Add NormalCase model, views, filters, and templates for managing normal cases

atlas/admin.py

@@ -3,6 +3,7 @@ from .models import (
     Case,
     CaseDetail,
     CaseCollection,
+    NormalCase,
     Differential,
     Series,
     SeriesImage,
@@ -79,6 +80,15 @@ class CaseCollectionAdmin(VersionAdmin):
 
 admin.site.register(CaseCollection, CaseCollectionAdmin)
 
+
+class NormalCaseAdmin(VersionAdmin):
+    list_display = ("case", "age_years", "examination", "modality", "added_by", "added_date")
+    list_filter = ("examination", "modality")
+    search_fields = ("case__title", "case__pk")
+
+
+admin.site.register(NormalCase, NormalCaseAdmin)
+
 class AtlasAdminForm(ModelForm):
     class Meta:
         model = Case

atlas/filters.py

@@ -11,6 +11,7 @@ from .models import (
     Series,
     Structure,
     Subspecialty,
+    NormalCase,
 )
 from django.contrib.auth.models import User
 from django.db.models import Q
@@ -286,6 +287,38 @@ class SubspecialtyFilter(django_filters.FilterSet):
         )
         pass
 
+
+class NormalCaseFilter(django_filters.FilterSet):
+    """FilterSet for the NormalCase model allowing filtering by
+    examination, modality and nearest-year age ranges.
+    """
+    examination = django_filters.ModelChoiceFilter(queryset=Series.objects.none())
+    modality = django_filters.ModelChoiceFilter(queryset=Series.objects.none())
+    min_age = django_filters.NumberFilter(field_name="age_years", lookup_expr="gte", label="Min age")
+    max_age = django_filters.NumberFilter(field_name="age_years", lookup_expr="lte", label="Max age")
+
+    class Meta:
+        model = NormalCase
+        fields = ("examination", "modality", "age_years")
+
+    def __init__(self, data=None, queryset=None, prefix=None, strict=None, user=None, request=None):
+        # Use the global Examination and Modality querysets from the Series model
+        from generic.models import Examination, Modality
+
+        # Set up the actual querysets for the filters
+        self.base_filters.get("examination").queryset = Examination.objects.all()
+        self.base_filters.get("modality").queryset = Modality.objects.all()
+
+        # If not an atlas editor restrict to cases authored by the user or open access cases
+        if request is not None and not request.user.groups.filter(name="atlas_editor").exists():
+            from django.db.models import Q
+
+            if queryset is None:
+                queryset = NormalCase.objects.select_related("case")
+            queryset = queryset.filter((Q(case__author__id=request.user.id) | Q(case__open_access=True)))
+
+        super(NormalCaseFilter, self).__init__(data=data, queryset=queryset, prefix=prefix, request=request)
+
 class QuestionSchemaFilter(django_filters.FilterSet):
     class Meta:
         model = QuestionSchema

atlas/migrations/0080_normalcase.py

@@ -0,0 +1,35 @@
+# Generated by Django 5.2.7 on 2025-11-13 21:43
+
+import django.core.validators
+import django.db.models.deletion
+import django.utils.timezone
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0079_casecollection_prerequisites'),
+        ('generic', '0029_add_unique_constraint_supervisor_email'),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='NormalCase',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('age_years', models.PositiveSmallIntegerField(blank=True, help_text='Age of the patient at scan in years (rounded to nearest year).', null=True, validators=[django.core.validators.MinValueValidator(0), django.core.validators.MaxValueValidator(150)])),
+                ('added_date', models.DateTimeField(default=django.utils.timezone.now)),
+                ('notes', models.TextField(blank=True, null=True)),
+                ('added_by', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='added_normals', to=settings.AUTH_USER_MODEL)),
+                ('case', models.OneToOneField(help_text='The Case that is marked as a normal example.', on_delete=django.db.models.deletion.CASCADE, related_name='normal_case', to='atlas.case')),
+                ('examination', models.ForeignKey(blank=True, help_text='Primary examination for this normal case (optional).', null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='normal_cases', to='generic.examination')),
+                ('modality', models.ForeignKey(blank=True, help_text='Primary modality for this normal case (optional).', null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='normal_cases', to='generic.modality')),
+            ],
+            options={
+                'ordering': ['-added_date'],
+            },
+        ),
+    ]

atlas/models.py

@@ -611,6 +611,83 @@ class Case(models.Model, AuthorMixin, QuestionMixin):
 
         return json.dumps(results)
 
