.

- Added logging configuration to WSGI for persistent log collection.
- Updated Docker Compose files for local and development environments, including Redis, PostgreSQL, and Grafana services.
- Introduced Promtail configuration for log scraping and integration with Loki.
- Created application log directory in Dockerfile for log persistence.

.env.dev

@@ -0,0 +1,22 @@
+# Django
+DEBUG=1
+SECRET_KEY=w(s0&(_eb058wvmg@44_repv8)r9@5p8fx*g_@c)1dm&d*ew^u
+DJANGO_ALLOWED_HOSTS=localhost 127.0.0.1 [::1]
+
+# External DB (you mentioned production uses an external DB)
+DB_HOST=db-postgresql-lon1-05515-jan-22-backup-do-user-8165014-0.c.db.ondigitalocean.com
+DB_PORT=25060
+DB_NAME=testing
+DB_USER=django
+DB_PASSWORD=AVNS_NG_s4i7SMMobWLO
+
+# Redis
+REDIS_URL=redis://redis:6379/0
+
+# Gunicorn tuning
+GUNICORN_WORKERS=3
+GUNICORN_LOGLEVEL=info
+
+# Nginx host ports for local development (override prod defaults)
+NGINX_HTTP_PORT=8000
+NGINX_HTTPS_PORT=8443

.env.prod.example

@@ -0,0 +1,20 @@
+# Copy this to .env.prod on the server and fill in production values (do NOT commit secrets).
+
+# Django
+SECRET_KEY=replace-me-with-a-secure-random-string
+DEBUG=0
+ALLOWED_HOSTS=example.com
+
+# External DB (you mentioned production uses an external DB)
+DATABASE_HOST=your.db.host
+DATABASE_PORT=5432
+DATABASE_NAME=rad
+DATABASE_USER=django
+DATABASE_PASSWORD=strong-db-password
+
+# Redis
+REDIS_URL=redis://redis:6379/0
+
+# Gunicorn tuning
+GUNICORN_WORKERS=3
+GUNICORN_LOGLEVEL=info

.gitignore

@@ -12,3 +12,7 @@ venv
 *.log
 
 temp/
+
+# Loki runtime data
+/docker/loki-data/
+/docker/loki-wal/

anatomy/api.py

@@ -19,51 +19,50 @@ from django.contrib.auth import get_user_model
 router = Router()
 
 class CidUserSchema(ModelSchema):
-    class Config:
+    class Meta:
         model = CidUser
 
-        model_fields = ["cid", "name", "email"]
+        fields = ["cid", "name", "email"]
 
 class UserUserSchema(ModelSchema):
-    class Config:
+    class Meta:
         model = get_user_model()
-        model_fields = ["id", "email"]
+        fields = ["id", "email"]
 
 class CidUserExamSchema(ModelSchema):
     cid_user : CidUserSchema | None
     user_user : UserUserSchema | None
-    class Config:
+    class Meta:
         model = CidUserExam
-        model_fields = ["id"]
+        fields = ["id"]
 
 class ExamStatusSchema(ModelSchema):
-    class Config:
+    class Meta:
         model = ExamUserStatus
-        model_fields = ["id", "datetime", "status", "extra"]
+        fields = ["id", "datetime", "status", "extra"]
 
 class ExamUserStatusSchema(ModelSchema):
 
     #cid_user : CidUserSchema | None
     #user_user : UserUserSchema | None
     cid_user_exam : CidUserExamSchema | None
-    class Config:
+    class Meta:
         model = ExamUserStatus
-        model_fields = ["id", "datetime", "status", "extra"]
+        fields = ["id", "datetime", "status", "extra"]
 
 class QuestionSchema(ModelSchema):
-    class Config:
+    class Meta:
         model = Question
 
-        #model_fields = ["question", "history", "feedback", "normal", "laterality"]
-        model_fields = "__all__"
+        fields = "__all__"
 
-        #model_exclude = ["answers"]
+        #exclude = ["answers"]
 
 class ExamSchema(ModelSchema):
-    class Config:
+    class Meta:
         model = Exam
 
-        model_fields = ["id", "name", "active", "publish_results"]
+        fields = ["id", "name", "active", "publish_results"]
 
 @router.get('/')
 def list_questions(request):

anatomy/templates/anatomy/exams.html

@@ -2,16 +2,30 @@
 
 {% block navigation %}
     {{block.super}}
-    <br/>
-    Exams: {{exam}}->
-    <a href="{% url 'anatomy:exam_overview' pk=exam.pk %}">Overview</a> /
-    {% if exam.exam_mode %}
-        <a href="{% url 'anatomy:mark_overview' pk=exam.pk %}">Mark</a> /
-        <a href="{% url 'anatomy:mark2_overview' pk=exam.pk %}">Mark2</a> /
-        <a href="{% url 'anatomy:exam_scores_all' pk=exam.pk %}">Scores</a> /
-        <a href="{% url 'anatomy:exam_cids' exam_id=exam.pk %}">Candidates</a> /
-        <a href="{% url 'anatomy:exam_stats' exam_id=exam.pk %}">Stats</a> /
-    {% endif %}
-    <a href="{% url 'anatomy:exam_review_start' pk=exam.pk %}">Review</a>
-{% comment %}     <a href="{% url 'anatomy:question_create_exam' pk=exam.pk %}" title="Add a new question directly into the exam.">Add New Question</a> {% endcomment %}
+    <nav class="navbar navbar-expand-lg navbar-dark bg-dark mt-2 rounded">
+        <div class="container-fluid px-3">
+            <span class="navbar-text me-3 text-white">
+                <strong>Exam:</strong> {{ exam.title|default:exam.name|default:exam }}
+            </span>
+            <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#examNav" aria-controls="examNav" aria-expanded="false" aria-label="Toggle navigation">
+                <span class="navbar-toggler-icon"></span>
+            </button>
+
+            <div class="collapse navbar-collapse" id="examNav">
+                <ul class="navbar-nav me-auto mb-2 mb-lg-0">
+                    <li class="nav-item"><a class="nav-link" href="{% url 'anatomy:exam_overview' pk=exam.pk %}">Overview</a></li>
+                    {% if exam.exam_mode %}
+                        <li class="nav-item"><a class="nav-link" href="{% url 'anatomy:mark_overview' pk=exam.pk %}">Mark</a></li>
+                        <li class="nav-item"><a class="nav-link" href="{% url 'anatomy:mark2_overview' pk=exam.pk %}">Mark2</a></li>
+                        <li class="nav-item"><a class="nav-link" href="{% url 'anatomy:exam_scores_all' pk=exam.pk %}">Scores</a></li>
+                        <li class="nav-item"><a class="nav-link" href="{% url 'anatomy:exam_cids' exam_id=exam.pk %}">Candidates</a></li>
+                        <li class="nav-item"><a class="nav-link" href="{% url 'anatomy:exam_stats' exam_id=exam.pk %}">Stats</a></li>
+                    {% endif %}
+                    <li class="nav-item"><a class="nav-link" href="{% url 'anatomy:exam_review_start' pk=exam.pk %}">Review</a></li>
+                </ul>
+
+                {% include 'generic/partials/exams/dropdown_menu.html'%}
+            </div>
+        </div>
+    </nav>
 {% endblock %}

anatomy/templates/anatomy/question_link_header.html

@@ -1,28 +1,95 @@
+<nav class="navbar navbar-expand-lg navbar-dark bg-dark mt-2 rounded">
+    <div class="container-fluid px-3">
+        <span class="navbar-text me-3 text-white">
+            <strong>Question:</strong>
+            {% if question.stem %}
+                {{ question.stem|striptags|truncatechars:80 }}
+            {% else %}
+                #{{ question.pk }}
+            {% endif %}
+        </span>
 
-    <div class="floating-header">
-        <a href="{% url 'anatomy:anatomy_question_update' question.id %}" title="Edit the Question">Edit</a>
-        <a href="{% url 'anatomy:question_clone' question.id %}" title="Clone the Question">Clone</a>
-        <a href="{% url 'anatomy:question_delete' pk=question.pk %}" title="Delete the Question">Delete</a>
-        <a href="{% url 'anatomy:question_answer_update' pk=question.pk %}" title="Update the question answers">Edit Answers</a>
-        <a href="#"
-           onclick="return window.create_popup_window('{% url 'feedback_create' question_type='anatomy' pk=question.pk %}')">
-            Add Note</a>
+        <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#questionNav" aria-controls="questionNav" aria-expanded="false" aria-label="Toggle navigation">
+            <span class="navbar-toggler-icon"></span>
+        </button>
 
-        {% if request.user.is_superuser %}
-            <a href="{% url 'admin:anatomy_anatomyquestion_change' question.id %}"
-               title="Edit the Question using the admin interface">Admin Edit</a>
-            <a href="{% url 'anatomy:question_user_answers' question.id %}" title="View user answers associated with this question">User answers</a>
-        {% endif %}
-        {% if exam %}
-            <div>
-
-                {% if previous > -1 %}
-                    <a href="{% url 'anatomy:exam_question_detail' exam.id previous %}">Previous question</a>
+        <div class="collapse navbar-collapse" id="questionNav">
+            <ul class="navbar-nav me-auto mb-2 mb-lg-0">
+                {% if exam %}
+                    <li class="nav-item">
+                        {% if previous > -1 %}
+                            <a class="nav-link" href="{% url 'anatomy:exam_question_detail' exam.id previous %}">Previous</a>
+                        {% endif %}
+                    </li>
+                    <li class="nav-item align-self-center">
+                        Viewing as part of exam: <a class="nav-link d-inline p-0" href="{% url 'anatomy:exam_overview' exam.id %}">{{ exam }}</a>
+                        <span class="navbar-text text-muted ms-2">[{{ pos }}/{{ exam_length }}]</span>
+                    </li>
+                    <li class="nav-item">
+                        {% if next %}
+                            <a class="nav-link" href="{% url 'anatomy:exam_question_detail' exam.id next %}">Next</a>
+                        {% endif %}
+                    </li>
                 {% endif %}
-                Viewing question as part of exam: <a href="{% url 'anatomy:exam_overview' exam.id %}">{{exam}}</a> [{{pos}}/{{exam_length}}]
-                {% if next %}
-                    <a href="{% url 'anatomy:exam_question_detail' exam.id next %}">Next question</a>
-                {% endif %}
-            </div>
-        {% endif %}
+            </ul>
+
+            <ul class="navbar-nav ms-auto">
+                <li class="nav-item dropdown">
+                    <a class="nav-link dropdown-toggle" href="#" id="questionActions" role="button" data-bs-toggle="dropdown" aria-expanded="false">Actions</a>
+                    <ul class="dropdown-menu dropdown-menu-end dropdown-menu-dark" aria-labelledby="questionActions">
+                        <li>
+                            <a class="dropdown-item text-primary" href="{% url 'anatomy:question_detail' question.id %}">
+                                <i class="bi bi-eye me-2"></i> View
+                            </a>
+                        </li>
+                        <li>
+                            <a class="dropdown-item text-primary" href="{% url 'anatomy:anatomy_question_update' question.id %}">
+                                <i class="bi bi-pencil-square me-2"></i> Edit
+                            </a>
+                        </li>
+
+                        <li>
+                            <a class="dropdown-item text-white" href="{% url 'anatomy:question_answer_update' pk=question.pk %}">
+                                <i class="bi bi-list-check me-2"></i> Edit Answers
+                            </a>
+                        </li>
+
+                        <li>
+                            <a class="dropdown-item text-white" href="{% url 'anatomy:question_clone' question.id %}">
+                                <i class="bi bi-files me-2"></i> Clone
+                            </a>
+                        </li>
+
+                        <li>
+                            <a class="dropdown-item text-info" href="#" onclick="return window.create_popup_window('{% url 'feedback_create' question_type='anatomy' pk=question.pk %}')">
+                                <i class="bi bi-chat-left-text me-2"></i> Add Note
+                            </a>
+                        </li>
+
+                        <li><hr class="dropdown-divider"></li>
+
+                        <li>
+                            <a class="dropdown-item text-danger" href="{% url 'anatomy:question_delete' pk=question.pk %}">
+                                <i class="bi bi-trash me-2"></i> Delete
+                            </a>
+                        </li>
+
+                        {% if request.user.is_superuser %}
+                            <li><hr class="dropdown-divider"></li>
+                            <li>
+                                <a class="dropdown-item text-warning" href="{% url 'admin:anatomy_anatomyquestion_change' question.id %}">
+                                    <i class="bi bi-tools me-2"></i> Admin Edit
+                                </a>
+                            </li>
+                            <li>
+                                <a class="dropdown-item text-muted" href="{% url 'anatomy:question_user_answers' question.id %}">
+                                    <i class="bi bi-people me-2"></i> User answers
+                                </a>
+                            </li>
+                        {% endif %}
+                    </ul>
+                </li>
+            </ul>
+        </div>
     </div>
+</nav>

atlas/api.py

@@ -32,9 +32,9 @@ router = Router()
 class SeriesSchema(ModelSchema):
     case_id: List[int] = []
 
-    class Config:
+    class Meta:
         model = Series
-        model_fields = [
+        fields = [
             "id",
             "modality",
             "examination",
@@ -48,9 +48,9 @@ class SeriesSchema(ModelSchema):
 
 
 class CaseSchema(ModelSchema):
-    class Config:
+    class Meta:
         model = Case
-        model_fields = ["id", "title"]
+        fields = ["id", "title"]
 
 
 @router.post("/upload_dicom", auth=django_auth)

atlas/filters.py

@@ -164,13 +164,16 @@ class SeriesFilter(django_filters.FilterSet):
 
 
 class ConditionFilter(django_filters.FilterSet):
+    # Replace legacy `primary` filter with `is_canonical` and provide a
+    # `synonym` filter which will filter by the canonical group of the
+    # selected condition.
+    is_canonical = django_filters.BooleanFilter(method="filter_is_canonical", label="Canonical")
+    synonym = django_filters.ModelChoiceFilter(queryset=Condition.objects.all(), method="filter_synonym", label="Synonym group")
+
     class Meta:
         model = Condition
         fields = {
             "name": ["icontains"],
-            "primary": ["exact"],
-            "synonym": ["exact"],
-            #"parent": ["exact"],
             "subspecialty": ["exact"],
             "rcr_curriculum": ["exact"],
         }
@@ -189,11 +192,32 @@ class ConditionFilter(django_filters.FilterSet):
         )
         pass
 
+    def filter_is_canonical(self, queryset, name, value):
+        if value in (True, "True", "true", 1, "1"):
+            return queryset.filter(canonical__isnull=True)
+        if value in (False, "False", "false", 0, "0"):
+            return queryset.filter(canonical__isnull=False)
+        return queryset
+
+    def filter_synonym(self, queryset, name, value):
+        # value is a Condition instance selected in the filter. Return all
+        # Conditions that belong to the same canonical group as `value`.
+        if not value:
+            return queryset
+        master = value.canonical if value.canonical else value
+        return queryset.filter(Q(canonical=master) | Q(pk=master.pk))
+
 
 class FindingFilter(django_filters.FilterSet):
+    # Replace legacy `primary`/`synonym` with canonical-based filters
+    is_canonical = django_filters.BooleanFilter(method="filter_is_canonical", label="Canonical")
+    synonym = django_filters.ModelChoiceFilter(queryset=Finding.objects.all(), method="filter_synonym", label="Synonym group")
+
     class Meta:
         model = Finding
-        fields = ("name", "primary", "synonym")
+        fields = {
+            "name": ["icontains"],
+        }
 
     def __init__(
         self,
@@ -209,11 +233,29 @@ class FindingFilter(django_filters.FilterSet):
         )
         pass
 
