rebase was broken

.gitignore

@@ -7,3 +7,4 @@
 rsnapshot/
 *.swp
 env/
+*.tar.gz

.pre-commit-config.yaml

@@ -69,7 +69,7 @@ repos:
 # On centos, with py36, this was locked to 4.0.1
 # Had to install anaconda3 and adjust INSTALL_PYTHON @ .git/hooks/pre-commit
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
     -   id: trailing-whitespace
         types: [python]
@@ -88,7 +88,7 @@ repos:
 # https://github.com/hadolint/hadolint/blob/master/docs/INTEGRATION.md#pre-commit
 
 -   repo: https://github.com/psf/black
-    rev: 22.8.0
+    rev: 22.12.0
     hooks:
     -   id: black
         language_version: python3
@@ -101,7 +101,7 @@ repos:
         additional_dependencies: [black==21.4b2]
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.38.2
+    rev: v3.3.1
     hooks:
     -   id: pyupgrade
         args: [--py38-plus]  # 3.8
@@ -116,7 +116,7 @@ repos:
 #        args: [--max-line-length, "222", --extend-ignore, "E203"]
 
 -   repo: https://github.com/pycqa/doc8
-    rev: v1.0.0
+    rev: v1.1.1
     hooks:
     -   id: doc8
 
@@ -131,13 +131,13 @@ repos:
     -   id: rst-directive-colons
 
 -   repo: https://github.com/adamchainz/django-upgrade
-    rev: 1.10.0
+    rev: 1.12.0
     hooks:
     -   id: django-upgrade
         args: [--target-version, "3.2"]
 
 -   repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.11.4
     hooks:
     -   id: isort
         args: [--profile, "black"]

Dockerfile

@@ -6,5 +6,6 @@ RUN --mount=type=cache,target=/root/.cache pip install -r requirements/prod.txt
 EXPOSE 8000
 ENV PYTHONBREAKPOINT ipdb.set_trace
 ENV PYTHONUNBUFFERED 1
+ENV PYTHONDONTWRITEBYTECODE 1
 #CMD ["python", "/usr/src/app/manage.py", "runserver_plus", "0.0.0.0:8000"]
 CMD ["gunicorn", "wui.wsgi:application", "-t", "600", "-w", "2", "-b", ":8000"]

docker-compose.yml

@@ -14,6 +14,8 @@ services:
       interval: 10s
       timeout: 2s
       retries: 10
+    ports:
+      - 5432:5432
 
   parkour2-django:
     container_name: parkour2-django
@@ -23,6 +25,7 @@ services:
       - ./parkour.env
     restart: always
     volumes:
+      - ./parkour_app:/usr/src/app
       - media:/usr/src/app/media
       - staticfiles:/usr/src/app/staticfiles
     depends_on:

nginx-ncdb.conf

@@ -0,0 +1,24 @@
+upstream ncdb {
+	server parkour2-nocodb:8080;
+}
+
+server {
+	listen 80;
+	listen [::]:80;
+	server_name db-test.ie-freiburg.mpg.de;
+	client_max_body_size 50M;
+	client_body_buffer_size 50M;
+	client_body_timeout 120;
+	client_header_timeout 120;
+	keepalive_timeout 120;
+	add_header X-Frame-Options SAMEORIGIN always;
+	location / {
+		proxy_connect_timeout 120;
+		proxy_read_timeout 120;
+		proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+		proxy_set_header X-Forwarded-Proto $scheme;
+		proxy_set_header Host $http_host;
+		proxy_redirect off;
+		proxy_pass http://ncdb;
+	}
+}

parkour_app/common/admin.py

@@ -75,6 +75,7 @@ def clean_password2(self):
         return password2
 
 
+@admin.register(User)
 class UserAdmin(NamedUserAdmin):
     add_form = UserCreationForm
     add_fieldsets = (
@@ -214,4 +215,3 @@ def save_model(self, request, obj, form, change):
 
 
 # admin.site.unregister(User)
-admin.site.register(User, UserAdmin)

parkour_app/common/serializers.py

@@ -1,9 +1,15 @@
 from rest_framework.serializers import ModelSerializer
 
-from .models import CostUnit
+from .models import CostUnit, User
 
 
 class CostUnitSerializer(ModelSerializer):
     class Meta:
         model = CostUnit
         fields = ("id", "name")
+
+
+class UserSerializer(ModelSerializer):
+    class Meta:
+        model = User
+        fields = ("email",)

parkour_app/flowcell/admin.py

@@ -26,32 +26,29 @@ class LaneInline(admin.TabularInline):
         "completed",
     )
 