+
+class NormalCase(models.Model):
+    """Marks a Case as a 'normal' example used in the Atlas normals section.
+
+    We store a nearest-year age (age_years) and optional primary
+    examination/modality to make filtering simple and fast. A OneToOne
+    relation keeps normal-specific fields separate from the main Case
+    object and is non-destructive.
+    """
+    case = models.OneToOneField(
+        Case,
+        on_delete=models.CASCADE,
+        related_name="normal_case",
+        help_text="The Case that is marked as a normal example.",
+    )
+
+    age_years = models.PositiveSmallIntegerField(
+        null=True,
+        blank=True,
+        validators=[MinValueValidator(0), MaxValueValidator(150)],
+        help_text="Age of the patient at scan in years (rounded to nearest year).",
+    )
+
+    examination = models.ForeignKey(
+        Examination,
+        null=True,
+        blank=True,
+        on_delete=models.SET_NULL,
+        related_name="normal_cases",
+        help_text="Primary examination for this normal case (optional).",
+    )
+
+    modality = models.ForeignKey(
+        Modality,
+        null=True,
+        blank=True,
+        on_delete=models.SET_NULL,
+        related_name="normal_cases",
+        help_text="Primary modality for this normal case (optional).",
+    )
+
+    added_by = models.ForeignKey(
+        settings.AUTH_USER_MODEL,
+        null=True,
+        blank=True,
+        on_delete=models.SET_NULL,
+        related_name="added_normals",
+    )
+
+    added_date = models.DateTimeField(default=timezone.now)
+
+    notes = models.TextField(null=True, blank=True)
+
+    class Meta:
+        ordering = ["-added_date"]
+
+    def __str__(self):
+        return f"Normal: {self.case} ({self.age_years or 'unknown'}y)"
+
+    def get_absolute_url(self):
+        return self.case.get_absolute_url()
+
+    def save(self, *args, **kwargs):
+        # If examination/modality not specified, try to infer from the first series
+        try:
+            if (self.examination is None or self.modality is None) and self.case.series.exists():
+                first_series = self.case.series.first()
+                if self.examination is None and getattr(first_series, 'examination', None) is not None:
+                    self.examination = first_series.examination
+                if self.modality is None and getattr(first_series, 'modality', None) is not None:
+                    self.modality = first_series.modality
+        except Exception:
+            # Be defensive: if anything goes wrong whilst inferring, continue and save as-is
+            pass
+
+        super().save(*args, **kwargs)
+
 def extract_image_dicom_json_from_ds(ds, url, image_index):
     to_keep = [
         "Columns",