+    def filter_is_canonical(self, queryset, name, value):
+        if value in (True, "True", "true", 1, "1"):
+            return queryset.filter(canonical__isnull=True)
+        if value in (False, "False", "false", 0, "0"):
+            return queryset.filter(canonical__isnull=False)
+        return queryset
+
+    def filter_synonym(self, queryset, name, value):
+        # value is a Finding instance selected in the filter. Return all
+        # Findings that belong to the same canonical group as `value`.
+        if not value:
+            return queryset
+        master = value.canonical if value.canonical else value
+        return queryset.filter(Q(canonical=master) | Q(pk=master.pk))
+
 
 class StructureFilter(django_filters.FilterSet):
+    is_canonical = django_filters.BooleanFilter(method="filter_is_canonical", label="Canonical")
+    synonym = django_filters.ModelChoiceFilter(queryset=Structure.objects.all(), method="filter_synonym", label="Synonym group")
+
     class Meta:
         model = Structure
-        fields = {"name": ["icontains"], "primary": ["exact"], "synonym": ["exact"]}
+        fields = {"name": ["icontains"]}
 
     def __init__(
         self,
@@ -229,6 +271,19 @@ class StructureFilter(django_filters.FilterSet):
         )
         pass
 
+    def filter_is_canonical(self, queryset, name, value):
+        if value in (True, "True", "true", 1, "1"):
+            return queryset.filter(canonical__isnull=True)
+        if value in (False, "False", "false", 0, "0"):
+            return queryset.filter(canonical__isnull=False)
+        return queryset
+
+    def filter_synonym(self, queryset, name, value):
+        if not value:
+            return queryset
+        master = value.canonical if value.canonical else value
+        return queryset.filter(Q(canonical=master) | Q(pk=master.pk))
+
 
 class PresentationFilter(django_filters.FilterSet):
     class Meta:

atlas/forms.py

@@ -40,6 +40,8 @@ from atlas.models import (
     Condition,
     Structure,
     Subspecialty,
+    Presentation,
+    PathologicalProcess,
     UncategorisedDicom,
     UserReportAnswer,
     CaseDisplaySet,
@@ -54,7 +56,8 @@ from generic.models import Examination  # , Sign
 
 from django.contrib.admin.widgets import FilteredSelectMultiple
 from django.forms.widgets import RadioSelect, TextInput, Textarea, Select
-from crispy_forms.layout import Submit, Layout, Fieldset, Field, Div, HTML
+from crispy_forms.layout import Submit, Layout, Fieldset, Field, Div, HTML, Button
+from django.urls import reverse
 from crispy_forms.bootstrap import Accordion, AccordionGroup
 
 from tinymce.widgets import TinyMCE
@@ -116,11 +119,10 @@ class ConditionForm(ModelForm):
     class Meta:
         model = Condition
         exclude = ["rcr_curriculum"]
-
         widgets = {
-            "synonym": autocomplete.ModelSelect2Multiple(
-                url="atlas:condition-autocomplete"
-            ),
+            # Use an AJAX/autocomplete single-select for canonical so users
+            # can search for existing canonical Conditions by name.
+            "canonical": autocomplete.ModelSelect2(url="atlas:condition-autocomplete"),
             "parent": autocomplete.ModelSelect2Multiple(
                 url="atlas:condition-autocomplete"
             ),
@@ -129,6 +131,32 @@ class ConditionForm(ModelForm):
             ),
         }
 
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        # Crispy helper to render a submit button consistently
+        try:
+            self.helper = FormHelper()
+            self.helper.form_method = "post"
+            self.helper.form_tag = True
+            # Primary submit
+            self.helper.add_input(Submit("submit", "Submit"))
+            # Cancel as a button that redirects back to the condition list
+            try:
+                cancel_url = reverse("atlas:condition_view")
+            except Exception:
+                cancel_url = "#"
+            self.helper.add_input(
+                Button(
+                    "cancel",
+                    "Cancel",
+                    css_class="btn btn-secondary ms-2",
+                    onclick=f"window.location='{cancel_url}'",
+                )
+            )
+        except Exception:
+            # If crispy not available or something goes wrong, don't break form
+            pass
+
 
 class CaseCollectionForm(ModelForm):
     class Meta:
@@ -313,9 +341,10 @@ class FindingForm(ModelForm):
     class Meta:
         model = Finding
         exclude = []
-
+        # Use the canonical FK in forms (if users want to mark this Finding
+        # as an alias of another). The old `synonym` M2M has been removed.
         widgets = {
-            "synonym": autocomplete.ModelSelect2Multiple(
+            "canonical": autocomplete.ModelSelect2(
                 url="atlas:finding-autocomplete"
             ),
         }
@@ -325,14 +354,31 @@ class StructureForm(ModelForm):
     class Meta:
         model = Structure
         exclude = []
-
         widgets = {
-            "synonym": autocomplete.ModelSelect2Multiple(
+            "canonical": autocomplete.ModelSelect2(
                 url="atlas:structure-autocomplete"
             ),
         }
 
 
+class SubspecialtyForm(ModelForm):
+    class Meta:
+        model = Subspecialty
+        exclude = []
+
+
+class PresentationForm(ModelForm):
+    class Meta:
+        model = Presentation
+        exclude = []
+
+
+class PathologicalProcessForm(ModelForm):
+    class Meta:
+        model = PathologicalProcess
+        exclude = []
+
+
 class SeriesFindingForm(ModelForm):
     class Meta:
         model = SeriesFinding
@@ -831,7 +877,7 @@ class BaseReportAnswerForm(ModelForm):
         #    "answer": "Write your answer in here."
         # }
 
-    def __init__(self, *args, case_detail, **kwargs):
+    def __init__(self, *args, casedetail, **kwargs):
         super(BaseReportAnswerForm, self).__init__(*args, **kwargs)
         self.fields["answer"].required = False
 
@@ -847,12 +893,12 @@ class BaseQuestionAnswerForm(ModelForm):
         #    "answer": "Write your answer in here."
         # }
 
-    def __init__(self, *args, case_detail, **kwargs):
+    def __init__(self, *args, casedetail, **kwargs):
         super(BaseQuestionAnswerForm, self).__init__(*args, **kwargs)
-        # self.fields["json_answer"].schema = case_detail.question_schema
-        if case_detail.question_schema is not None:
+        # self.fields["json_answer"].schema = casedetail.question_schema
+        if casedetail.question_schema is not None:
             self.fields["json_answer"] = JSONSchemaField(
-                schema=case_detail.question_schema, options="schema/options.json"
+                schema=casedetail.question_schema, options="schema/options.json"
             )
             self.fields["json_answer"].label = ""
 
@@ -1013,6 +1059,37 @@ class ConditionAutocomplete(ModelAutocomplete):
     model = Condition
     search_attrs = ["name"]
 
+    @classmethod
+    def get_items_from_keys(cls, keys, context_obj=None):
+        """Return items for given keys, ignoring empty strings.
+
+        The autocomplete frontend sometimes sends empty string keys which
+        causes the ORM to raise ValueError when filtering numeric PK fields.
+        Filter out falsy/blank keys before querying. If no valid keys remain
+        return an empty queryset.
+        """
+        # normalize and remove empty/blank values
+        clean_keys = [k for k in keys if k is not None and str(k).strip() != ""]
+        if not clean_keys:
+            return cls.model.objects.none()
+
+        # try to convert numeric keys to ints where possible
+        parsed_keys = []
+        for k in clean_keys:
+            try:
+                parsed_keys.append(int(k))
+            except Exception:
+                parsed_keys.append(k)
+
+        qs = cls.model.objects.filter(pk__in=parsed_keys)
+
+        # Return a list of dicts matching the autocomplete core expectations
+        # (items subscriptable by keys like 'key' / 'label').
+        return [
+            {"key": obj.pk, "label": getattr(obj, "name", str(obj)), "value": str(obj)}
+            for obj in qs
+        ]
+
 
 class ConditionAutocompleteForm(Form):
     condition = ModelChoiceField(
@@ -1153,23 +1230,6 @@ class PriorCaseForm(Form):
 
     prior_visibility = CharField(max_length=2, required=True)
 
-    # def __init__(self, *args, **kwargs):
-    #    self.case_detail = kwargs.pop(
-    #        "case_detail"
-    #    )  # To get request.user. Do not use kwargs.pop('user', None) due to potential security hole
-
-    #    super(PriorCaseForm, self).__init__(*args, **kwargs)
-
-    #    prior_cases = self.case_detail.case.get_all_prior_cases()
-
-    #    if not prior_cases:
-    #        prior_cases = Case.objects.none()
-
-    #    self.fields["case"] = ChoiceField(
-    #        required=False,
-    #        # widget=Select(verbose_name="Series", is_stacked=False),
-    #    )
-
 
 class CaseSeriesForm(forms.ModelForm):
     def __init__(self, *args, queryset, user=None, is_atlas_editor=False, **kwargs):

atlas/migrations/0085_rename_case_detail_caseprior_casedetail_and_more.py

@@ -0,0 +1,22 @@
+# Generated by Django 5.2.7 on 2025-11-17 10:28
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0084_resource_open_access'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='caseprior',
+            old_name='case_detail',
+            new_name='casedetail',
+        ),
+        migrations.AlterUniqueTogether(
+            name='caseprior',
+            unique_together={('casedetail', 'prior_case')},
+        ),
+    ]

atlas/migrations/0086_add_canonical.py

@@ -0,0 +1,69 @@
+from django.db import migrations, models
+
+
+def forwards(apps, schema_editor):
+    Condition = apps.get_model("atlas", "Condition")
+    # Build connected components using existing M2M 'synonym' links
+    visited = set()
+
+    for cond in Condition.objects.all():
+        if cond.pk in visited:
+            continue
+        # BFS/DFS to collect component
+        stack = [cond]
+        comp = []
+        while stack:
+            c = stack.pop()
+            if c.pk in visited:
+                continue
+            visited.add(c.pk)
+            comp.append(c)
+            # access existing M2M relations
+            for s in c.synonym.all():
+                if s.pk not in visited:
+                    stack.append(s)
+
+        # choose canonical: prefer primary==True else lowest pk
+        canon = None
+        for c in comp:
+            if getattr(c, "primary", False):
+                canon = c
+                break
+        if not canon:
+            canon = min(comp, key=lambda x: x.pk)
+
+        # set canonical for all non-canonical members
+        for c in comp:
+            if c.pk != canon.pk:
+                c.canonical_id = canon.pk
+                c.save()
+
+
+def backwards(apps, schema_editor):
+    Condition = apps.get_model("atlas", "Condition")
+    for c in Condition.objects.all():
+        if c.canonical_id:
+            c.canonical_id = None
+            c.save()
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("atlas", "0085_rename_case_detail_caseprior_casedetail_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="condition",
+            name="canonical",
+            field=models.ForeignKey(
+                related_name="aliases",
+                null=True,
+                on_delete=models.SET_NULL,
+                to="atlas.condition",
+                blank=True,
+            ),
+        ),
+        migrations.RunPython(forwards, backwards),
+    ]

atlas/migrations/0087_alter_condition_canonical.py

@@ -0,0 +1,19 @@
+# Generated by Django 5.2.7 on 2025-11-20 22:35
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0086_add_canonical'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='condition',
+            name='canonical',
+            field=models.ForeignKey(blank=True, help_text='If set, this Condition is an alias and points to the canonical Condition.', null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='aliases', to='atlas.condition'),
+        ),
+    ]

atlas/migrations/0088_remove_finding_primary_remove_finding_synonym_and_more.py

@@ -0,0 +1,40 @@
+# Generated by Django 5.2.7 on 2025-11-24 10:17
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0087_alter_condition_canonical'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='finding',
+            name='primary',
+        ),
+        migrations.RemoveField(
+            model_name='finding',
+            name='synonym',
+        ),
+        migrations.RemoveField(
+            model_name='structure',
+            name='primary',
+        ),
+        migrations.RemoveField(
+            model_name='structure',
+            name='synonym',
+        ),
+        migrations.AddField(
+            model_name='finding',
+            name='canonical',
+            field=models.ForeignKey(blank=True, help_text='If set, this Finding is an alias and points to the canonical Finding.', null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='aliases', to='atlas.finding'),
+        ),
+        migrations.AddField(
+            model_name='structure',
+            name='canonical',
+            field=models.ForeignKey(blank=True, help_text='If set, this Structure is an alias and points to the canonical Structure.', null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='aliases', to='atlas.structure'),
+        ),
+    ]

atlas/migrations/0089_remove_condition_primary_remove_condition_synonym.py

@@ -0,0 +1,21 @@
+# Generated by Django 5.2.7 on 2025-11-24 10:31
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0088_remove_finding_primary_remove_finding_synonym_and_more'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='condition',
+            name='primary',
+        ),
+        migrations.RemoveField(
+            model_name='condition',
+            name='synonym',
+        ),
+    ]

atlas/models.py

@@ -110,36 +110,121 @@ class SynMixin(object):
     #    abstract = True
 
     def __str__(self) -> str:
-        if self.primary:
-            return self.name
-        else:
-            return f"{self.name} [syn]"
+        # Determine whether this record should be displayed as the
+        # canonical/primary entry. Prefer the new canonical FK pattern
+        # (`canonical is None` means this object is the master). Fallback
+        # to legacy `primary` boolean when present.
+        # If the model supports canonical FK, consider canonical==None as
+        # the primary/master entry. For models without canonical (legacy
+        # edge-cases), treat the instance as primary by default.
+        if hasattr(self, "canonical"):
+            try:
+                if self.canonical is None or self.canonical == self:
+                    return self.name
+                return f"{self.name} [syn]"
+            except Exception:
+                # defensive fallback
+                return f"{self.name} [syn]"
+
+        # No canonical support: assume primary
+        return self.name
 
     def get_old_str(self) -> str:
-        if self.primary:
-            if self.synonym.count() == 0:
-                return self.name
-            else:
-                synonyms = ",".join([i.name for i in self.synonym.all()])
-                return f"{self.name} ({synonyms})"
+        # Prefer using a model-specific get_synonyms (e.g. Condition.get_synonyms)
+        try:
+            syns = self.get_synonyms()
+        except Exception:
+            syns = None
+        # If the model supports canonical, only canonical==None entries
+        # should be rendered as the primary name. For models without
+        # canonical, treat instance as primary.
+        if hasattr(self, "canonical"):
+            try:
+                is_primary = self.canonical is None or self.canonical == self
+            except Exception:
+                is_primary = False
         else:
-            return f"{self.name} [syn]"
+            is_primary = True
+
+        if is_primary:
+            if syns is None:
+                synonyms_field = getattr(self, "synonym", None)
+                if synonyms_field is None or (hasattr(synonyms_field, "count") and synonyms_field.count() == 0):
+                    return self.name
+                synonyms = ",".join([i.name for i in synonyms_field.all()])
+                return f"{self.name} ({synonyms})"
+            else:
+                if not syns:
+                    return self.name
+                synonyms = ",".join([i.name for i in syns])
+                return f"{self.name} ({synonyms})"
+
+        return f"{self.name} [syn]"
 
     def get_synonym(self):
-        if self.primary:
-            return "[Primary]"
-        else:
-            s = self.synonym.filter(primary=True).values_list("name", flat=True)
+        # Return a readable synonym string. For models that implement
+        # get_synonyms (Condition with canonical/aliases), use that.
+        try:
+            syns = self.get_synonyms()
+        except Exception:
+            syns = None
+        # If canonical is present and this instance is the master, mark Primary
+        if hasattr(self, "canonical"):
+            try:
+                if self.canonical is None or self.canonical == self:
+                    return "[Primary]"
+            except Exception:
+                pass
+
+        if syns is None:
+            synonyms_field = getattr(self, "synonym", None)
+            if synonyms_field is None:
+                return ""
+            # If the old M2M exists, prefer those marked primary if such a
+            # attribute exists on the related objects.
+            try:
+                # Select all synonym names; legacy `primary` flag removed.
+                s = synonyms_field.values_list("name", flat=True)
+            except Exception:
+                s = []
             return ", ".join(s)
 
