Merge pull request #815 from sanger/develop

Develop into master

.github/workflows/automated_release.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     services:
       mysql:
-        image: mysql:5.7
+        image: mysql:8.0
         ports:
           - 3306:3306
         env:

.github/workflows/ci.yml

@@ -86,7 +86,7 @@ jobs:
     runs-on: ubuntu-latest
     services:
       mysql:
-        image: mysql:5.7
+        image: mysql:8.0
         ports:
           - 3306:3306
         env:

.release-version

@@ -1 +1 @@
-2.34.0
+2.35.0

Pipfile

@@ -20,7 +20,7 @@ colorlog = "~=6.7"
 eve = "~=2.1"
 flask-apscheduler = "~=1.12"
 flask-cors = "~=4.0"
-gunicorn = "~=20.0"
+gunicorn = "~=21.2"
 openpyxl = "~=3.1"
 pandas = "~=2.0"
 pika = "~=1.3"
@@ -30,7 +30,7 @@ python-dotenv = "~=1.0"
 requests = "~=2.31"
 slackclient = "~=2.9"
 sqlalchemy = "~=2.0"
-pymongo = "~=4.4.0"
+pymongo = "~=4.4.1"
 
 [requires]
 python_version = "3.8"

dependencies/docker-compose.yml

@@ -2,11 +2,11 @@ version: "3.8"
 services:
   # A MySQL service as close to production as currently possible
   # To run it as a standalone container:
-  #   docker run --name mysql-5.7 -e MYSQL_ALLOW_EMPTY_PASSWORD=yes -d -p 3306:3306 mysql:5.7
-  mysql-5.7:
+  #   docker run --name mysql-8.0 -e MYSQL_ALLOW_EMPTY_PASSWORD=yes -d -p 3306:3306 mysql:8.0
+  mysql-8.0:
     # Use the following on M1; for Docker Rosetta support on macOS Ventura.
     # platform: linux/amd64
-    image: mysql:5.7
+    image: mysql:8.0
     ports:
       - "3306:3306"
     environment:

lighthouse/validator.py

@@ -4,10 +4,7 @@
 
 from lighthouse.classes.beckman import Beckman
 from lighthouse.classes.biosero import Biosero
-from lighthouse.constants.error_messages import (
-    ERROR_PLATE_SPECS_EMPTY_LIST,
-    ERROR_PLATE_SPECS_INVALID_FORMAT,
-)
+from lighthouse.constants.error_messages import ERROR_PLATE_SPECS_EMPTY_LIST, ERROR_PLATE_SPECS_INVALID_FORMAT
 from lighthouse.constants.fields import FIELD_EVENT_RUN_ID
 
 logger = logging.getLogger(__name__)
@@ -95,7 +92,7 @@ def _check_with_validate_cptd_plate_specs(self, field, value):
         if len(value) == 0:
             self._error(field, ERROR_PLATE_SPECS_EMPTY_LIST)
 
-        if not all([type(ps) == list and len(ps) == 2 for ps in value]) or not all(
-            [type(s) == int for ps in value for s in ps]
+        if not all([type(ps) is list and len(ps) == 2 for ps in value]) or not all(
+            [type(s) is int for ps in value for s in ps]
         ):
             self._error(field, ERROR_PLATE_SPECS_INVALID_FORMAT)