Timezone parameter in docker (#937)

* Timezone parameter in docker

- This allows users to change the timezone without requiring model migrations.
- This commit itself will require a model migration
- Containers by default would be in UTC
- Users can override Alyx timezone although logs etc. will remain UTC

* Initial form value

* Add migrations

* Admin form tests

* Correct settings import

Author: k1o0

alyx/alyx/environment_template.env

@@ -10,7 +10,8 @@ DJANGO_DEBUG=False
 DJANGO_LOG_LEVEL=INFO
 DJANGO_SECRET_KEY='create_a_secret_key_here_and_make_sure_you_use_single_quotes'
 GLOBUS_CLIENT_ID=525cc543-8ccb-4d11-8036-af332da5eafd
+TZ=UTC  # Alyx datetime timezone. See https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
 # DJANGO_MEDIA_ROOT=https://alyx-uploaded.s3.eu-west-2.amazonaws.com/uploaded/  # add if s3
 # DJANGO_MEDIA_ROOT=/home/olivier/scratch/uploaded  # add if local instance (for docker deployment leave it commented)
 # DJANGO_TABLES_ROOT=https://ibl-brain-wide-map-public.s3.amazonaws.com/caches/alyx  # add if s3
-# DJANGO_TABLES_ROOT=/home/olivier/scratch/uploaded  # add if local instance (for docker deployment leave it commented)
+# DJANGO_TABLES_ROOT=/home/olivier/scratch/uploaded  # add if local instance (for docker deployment leave it commented)

alyx/data/migrations/0022_alter_datarepository_timezone.py

@@ -0,0 +1,18 @@
+# Generated by Django 5.2.8 on 2025-11-05 23:51
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('data', '0021_alter_dataset_collection_alter_dataset_hash_and_more'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='datarepository',
+            name='timezone',
+            field=models.CharField(blank=True, default='Africa/Djibouti', help_text='Timezone of the server (see https://en.wikipedia.org/wiki/List_of_tz_database_time_zones)', max_length=64),
+        ),
+    ]

alyx/misc/admin.py

@@ -3,6 +3,7 @@
 from django import forms
 from django.db import models
 from django.db.models import Q
+from django.conf import settings
 from django.contrib import admin
 from django.contrib.admin.widgets import AdminFileWidget
 from django.contrib.contenttypes.admin import GenericTabularInline
@@ -49,7 +50,7 @@ def clean_timezone(self):
         ref = self.cleaned_data['timezone']
         if ref not in all_timezones:
             raise forms.ValidationError(
-                ("Time Zone is incorrect here is the list (column TZ Database Name):  "
+                ("Time Zone is incorrect. Here is the list (column TZ Database Name):  "
                  "https://en.wikipedia.org/wiki/List_of_tz_database_time_zones"))
         return ref
 
@@ -70,6 +71,12 @@ def local(self, obj):
     def server(self, obj):
         return ','.join([p.name for p in obj.repositories.filter(globus_is_personal=False)])
 
+    def get_form(self, request, obj=None, **kwargs):
+        form = super().get_form(request, obj, **kwargs)
+        if not obj:
+            form.base_fields['timezone'].initial = settings.TIME_ZONE
+        return form
+
 
 class LabMembershipAdmin(BaseAdmin):
     fields = ['user', 'lab', 'role', 'start_date', 'end_date']

alyx/misc/migrations/0012_alter_lab_timezone.py

@@ -0,0 +1,18 @@
+# Generated by Django 5.2.8 on 2025-11-05 23:51
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('misc', '0011_alter_lab_name'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='lab',
+            name='timezone',
+            field=models.CharField(blank=True, help_text='Timezone of the server (see https://en.wikipedia.org/wiki/List_of_tz_database_time_zones)', max_length=64),
+        ),
+    ]

alyx/misc/models.py

@@ -19,11 +19,10 @@
 from django.utils import timezone
 
 from alyx.base import BaseModel, modify_fields, ALF_SPEC
-from alyx.settings import TIME_ZONE, UPLOADED_IMAGE_WIDTH, DEFAULT_LAB_PK
 
 
 def default_lab():
-    return DEFAULT_LAB_PK
+    return settings.DEFAULT_LAB_PK
 
 
 class LabMember(AbstractUser):
@@ -78,7 +77,7 @@ class Lab(BaseModel):
     institution = models.CharField(max_length=255, blank=True)
     address = models.CharField(max_length=255, blank=True)
     timezone = models.CharField(
-        max_length=64, blank=True, default=TIME_ZONE,
+        max_length=64, blank=True,
         help_text="Timezone of the server "
         "(see https://en.wikipedia.org/wiki/List_of_tz_database_time_zones)")
 
@@ -106,6 +105,10 @@ class Lab(BaseModel):
     def __str__(self):
         return self.name
 