+        # prefer primary names among synonyms if present
+        primary_names = []
+        for i in syns:
+            # Prefer items that are canonical/master in the group
+            if getattr(i, "canonical", None) is None:
+                primary_names.append(i.name)
+        if primary_names:
+            return ", ".join(primary_names)
+        return ", ".join([i.name for i in syns])
+
     def get_synonym_link(self):
-        if self.primary:
-            return "[Primary]"
-        else:
-            syns = self.synonym.filter(primary=True)
-            return ", ".join(
-                [f"<a href='{s.get_absolute_url()}'>{s.name}</a>" for s in syns]
-            )
+        try:
+            syns = self.get_synonyms()
+        except Exception:
+            syns = None
+        # Prefer canonical/master check
+        if hasattr(self, "canonical"):
+            try:
+                if self.canonical is None or self.canonical == self:
+                    return "[Primary]"
+            except Exception:
+                pass
+
+        if syns is None:
+            # fall back to all M2M synonyms (not just primary) for models
+            # that still use the old synonym field (e.g. Finding, Structure)
+            synonyms_field = getattr(self, "synonym", None)
+            if synonyms_field is None:
+                return ""
+            syns_qs = synonyms_field.all()
+            items = [f"<a href='{s.get_absolute_url()}'>{s.name}</a>" for s in syns_qs]
+            return ", ".join(items)
+
+        # render links for synonyms/canonical group
+        items = [f"<a href='{s.get_absolute_url()}'>{s.name}</a>" for s in syns]
+        return ", ".join(items)
 
     def get_link(self):
         return format_html("<a href='{}'>{}</a>", self.get_absolute_url(), self.name)
@@ -147,21 +232,49 @@ class SynMixin(object):
 
 class Finding(SynMixin, models.Model):
     name = models.CharField(max_length=255, unique=True)
-    synonym = models.ManyToManyField("self", blank=True)
-
-    primary = models.BooleanField(default="True")
+    # New canonical/alias field: if set, this Finding is an alias and points
+    # to the canonical/master Finding. We remove the old M2M `synonym` and
+    # `primary` boolean in favour of this single canonical FK.
+    canonical = models.ForeignKey(
+        "self",
+        null=True,
+        blank=True,
+        on_delete=models.SET_NULL,
+        related_name="aliases",
+        help_text="If set, this Finding is an alias and points to the canonical Finding.",
+    )
 
     def get_absolute_url(self):
         return reverse("atlas:finding_detail", kwargs={"pk": self.pk})
 
+    @property
+    def canonical_finding(self):
+        return self.canonical if self.canonical else self
+
+    def get_synonyms(self):
+        """Return other Findings that are aliases/synonyms for this concept.
+
+        Behaviour mirrors Condition.get_synonyms: if this Finding is an alias
+        (has canonical set) return the canonical and other aliases (excluding
+        self). If this Finding is canonical, return all aliases (excluding
+        self).
+        """
+        master = self.canonical_finding
+        qs = Finding.objects.filter(models.Q(canonical=master) | models.Q(pk=master.pk)).exclude(pk=self.pk)
+        return qs
+
 
 class Condition(SynMixin, models.Model):
     name = models.CharField(max_length=255, unique=True)
-
-    synonym = models.ManyToManyField(
+    # New canonical/alias field (Option B): if set, this Condition is an alias
+    # and points to the canonical/master Condition.
+    canonical = models.ForeignKey(
         "self",
+        null=True,
         blank=True,
-        help_text="Use if a direct synonym for the condition exists, e.g. 'Wegener granulomatosis' and 'Granulomatosis with Polyangitis'.",
+        on_delete=models.SET_NULL,
+        related_name="aliases",
+        help_text="If set, this Condition is an alias and points to the canonical Condition.",
     )
     parent = models.ManyToManyField(
         "self",
@@ -172,10 +285,10 @@ class Condition(SynMixin, models.Model):
         help_text="Use if the condition could be considered a subset of another, e.g. 'Alzheimer disease' and 'Dementia'.",
     )
 
-    primary = models.BooleanField(
-        default="True",
-        help_text="Sets if this should be the canonical item, all other synonyms will then redirect to this by default.",
-    )
+    # Legacy fields `synonym` (M2M) and `primary` (boolean) have been removed.
+    # Canonical/aliases are represented by the `canonical` ForeignKey and
+    # the reverse `aliases` related_name. Use `get_synonyms()` /
+    # `canonical_condition` to access canonical groups.
 
     subspecialty = models.ManyToManyField(
         "subspecialty",
@@ -198,6 +311,23 @@ class Condition(SynMixin, models.Model):
     def get_absolute_url(self):
         return reverse("atlas:condition_detail", kwargs={"pk": self.pk})
 
+    @property
+    def canonical_condition(self):
+        """Return the canonical/master condition for this Condition (self if none)."""
+        return self.canonical if self.canonical else self
+
+    def get_synonyms(self):
+        """Return other Conditions that are synonyms/aliases for this concept.
+
+        Behaviour:
+        - If this Condition is an alias (canonical set), return the canonical and
+          any other aliases (excluding self).
+        - If this Condition is canonical, return all aliases (and exclude self).
+        """
+        master = self.canonical_condition
+        qs = Condition.objects.filter(models.Q(canonical=master) | models.Q(pk=master.pk)).exclude(pk=self.pk)
+        return qs
+
     def get_children(self):
         return self.child.all()
 
@@ -276,14 +406,28 @@ class Differential(models.Model):
 
 class Structure(SynMixin, models.Model):
     name = models.CharField(max_length=255, unique=True)
-
-    synonym = models.ManyToManyField("self", blank=True)
-
-    primary = models.BooleanField(default="True")
+    # Migrate to canonical/aliases model like Condition and Finding
+    canonical = models.ForeignKey(
+        "self",
+        null=True,
+        blank=True,
+        on_delete=models.SET_NULL,
+        related_name="aliases",
+        help_text="If set, this Structure is an alias and points to the canonical Structure.",
+    )
 
     def get_absolute_url(self):
         return reverse("atlas:structure_detail", kwargs={"pk": self.pk})
 
+    @property
+    def canonical_structure(self):
+        return self.canonical if self.canonical else self
+
+    def get_synonyms(self):
+        master = self.canonical_structure
+        qs = Structure.objects.filter(models.Q(canonical=master) | models.Q(pk=master.pk)).exclude(pk=self.pk)
+        return qs
+
 
 @reversion.register
 class Case(models.Model, AuthorMixin, QuestionMixin):
@@ -1443,6 +1587,13 @@ class CaseDetail(models.Model):
     def __str__(self) -> str:
         return f"{self.case} -> {self.collection}"
 
+
+    def get_case_index(self):
+        """Returns the question index (number) in the collection (0 indexed)"""
+        case_details = list(self.collection.casedetail_set.all().order_by("sort_order"))
+
+        return case_details.index(self)
+
     def get_question_schema(self):
         return json.dumps(self.question_schema)
 
@@ -1545,7 +1696,7 @@ class CaseDetail(models.Model):
         return mark_safe(html)
 
 class CasePrior(models.Model):
-    case_detail = models.ForeignKey(CaseDetail, on_delete=models.CASCADE)
+    casedetail = models.ForeignKey(CaseDetail, on_delete=models.CASCADE)
     prior_case = models.ForeignKey(Case, on_delete=models.CASCADE, related_name="prior_case")
 
     relation_text = models.CharField(max_length=255, blank=True, help_text="Text to describe the relationship between the cases")
@@ -1564,10 +1715,10 @@ class CasePrior(models.Model):
     )
 
     class Meta:
-        unique_together = ("case_detail", "prior_case")
+        unique_together = ("casedetail", "prior_case")
 
     def __str__(self) -> str:
-        return f"{self.case_detail.case} -> {self.prior_case}"
+        return f"{self.casedetail.case} -> {self.prior_case}"
 
 class BaseReportAnswer(models.Model):
     question = models.ForeignKey(CaseDetail, on_delete=models.CASCADE)

atlas/tables.py

@@ -276,7 +276,7 @@ class ConditionTable(SelectionTable):
     class Meta(SelectionTable.Meta):
         model = Condition
         template_name = "django_tables2/bootstrap4.html"
-        fields = ("primary", "subspecialty", "rcr_curriculum_map", "rcr_curriculum")
+        fields = ("subspecialty", "rcr_curriculum_map", "rcr_curriculum")
         sequence = ("name",)
 
 
@@ -312,7 +312,7 @@ class FindingTable(SelectionTable):
     class Meta(SelectionTable.Meta):
         model = Finding
         template_name = "django_tables2/bootstrap4.html"
-        fields = ("name", "primary")
+        fields = ("name",)
         sequence = ("name",)
 
 
@@ -339,7 +339,7 @@ class StructureTable(SelectionTable):
     class Meta(SelectionTable.Meta):
         model = Structure
         template_name = "django_tables2/bootstrap4.html"
-        fields = ("name", "primary")
+        fields = ("name",)
         sequence = ("name",)
 
 

atlas/templates/atlas/add_case_to_collection.html

@@ -1,14 +1,9 @@
-<span id="add-case-form">
-    This form allows you to add an existing case to the collection. You may find it easier to do this from the individual case pages or the <a href="{% url 'atlas:case_view' %}">case overview view</a> which allows you to add multiple cases at once.
-<form hx-post="{% url 'atlas:add_case_to_collection' collection.id %}" hx-swap="outerHTML">
-    {% csrf_token %}
-    <label for="case">Select Case to add:</label>
-    <select name="case" id="case">
-        {% for case in cases %}
-            <option value="{{ case.id }}">{{ case.title }}</option>
-        {% endfor %}
-    </select>
-    <button type="submit">Add</button>
-    <button _="on click remove #add-case-form">Cancel</button>
-</form>
-</span
+<div id="add-case-form" class="p-2 border rounded">
+    <p class="mb-2">Add an existing case to this collection. You can also use the case overview view to add multiple cases at once: <a href="{% url 'atlas:case_view' %}">case overview</a>.</p>
+
+    {% include 'atlas/partials/case_search_widget.html' %}
+
+    <div class="mt-2">
+        <button class="btn btn-sm btn-secondary" _="on click remove #add-case-form">Close</button>
+    </div>
+</div>

atlas/templates/atlas/base.html

@@ -66,8 +66,32 @@
                                 </li>
                             </ul>
                         </li>
-                        <li class="nav-item">
-                            <a class="nav-link" href="{% url 'atlas:categories_list' %}"><i class="bi bi-tags me-1" aria-hidden="true"></i>Categories</a>
+                        <li class="nav-item dropdown">
+                            <a class="nav-link d-inline" href="{% url 'atlas:categories_list' %}"><i class="bi bi-tags me-1" aria-hidden="true"></i>Categories</a>
+                            <a class="nav-link d-inline dropdown-toggle dropdown-toggle-split" data-bs-toggle="dropdown" aria-expanded="false">
+                                <span class="visually-hidden">Toggle Dropdown</span>
+                            </a>
+
+                            <ul class="dropdown-menu">
+                                <li><a class="dropdown-item" href="{% url 'atlas:categories_list' %}"><i class="bi bi-list-ul me-1" aria-hidden="true"></i>All categories</a></li>
+                                <li><hr class="dropdown-divider"></li>
+                                <li><a class="dropdown-item" href="{% url 'atlas:condition_view' %}">Conditions</a></li>
+                                <li><a class="dropdown-item" href="{% url 'atlas:finding_view' %}">Findings</a></li>
+                                <li><a class="dropdown-item" href="{% url 'atlas:structure_view' %}">Structures</a></li>
+                                <li><a class="dropdown-item" href="{% url 'atlas:subspecialty_view' %}">Subspecialties</a></li>
+                                <li><a class="dropdown-item" href="{% url 'atlas:presentation_view' %}">Presentations</a></li>
+                                <li><a class="dropdown-item" href="{% url 'atlas:pathological_process_view' %}">Pathological process</a></li>
+                                {% if request.user.is_staff %}
+                                    <li><hr class="dropdown-divider"></li>
+                                    <li class="dropdown-item-text small text-muted px-3">Create</li>
+                                    <li><a class="dropdown-item" href="{% url 'atlas:condition_create' %}">New condition</a></li>
+                                    <li><a class="dropdown-item" href="{% url 'atlas:finding_create' %}">New finding</a></li>
+                                    <li><a class="dropdown-item" href="{% url 'atlas:structure_create' %}">New structure</a></li>
+                                    <li><a class="dropdown-item" href="{% url 'atlas:subspecialty_create' %}">New subspecialty</a></li>
+                                    <li><a class="dropdown-item" href="{% url 'atlas:presentation_create' %}">New presentation</a></li>
+                                    <li><a class="dropdown-item" href="{% url 'atlas:pathological_process_create' %}">New pathological process</a></li>
+                                {% endif %}
+                            </ul>
                         </li>
                         <li class="nav-item dropdown">
                             <a class="nav-link d-inline" href="{% url 'atlas:resource_view' %}" title="Resources"><i class="bi bi-folder2-open me-1" aria-hidden="true"></i>Resources</a>

atlas/templates/atlas/case_display_block.html

@@ -464,7 +464,7 @@
 
     
     {% if casedetail %}
-        {% include 'atlas/partials/collection_question_block.html' with case_detail=casedetail can_edit=can_edit %}
+        {% include 'atlas/partials/collection_question_block.html' with can_edit=can_edit %}
         
     {% endif %}
         

atlas/templates/atlas/collection_case_details.html

@@ -3,17 +3,9 @@
 
 {% block content %}
 
-    <div>
-        {% if previous %}
-            <a href="{% url 'atlas:collection_case_details' collection.id previous.id %}">Previous question</a>
-        {% endif %}
-        Viewing question as part of collection: <a href="{% url 'atlas:collection_detail' collection.id %}">{{collection.name}}</a> [{{case_number|add:1}}/{{collection_length}}]
-        {% if next %}
-            <a href="{% url 'atlas:collection_case_details' collection.id next.id %}">Next question</a>
-        {% endif %}
-    </div>
+    {% include 'atlas/partials/_viewing_case_as_part_of_collection.html' with nav_link_view="atlas:collection_case_details" %}
 
-    <h2>Case: <a href="{% url 'atlas:case_detail' case_detail.case.pk %}">{{case_detail.case.title}}</a></h2>
+    <h2>Case: <a href="{% url 'atlas:case_detail' casedetail.case.pk %}">{{casedetail.case.title}}</a></h2>
 
     <p>This page allows you to configure how the case is displayed as part of the collection.</p>
 

atlas/templates/atlas/collection_case_displaysetup.html

@@ -3,66 +3,67 @@
 
 
 {% block content %}
-<h2>Setup default display for case</h2>
+    {% include 'atlas/partials/_viewing_case_as_part_of_collection.html' with nav_link_view="atlas:collection_case_displaysetup" %}
+    <h2>Setup default display for case</h2>
 