+    @admin.display(description="Name")
     def name(self, instance):
         return instance.lane.name
 
-    name.short_description = "Name"
-
+    @admin.display(description="Pool")
     def pool(self, instance):
         return instance.lane.pool.name
 
-    pool.short_description = "Pool"
-
+    @admin.display(description="Loading Concentration")
     def loading_concentration(self, instance):
         return instance.lane.loading_concentration
 
-    loading_concentration.short_description = "Loading Concentration"
-
+    @admin.display(description="PhiX %")
     def phix(self, instance):
         return instance.lane.phix
 
-    phix.short_description = "PhiX %"
-
+    @admin.display(
+        description="Completed",
+        boolean=True,
+    )
     def completed(self, instance):
         return instance.lane.completed
 
-    completed.short_description = "Completed"
-    completed.boolean = True
-
     def has_add_permission(self, request, obj=None):
         return False
 
@@ -64,21 +61,18 @@ class SequencerAdmin(admin.ModelAdmin):
         "mark_as_non_obsolete",
     )
 
+    @admin.action(description="Mark sequencer as obsolete")
     def mark_as_obsolete(self, request, queryset):
         queryset.update(obsolete=settings.OBSOLETE)
 
-    mark_as_obsolete.short_description = "Mark sequencer as obsolete"
-
+    @admin.action(description="Mark sequencer as non-obsolete")
     def mark_as_non_obsolete(self, request, queryset):
         queryset.update(obsolete=settings.NON_OBSOLETE)
 
-    mark_as_non_obsolete.short_description = "Mark sequencer as non-obsolete"
-
+    @admin.display(description="STATUS")
     def obsolete_name(self, obj):
         return "Non-obsolete" if obj.obsolete == settings.NON_OBSOLETE else "Obsolete"
 
-    obsolete_name.short_description = "STATUS"
-
 
 @admin.register(Flowcell)
 class FlowcellAdmin(admin.ModelAdmin):

parkour_app/index_generator/admin.py

@@ -21,26 +21,22 @@ class BaseInline(admin.TabularInline):
     can_delete = False
     extra = 0
 
+    @admin.display(description="Name")
     def name(self, instance):
         return getattr(instance, self.verbose_name.lower()).name
 
-    name.short_description = "Name"
-
+    @admin.display(description="Barcode")
     def barcode(self, instance):
         return getattr(instance, self.verbose_name.lower()).barcode
 
-    barcode.short_description = "Barcode"
-
+    @admin.display(description="Status")
     def status(self, instance):
         return getattr(instance, self.verbose_name.lower()).status
 
-    status.short_description = "Status"
-
+    @admin.display(description="Request")
     def request(self, instance):
         return getattr(instance, self.verbose_name.lower()).request.get().name
 
-    request.short_description = "Request"
-
     def has_add_permission(self, request, obj=None):
         return False
 
@@ -84,17 +80,14 @@ class PoolSizeAdmin(admin.ModelAdmin):
         "mark_as_non_obsolete",
     )
 
+    @admin.action(description="Mark pool size as obsolete")
     def mark_as_obsolete(self, request, queryset):
         queryset.update(obsolete=settings.OBSOLETE)
 
-    mark_as_obsolete.short_description = "Mark pool size as obsolete"
-
+    @admin.action(description="Mark pool size as non-obsolete")
     def mark_as_non_obsolete(self, request, queryset):
         queryset.update(obsolete=settings.NON_OBSOLETE)
 
-    mark_as_non_obsolete.short_description = "Mark pool size as non-obsolete"
-
+    @admin.display(description="STATUS")
     def obsolete_name(self, obj):
         return "Non-obsolete" if obj.obsolete == settings.NON_OBSOLETE else "Obsolete"
-
-    obsolete_name.short_description = "STATUS"

parkour_app/invoicing/migrations/0004_alter_librarypreparationcosts_library_protocol.py