+    def save(self, *args, timezone=None, **kwargs):
+        self.timezone = timezone or self.timezone or settings.TIME_ZONE
+        super().save(*args, **kwargs)
+
 
 class LabMembership(BaseModel):
     user = models.ForeignKey(settings.AUTH_USER_MODEL, on_delete=models.CASCADE)
@@ -158,7 +161,7 @@ def save(self, image_width=None, **kwargs):
             with Image.open(self.image) as im:
                 with BytesIO() as output:
                     # Compute new size by keeping the aspect ratio.
-                    width = int(image_width or UPLOADED_IMAGE_WIDTH)
+                    width = int(image_width or settings.UPLOADED_IMAGE_WIDTH)
                     wpercent = width / float(im.size[0])
                     height = int((float(im.size[1]) * float(wpercent)))
                     im.thumbnail((width, height))

alyx/misc/tests_admin.py

@@ -0,0 +1,53 @@
+from unittest.mock import MagicMock
+
+from django.test import TestCase, Client, override_settings
+from django.contrib.admin.sites import AdminSite
+
+from misc.models import LabMember, Lab
+from misc.management.commands.set_user_permissions import Command
+from misc.admin import LabAdmin
+
+
+class TestLabAdminViews(TestCase):
+
+    def setUp(self):
+        self.client = Client()
+        self.user = LabMember.objects.create_user(
+            username='foo', password='bar123', email='[email protected]')
+        self.user.is_staff = self.user.is_active = True  # used by below Command instance
+        self.user.save()
+
+        self.superuser = LabMember.objects.create_superuser(
+            username='admin', password='admin', email='[email protected]')
+        Command().handle()  # set user group permissions
+        self.client.login(username='foo', password='bar123')
+
+    @override_settings(TIME_ZONE='Africa/Djibouti')
+    def test_admin_add_form_view(self):
+        """Test the lab add form view."""
+        response = self.client.get('/admin/misc/lab/add/', follow=True)
+        self.assertEqual(response.status_code, 200)
+        self.client.login(username='admin', password='admin')
+        response = self.client.get('/admin/misc/lab/add/', follow=True)
+        self.assertEqual(response.status_code, 200)
+        la = LabAdmin(model=Lab, admin_site=AdminSite())
+        request = MagicMock()
+        request.user = self.user
+        LabForm = la.get_form(request)
+        # Check initial value of timezone field
+        form = LabForm(data={})
+        self.assertEqual(form.fields['timezone'].initial, 'Africa/Djibouti')
+        # Check form cleaning
+        data = {
+            'timezone': 'Africa/Djibouti',
+            'name': 'TestLab',
+            'reference_weight_pct': 0.8,
+            'zscore_weight_pct': 0
+        }
+        form = LabForm(data=data)
+        self.assertTrue(form.is_valid())
+        data['timezone'] = 'Africa/Zaire'  # Invalid timezone
+        form = LabForm(data=data)
+        self.assertFalse(form.is_valid())
+        error = form.errors.get('timezone')[0]
+        self.assertIn('Time Zone is incorrect. Here is the list', error)

deploy/docker/Dockerfile_base

@@ -2,7 +2,8 @@ FROM ubuntu/apache2:2.4-22.04_beta
 
 # python unbuffered allows to get real-time logs
 ENV PYTHONUNBUFFERED=1
-ENV TZ=Europe/London
+ARG TZ=UTC
+ENV TZ=${TZ}
 RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
 
 RUN cat /etc/lsb-release && apt-get update

deploy/docker/settings_lab-deploy.py

@@ -1,10 +1,15 @@
 import os
+import zoneinfo
 from textwrap import dedent
 
 LANGUAGE_CODE = 'en-us'
-TIME_ZONE = 'Europe/London'
+TIME_ZONE = os.getenv('TZ', 'Europe/London').strip()
+if TIME_ZONE not in zoneinfo.available_timezones():
+    raise ValueError(f'Invalid TIME_ZONE: "{TIME_ZONE}". '
+                     'Please set a valid timezone with TZ env variable. '
+                     'See https://en.wikipedia.org/wiki/List_of_tz_database_time_zones.')
 GLOBUS_CLIENT_ID = os.getenv('GLOBUS_CLIENT_ID')
-SUBJECT_REQUEST_EMAIL_FROM = 'alyx@internationalbrainlab.org'
+SUBJECT_REQUEST_EMAIL_FROM = os.getenv('APACHE_SERVER_ADMIN', 'alyx@localhost')
 DEFAULT_SOURCE = 'IBL'
 DEFAULT_PROTOCOL = '1'
 SUPERUSERS = ('root',)
@@ -13,8 +18,8 @@
 DEFAULT_LAB_NAME = 'cortexlab'
 WATER_RESTRICTIONS_EDITABLE = False  # if set to True, all users can edit water restrictions
 DEFAULT_LAB_PK = '4027da48-7be3-43ec-a222-f75dffe36872'
-SESSION_REPO_URL = \
-    "http://ibl.flatironinstitute.org/{lab}/Subjects/{subject}/{date}/{number:03d}/"
+SESSION_REPO_URL = f'https://{os.getenv("APACHE_SERVER_NAME", "localhost")}/'
+SESSION_REPO_URL += "{lab}/Subjects/{subject}/{date}/{number:03d}/"
 NARRATIVE_TEMPLATES = {
     'Headplate implant': dedent('''
     == General ==