-    <div id="root" class="dicom-viewer-root" data-images="{{case_detail.case.get_series_images_nested}}"
-        style="box-sizing: border-box; background: #222; width: 100vw; height: 800px; max-width: 1600px;"
-        data-auto-cache-stack="true" 
-        {% if case_detail.default_viewerstate %}
-           data-viewerstate={{ case_detail.default_viewerstate }} 
-        {% endif %}
+    <div id="root" class="dicom-viewer-root" data-images="{{casedetail.case.get_series_images_nested}}"
+         style="box-sizing: border-box; background: #222; width: 100vw; height: 800px; max-width: 1600px;"
+         data-auto-cache-stack="true"
+         {% if casedetail.default_viewerstate %}
+             data-viewerstate={{ casedetail.default_viewerstate }}
+         {% endif %}
 
     ></div>
 
-<button id="save-viewerstate" type="button" class="btn btn-primary mt-3">
-    Save Viewer State
-</button>
-<button id="reset-viewerstate" type="button" class="btn btn-secondary mt-3 ms-2">
-    Reset to Default
-</button>
-<div id="viewerstate-save-response" class="mt-2"></div>
+    <button id="save-viewerstate" type="button" class="btn btn-primary mt-3">
+        Save Viewer State
+    </button>
+    <button id="reset-viewerstate" type="button" class="btn btn-secondary mt-3 ms-2">
+        Reset to Default
+    </button>
+    <div id="viewerstate-save-response" class="mt-2"></div>
 
-<script>
-document.getElementById('save-viewerstate').addEventListener('click', function() {
-    let viewerState = window.exportViewerState_root();
-    if (!viewerState) {
-        document.getElementById('viewerstate-save-response').innerHTML = "<span class='text-danger'>Viewer state could not be retrieved.</span>";
-        return;
-    }
-    fetch("{% url 'atlas:collection_case_displaysetup' case_detail.collection.pk case_detail.case.pk %}", {
-        method: "POST",
-        headers: {
-            "Content-Type": "application/json",
-            "X-CSRFToken": "{{ csrf_token }}"
-        },
-        body: JSON.stringify({viewerstate: viewerState})
-    })
-    .then(response => response.text())
-    .then(html => {
-        document.getElementById('viewerstate-save-response').innerHTML = html;
-    })
-    .catch(error => {
-        document.getElementById('viewerstate-save-response').innerHTML = "<span class='text-danger'>Error saving viewer state.</span>";
-    });
-});
-document.getElementById('reset-viewerstate').addEventListener('click', function() {
-    fetch("{% url 'atlas:collection_case_displaysetup' case_detail.collection.pk case_detail.case.pk %}", {
-        method: "POST",
-        headers: {
-            "Content-Type": "application/json",
-            "X-CSRFToken": "{{ csrf_token }}"
-        },
-        body: JSON.stringify({reset_viewerstate: true})
-    })
-    .then(response => response.text())
-    .then(html => {
-        document.getElementById('viewerstate-save-response').innerHTML = html;
+    <script>
+        document.getElementById('save-viewerstate').addEventListener('click', function() {
+            let viewerState = window.exportViewerState_root();
+            if (!viewerState) {
+                document.getElementById('viewerstate-save-response').innerHTML = "<span class='text-danger'>Viewer state could not be retrieved.</span>";
+                return;
+            }
+            fetch({% if case_number %}"{% url 'atlas:collection_case_displaysetup' casedetail.collection.pk case_number %}"{% else %}"{% url 'atlas:collection_case_displaysetup_legacy' casedetail.collection.pk casedetail.case.pk %}"{% endif %}, {
+                method: "POST",
+                headers: {
+                    "Content-Type": "application/json",
+                    "X-CSRFToken": "{{ csrf_token }}"
+                },
+                body: JSON.stringify({viewerstate: viewerState})
+            })
+                .then(response => response.text())
+                .then(html => {
+                    document.getElementById('viewerstate-save-response').innerHTML = html;
+                })
+                .catch(error => {
+                    document.getElementById('viewerstate-save-response').innerHTML = "<span class='text-danger'>Error saving viewer state.</span>";
+                });
+        });
+        document.getElementById('reset-viewerstate').addEventListener('click', function() {
+            fetch({% if case_number %}"{% url 'atlas:collection_case_displaysetup' casedetail.collection.pk case_number %}"{% else %}"{% url 'atlas:collection_case_displaysetup_legacy' casedetail.collection.pk casedetail.case.pk %}"{% endif %}, {
+                method: "POST",
+                headers: {
+                    "Content-Type": "application/json",
+                    "X-CSRFToken": "{{ csrf_token }}"
+                },
+                body: JSON.stringify({reset_viewerstate: true})
+            })
+                .then(response => response.text())
+                .then(html => {
+                    document.getElementById('viewerstate-save-response').innerHTML = html;
         // Optionally reload the page or viewer here if needed
-    })
-    .catch(error => {
-        document.getElementById('viewerstate-save-response').innerHTML = "<span class='text-danger'>Error resetting viewer state.</span>";
-    });
-});
-</script>
+                })
+                .catch(error => {
+                    document.getElementById('viewerstate-save-response').innerHTML = "<span class='text-danger'>Error resetting viewer state.</span>";
+                });
+        });
+    </script>
 
 {% endblock %}

atlas/templates/atlas/collection_case_priors.html

@@ -4,106 +4,28 @@
 
 {% block content %}
 
-    <div>
+    {% include 'atlas/partials/_viewing_case_as_part_of_collection.html' with nav_link_view="atlas:collection_case_priors" %}
 
-        {% if previous %}
-            <a href="{% url 'atlas:collection_case_questions' collection.id previous.id %}">Previous question</a>
-        {% endif %}
-        Viewing question as part of collection: <a href="{% url 'atlas:collection_detail' collection.id %}">{{collection.name}}</a> [{{case_number|add:1}}/{{collection_length}}]
-        {% if next %}
-            <a href="{% url 'atlas:collection_case_questions' collection.id next.id %}">Next question</a>
-        {% endif %}
+    <h2 class="mb-3">Managing Priors for Case: <a href="{% url 'atlas:case_detail' casedetail.case.pk %}" class="text-decoration-none">{{casedetail.case.title}}</a></h2>
+
+    <div class="card mb-4">
+        <div class="card-body">
+            <p class="mb-1">This page allows you to add series from prior cases to a case in a collection. In order to be available here the cases must be linked on the system.</p>
+            <p class="mb-0">It is necessary to give a description of how the cases are related that will be displayed to the user when viewing the case.</p>
+        </div>
     </div>
 
+    <h3 class="mb-3">Available priors</h3>
 
-    <h2>Case: <a href="{% url 'atlas:case_detail' case_detail.case.pk %}">{{case_detail.case.title}}</a></h2>
-
-    <p>This page allows you to add series from prior cases to a case in a collection. In order to be available here the cases must be linked on the system.</p>
-    <p>It is necessary to give a description of how the cases are related that will be displayed to the user when viewing the case.</p>
-
-    <h3>Available priors</h3>
-
-    <ul>
+    <div class="row g-3">
         {% for case, added, relation, visibility in available_priors %}
-
-            <li class='
-                       {% if added %}
-                           added
-                       {% else %}
-                           not-added
-                       {% endif %}
-                      ' data-case={{case.id}}>
-                {{case.title}} / {{added}} / {{relation}} / <a href="{% url 'atlas:case_detail' case.id %}">View case</a>
-                <br/>{{case.get_series_blocks|safe}}
-
-                <br/>
-
-                {% if not added %}
-                    <form hx-post="{% url 'atlas:collection_case_priors' collection.id case_detail.case.pk %}"
-                          hx-target="#htmx-response-{{case.id}}"
-                          _="on htmx:afterRequest log 'test' then remove me">
-                        {% csrf_token %}
-                        <input type="hidden" name="prior_case_id" value="{{case.id}}" />
-                        <input type="text" name="relation" value="{{relation}}" placeholder="relation to case" />
-                        <br />
-                        <label for="prior_visibility_{{case.id}}">Visibility:</label>
-                        <select name="prior_visibility" id="prior_visibility_{{case.id}}">
-                            <option value="AL" 
-                            {% if visibility == 'AL' %}
-                               selected 
-                            {% endif %}
-                                >Always</option>
-                            <option value="RE"
-                            {% if visibility == 'RE' %}
-                               selected 
-                            {% endif %}
-
-                            >Review</option>
-                            <option value="NO"
-                            {% if visibility == 'NO' %}
-                               selected 
-                            {% endif %}
-                            >None</option>
-                        </select>
-                        <br />
-                        <button class="btn primary">Add to case</button>
-                    </form>
-                {% else %}
-                    <form hx-post="{% url 'atlas:collection_case_priors' collection.id case_detail.case.pk %}"
-                          hx-target="#htmx-response-{{case.id}}"
-                          _="on htmx:afterRequest log 'test' then remove me">
-                        Case available: {{relation}}
-                        <input type="hidden" name="remove" value="{{case.id}}" />
-                        <br />
-                        <label for="prior_visibility_{{case.id}}">Visibility:</label>
-                        <select name="prior_visibility" id="prior_visibility_{{case.id}}" disabled>
-                            <option value="AL" 
-                            {% if visibility == 'AL' %}
-                               selected 
-                            {% endif %}
-                                >Always</option>
-                            <option value="RE"
-                            {% if visibility == 'RE' %}
-                               selected 
-                            {% endif %}
-
-                            >Review</option>
-                            <option value="NO"
-                            {% if visibility == 'NO' %}
-                               selected 
-                            {% endif %}
-                            >None</option>
-                        </select>
-                        <br />
-                        <button class="btn primary">Remove from case</button>
-                    </form>
-                {% endif %}
-                <span id="htmx-response-{{case.id}}"></span>
-
-            </li>
-
+            {% include 'atlas/partials/_prior_card.html' with case=case added=added relation=relation visibility=visibility collection=collection %}
+        {% empty %}
+            <div class="col-12">
+                <div class="alert alert-info">No available prior cases found for the case.</div>
+            </div>
         {% endfor %}
-    </ul>
+    </div>
 
 
 

atlas/templates/atlas/collection_case_questions.html

@@ -4,21 +4,11 @@
 
 {% block content %}
 
-    <div>
+    {% include 'atlas/partials/_viewing_case_as_part_of_collection.html' with nav_link_view="atlas:collection_case_questions" %}
 
-        {% if previous %}
-            <a href="{% url 'atlas:collection_case_questions' collection.id previous.id %}">Previous question</a>
-        {% endif %}
-        Viewing question as part of collection: <a href="{% url 'atlas:collection_detail' collection.id %}">{{collection.name}}</a> [{{case_number|add:1}}/{{collection_length}}]
-        {% if next %}
-            <a href="{% url 'atlas:collection_case_questions' collection.id next.id %}">Next question</a>
-        {% endif %}
-    </div>
+    <h2>Case: <a href="{% url 'atlas:case_detail' casedetail.case.pk %}">{{casedetail.case.title}}</a></h2>
 
-
-    <h2>Case: <a href="{% url 'atlas:case_detail' case_detail.case.pk %}">{{case_detail.case.title}}</a></h2>
-
-    {% if case_detail.question_schema is not None and not case_detail.question_answers %}
+    {% if casedetail.question_schema is not None and not casedetail.question_answers %}
 
 
         <div class="alert alert-danger" role="alert">
@@ -42,7 +32,7 @@
 
     Import schema from:
     <button class="btn btn-primary btn-sm" type="button" data-bs-toggle="offcanvas" data-bs-target="#offcanvasRight" aria-controls="offcanvasRight"
-            hx-get="{% url 'atlas:collection_question_schemas' case_detail.collection.id %}"
+            hx-get="{% url 'atlas:collection_question_schemas' casedetail.collection.id %}"
             hx-target=".offcanvas-body"
     >Collection questions</button>
     <button class="btn btn-primary btn-sm" type="button" data-bs-toggle="offcanvas" data-bs-target="#offcanvasRight" aria-controls="offcanvasRight"
@@ -54,7 +44,7 @@
         Question Block Title
     </summary>
         <p>Title of the question block.</p>
-        <input id="question_block_title_input" type="text" name="title" value="{{case_detail.question_schema.title}}" class="form-control" placeholder="Question title" aria-label="Question title">
+        <input id="question_block_title_input" type="text" name="title" value="{{casedetail.question_schema.title}}" class="form-control" placeholder="Question title" aria-label="Question title">
     </details>
     <details><summary>Modify Questions</summary>
         <div id="questions-container" style="margin-top: 20px;">
@@ -123,7 +113,7 @@
     </form> {% endcomment %}
 
 
-    {% if case_detail.question_schema %}
+    {% if casedetail.question_schema %}
         <h2>Question display</h2>
         This shows the form as it will be displayed (with the correct answers). If you wish to edit a correct answer you can change it below.
 

atlas/templates/atlas/collection_case_view_take.html

@@ -2,28 +2,48 @@
 {% load crispy_forms_tags %}
 
 {% block content %}
-    <span class="collection-name-blend">Collection: {{collection}}</span>
-    <h2>Case {{case_number|add:1}}
+    <div class="mb-2"><small class="text-muted">Collection: <strong>{{collection}}</strong></small></div>
 
-        {% if show_title %}
-            : {{case.title}}
-        {% endif %}
+    <div class="d-flex justify-content-between align-items-start mb-3">
+        <div>
+            <h2 class="h4 mb-0">Case {{case_number|add:1}}
+
+                {% if show_title %}
+                    : {{case.title}}
+                {% endif %}
 
 
-        {% if question_completed %}
-            <span class="stamp-white">REVIEW</span>
-        {% endif %}
+                {% if question_completed %}
+                    <span class="badge bg-warning text-dark ms-2 small">REVIEW</span>
+                {% endif %}
 
+            </h2>
+        </div>
 
-    </h2>
+        <div class="d-flex align-items-center ms-3">
+            <div class="dropdown">
+                <a class="btn btn-outline-secondary btn-sm dropdown-toggle" href="#" role="button" id="caseJump" data-bs-toggle="dropdown" aria-expanded="false"
+                   hx-get="{% url 'atlas:collection_case_jump_partial' pk=collection.pk %}?current={{case_number}}{% if cid %}&cid={{cid}}&passcode={{passcode}}{% endif %}"
+                   hx-target="#case-jump-menu"
+                   hx-swap="innerHTML"
+                   hx-trigger="click">
+                    Jump
+                </a>
+                <div class="dropdown-menu dropdown-menu-end" id="case-jump-menu">
+                    <div class="px-3 py-2 text-muted">Loading...</div>
+                </div>
+            </div>
+        </div>
+    </div>
 
     {% if not question_completed and collection.question_time_limit is not None %}
-        <div id="question-timer-block" style="margin-top:8px; margin-bottom:8px;" title="This question has a time limit of {{ collection.question_time_limit }} seconds. The timer will start when the page loads.">
-            <strong>Time remaining:</strong>
-            <span id="question-timer" aria-live="polite">&nbsp;</span>
-            <div id="question-timer-progress" style="display:inline-block; vertical-align: middle; width: 200px; margin-left:12px;">
-                <div id="question-timer-progress-outer" style="background:#e9ecef; border-radius:6px; height:10px; overflow:hidden;">
-                    <div id="question-timer-progress-inner" style="width:100%; height:100%; background:var(--timer-color, #28a745);"></div>
+        <div id="question-timer-block" class="mb-3" title="This question has a time limit of {{ collection.question_time_limit }} seconds. The timer will start when the page loads.">
+            <div class="d-flex align-items-center gap-3">
+                <div><strong>Time remaining:</strong> <span id="question-timer" aria-live="polite">&nbsp;</span></div>
+                <div style="flex:1; max-width:320px;">
+                    <div class="progress" style="height:10px;">
+                        <div id="question-timer-progress-inner" class="progress-bar" role="progressbar" style="width:100%; background:var(--timer-color, #28a745);"></div>
+                    </div>
                 </div>
             </div>
             <div id="timer-htmx-target" style="display:none;"></div>
@@ -38,12 +58,10 @@
 
