17,11 @@ from uploader.files import save_file
 from uploader.ui import make_template_renderer
 from uploader.authorisation import require_login
 from uploader.input_validation import is_integer_input
-from uploader.datautils import order_by_family, enumerate_sequence
-from uploader.db_utils import (
-    with_db_connection,
-    database_connection,
-    with_redis_connection)
+from uploader.datautils import safe_int, order_by_family, enumerate_sequence
+from uploader.population.models import population_by_id, populations_by_species
+from uploader.db_utils import (with_db_connection,
+                               database_connection,
+                               with_redis_connection)
 from uploader.species.models import (all_species,
                                      species_by_id,
                                      order_species_by_family)
@@ -110,9 +107,7 @@ def list_samples(species_id: int, population_id: int):
         all_samples = enumerate_sequence(samples_by_species_and_population(
             conn, species_id, population_id))
         total_samples = len(all_samples)
-        offset = int(request.args.get("from") or 0)
-        if offset < 0:
-            offset = 0
+        offset = max(safe_int(request.args.get("from") or 0), 0)
         count = int(request.args.get("count") or 20)
         return render_template("samples/list-samples.html",
                                species=species,
-- 
cgit v1.2.3