@@ -0,0 +1,25 @@
+# Generated by Django 3.2.16 on 2023-01-24 14:20
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("library_sample_shared", "0008_optional_index1_long"),
+        ("invoicing", "0003_dj32_upgrade"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="librarypreparationcosts",
+            name="library_protocol",
+            field=models.OneToOneField(
+                limit_choices_to={"obsolete": 1},
+                null=True,
+                on_delete=django.db.models.deletion.SET_NULL,
+                to="library_sample_shared.libraryprotocol",
+            ),
+        ),
+    ]

parkour_app/invoicing/models.py

@@ -40,9 +40,8 @@ def __str__(self):
 
 
 class LibraryPreparationCosts(models.Model):
-    library_protocol = models.ForeignKey(
+    library_protocol = models.OneToOneField(
         LibraryProtocol,
-        unique=True,
         limit_choices_to={"obsolete": 1},
         on_delete=models.SET_NULL,
         null=True,

parkour_app/library_sample_shared/admin.py

@@ -38,22 +38,19 @@ class ReadLengthAdmin(admin.ModelAdmin):
     list_display = ("name", "obsolete_name")
     actions = ("mark_as_obsolete", "mark_as_non_obsolete")
 
+    @admin.action(description="Mark read length as obsolete")
     def mark_as_obsolete(self, request, queryset):
         queryset.update(obsolete=settings.OBSOLETE)
 
-    mark_as_obsolete.short_description = "Mark read length as obsolete"
-
+    @admin.action(description="Mark read length as non-obsolete")
     def mark_as_non_obsolete(self, request, queryset):
         queryset.update(obsolete=settings.NON_OBSOLETE)
 
-    mark_as_non_obsolete.short_description = "Mark read length as non-obsolete"
-
+    @admin.display(description="STATUS")
     def obsolete_name(self, obj):
 
         return "Non-obsolete" if obj.obsolete == settings.NON_OBSOLETE else "Obsolete"
 
-    obsolete_name.short_description = "STATUS"
-
 
 class IndexI7Inline(admin.TabularInline):
     model = IndexI7
@@ -107,22 +104,19 @@ class IndexTypeAdmin(admin.ModelAdmin):
         ),
     )
 
+    @admin.action(description="Mark index type as obsolete")
     def mark_as_obsolete(self, request, queryset):
         queryset.update(obsolete=settings.OBSOLETE)
 
-    mark_as_obsolete.short_description = "Mark index type as obsolete"
-
+    @admin.action(description="Mark index type as non-obsolete")
     def mark_as_non_obsolete(self, request, queryset):
         queryset.update(obsolete=settings.NON_OBSOLETE)
 
-    mark_as_non_obsolete.short_description = "Mark index type as non-obsolete"
-
+    @admin.display(description="STATUS")
     def obsolete_name(self, obj):
 
         return "Non-obsolete" if obj.obsolete == settings.NON_OBSOLETE else "Obsolete"
 
-    obsolete_name.short_description = "STATUS"
-
     def change_view(self, request, object_id, form_url="", extra_context=None):
         # Display inline when the object has been saved and
         # the format has been set to 'plate'
@@ -184,11 +178,10 @@ class IndexI5Admin(ImportExportModelAdmin):
 
     resource_class = IndexI5Resource
 
+    @admin.display(description="Index ID")
     def idx_id(sef, obj):
         return obj.prefix + obj.number
 
-    idx_id.short_description = "Index ID"
-
 
 class IndexI7Resource(resources.ModelResource):
     class Meta:
@@ -218,11 +211,10 @@ class IndexI7Admin(ImportExportModelAdmin):
 
     resource_class = IndexI7Resource
 
+    @admin.display(description="Index ID")
     def idx_id(sef, obj):
         return obj.prefix + obj.number
 
-    idx_id.short_description = "Index ID"
-
 
 @admin.register(LibraryProtocol)
 class LibraryProtocolAdmin(admin.ModelAdmin):
@@ -246,22 +238,19 @@ class LibraryProtocolAdmin(admin.ModelAdmin):
         "mark_as_non_obsolete",
     )
 
+    @admin.action(description="Mark library protocol as obsolete")
     def mark_as_obsolete(self, request, queryset):
         queryset.update(obsolete=settings.OBSOLETE)
 
-    mark_as_obsolete.short_description = "Mark library protocol as obsolete"
-
+    @admin.action(description="Mark library protocol as non-obsolete")
     def mark_as_non_obsolete(self, request, queryset):
         queryset.update(obsolete=settings.NON_OBSOLETE)
 
-    mark_as_non_obsolete.short_description = "Mark library protocol as non-obsolete"
-
+    @admin.display(description="STATUS")
     def obsolete_name(self, obj):
 
         return "Non-obsolete" if obj.obsolete == settings.NON_OBSOLETE else "Obsolete"
 
-    obsolete_name.short_description = "STATUS"
-
 
 @admin.register(LibraryType)
 class LibraryTypeAdmin(admin.ModelAdmin):