     {% if not question_completed %}
         {% if resources %}
-            <h5>Resources</h4>
-            <ul class="no-list-style">
+            <h5 class="mt-3">Resources</h5>
+            <ul class="list-group list-group-flush mb-3">
                 {% for caseresource in resources %}
-                    <li>
-                        {{caseresource.resource.get_display}}
-                    </li>
+                    <li class="list-group-item py-1 small">{{caseresource.resource.get_display}}</li>
                 {% endfor %}
             </ul>
         {% endif %}
@@ -51,14 +69,21 @@
 
 
     {% if show_description and case.description %}
-        <div>
-            Description: {{case.description}}
+        <div class="mb-3">
+            <h6 class="mb-1">Description</h6>
+            <p class="mb-0">{{case.description}}</p>
         </div>
     {% endif %}
     {% if show_history %}
-        <div>
-            History: {{case_detail.get_history_pre|linebreaks}}
-
+        <div class="card mb-3">
+            <div class="card-body p-2 d-flex justify-content-between align-items-start">
+                <div class="me-3 small text-muted">History: {{casedetail.get_history_pre|linebreaks}}</div>
+                {% if has_priors %}
+                    <div class="ms-2">
+                        <span title="This case has priors available for comparison" class="badge bg-secondary text-white rounded-pill small">Priors{% if prior_count %} ({{ prior_count }}){% endif %}</span>
+                    </div>
+                {% endif %}
+            </div>
         </div>
     {% endif %}
 
@@ -66,9 +91,9 @@
         <div>
 
             {% if question_completed %}
-                <iframe id="viewer" style="width: 100%; height: 100%; border: none; padding: 0px; min-height: 700px" src="/ohif/viewer/dicomjson?url=https://www.penracourses.org.uk{% url 'atlas:collection_case_dicom_json_review' collection.pk case.pk %}"></iframe>
+                <iframe id="viewer" style="width: 100%; height: 100%; border: none; padding: 0px; min-height: 700px" src="/ohif/viewer/dicomjson?url=https://www.penracourses.org.uk{% if case_number %}{% url 'atlas:collection_case_dicom_json_review' collection.pk case_number %}{% else %}{% url 'atlas:collection_case_dicom_json_review_legacy' collection.pk case.pk %}{% endif %}"></iframe>
             {% else %}
-                <iframe id="viewer" style="width: 100%; height: 100%; border: none; padding: 0px; min-height: 700px" src="/ohif/viewer/dicomjson?url=https://www.penracourses.org.uk{% url 'atlas:collection_case_dicom_json' collection.pk case.pk %}"></iframe>
+                <iframe id="viewer" style="width: 100%; height: 100%; border: none; padding: 0px; min-height: 700px" src="/ohif/viewer/dicomjson?url=https://www.penracourses.org.uk{% if case_number %}{% url 'atlas:collection_case_dicom_json' collection.pk case_number %}{% else %}{% url 'atlas:collection_case_dicom_json_legacy' collection.pk case.pk %}{% endif %}"></iframe>
             {% endif %}
 
         </div>
@@ -78,9 +103,9 @@
     {% if collection.show_ohif_viewer_link %}
         <div>
             {% if question_completed %}
-                <a target="_blank" href="/ohif/viewer/dicomjson?url=https://www.penracourses.org.uk{% url 'atlas:collection_case_dicom_json_review' collection.pk case.pk %}" title="Click to open the case in the advanced viewer. This will open in a new tab/window."><button class="viewer"><i class="bi bi-collection"></i> Launch advanced viewer.</button></a>
+                <a target="_blank" href="/ohif/viewer/dicomjson?url=https://www.penracourses.org.uk{% if case_number %}{% url 'atlas:collection_case_dicom_json_review' collection.pk case_number %}{% else %}{% url 'atlas:collection_case_dicom_json_review_legacy' collection.pk case.pk %}{% endif %}" title="Click to open the case in the advanced viewer. This will open in a new tab/window."><button class="viewer"><i class="bi bi-collection"></i> Launch advanced viewer.</button></a>
             {% else %}
-                <a target="_blank" href="/ohif/viewer/dicomjson?url=https://www.penracourses.org.uk{% url 'atlas:collection_case_dicom_json' collection.pk case.pk %}" title="Click to open the case in the advanced viewer. This will open in a new tab/window."><button class="viewer"><i class="bi bi-collection"></i> Launch advanced viewer.</button></a>
+                <a target="_blank" href="/ohif/viewer/dicomjson?url=https://www.penracourses.org.uk{% if case_number %}{% url 'atlas:collection_case_dicom_json' collection.pk case_number %}{% else %}{% url 'atlas:collection_case_dicom_json_legacy' collection.pk case.pk %}{% endif %}" title="Click to open the case in the advanced viewer. This will open in a new tab/window."><button class="viewer"><i class="bi bi-collection"></i> Launch advanced viewer.</button></a>
             {% endif %}
         </div>
     {% endif %}
@@ -92,7 +117,7 @@
             <div id="main_viewer" class="dicom-viewer-root"
                  style="box-sizing: border-box; background: #222; width: 100%; height: 600px;"
                  data-auto-cache-stack="false"
-                 data-named-stacks='{{case_detail.get_case_named_stacks}}'
+                 data-named-stacks='{{casedetail.get_case_named_stacks}}'
             ></div>
         </details>
 
@@ -131,28 +156,24 @@
     {% endif %}
 
     {% if show_discussion and case.discussion %}
-        <p>
-            <details>
-                <summary>
-                    Discussion:
-                </summary>
-                <div>
-                    {{case.discussion|linebreaks}}
-                </div>
-            </details>
-        </p>
+        <details class="card mb-3">
+            <summary class="card-header p-2" style="cursor: pointer;">
+                <strong>Discussion</strong>
+            </summary>
+            <div class="card-body p-2 small">
+                {{case.discussion|linebreaks}}
+            </div>
+        </details>
     {% endif %}
     {% if show_report and case.report %}
-        <p>
-            <details>
-                <summary>
-                    Report:
-                </summary>
-                <div>
-                    {{case.report|linebreaks}}
-                </div>
-            </details>
-        </p>
+        <details class="card mb-3">
+            <summary class="card-header p-2" style="cursor: pointer;">
+                <strong>Report</strong>
+            </summary>
+            <div class="card-body p-2 small">
+                {{case.report|linebreaks}}
+            </div>
+        </details>
     {% endif %}
 
     {% if question_completed %}
@@ -246,25 +267,28 @@
             {% endif %}
 
         {% endif %}
-        {% if previous %}
-            <button type="submit" name="previous" class="save btn btn-default">Previous</button>
-        {% endif %}
-        {% if next %}
-            <button type="submit" name="next" class="save btn btn-default">Next</button>
-        {% elif collection.collection_type == "REP" %}
-            {% if not exam.publish_results %}
-                <button type="submit" name="save" class="save btn btn-default">Save</button>
+        <div class="mb-2">
+            {% if previous %}
+                <button type="submit" name="previous" class="btn btn-outline-secondary btn-sm me-2">Previous</button>
             {% endif %}
-        {% endif %}
+            {% if next %}
+                <button type="submit" name="next" class="btn btn-primary btn-sm me-2">Next</button>
+            {% elif collection.collection_type == "REP" %}
+                {% if not exam.publish_results %}
+                    <button type="submit" name="save" class="btn btn-primary btn-sm me-2">Save</button>
+                {% endif %}
+            {% endif %}
+        </div>
 
         {% if collection.self_review and not collection.feedback_once_collection_complete and not question_completed %}
-            <button type="submit" name="complete_case" class="save btn btn-default">Finish Case</button>
+            <button type="submit" name="complete_case" class="btn btn-success btn-sm">Finish Case</button>
         {% endif %}
 
 
-        <br />
-        <button type="submit" name="finish" class="save btn btn-default">Overview</button>
-        <button type="submit" id="goto-button" value="test" name="goto" class="hide">goto</button>
+        <div class="mt-3">
+            <button type="submit" name="finish" class="btn btn-outline-secondary btn-sm">Overview</button>
+            <button type="submit" id="goto-button" value="test" name="goto" class="hide">goto</button>
+        </div>
     </form>
     <style>
         label {

atlas/templates/atlas/collection_case_view_take_answers.html

@@ -3,10 +3,10 @@
 
 {% block content %}
 
-<h2>Case: {{ case.title }}</h2>
-{{ case_detail.question_schema }}
+    <h2>Case: {{ case.title }}</h2>
+    {{ casedetail.question_schema }}
 
 
-{{ case.question_answers }}
+    {{ case.question_answers }}
 
 {% endblock %}

atlas/templates/atlas/collection_detail.html

@@ -4,139 +4,154 @@
 
 {% partialdef casedetails-management-links %}
 
-    (<a href="{% url 'atlas:collection_case_displaysetup' casedetail.collection.pk casedetail.case.pk %}"><i class="bi bi-display" title="Setup default display"></i></a>
+<div class="btn-toolbar" role="toolbar" aria-label="Case management links">
+    {% include 'atlas/partials/casedetails_management_links.html' %}
+</div>
 
-    {% if casedetail.default_viewerstate %}
-        <i class="bi bi-check text-success" title="This case has a default viewerstate defined"></i>
-    {% endif %}
-    )
-
-    (<a href="{% url 'atlas:collection_case_details' casedetail.collection.pk casedetail.case.pk %}"><i class="bi bi-info-square" title="Case details"></i></a>)
-
-    {% if collection.collection_type == "QUE" %}
-        (<a href='{% url "atlas:collection_case_questions" casedetail.collection.pk casedetail.case.pk %}'>
-            {% if casedetail.question_schema %}
-                <i class="bi bi-question-square text-success" title="This case has questions defined."></i>
-            {% else %}
-                <i class="bi bi-question-square text-danger" title="This case has no questions defined."></i>
-            {% endif %}
-        </a>
-        )
-    {% endif %}
-
-    {% if casedetail.case.previous_case %}
-        (<a href='{% url "atlas:collection_case_priors" casedetail.collection.pk casedetail.case.pk %}'>
-            <i class="bi bi-link-45deg" title="Manage priors"></i></a>)
-    {% endif %}
 {% endpartialdef %}
 
 {% block content %}
-    <h2>{{collection.name}}</h2>
 
-    {% include 'exam_notes.html' %}
+<div class="container">
+    <div class="card mb-4">
+        <div class="card-body">
+            <div class="row">
+                <div class="col-md-8">
+                    <h2 class="card-title mb-2">{{ collection.name }}</h2>
 
-    <div>
-        Exam mode: {{collection.exam_mode}} (open access: {{collection.exam_open_access}})<br />
-        {% include "generic/partials/exams/exam_status.html#publish-results" %}
-        {% include "generic/partials/exams/exam_status.html#exam-active" %}
-        Collection Type: {{collection.get_collection_type_display}}<br />
-        Self review: {{collection.self_review}}<br />
-        Open access: {{collection.open_access}}<br />
-        {% if collection.prerequisites.exists %}
-            Prerequisite collections:
-            <ul>
-                {% for prereq in collection.prerequisites.all %}
-                    <li>
-                        <a href="{% url 'atlas:collection_detail' prereq.pk %}">{{ prereq.name }}</a>
-                        &nbsp;
-                    </li>
-                {% endfor %}
-            </ul>
+                    {% include 'exam_notes.html' %}
 
-        <p>
-            <button
-                title="Sync users from all prerequisite collections into this collection"
-                hx-post="{% url 'atlas:collection_sync_prerequisite_users' collection.pk %}"
-                hx-swap="outerHTML"
-                class="btn btn-sm btn-secondary"
-            >Sync prerequisite users</button>
-        </p>
-        {% endif %}
+                    <p class="mb-1">
+                        <span class="badge bg-info text-dark me-2">{{ collection.exam_mode }}</span>
+                        <small class="text-muted">(open access: {{ collection.exam_open_access }})</small>
+                    </p>
+
+                    <p class="mb-2">
+                        {% include "generic/partials/exams/exam_status.html#publish-results" %}
+                        {% include "generic/partials/exams/exam_status.html#exam-active" %}
+                    </p>
+
+                    <p class="mb-1">
+                        <span class="badge bg-secondary me-2">{{ collection.get_collection_type_display }}</span>
+                        <span class="badge bg-light text-dark me-2">Self review: {{ collection.self_review }}</span>
+                        {% if collection.open_access %}
+                            <span class="badge bg-success">Open</span>
+                        {% else %}
+                            <span class="badge bg-warning text-dark">Restricted</span>
+                        {% endif %}
+                    </p>
+
+                    {% if collection.prerequisites.exists %}
+                        <div class="mt-3 mb-2">
+                            <strong>Prerequisites</strong>
+                            <ul class="mb-0">
+                                {% for prereq in collection.prerequisites.all %}
+                                    <li><a href="{% url 'atlas:collection_detail' prereq.pk %}">{{ prereq.name }}</a></li>
+                                {% endfor %}
+                            </ul>
+                        </div>
+                    {% endif %}
+                </div>
+
+                <div class="col-md-4 d-flex flex-column align-items-md-end mt-3 mt-md-0">
+                    <div class="mb-2 w-100 text-md-end">
+                        {% if collection.collection_type == "VIV" %}
+                            <a href="{% url 'atlas:collection_viva' collection.pk %}" class="btn btn-primary mb-2">Start Viva</a>
+                        {% else %}
+                            <div class="d-inline-block">
+                                <a class="btn btn-outline-secondary btn-sm" href="{{ collection.get_take_url }}" id="take-url-link">Open</a>
+                                <button
+                                    _="on click
+                                         writeText(#take-url-link's href) on navigator.clipboard
+                                         put 'copied url!' into me
+                                         wait 1s
+                                         put 'copy link' into me"
+                                    class="btn btn-sm btn-outline-secondary ms-1">Copy link</button>
+                            </div>
+                        {% endif %}
+                    </div>
+
+                    {% if collection.prerequisites.exists %}
+                        <div class="w-100 text-md-end">
+                            <button
+                                title="Sync users from all prerequisite collections into this collection"
+                                hx-post="{% url 'atlas:collection_sync_prerequisite_users' collection.pk %}"
+                                hx-swap="outerHTML"
+                                class="btn btn-sm btn-secondary"
+                            >Sync prerequisite users</button>
+                        </div>
+                    {% endif %}
+                </div>
+            </div>
+        </div>
     </div>
 
+    <div class="row">
+        <div class="col-12">
+            <h3 class="mb-3">Cases</h3>
 
-    {% if collection.collection_type == "VIV" %}
-        <p><a href='{% url "atlas:collection_viva" collection.pk %}'><button class="btn btn-primary">Start Viva</button></a>
-    {% else %}
-        <p>This collection will be available to view/take <a href='{{collection.get_take_url}}' id="take-url">here</a>{% if not collection.active %} (when active){% endif %} <button
-            _="on click
-               writeText(#take-url's href) on navigator.clipboard
-               put 'copied url!' into me
-               wait 1s
-               put 'copy url' into me"
-            class="btn btn-sm">copy link</button>
-            <p>Review collection <a href='{% url "atlas:collection_viva" collection.pk %}'>here</a>
-    {% endif %}
-
-
-
-
-    <h3>Cases</h3>
-    <ol id="full-question-list" class="sortable">
-        {% for casedetail in casesdetails %}
-            <li data-question_pk={{casedetail.case.pk}}>
-
-
-                <a href="{% url 'atlas:collection_case_view' pk=collection.pk case_number=forloop.counter0 %}">Case {{forloop.counter}}</a>
-                :
-                {% if casedetail.case.series.count == 0 %}
-                    &nbsp;<i class="bi bi-exclamation-circle text-warning" title="No series attached to this case"></i>&nbsp;
-                {% endif %}
-                {{casedetail.case.title}}
-
-                {% partial casedetails-management-links %}
-
-            </li>
-
-        {% endfor %}
-    </ol>
-
-
-
+            <ol id="full-question-list" class="sortable list-group list-group-numbered">
+                {% for casedetail in casesdetails %}
+                    {% include 'atlas/partials/case_list_item.html' %}
+                {% endfor %}
+            </ol>
+        </div>
+    </div>
 
