Schema Migration: Shared FluorState MTI for protein and dye states, introduce FluorescenceMeasurement

.github/workflows/ci.yml

@@ -49,6 +49,17 @@ jobs:
       - name: Run TypeScript type checking
         run: pnpm typecheck
 
+  check-migrations:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Code Repository
+        uses: actions/checkout@v5
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+      - name: Check for new migrations
+        run: uv run backend/manage.py makemigrations --check --noinput
+
   test:
     runs-on: ubuntu-latest
     services:

backend/config/settings/base.py

@@ -63,7 +63,6 @@
 
 THIRD_PARTY_APPS = [
     "django_structlog",  # Structured logging
-    "scout_apm.django",  # APM monitoring
     "crispy_forms",  # Form layouts
     "crispy_bootstrap5",
     "allauth",  # registration

backend/config/settings/production.py

@@ -211,6 +211,7 @@ def WHITENOISE_IMMUTABLE_FILE_TEST(path, url):
 # Scout APM Configuration
 # ------------------------------------------------------------------------------
 # SCOUT_MONITOR and SCOUT_KEY are automatically set by the Heroku addon
+INSTALLED_APPS += ["scout_apm.django"]
 SCOUT_NAME = "FPbase"
 
 # Structlog Configuration for Production

backend/favit/models.py

@@ -1,3 +1,7 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
 from django.conf import settings
 from django.contrib.contenttypes.fields import GenericForeignKey
 from django.contrib.contenttypes.models import ContentType
@@ -6,19 +10,24 @@
 
 from .managers import FavoriteManager
 
+if TYPE_CHECKING:
+    from fpbase.users.models import User
+
 
 class Favorite(models.Model):
-    user = models.ForeignKey(
+    user_id: int
+    user: models.ForeignKey[User] = models.ForeignKey(
         getattr(settings, "AUTH_USER_MODEL", "auth.User"),
         related_name="favorites",
         on_delete=models.CASCADE,
     )
-    target_content_type = models.ForeignKey(ContentType, on_delete=models.CASCADE)
+    target_content_type_id: int
+    target_content_type: models.ForeignKey[ContentType] = models.ForeignKey(ContentType, on_delete=models.CASCADE)
     target_object_id = models.PositiveIntegerField()
     target = GenericForeignKey("target_content_type", "target_object_id")
     timestamp = models.DateTimeField(auto_now_add=True, db_index=True)
 
-    objects = FavoriteManager()
+    objects: FavoriteManager = FavoriteManager()
 
     class Meta:
         ordering = ["-timestamp"]

backend/fpbase/cache_utils.py

@@ -62,6 +62,7 @@ def _invalidate_optical_config_cache() -> None:
 SPECTRUM_OWNER_MODELS = {
     "proteins.Camera",
     "proteins.Dye",
+    "proteins.DyeState",
     "proteins.Filter",
     "proteins.Light",
     "proteins.Protein",

backend/fpbase/celery.py

@@ -10,7 +10,8 @@
 app = Celery("fpbase", namespace="CELERY")
 app.config_from_object("django.conf:settings", namespace="CELERY")
 
-scout_apm.celery.install(app)
+if getattr(settings, "SCOUT_NAME", False):
+    scout_apm.celery.install(app)
 
 # Load task modules from all registered Django app configs.
 app.autodiscover_tasks(lambda: settings.INSTALLED_APPS)

backend/fpbase/users/models.py

@@ -1,9 +1,18 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
 from django.contrib.auth.models import AbstractUser
 from django.contrib.auth.signals import user_logged_in
 from django.db import models
 from django.urls import reverse
 from django.utils.translation import gettext_lazy as _
 
+if TYPE_CHECKING:
+    from favit.models import Favorite
+    from proteins.models import Microscope, OpticalConfig, ProteinCollection
+    from references.models import Reference
+
 
 class User(AbstractUser):
     # # AbstractUser Fields
@@ -19,6 +28,15 @@ class User(AbstractUser):
     # around the globe.
     name = models.CharField(_("Name of User"), blank=True, max_length=255)
 
+    if TYPE_CHECKING:
+        logins: models.QuerySet[UserLogin]
+        favorites: models.QuerySet[Favorite]
+        reference_author: models.QuerySet[Reference]
+        reference_modifier: models.QuerySet[Reference]
+        microscopes: models.QuerySet[Microscope]
+        opticalconfigs: models.QuerySet[OpticalConfig]
+        proteincollections: models.QuerySet[ProteinCollection]
+
     def __str__(self):
         return self.username
 
@@ -29,7 +47,8 @@ def get_absolute_url(self):
 class UserLogin(models.Model):
     """Represent users' logins, one per record"""
 