atlas/templates/atlas/normals_list.html

@@ -0,0 +1,45 @@
+{% extends "atlas/base.html" %}
+{% load static %}
+
+{% block content %}
+<div class="container">
+  <h1>Normals</h1>
+
+  <div class="row mb-3">
+    <div class="col-md-4">
+      <form method="get" class="form-inline">
+        {% for field in filter.form.visible_fields %}
+          <div class="mb-2">
+            {{ field.label_tag }}
+            {{ field }}
++          </div>
+        {% endfor %}
+        <div class="mb-2">
+          <button class="btn btn-primary" type="submit">Filter</button>
+          <a class="btn btn-link" href="?">Clear</a>
+        </div>
+      </form>
+    </div>
+  </div>
+
+  <div class="list-group">
+    {% for normal in page_obj.object_list %}
+      {% include "atlas/partials/_normal_row.html" with normal=normal %}
+    {% empty %}
+      <div class="list-group-item">No normal cases found.</div>
+    {% endfor %}
+  </div>
+
+  <nav aria-label="Page navigation">
+    <ul class="pagination mt-3">
+      {% if page_obj.has_previous %}
+        <li class="page-item"><a class="page-link" href="?page={{ page_obj.previous_page_number }}">Previous</a></li>
+      {% endif %}
+      <li class="page-item disabled"><span class="page-link">Page {{ page_obj.number }} of {{ page_obj.paginator.num_pages }}</span></li>
+      {% if page_obj.has_next %}
+        <li class="page-item"><a class="page-link" href="?page={{ page_obj.next_page_number }}">Next</a></li>
+      {% endif %}
+    </ul>
+  </nav>
+</div>
+{% endblock %}

atlas/templates/atlas/partials/_normal_row.html

@@ -0,0 +1,11 @@
+<div class="list-group-item">
+  <div class="d-flex w-100 justify-content-between">
+    <h5 class="mb-1"><a href="{{ normal.case.get_absolute_url }}">{{ normal.case.title }}</a></h5>
+    <small>{{ normal.added_date|date:"Y-m-d" }}</small>
+  </div>
+  <p class="mb-1">Age: {{ normal.age_years|default:"unknown" }} years</p>
+  <p class="mb-1">Examination: {{ normal.examination }} | Modality: {{ normal.modality }}</p>
+  {% if normal.notes %}
+    <p class="mb-0">Notes: {{ normal.notes }}</p>
+  {% endif %}
+</div>

atlas/urls.py

@@ -349,6 +349,7 @@ urlpatterns = [
     path("categories/", views.categories_list, name="categories_list"),
     path("categories/search_partial/", views.categories_search_partial, name="categories_search_partial"),
     path("search/cases/", views.case_search_partial, name="case_search_partial"),
+    path("normals/", views.NormalCaseList.as_view(), name="normals_list"),
     path("condition/<int:pk>", views.condition_detail, name="condition_detail"),
     path(
         "condition/<int:pk>/delete",

atlas/views.py

@@ -5,6 +5,7 @@ from dal import autocomplete
 from django.db.models.base import Model as Model
 from django.db.models.query import QuerySet
 from django.db.models import Prefetch
+from django.db.models import Q
 from django.shortcuts import render, get_object_or_404, redirect
 from django import forms
 from django.utils import timezone
@@ -107,6 +108,7 @@ from .models import (
     UserReportAnswer,
     PrerequisiteRequired
 )
+from .models import NormalCase
 from .tables import (
     CaseCollectionTable,
     CaseTable,
@@ -130,6 +132,7 @@ from .filters import (
     SeriesFilter,
     StructureFilter,
     SubspecialtyFilter,
+    NormalCaseFilter,
 )
 
 from .tasks import push_case_to_cimar_task
@@ -288,6 +291,22 @@ class AtlasEditorRequiredMixin(object):
             return obj
         raise PermissionDenied("You must be an atlas editor to do this.")  # or Http404
 
+
+
+class NormalCaseList(LoginRequiredMixin, FilterView):
+    model = NormalCase
+    template_name = "atlas/normals_list.html"
+    filterset_class = NormalCaseFilter
+    paginate_by = 25
+
+    def get_queryset(self):
+        qs = NormalCase.objects.select_related("case", "examination", "modality", "added_by")
+        # Restrict similar to CaseFilter: non-editors only see authored or open_access
+        if not self.request.user.groups.filter(name="atlas_editor").exists():
+            qs = qs.filter((Q(case__author__id=self.request.user.id) | Q(case__open_access=True)))
+
+        return qs.order_by("-added_date")
+
 @login_required
 @user_has_case_view_access
 def case_displaysets(request, pk):