     {% if can_edit %}
-        <p><button id='button-edit-order' title='click and drag questions to change order' data-posturl="{% url 'atlas:exam_json_edit' pk=collection.pk %}">Edit case order / Remove cases</button></p>
-        <p><button id='button-add-case'
-                   title='click to add a case to this collection'
-                   hx-get="{% url 'atlas:add_case_to_collection' collection.pk %}" hx-swap="innerHTML" hx-target="#case-list">
-            Add case
-        </button>
-            <div id='case-list'></div>
-        </p>
+        <div class="row mt-4">
+            <div class="col-12 d-flex gap-2">
+                <button id='button-edit-order'
+                                title='click and drag questions to change order'
+                                data-posturl="{% url 'atlas:exam_json_edit' pk=collection.pk %}"
+                                class="btn btn-sm btn-outline-secondary">
+                        Edit case order / Remove cases
+                </button>
 
-        <details>
-            <summary>Answer management</summary>
+                <button id='button-add-case'
+                             title='click to add a case to this collection'
+                             hx-get="{% url 'atlas:add_case_to_collection' collection.pk %}" hx-swap="innerHTML" hx-target="#case-list"
+                             class="btn btn-sm btn-secondary">
+                        Add case
+                </button>
 
-            <div class="alert alert-danger">
-                <p>Manage answers for this collection. </p>
-
-                Please note these are permanant and cannot be undone.
+                <div id='case-list'></div>
             </div>
+        </div>
 
-            <button title="This will clear all user answers and attempts"
-                    hx-post="{% url 'atlas:collection_reset_answers' collection.pk %}"
-                    hx-swap="outerHTML"
-                    hx-confirm="Are you sure you want to reset all answers? This action cannot be undone."
-            >Reset all answers</button>
+        <div class="row mt-3">
+            <div class="col-12">
+                <details>
+                    <summary>Answer management</summary>
 
-            <button title="This will specific user answers and attempts"
-                    hx-post="{% url 'atlas:collection_reset_answers_user_list' collection.pk %}"
-                    hx-swap="innerHTML"
-                    hx-target="#user-list"
-            >Reset user answers</button>
-            <div id="user-list"></div>
+                    <div class="alert alert-danger mt-3">
+                        <p class="mb-1">Manage answers for this collection.</p>
+                        <small class="text-muted">Please note these are permanent and cannot be undone.</small>
+                    </div>
 
-        </details>
+                    <div class="d-flex gap-2">
+                        <button title="This will clear all user answers and attempts"
+                                        hx-post="{% url 'atlas:collection_reset_answers' collection.pk %}"
+                                        hx-swap="outerHTML"
+                                        hx-confirm="Are you sure you want to reset all answers? This action cannot be undone."
+                                        class="btn btn-danger btn-sm"
+                        >Reset all answers</button>
+
+                        <button title="This will specific user answers and attempts"
+                                        hx-post="{% url 'atlas:collection_reset_answers_user_list' collection.pk %}"
+                                        hx-swap="innerHTML"
+                                        hx-target="#user-list"
+                                        class="btn btn-warning btn-sm">
+                                Reset user answers</button>
+                    </div>
+
+                    <div id="user-list" class="mt-3"></div>
+                </details>
+            </div>
+        </div>
     {% endif %}
+
     {% include 'exam_overview_js.html' %}
+</div>
+
 {% endblock %}

atlas/templates/atlas/collection_headers.html

@@ -16,7 +16,6 @@
                 <li class="nav-item"><a class="nav-link" href="{% url 'atlas:collection_mark_overview' collection.pk %}">Mark</a></li>
                 <li class="nav-item"><a class="nav-link" href="{% url 'atlas:collection_scores_cid' collection.pk %}">Scores</a></li>
                 <li class="nav-item"><a class="nav-link" href="{% url 'atlas:exam_cids' collection.pk %}">Candidates</a></li>
-                <li class="nav-item"><a class="nav-link" href="{% url 'atlas:atlas_create_exam' pk=collection.pk %}">Add New Case</a></li>
             </ul>
 
             <ul class="navbar-nav ms-auto">
@@ -32,6 +31,7 @@
                         {% if request.user.is_superuser %}
                             <li><hr class="dropdown-divider"></li>
                             <li><a class="dropdown-item" href="{% url 'admin:atlas_casecollection_change' collection.id %}">Admin Edit</a></li>
+                            <li><a class="dropdown-item" href="{% url 'atlas:atlas_create_exam' pk=collection.pk %}">Add New Case</a></li>
                         {% endif %}
                     </ul>
                 </li>

atlas/templates/atlas/collection_mark_overview.html

@@ -2,9 +2,9 @@
 
 {% block content %}
     <div class="vstack gap-3">
-        {% for case_detail, answers in case_map.items %}
+        {% for casedetail, answers in case_map.items %}
             <div class="border border-dark">
-                <h4>Case: {{case_detail.case.title}}</h4>
+                <h4>Case: {{casedetail.case.title}}</h4>
                 Answers
                 <ul>
                     {% for answer in answers %}

atlas/templates/atlas/collection_question_schemas.html

@@ -3,15 +3,15 @@
 {% comment %} <script src="{% static 'js/jquery-3.7.1.min.js' %}"></script>
 <script src="https://cdn.jsdelivr.net/npm/@json-editor/json-editor@latest/dist/jsoneditor.min.js"></script> {% endcomment %}
 <ol>
-    {% for case_detail in case_details %}
+    {% for casedetail in casedetails %}
 
-        <li id="case-detail-{{case_detail.pk}}"{% if case_detail.question_schema %} class="cases"{% endif %}>
-            <h2>Case: {{ case_detail.case.title }}</h2>
+        <li id="case-detail-{{casedetail.pk}}"{% if casedetail.question_schema %} class="cases"{% endif %}>
+            <h2>Case: {{ casedetail.case.title }}</h2>
             
-            {% if case_detail.question_schema %}
+            {% if casedetail.question_schema %}
                 <button class="btn btn-sm btn-secondary use-layout">Use schema</button>
                 <details><summary>Schema:</summary>
-                <div class="schema" data-schema='{{ case_detail.get_question_schema }}'>{{ case_detail.question_schema }}</div>
+                <div class="schema" data-schema='{{ casedetail.get_question_schema }}'>{{ casedetail.question_schema }}</div>
                 </details>
                 <div class="form"></div>
             {% else %}

atlas/templates/atlas/collection_view.html

@@ -0,0 +1,22 @@
+{% extends 'atlas/base.html' %}
+
+{% load render_table from django_tables2 %}
+
+{% block content %}
+
+<div class="container-fluid">
+    <div class="d-flex align-items-start justify-content-between mb-3">
+        <h2 class="mb-0">Collections</h2>
+        {% if request.user.is_staff %}
+            <a class="btn btn-sm btn-primary" href="{% url 'atlas:exam_create' %}">Create collection</a>
+        {% endif %}
+    </div>
+
+    <p class="mb-3">Manage and browse case collections. Use filters to narrow results.</p>
+
+    {% render_table table %}
+
+    {% include "generic/partials/filter_bar.html" with filter=filter app_name=app_name collapse_id="bottom-filter-body" %}
+</div>
+
+{% endblock %}

atlas/templates/atlas/collection_viva.html

@@ -69,7 +69,7 @@
                                     </div>
                                     {# Hidden per-case question snippet to inject when case is loaded #}
                                     <div class="question-block-snippet" style="display:none;">
-                                        {% include 'atlas/partials/collection_question_block.html' with case_detail=casedetail %}
+                                        {% include 'atlas/partials/collection_question_block.html' with casedetail=casedetail %}
                                     </div>
                                     {% if case.display_sets.all %}
                                         <details class="displayset-detail"><summary>Display Sets:</summary>
@@ -212,14 +212,14 @@
                 let c = this.closest(".case-item");
                 console.log('clicked local', c)
                 console.log('open local', c.dataset.case)
-                case_details = JSON.parse(c.dataset.casejson);
+                casedetails = JSON.parse(c.dataset.casejson);
                 let viewerstate = JSON.parse(c.dataset.viewerstate) || {};
                 $('#loading-case').show()
                 $("#open-viewer-local").addClass("flash-button");
                 $('#current-case-title').html("<span class='title'>Case:</span> "+c.dataset.title);
-                $("#current-case-history").html("<span class='title'>History:</span> "+case_details['history']);
-                $("#current-case-discussion").html("<span class='title'>Discussion:</span> "+case_details['discussion']);
-                $("#current-case-report").html("<span class='title'>Report:</span> "+case_details['report']);
+                $("#current-case-history").html("<span class='title'>History:</span> "+casedetails['history']);
+                $("#current-case-discussion").html("<span class='title'>Discussion:</span> "+casedetails['discussion']);
+                $("#current-case-report").html("<span class='title'>Report:</span> "+casedetails['report']);
 
                 bc.postMessage({"type": "open",
                     "case" : c.dataset.case, "images": c.dataset.images,
@@ -239,15 +239,15 @@
                 let c = this;
                 console.log('clicked local', c)
                 console.log('open local', c.dataset.case)
-                case_details = JSON.parse(c.dataset.casejson);
+                casedetails = JSON.parse(c.dataset.casejson);
                 let viewerstate = JSON.parse(c.dataset.viewerstate) || {};
                 let annotations = JSON.parse(c.dataset.annotations) || {};
                 $('#loading-case').show()
                 $("#open-viewer-local").addClass("flash-button");
                 $('#current-case-title').html("<span class='title'>Case:</span> "+c.dataset.title);
-                $("#current-case-history").html("<span class='title'>History:</span> "+case_details['history']);
-                $("#current-case-discussion").html("<span class='title'>Discussion:</span> "+case_details['discussion']);
-                $("#current-case-report").html("<span class='title'>Report:</span> "+case_details['report']);
+                $("#current-case-history").html("<span class='title'>History:</span> "+casedetails['history']);
+                $("#current-case-discussion").html("<span class='title'>Discussion:</span> "+casedetails['discussion']);
+                $("#current-case-report").html("<span class='title'>Report:</span> "+casedetails['report']);
 
                 bc.postMessage({"type": "open",
                     "case" : c.dataset.case, "images": c.dataset.images,
@@ -302,15 +302,15 @@
 
                 let c = $(this).closest(".case-item");
 
-                case_details = c.data('casejson');
-                console.log(case_details);
+                casedetails = c.data('casejson');
+                console.log(casedetails);
 
                 $('#loading-case').show()
                 $("#open-viewer").addClass("flash-button");
                 $('#current-case-title').html("<span class='title'>Case:</span> "+c.data('title'));
-                $("#current-case-history").html("<span class='title'>History:</span> "+case_details['history']);
-                $("#current-case-discussion").html("<span class='title'>Discussion:</span> "+case_details['discussion']);
-                $("#current-case-report").html("<span class='title'>Report:</span> "+case_details['report']);
+                $("#current-case-history").html("<span class='title'>History:</span> "+casedetails['history']);
+                $("#current-case-discussion").html("<span class='title'>Discussion:</span> "+casedetails['discussion']);
+                $("#current-case-report").html("<span class='title'>Report:</span> "+casedetails['report']);
 
                 console.log($(this).data('type'))
                 if ($(this).data('type') == 'case') {

atlas/templates/atlas/condition_detail.html

@@ -18,7 +18,7 @@
                 <h5 class="mb-2">Details</h5>
                 <dl class="row">
                         <dt class="col-sm-4">Primary name</dt>
-                        <dd class="col-sm-8">{{ condition.primary }}</dd>
+                        <dd class="col-sm-8">{% if condition.canonical %}No (alias of <a href="{{ condition.canonical.get_absolute_url }}">{{ condition.canonical.name }}</a>){% else %}Yes{% endif %}</dd>
 
                         <dt class="col-sm-4">Subspecialty</dt>
                         <dd class="col-sm-8">
@@ -31,11 +31,9 @@
 
                         <dt class="col-sm-4">Synonyms</dt>
                         <dd class="col-sm-8">
-                            {% for syn in condition.synonym.all %}
-                                <a class="badge bg-secondary text-decoration-none text-white me-1" href="{{ syn.get_absolute_url }}">{{ syn }}</a>
-                            {% empty %}
-                                &mdash;
-                            {% endfor %}
+                            <div id="synonyms-container">
+                                {% include 'atlas/partials/_synonyms_list.html' %}
+                            </div>
                         </dd>
 
                         <dt class="col-sm-4">Parent</dt>

atlas/templates/atlas/condition_form.html

@@ -1,27 +1,20 @@
 {% extends "atlas/base.html" %}
-<!-- {% load static from static %} -->
+{% load crispy_forms_tags %}
+
+{% block css %}{% endblock %}
 