-    user = models.ForeignKey(User, on_delete=models.CASCADE, related_name="logins")
+    user_id: int
+    user: models.ForeignKey[User] = models.ForeignKey(User, on_delete=models.CASCADE, related_name="logins")
     timestamp = models.DateTimeField(auto_now_add=True)
 
     def __str__(self) -> str:

backend/fpbase/views.py

@@ -149,7 +149,7 @@ def get_context_data(self):
         data = super().get_context_data()
         data["stats"] = {
             "proteins": Protein.objects.count(),
-            "protspectra": Spectrum.objects.exclude(owner_state=None).count(),
+            "protspectra": Spectrum.objects.exclude(owner_fluor=None).count(),
         }
         return data
 

backend/proteins/admin.py

@@ -15,10 +15,11 @@
     BleachMeasurement,
     Camera,
     Dye,
+    DyeState,
     Excerpt,
     Filter,
     FilterPlacement,
-    Fluorophore,
+    FluorState,
     Light,
     Lineage,
     Microscope,
@@ -41,7 +42,7 @@
 class SpectrumOwner:
     list_display = ("__str__", "spectra", "created_by", "created")
     list_select_related = ("created_by",)
-    list_filter = ("created", "manufacturer")
+    list_filter = ("created",)
     search_fields = ("name",)
 
     def __init__(self, *args, **kwargs):
@@ -56,7 +57,7 @@ def _makelink(sp):
             return f'<a href="{url}">{sp.get_subtype_display()}{pending}</a>'
 
         links = []
-        if isinstance(obj, Fluorophore):
+        if isinstance(obj, FluorState):
             [links.append(_makelink(sp)) for sp in obj.spectra.all()]
         else:
             links.append(_makelink(obj.spectrum))
@@ -98,10 +99,8 @@ class OSERInline(admin.StackedInline):
     ]
 
 
-class StateInline(MultipleSpectraOwner, admin.StackedInline):
-    # form = StateForm
-    # formset = StateFormSet
-    model = State
+class FluorStateInline(MultipleSpectraOwner):
+    model = FluorState
     extra = 0
     can_delete = True
     show_change_link = True
@@ -113,10 +112,9 @@ class StateInline(MultipleSpectraOwner, admin.StackedInline):
                 "fields": (
                     ("ex_max", "em_max"),
                     ("ext_coeff", "qy"),
-                    ("twop_ex_max", "twop_peakGM", "twop_qy"),
-                    ("pka", "maturation"),
+                    ("twop_ex_max", "twop_peak_gm", "twop_qy"),
+                    "pka",
                     "lifetime",
-                    "bleach_links",
                     "spectra",
                 )
             },
@@ -131,13 +129,25 @@ class StateInline(MultipleSpectraOwner, admin.StackedInline):
     ]
     readonly_fields = (
         "slug",
-        "bleach_links",
         "created",
         "created_by",
         "modified",
         "updated_by",
     )
 
+
+class StateInline(FluorStateInline, admin.StackedInline):
+    # form = StateForm
+    # formset = StateFormSet
+    model = State
+    fieldsets = [
+        *FluorStateInline.fieldsets,
+        (None, {"fields": ("bleach_links",)}),
+        (None, {"fields": ("maturation",)}),
+    ]
+
+    readonly_fields = (*FluorStateInline.readonly_fields, "bleach_links")
+
     @admin.display(description="BleachMeasurements")
     def bleach_links(self, obj):
         links = []
@@ -148,6 +158,10 @@ def bleach_links(self, obj):
         return mark_safe(", ".join(links))
 
 
+class DyeStateInline(FluorStateInline, admin.StackedInline):
+    model = DyeState
+
+
 class LineageInline(admin.TabularInline):
     model = Lineage
     autocomplete_fields = ("parent", "root_node")
@@ -165,9 +179,24 @@ class LightAdmin(SpectrumOwner, admin.ModelAdmin):
 
 
 @admin.register(Dye)
-class DyeAdmin(MultipleSpectraOwner, VersionAdmin):
+class DyeAdmin(admin.ModelAdmin):
     model = Dye
+    list_display = ("__str__", "created_by", "created")
     ordering = ("-created",)
+    list_filter = ("created", "manufacturer")
+    fields = (
+        "name",
+        "slug",
+        "manufacturer",
+        "default_state",
+        "primary_reference",
+        "created",
+        "modified",
+        "created_by",
+        "updated_by",
+    )
+    readonly_fields = ("created", "modified")
+    inlines = (DyeStateInline,)
 
