Breeding Pair form validation removes parents when culled (#944)

* breeding pair form should not exclude parent if culled. Fixes #941

* hopefully fixes the tests

* fix timezone failing test

Author: oliche

alyx/jobs/tests.py

@@ -68,7 +68,7 @@ def test_cleanup(self):
         """Test for cleanup action."""
         # First run in dry mode, expect submit_delete to not be called
         n = self.n_tasks - 10
-        before_date = (self.base - timedelta(days=n)).date()
+        before_date = (self.base - timedelta(days=n - .1)).date()
         with patch.object(self.command.stdout, 'write') as stdout_mock:
             self.command.handle(action='cleanup', before=str(before_date), dry=True)
             stdout_mock.assert_called()

alyx/subjects/admin.py

@@ -1,3 +1,5 @@
+import uuid
+
 from django import forms
 from django_admin_listfilter_dropdown.filters import RelatedDropdownFilter
 from django.contrib import admin
@@ -836,10 +838,12 @@ def queryset(self, request, queryset):
             return queryset.all()
 
 
-def _bp_subjects(line, sex):
+def _bp_subjects(line, sex, current_subjects=None):
     # All alive subjects of the given sex.
     qs = Subject.objects.filter(
-        sex=sex, responsible_user__is_stock_manager=True, cull__isnull=True)
+        Q(sex=sex, responsible_user__is_stock_manager=True, cull__isnull=True) |
+        Q(pk__in=[current_subjects] if isinstance(current_subjects, uuid.UUID) else []),
+    )
     qs = qs.order_by('nickname')
     ids = [item.id for item in qs]
     if ids:
@@ -876,7 +880,9 @@ def __init__(self, *args, **kwargs):
         for w in ('father', 'mother1', 'mother2'):
             sex = 'M' if w == 'father' else 'F'
             if w in self.fields:
-                self.fields[w].queryset = _bp_subjects(self.instance.line, sex)
+                self.fields[w].queryset = _bp_subjects(
+                    self.instance.line, sex, current_subjects=
+                    getattr(getattr(self.instance, w), 'id', None))
 
     def save(self, commit=True):
         cage = self.cleaned_data.get('cage')
@@ -1076,7 +1082,7 @@ def formfield_for_foreignkey(self, db_field, request=None, **kwargs):
             return field
         if db_field.name in ('father', 'mother1', 'mother2'):
             sex = 'M' if db_field.name == 'father' else 'F'
-            field.queryset = _bp_subjects(obj, sex)
+            field.queryset = _bp_subjects(obj, sex, BreedingPair.objects.filter(line=obj).values_list(f'{db_field.name}__pk'))
         return field
 
 

alyx/subjects/tests_admin.py

@@ -7,9 +7,45 @@
 
 from alyx.test_base import setup_admin_subject_user
 from misc.models import LabMember
-from subjects.models import Subject
+from subjects.models import Subject, BreedingPair
 from actions.models import Cull, CullMethod, CullReason
-from subjects.admin import CullForm, SubjectAdmin
+from subjects.admin import CullForm, SubjectAdmin, BreedingPairAdminForm
+
+
+class TestBreedingPairAdmin(TestCase):
+    fixtures = ['misc.lab.json']
+
+    def setUp(self):
+        self.site = AdminSite()
+        setup_admin_subject_user(self)
+
+    def test_set_end_date_with_culled_subject(self):
+        lab_member_stock_manager = LabMember.objects.create_user(
+            username='stock_manager', password='bar123', email='foo@example.com', is_staff=True, is_active=True, is_stock_manager=True)
+        kwargs_subjects = dict(birth_date=date(2025, 1, 1), lab=self.lab, responsible_user=lab_member_stock_manager)
+        father = Subject.objects.create(nickname='father', sex='M', **kwargs_subjects)
+        mother1 = Subject.objects.create(nickname='mother1', sex='F', **kwargs_subjects)
+        breeding_pair = BreedingPair.objects.create(father=father, mother1=mother1, mother2=None)
+        # the form is valid as both parents are alive
+        form_data = {
+        'json': breeding_pair.json,
+            'description': breeding_pair.description,
+            'name': breeding_pair.name,
+         'line': breeding_pair.line,
+         'start_date': breeding_pair.start_date,
+         'end_date': breeding_pair.end_date,
+         'father': breeding_pair.father,
+         'mother1': breeding_pair.mother1,
+         'mother2': breeding_pair.mother2,
+         }
+        form_instance = BreedingPairAdminForm(data=form_data, instance=breeding_pair)
+        self.assertTrue(form_instance.is_valid())
+        # the form is still valid once the father is culled: it can´t  be set on a new breeding pair,
+        # but it can remain on this one and the form is valid
+        Cull(subject=father, user=lab_member_stock_manager, date=date(2025, 6, 1))
+        father.save()
+        form_instance = BreedingPairAdminForm(data=form_data, instance=breeding_pair)
+        self.assertTrue(form_instance.is_valid())
 