-{% block css %}
-{% endblock %}
 {% block js %}
-    <!--<script type="text/javascript" src="/admin/jsi18n/"></script>-->
-    {{form.media}}
-
-    <script type="text/javascript">
-    </script>
-
-    <!-- {{ form.media }} -->
+    {{ form.media }}
 {% endblock %}
+
 {% block content %}
-    <h2>Add/Edit Condition</h2>
+    <h2>Add / Edit Condition</h2>
     <p>Use this form to create or edit a condition.</p>
     <p>Please check if it already <a href='{% url "atlas:condition_view" %}'>exists</a> before doing so!</p>
+
     <form action="" method="post" enctype="multipart/form-data" id="condition-form">
         {% csrf_token %}
-
-        <table>
-            {{ form.as_table }}
-        </table>
-        <input type="submit" class="submit-button" value="Submit" name="submit">
+        {% crispy form %}
     </form>
+
 {% endblock %}

atlas/templates/atlas/finding_detail.html

@@ -12,8 +12,8 @@
     </div>
     <div>
         <h3>Name: {{finding.name}}</h3>
-        Primary name: {{finding.primary}}<br />
-        Synonyms: {{finding.synonym.all|join:", "}}<br />
+    Primary name: {% if finding.canonical %}No (alias of <a href="{{ finding.canonical.get_absolute_url }}">{{ finding.canonical.name }}</a>){% else %}Yes{% endif %}<br />
+    Synonyms: {{ finding.get_synonym_link|safe }}<br />
     </div>
     {% if finding.seriesfinding_set.all %}
         <h4>Associated Cases</h4>

atlas/templates/atlas/partials/_collection_case_jump.html

@@ -0,0 +1,11 @@
+{% for cd in casedetails %}
+    {% with idx=forloop.counter0 %}
+        {% if cid %}
+            <a class="dropdown-item {% if idx == current %}active{% endif %}" href="{% url 'atlas:collection_case_view_take' pk=collection.pk case_number=idx cid=cid passcode=passcode %}">
+        {% else %}
+            <a class="dropdown-item {% if idx == current %}active{% endif %}" href="{% url 'atlas:collection_case_view_take_user' pk=collection.pk case_number=idx %}">
+        {% endif %}
+        Case {{ forloop.counter }}: {{ cd.case.title|default:cd.case.pk|truncatechars:60 }}
+        </a>
+    {% endwith %}
+{% endfor %}

atlas/templates/atlas/partials/_prior_card.html

@@ -0,0 +1,80 @@
+<div id="prior-card-{{case.id}}" class="col-12 col-md-6 col-lg-4" data-case="{{case.id}}">
+    <div class="card h-100 shadow-sm {% if added %}border-success{% else %}border-secondary{% endif %}">
+        <div class="card-body d-flex flex-column">
+            {% if error %}
+                <div class="alert alert-danger py-1 mb-2 small">{{ error }}</div>
+            {% endif %}
+            <div class="d-flex justify-content-between align-items-start mb-2">
+                <h5 class="card-title mb-0">{{case.title}}</h5>
+                <div>
+                    {% if added %}
+                        <span class="badge bg-success">Added</span>
+                    {% else %}
+                        <span class="badge bg-secondary">Available</span>
+                    {% endif %}
+                </div>
+            </div>
+
+            <p class="card-text small text-muted mb-2">Relation: <span class="fw-medium">{{ relation }}</span></p>
+
+            <div class="mb-3 small">{{case.get_series_blocks|safe}}</div>
+
+            <div class="mt-auto">
+                <div class="d-flex gap-2 mb-2">
+                    <a href="{% url 'atlas:case_detail' case.id %}" class="btn btn-sm btn-outline-primary">View case</a>
+                </div>
+
+                {% if not added %}
+                    <form class="row g-2"
+                          {% if case_number %}
+                              hx-post="{% url 'atlas:collection_case_priors' collection.id case_number %}"
+                          {% else %}
+                              hx-post="{% url 'atlas:collection_case_priors_legacy' collection.id casedetail.case.pk %}"
+                          {% endif %}
+                          hx-target="#prior-card-{{case.id}}" hx-swap="outerHTML">
+                        {% csrf_token %}
+                        <input type="hidden" name="prior_case_id" value="{{case.id}}" />
+                        <div class="col-12">
+                            <input class="form-control form-control-sm" type="text" name="relation" value="{{relation}}" placeholder="Relation to case" />
+                        </div>
+                        <div class="col-8">
+                            <select class="form-select form-select-sm" name="prior_visibility" id="prior_visibility_{{case.id}}">
+                                <option value="AL" {% if visibility == 'AL' %}selected{% endif %}>Always</option>
+                                <option value="RE" {% if visibility == 'RE' %}selected{% endif %}>Review</option>
+                                <option value="NO" {% if visibility == 'NO' %}selected{% endif %}>None</option>
+                            </select>
+                        </div>
+                        <div class="col-4 d-grid">
+                            <button class="btn btn-sm btn-primary" type="submit">Add</button>
+                        </div>
+                    </form>
+                {% else %}
+                    <form
+                        {% if case_number %}
+                            hx-post="{% url 'atlas:collection_case_priors' collection.id case_number %}"
+                        {% else %}
+                            hx-post="{% url 'atlas:collection_case_priors_legacy' collection.id casedetail.case.pk %}"
+                        {% endif %}
+                        hx-target="#prior-card-{{case.id}}" hx-swap="outerHTML">
+                        {% csrf_token %}
+                        <input type="hidden" name="remove" value="{{case.id}}" />
+                        <div class="mb-2 small text-muted">Current relation: <strong>{{relation}}</strong></div>
+                        <div class="d-flex gap-2">
+                            <select class="form-select form-select-sm w-50" name="prior_visibility" id="prior_visibility_{{case.id}}" disabled>
+                                <option value="AL" {% if visibility == 'AL' %}selected{% endif %}>Always</option>
+                                <option value="RE" {% if visibility == 'RE' %}selected{% endif %}>Review</option>
+                                <option value="NO" {% if visibility == 'NO' %}selected{% endif %}>None</option>
+                            </select>
+                            <button class="btn btn-sm btn-danger" type="submit">Remove</button>
+                        </div>
+                    </form>
+                {% endif %}
+
+            </div>
+        </div>
+
+        <div class="card-footer bg-transparent">
+            <small class="text-muted">Case ID: {{ case.id }}</small>
+        </div>
+    </div>
+</div>

atlas/templates/atlas/partials/_synonyms_list.html

@@ -0,0 +1,56 @@
+{% comment %}Partial that renders the synonyms list + add form. Used by condition_detail and HTMX responses.{% endcomment %}
+{% load static %}
+
+{% with syns=condition.get_synonyms %}
+    {% if syns %}
+        {% for syn in syns %}
+            <a class="badge bg-secondary text-decoration-none text-white me-1" href="{{ syn.get_absolute_url }}">{{ syn }}</a>
+        {% endfor %}
+    {% else %}
+        &mdash;
+    {% endif %}
+{% endwith %}
+
+{% if request.user.is_authenticated and can_merge %}
+    <div class="mt-2 d-flex gap-2">
+        <!-- Button to add an existing condition as a synonym -->
+        <a class="btn btn-sm btn-outline-primary" data-bs-toggle="collapse" href="#addSynonymCollapse" role="button" aria-expanded="false" aria-controls="addSynonymCollapse">Add synonym</a>
+
+        <!-- Button to create a new condition and add it as a synonym -->
+        <a class="btn btn-sm btn-outline-success" data-bs-toggle="collapse" href="#createSynonymCollapse" role="button" aria-expanded="false" aria-controls="createSynonymCollapse">Create synonym</a>
+    </div>
+
+    <!-- Collapse: add existing condition -->
+    <div class="collapse mt-2" id="addSynonymCollapse">
+        <div class="card card-body">
+            <form method="POST"
+                  hx-post="{% url 'atlas:condition_detail' condition.pk %}"
+                  hx-target="#synonyms-container" hx-swap="innerHTML">
+                {% csrf_token %}
+                <input type="hidden" name="action" value="add_synonym" />
+                <div class="mb-2">
+                    <label class="form-label small">Select existing condition</label>
+                    {{ synonym_form.condition }}
+                </div>
+                <button class="btn btn-primary btn-sm" type="submit">Add</button>
+            </form>
+        </div>
+    </div>
+
+    <!-- Collapse: create new condition -->
+    <div class="collapse mt-2" id="createSynonymCollapse">
+        <div class="card card-body">
+            <form method="POST"
+                  hx-post="{% url 'atlas:condition_detail' condition.pk %}"
+                  hx-target="#synonyms-container" hx-swap="innerHTML">
+                {% csrf_token %}
+                <input type="hidden" name="action" value="add_synonym" />
+                <div class="mb-2">
+                    <label class="form-label small">Create new synonym name</label>
+                    <input class="form-control" type="text" name="synonym_name" placeholder="e.g. Granulomatosis with Polyangitis" required />
+                </div>
+                <button class="btn btn-success btn-sm" type="submit">Create</button>
+            </form>
+        </div>
+    </div>
+{% endif %}

atlas/templates/atlas/partials/_viewing_case_as_part_of_collection.html

@@ -0,0 +1,24 @@
+
+<div class="d-flex justify-content-between align-items-center mb-3">
+    <div>
+        {% if previous %}
+            <a class="btn btn-outline-secondary btn-sm" href="{% url nav_link_view collection.id case_number|add:-1 %}">&larr; Previous</a>
+        {% endif %}
+    </div>
+    <div class="text-center">
+        <div class="h6 mb-0">Viewing as part of a collection</div>
+        <div>
+            <a href="{% url 'atlas:collection_detail' collection.id %}" class="fw-bold">{{collection.name}}</a>
+            <small class="text-muted">[{{case_number|add:1}}/{{collection_length}}]</small>
+        </div>
+    </div>
+    <div>
+        {% if next %}
+            <a class="btn btn-outline-secondary btn-sm" href="{% url nav_link_view collection.id case_number|add:1 %}">Next &rarr;</a>
+        {% endif %}
+    </div>
+
+    <div class="mb-1">
+        {% include "atlas/collection_detail.html#casedetails-management-links" %}
+    </div>
+</div>

atlas/templates/atlas/partials/case_list_item.html

@@ -0,0 +1,31 @@
+<li class="list-group-item d-flex gap-3 align-items-start" data-question_pk="{{ casedetail.case.pk }}">
+
+    <div class="flex-fill">
+        <div class="d-flex justify-content-between align-items-start">
+            <div>
+                <a class="h6 mb-0 text-decoration-none case-link"
+                   href="{% url 'atlas:collection_case_view' pk=collection.pk case_number=forloop.counter0 %}"
+                   data-case-base-href="{% url 'atlas:collection_case_view' pk=collection.pk case_number=0 %}">
+                    {{ casedetail.case.title }}
+                </a>
+                <div class="small text-muted"><span class="case-number">Case {{ forloop.counter }}</span> &mdash; <span class="text-truncate">{{ casedetail.case.description|default_if_none:""|truncatechars:80 }}</span></div>
+            </div>
+        </div>
+
+        <div class="mt-2 small text-muted">
+            {% if casedetail.case.series.count == 0 %}
+                <span class="text-warning">This case has no series / stacks attached</span>
+            {% else %}
+                {{ casedetail.case.series.count }} series
+            {% endif %}
+            {% if casedetail.question_schema %}
+                &nbsp;•&nbsp;<span class="text-success">Questions defined</span>
+            {% endif %}
+        </div>
+    </div>
+
+    <div class="d-flex align-items-center ms-3">
+        {% include 'atlas/partials/casedetails_management_links.html' %}
+    </div>
+
+</li>

atlas/templates/atlas/partials/case_search_results.html

@@ -0,0 +1,45 @@
+{# Search results #}
+{% if q %}
+  {% if cases and cases.exists %}
+    <div class="list-group mb-2">
+  {% for case in cases %}
+  <div class="list-group-item d-flex justify-content-between align-items-center" data-case-pk="{{ case.pk }}">
+          <div class="flex-fill me-3">
+            <div class="fw-semibold">{{ case.title }}</div>
+            <div class="small text-muted">{% if case.description %}{{ case.description|truncatechars:100 }}{% endif %}</div>
+          </div>
+
+          <form class="m-0" hx-post="{% url 'atlas:add_case_to_collection' collection.pk %}" hx-target="#full-question-list" hx-swap="beforeend">
+            {% csrf_token %}
+            <input type="hidden" name="case" value="{{ case.pk }}">
+            <button type="submit" class="btn btn-sm btn-primary">Add</button>
+          </form>
+        </div>
+      {% endfor %}
+    </div>
+  {% else %}
+    <div class="text-muted small mb-2">No cases found.</div>
+  {% endif %}
+{% endif %}
+
+{# Recent cases quick-add (rendered below search results) #}
+{% if recent_cases and recent_cases|length > 0 %}
+  <div>
+    <div class="small text-muted mb-1">Recently created</div>
+    <div class="list-group">
+      {% for case in recent_cases %}
+        <div class="list-group-item d-flex justify-content-between align-items-center" data-case-pk="{{ case.pk }}">
+          <div class="flex-fill me-3">
+            <div class="fw-semibold">{{ case.title }}</div>
+            <div class="small text-muted">{% if case.description %}{{ case.description|truncatechars:100 }}{% endif %}</div>
+          </div>
+          <form class="m-0" hx-post="{% url 'atlas:add_case_to_collection' collection.pk %}" hx-target="#full-question-list" hx-swap="beforeend">
+            {% csrf_token %}
+            <input type="hidden" name="case" value="{{ case.pk }}">
+            <button type="submit" class="btn btn-sm btn-outline-primary">Add</button>
+          </form>
+        </div>
+      {% endfor %}
+    </div>
+  </div>
+{% endif %}

atlas/templates/atlas/partials/case_search_widget.html

@@ -0,0 +1,46 @@
+<div class="case-search-widget">
+  <label for="case-search-input" class="form-label">Search cases</label>
+  <input id="case-search-input" name="q" class="form-control" type="search"
+    placeholder="Type to search cases..."
+    hx-get="{% url 'atlas:case_search' %}"
+    hx-include="#case-search-input"
+    hx-vals='{"collection": "{{ collection.pk }}"}'
+    hx-target="#case-search-results"
+    hx-trigger="keyup changed delay:400ms"
+    autocomplete="off">
+
+  <div id="case-search-results" class="mt-2">
+    {# Render initial results (search + recent) on initial GET; HTMX searches will replace this div with partial results #}
+    {% include 'atlas/partials/case_search_results.html' with cases=cases recent_cases=recent_cases collection=collection %}
+  </div>
+</div>
+
+<script>
+  (function(){
+    // Robust fallback: ensure repeated searches always work by using htmx.ajax when available.
+    try {
+      var input = document.getElementById('case-search-input');
+      if (!input) return;
+      var timer = null;
+      input.addEventListener('input', function(){
+        if (timer) clearTimeout(timer);
+        timer = setTimeout(function(){
+          try {
+            var q = encodeURIComponent(input.value || '');
+            var url = "{% url 'atlas:case_search' %}?q=" + q + "&collection={{ collection.pk }}";
+            if (window.htmx && typeof window.htmx.ajax === 'function') {
+              window.htmx.ajax('GET', url, { target: '#case-search-results', swap: 'innerHTML' });
+            } else {
+              // fallback to fetch
+              fetch(url, { credentials: 'same-origin' }).then(function(r){ return r.text(); }).then(function(html){
+                var el = document.getElementById('case-search-results');
+                if (el) el.innerHTML = html;
+              }).catch(function(e){ console.error('case search fetch error', e); });
+            }
+          } catch(e) { console.error(e); }
+        }, 400);
+      });
+    } catch(e) { console.error('case search widget init error', e); }
+  })();
+</script>
+

atlas/templates/atlas/partials/casedetails_management_links.html

@@ -0,0 +1,42 @@
+    <div class="btn-group btn-group-sm me-2" role="group" aria-label="management-actions">
+        <a class="btn btn-outline-secondary" href="{% url 'atlas:collection_case_displaysetup_legacy' casedetail.collection.pk casedetail.case.pk %}" title="Setup default display">
+            <i class="bi bi-display"></i>
+        </a>
+
+        <a class="btn btn-outline-secondary" href="{% url 'atlas:collection_case_details_legacy' casedetail.collection.pk casedetail.case.pk %}" title="Case details">
+            <i class="bi bi-info-square"></i>
+        </a>
+
+        {% if collection.collection_type == "QUE" %}
+            <a class="btn btn-outline-secondary" href='{% url "atlas:collection_case_questions_legacy" casedetail.collection.pk casedetail.case.pk %}' title="Manage questions">
+                {% if casedetail.question_schema %}
+                    <i class="bi bi-question-square text-success"></i>
+                {% else %}
+                    <i class="bi bi-question-square text-danger"></i>
+                {% endif %}
+            </a>
+        {% endif %}
+
+        {% if casedetail.case.previous_case %}
+            <a class="btn btn-outline-secondary" href='{% url "atlas:collection_case_priors_legacy" casedetail.collection.pk casedetail.case.pk %}' title="Manage priors">
+                <i class="bi bi-link-45deg"></i>
+            </a>
+        {% endif %}
+    </div>
+
+    <div class="btn-group btn-group-sm" role="group" aria-label="status-indicator">
+        {% if casedetail.default_viewerstate %}
+            <button type="button" class="btn btn-sm btn-outline-success" aria-disabled="true" title="This case has a default viewerstate defined">
+                <i class="bi bi-check"></i>
+            </button>
+        {% endif %}
+    </div>
+
+        {# Remove button (HTMX) - only shown when the surrounding template has `can_edit` true #}
+        {% if can_edit %}
+            <form class="d-inline ms-2 m-0" hx-post="{% url 'atlas:remove_case_from_collection' casedetail.case.pk casedetail.collection.pk %}" hx-target="closest li" hx-swap="outerHTML" hx-confirm="Remove this case from the collection?">
+                <button type="submit" class="btn btn-outline-danger btn-sm case-remove" title="Remove this case from the collection">
+                    <i class="bi bi-trash"></i>
+                </button>
+            </form>
+        {% endif %}

atlas/templates/atlas/partials/collection_question_block.html

@@ -1,10 +1,10 @@
 {# Partial: render questions and answers as HTML. #}
 
-{% if case_detail.question_schema %}
+{% if casedetail.question_schema %}
   <div class="collection-question-block">
     <h4>Questions</h4>
     <dl class="row">
-      {% for name, prop in case_detail.question_schema.properties.items %}
+      {% for name, prop in casedetail.question_schema.properties.items %}
         <dt class="col-sm-4">{{ prop.title|default:name }}</dt>
         <dd class="col-sm-8">
           {% if prop.description %}
@@ -18,8 +18,8 @@
           {% endif %}
 