 
 @admin.register(Filter)
@@ -198,39 +227,42 @@ class SpectrumAdmin(VersionAdmin):
     model = Spectrum
     autocomplete_fields = ["reference"]
     list_select_related = (
-        "owner_state__protein",
+        "owner_fluor",
         "owner_filter",
         "owner_camera",
         "owner_light",
-        "owner_dye",
         "created_by",
     )
     list_display = ("__str__", "category", "subtype", "owner", "created_by")
     list_filter = ("status", "created", "category", "subtype")
     readonly_fields = ("owner", "name", "created", "modified", "spectrum_preview")
     search_fields = (
-        "owner_state__protein__name",
+        "owner_fluor__name",
         "owner_filter__name",
         "owner_camera__name",
         "owner_light__name",
-        "owner_dye__name",
     )
 
     def get_fields(self, request, obj=None):
         fields = []
         if not obj or not obj.category:
+            # If no category yet, allow selecting any owner type
             own = [
-                "owner_state",
+                "owner_fluor",
                 "owner_filter",
                 "owner_camera",
                 "owner_light",
-                "owner_dye",
             ]
-        elif obj.category == Spectrum.PROTEIN:
-            own = ["owner_state"]
+        elif obj.category in (Spectrum.PROTEIN, Spectrum.DYE):
+            # Protein and Dye both use owner_fluor (Fluorophore)
+            own = ["owner_fluor"]
         else:
+            # Filter, Camera, Light
             own = ["owner_" + obj.get_category_display().split(" ")[0].lower()]
         fields.extend(own)
+        # Add clickable link to owner's admin page (for existing objects)
+        if obj and obj.owner:
+            fields.append("owner")
         self.autocomplete_fields.extend(own)
         fields += [
             "category",
@@ -249,11 +281,18 @@ def get_fields(self, request, obj=None):
 
     @admin.display(description="Owner")
     def owner(self, obj):
-        url = reverse(
-            f"admin:proteins_{obj.owner._meta.model.__name__.lower()}_change",
-            args=(obj.owner.pk,),
-        )
-        link = f'<a href="{url}">{obj.owner}</a>'
+        owner = obj.owner
+        # FluorState is a base class - resolve to the actual subclass admin
+        if isinstance(owner, FluorState):
+            if owner.entity_type == FluorState.EntityTypes.PROTEIN:
+                model_name = "state"
+            else:
+                model_name = "dyestate"
+        else:
+            model_name = owner._meta.model.__name__.lower()
+
+        url = reverse(f"admin:proteins_{model_name}_change", args=(owner.pk,))
+        link = f'<a href="{url}">{owner}</a>'
         return mark_safe(link)
 
     @admin.display(description="Spectrum Preview")
@@ -342,7 +381,7 @@ class StateAdmin(CompareVersionAdmin):
                 "fields": (
                     ("ex_max", "em_max"),
                     ("ext_coeff", "qy"),
-                    ("twop_ex_max", "twop_peakGM", "twop_qy"),
+                    ("twop_ex_max", "twop_peak_gm", "twop_qy"),
                     ("pka", "maturation"),
                     "lifetime",
                 )
@@ -356,6 +395,49 @@ def protein_link(self, obj):
         return mark_safe(f'<a href="{url}">{obj.protein}</a>')
 
 
+@admin.register(DyeState)
+class DyeStateAdmin(MultipleSpectraOwner, CompareVersionAdmin):
+    # form = StateForm
+    model = State
+    list_select_related = ("dye", "created_by", "updated_by")
+    search_fields = ("dye__name",)
+    list_display = (
+        "__str__",
+        "dye_link",
+        "ex_max",
+        "em_max",
+        "created_by",
+        "updated_by",
+        "modified",
+    )
+    list_filter = ("created", "modified")
+    fieldsets = [
+        (None, {"fields": (("name", "slug", "is_dark"),)}),
+        (
+            None,
+            {
+                "fields": (
+                    ("ex_max", "em_max"),
+                    ("ext_coeff", "qy"),
+                    ("twop_ex_max", "twop_peak_gm", "twop_qy"),
+                    ("pka", "lifetime"),
+                )
+            },
+        ),
+        (
+            None,
+            {
+                "fields": ("spectra",),
+            },
+        ),
+    ]
+
+    @admin.display(description="Dye")
+    def dye_link(self, obj):
+        url = reverse("admin:proteins_dye_change", args=([obj.dye.pk]))
+        return mark_safe(f'<a href="{url}">{obj.dye}</a>')
+
+
 class StateTransitionAdmin(VersionAdmin):
     model = StateTransition
     list_select_related = ("protein", "from_state", "to_state")