 
 class TestSubjectCullForm(TestCase):

deploy/docker/Dockerfile

@@ -4,12 +4,13 @@ COPY settings-deploy.py /var/www/alyx/alyx/alyx/settings.py
 COPY settings_lab-deploy.py /var/www/alyx/alyx/alyx/settings_lab.py
 COPY settings_lab-user.py* /var/www/alyx/alyx/alyx/settings_lab.py
 
-ARG alyx_branch=deploy
+ARG alyx_branch=dev
+ARG iblalyx_branch=deploy
 
 RUN git -C /var/www/alyx fetch origin ${alyx_branch}
 RUN git -C /var/www/alyx checkout -B ${alyx_branch} origin/${alyx_branch}
-RUN git -C /home/iblalyx fetch origin ${alyx_branch}
-RUN git -C /home/iblalyx checkout -B ${alyx_branch} origin/${alyx_branch}
+RUN git -C /home/iblalyx fetch origin ${iblalyx_branch}
+RUN git -C /home/iblalyx checkout -B ${iblalyx_branch} origin/${iblalyx_branch}
 
 RUN pip install -r /var/www/alyx/requirements.txt
 

deploy/docker/Dockerfile_base

@@ -1,13 +1,13 @@
-FROM ubuntu/apache2:latest
+FROM ubuntu/apache2:2.4-22.04_beta
 
 # python unbuffered allows to get real-time logs
-ENV PYTHONUNBUFFERED 1
+ENV PYTHONUNBUFFERED=1
 ENV TZ=Europe/London
 RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
 
-
+RUN cat /etc/lsb-release && apt-get update
 # Install services, packages and perform cleanup
-RUN apt-get update && apt-get install -y \
+RUN apt-get install -y \
     awscli \
     bash \
     build-essential \
@@ -23,16 +23,16 @@ RUN apt-get update && apt-get install -y \
     wget
 
 # The apt-add-repository command is installed by software-properties common above
-ARG PYTHON=python3.12
-RUN apt-get update && apt-get install -y ${PYTHON} ${PYTHON}-venv
+ARG PYTHON=python3.13
+RUN apt-add-repository -y ppa:deadsnakes/ppa && apt-get update && apt-get install -y ${PYTHON} ${PYTHON}-venv
 
 # Clean up
 RUN apt-get clean && rm -rf /var/lib/apt/lists/*
 
 RUN echo "root:Docker!" | chpasswd
 
 # Alyx application installation
-RUN git clone --branch master https://github.com/cortex-lab/alyx.git /var/www/alyx
+RUN git clone --branch dev https://github.com/cortex-lab/alyx.git /var/www/alyx
 # Best practice for configuring python venv
 ENV VIRTUAL_ENV=/var/www/alyx/.venv
 RUN ${PYTHON} -m venv ${VIRTUAL_ENV}
@@ -48,11 +48,11 @@ RUN git clone --branch main https://github.com/int-brain-lab/iblalyx.git /home/i
     && pip install --no-cache-dir -r /home/iblalyx/requirements.txt
 
 # Apache ENVs
-ENV APACHE_RUN_USER www-data
-ENV APACHE_RUN_GROUP www-data
-ENV APACHE_LOCK_DIR /var/lock/apache2
-ENV APACHE_LOG_DIR /var/log/apache2
-ENV APACHE_PID_FILE /var/run/apache2/apache2.pid
+ENV APACHE_RUN_USER=www-data
+ENV APACHE_RUN_GROUP=www-data
+ENV APACHE_LOCK_DIR=/var/lock/apache2
+ENV APACHE_LOG_DIR=/var/log/apache2
+ENV APACHE_PID_FILE=/var/run/apache2/apache2.pid
 
 RUN mkdir -p ${APACHE_LOG_DIR} \
     && touch ${APACHE_LOG_DIR}/django.log \