           {# Safely fetch the stored/example answer using the project's `get_item` filter. #}
-          {% if case_detail.question_answers %}
-            {% with correct=case_detail.question_answers|get_item:name %}
+          {% if casedetail.question_answers %}
+            {% with correct=casedetail.question_answers|get_item:name %}
               <div class="mt-2">
                 <strong>Example / Correct:</strong>
                 {% if correct %}
@@ -37,7 +37,7 @@
           {% if user_answer %}
             {% if user_answer|get_item:name %}
               {% with ua=user_answer|get_item:name %}
-                {% with correct=case_detail.question_answers|get_item:name %}
+                {% with correct=casedetail.question_answers|get_item:name %}
                   <div class="mt-1">
                     <strong>Your answer:</strong>
                     <span class="ms-2 {% if ua == correct %}text-success{% else %}text-danger{% endif %}">{{ ua }}</span>

atlas/templates/atlas/partials/series_images.html

@@ -0,0 +1,31 @@
+{% load static %}
+
+<div class="series-images-list">
+    {% for image in images %}
+        <div class="d-flex align-items-center mb-2">
+            {% if image.image %}
+                <a href="{% url 'atlas:series_image_dicom' pk=image.pk %}" target="_blank" class="me-2">
+                    <img src="{{ image.image.url }}" alt="image-{{ image.pk }}" style="width:96px;height:auto;object-fit:cover;border-radius:.25rem;" class="img-thumbnail">
+                </a>
+            {% else %}
+                <div class="me-2 bg-secondary" style="width:96px;height:72px;border-radius:.25rem;"></div>
+            {% endif %}
+
+            <div class="flex-grow-1">
+                <div><strong>{{ image.image.name|default:"(no file)" }}</strong></div>
+                {% if image.image %}
+                    <div class="small text-muted">{{ image.image.size|filesizeformat }}</div>
+                {% endif %}
+                {% if image.image_blake3_hash %}
+                    <div class="small text-muted">hash: {{ image.image_blake3_hash|truncatechars:12 }}</div>
+                {% endif %}
+            </div>
+
+            <div class="ms-auto text-end">
+                <a href="{% url 'atlas:series_image_dicom' pk=image.pk %}" class="btn btn-sm btn-outline-secondary">View DICOM</a>
+            </div>
+        </div>
+    {% empty %}
+        <p class="text-muted">No images found for this series.</p>
+    {% endfor %}
+</div>

atlas/templates/atlas/pathological_process_form.html

@@ -0,0 +1,23 @@
+{% extends "atlas/base.html" %}
+{% load crispy_forms_tags %}
+
+{% block js %}
+    {{ form.media }}
+{% endblock %}
+
+{% block content %}
+    <h2>Add / Edit Pathological process</h2>
+    <p>Use this form to create or edit a pathological process.</p>
+    <p>Please check if it already <a href='{% url "atlas:pathological_process_view" %}'>exists</a> before doing so!</p>
+
+    <form action="" method="post" enctype="multipart/form-data" id="pathological-process-form">
+        {% csrf_token %}
+        {% crispy form %}
+
+        <div class="mt-3">
+            <button type="submit" class="btn btn-primary">Submit</button>
+            <a class="btn btn-secondary ms-2" href="{% url 'atlas:pathological_process_view' %}">Cancel</a>
+        </div>
+    </form>
+
+{% endblock %}

atlas/templates/atlas/presentation_form.html

@@ -0,0 +1,23 @@
+{% extends "atlas/base.html" %}
+{% load crispy_forms_tags %}
+
+{% block js %}
+    {{ form.media }}
+{% endblock %}
+
+{% block content %}
+    <h2>Add / Edit Presentation</h2>
+    <p>Use this form to create or edit a presentation.</p>
+    <p>Please check if it already <a href='{% url "atlas:presentation_view" %}'>exists</a> before doing so!</p>
+
+    <form action="" method="post" enctype="multipart/form-data" id="presentation-form">
+        {% csrf_token %}
+        {% crispy form %}
+
+        <div class="mt-3">
+            <button type="submit" class="btn btn-primary">Submit</button>
+            <a class="btn btn-secondary ms-2" href="{% url 'atlas:presentation_view' %}">Cancel</a>
+        </div>
+    </form>
+
+{% endblock %}

atlas/templates/atlas/question_link_header.html

@@ -18,22 +18,8 @@
             </div>
         </div>
 
-        {% if collection %}
-            <div class="text-end mb-2">
-                <div class="small text-muted">Collection</div>
-                <div class="mb-1">
-                    {% include "atlas/collection_detail.html#casedetails-management-links" %}
-                </div>
-                <div class="small">
-                    {% if previous %}
-                        <a class="me-2" href="{% url 'atlas:collection_case_view' collection.id case_number|add:-1 %}">Previous</a>
-                    {% endif %}
-                    Viewing question as part of a collection: <a href="{% url 'atlas:collection_detail' collection.id %}">{{ collection.name }}</a>
-                    [{{ case_number|add:1 }} / {{ collection_length }}]
-                    {% if next %}
-                        <a class="ms-2" href="{% url 'atlas:collection_case_view' collection.id case_number|add:1 %}">Next</a>
-                    {% endif %}
-                </div>
-            </div>
-        {% endif %}
     </div>
+
+    {% if collection %}
+        {% include 'atlas/partials/_viewing_case_as_part_of_collection.html' with nav_link_view="atlas:collection_case_view" %}
+    {% endif %}

atlas/templates/atlas/series_viewer.html

@@ -1,337 +1,361 @@
 {% load crispy_forms_tags %}
 {% with image_url_array_and_count=series.get_image_url_array_and_count %}
 
-<div class="container my-4">
-    <div class="row">
-        <div class="col-12 mb-3">
-            <div class="card shadow-sm">
-                <div class="card-body d-flex flex-column flex-md-row justify-content-between align-items-start gap-3">
-                    <div>
-                        <h4 class="card-title mb-1">Series: {{ series.modality }} - {{ series.examination }}</h4>
-                        <div class="text-muted small">{{ series.plane }}, {{ series.contrast }}</div>
-                        <div class="mt-2">Description: <span class="text-break">{{ series.description }}</span></div>
-                        <div class="mt-2 text-muted">Author: {{ series.get_author_display }}</div>
+    <div class="container my-4">
+        <div class="row">
+            <div class="col-12 mb-3">
+                <div class="card shadow-sm">
+                    <div class="card-body d-flex flex-column flex-md-row justify-content-between align-items-start gap-3">
+                        <div>
+                            <h4 class="card-title mb-1">Series: {{ series.modality }} - {{ series.examination }}</h4>
+                            <div class="text-muted small">{{ series.plane }}, {{ series.contrast }}</div>
+                            <div class="mt-2">Description: <span class="text-break">{{ series.description }}</span></div>
+                            <div class="mt-2 text-muted">Author: {{ series.get_author_display }}</div>
+                        </div>
+                        <div class="ms-auto d-flex gap-2">
+                            <a class="btn btn-outline-secondary btn-sm" href="{% url 'atlas:series_detail' pk=series.pk %}">View series</a>
+                            {% if can_edit %}
+                                <button id="reset-viewport-button" class="btn btn-secondary btn-sm">Reset viewport</button>
+                            {% else %}
+                                <button id="reset-viewport-button" class="btn btn-secondary btn-sm">Reset viewport</button>
+                            {% endif %}
+                        </div>
                     </div>
-                    <div class="ms-auto d-flex gap-2">
-                        <a class="btn btn-outline-secondary btn-sm" href="{% url 'atlas:series_detail' pk=series.pk %}">View series</a>
+                </div>
+            </div>
+        </div>
+
+        <div class="row">
+            <div class="col-md-8 mb-3">
+                <div class="card">
+                    <div class="card-body p-2">
+                        {% with image_url_array_and_count=series.get_image_url_array_and_count %}
+                            <div id="root" class="dicom-viewer-root w-100" data-images="{{ image_url_array_and_count.0 }}"
+                                 style="height: 600px; box-sizing: border-box; background: #222;" data-auto-cache-stack=false>
+                            </div>
+                        {% endwith %}
+                    </div>
+                    <div class="card-footer bg-white d-flex flex-wrap gap-2 align-items-center">
+                        {% if can_edit and editing_finding < 1 %}
+                            <button id="add-finding-button" class="btn btn-primary btn-sm">Add finding</button>
+                            <button id="clone-finding-button" class="btn btn-outline-primary btn-sm"
+                                    title="Clone an existing finding"
+                                    hx-get="{% url 'atlas:series_finding_related' series.pk %}"
+                                    hx-target="#clone-findings-modal"
+                                    hx-trigger="click"
+                                    data-bs-toggle="modal"
+                                    data-bs-target="#clone-findings-modal">Clone finding</button>
+                        {% endif %}
+                        <div class="ms-auto text-muted small">{{ series.get_image_count }} images</div>
+                    </div>
+                </div>
+                <div class="mt-3">
+                <!-- Finding form moved below the viewport -->
+                    <div class="card mt-3">
+                        <div class="card-header">Finding form</div>
+                        <div class="card-body">
+                            <div id="finding-form">
+                                <div class="hide" id="hidden-form">
+                                    {% if editing_finding > 0 %}
+                                        <h5>Editing Finding</h5>
+                                        <p class="small">Editing finding with ID: {{editing_finding}}</p>
+                                    {% else %}
+                                        <h5>Add Finding</h5>
+                                        <p class="small">Click the button below to add a new finding.</p>
+                                    {% endif %}
+                                    <form method="post" id="series_finding_form">
+                                        {% csrf_token %}
+                                        {{series_finding_form|crispy}}
+                                        <div class="d-flex gap-2 mt-2">
+                                            <input type="submit" value="Submit" class="btn btn-success btn-sm">
+                                            <button id="cancel-add-finding-button" class="btn btn-secondary btn-sm">Cancel</button>
+                                        </div>
+                                    </form>
+                                </div>
+                            </div>
+                        </div>
+                    </div>
+                    <details class="styled-detail open">
+                        <summary>Findings</summary>
+                        <div class="mt-2">
+                            {% for finding in series.findings.all %}
+                                <div class="card mb-2">
+                                    <div class="card-body d-flex flex-column flex-md-row justify-content-between gap-2">
+                                        <div>
+                                            <button id="finding-{{finding.pk}}-3d" class="btn btn-sm btn-outline-secondary view-finding-button-3d me-2"
+                                                    data-annotationjson3d='{{finding.annotation_json_3d}}' data-viewerstatejson='{{finding.viewer_state_3d}}' data-findingid='{{finding.pk}}'>View 3D</button>
+                                            <strong>Finding(s):</strong>
+                                            {% for f in finding.findings.all %}{{f.get_link}}{% endfor %}<br />
+                                            <strong>Structure(s):</strong> {% for s in finding.structures.all %}{{s.get_link}}{% endfor %}<br />
+                                            <strong>Condition(s):</strong> {% for s in finding.conditions.all %}{{s.get_link}}{% endfor %}<br />
+                                            <div class="mt-2">{{finding.description}}</div>
+                                        </div>
+                                        <div class="text-end">
+                                            {% if request.user.is_superuser %}
+                                                <button class="btn btn-sm btn-outline-dark mb-2" type="button" data-bs-toggle="collapse" data-bs-target="#extra-{{finding.pk}}">Raw JSON</button>
+                                                <div class="collapse" id="extra-{{finding.pk}}">
+                                                <pre class="small bg-light p-2">{{finding.annotation_json}}</pre>
+                                                <pre class="small bg-light p-2">{{finding.viewport_json}}</pre>
+                                                </div>
+                                            {% endif %}
+                                            {% if can_edit %}
+                                                <div class="d-flex flex-column">
+                                                    <a href="{% url 'atlas:series_edit_finding' pk=series.pk finding_pk=finding.pk %}" class="btn btn-sm btn-outline-primary mb-1">Edit</a>
+                                                    <a href="{% url 'atlas:delete_finding' pk=finding.pk %}" class="btn btn-sm btn-outline-danger">Delete</a>
+                                                </div>
+                                            {% endif %}
+                                        </div>
+                                    </div>
+                                </div>
+                            {% empty %}
+                                <p class="text-muted">No findings available.</p>
+                            {% endfor %}
+                        </div>
+                    </details>
+                </div>
+
+            <!-- Images (loaded on demand via HTMX) -->
+                <div class="card mt-3">
+                    <div class="card-header d-flex justify-content-between align-items-center">
+                        <span>Images</span>
+                        <div>
+                            <button id="load-images-button" class="btn btn-sm btn-outline-primary"
+                                    hx-get="{% url 'atlas:series_images' series.pk %}"
+                                    hx-target="#series-images-container"
+                                    hx-swap="innerHTML"
+                                    hx-trigger="click"
+                                    hx-on="htmx:beforeRequest: document.getElementById('images-loading-indicator').style.display='inline-block'; htmx:afterSwap: document.getElementById('images-loading-indicator').style.display='none'; document.getElementById('load-images-button').disabled = true">
+                                Load images
+                            </button>
+                            <a href="{% url 'atlas:series_download' series.pk %}" class="btn btn-sm btn-outline-success ms-2" target="_blank" rel="noopener">Download</a>
+                            <span id="images-loading-indicator" class="spinner-border spinner-border-sm ms-2" role="status" aria-hidden="true" style="display:none"></span>
+                        </div>
+                    </div>
+                    <div class="card-body">
+                        <div id="series-images-container">
+                            <p class="text-muted small">Click 'Load images' to fetch.</p>
+                        </div>
+                    </div>
+                </div>
+
+            </div>
+
+            <div class="col-md-4 mb-3">
+                <div class="card mb-3">
+                    <div class="card-header">Cases</div>
+                    <div class="card-body">
+                        <div id="cases-list">
+                            {% include 'atlas/partials/series_cases_list.html' %}
+                        </div>
                         {% if can_edit %}
-                            <button id="reset-viewport-button" class="btn btn-secondary btn-sm">Reset viewport</button>
-                        {% else %}
-                            <button id="reset-viewport-button" class="btn btn-secondary btn-sm">Reset viewport</button>
+                            <details id="add-series-to-case-details" class="mt-2">
+                                <summary>Add Series to Case</summary>
+                                <form hx-post="{% url 'atlas:add_series_to_case' series.pk %}" hx-target="#cases-list" hx-swap="innerHTML" class="mt-2">
+                                    {% csrf_token %}
+                                    <div class="mb-2">
+                                        <label for="case-select" class="form-label">Select Case</label>
+                                        <select name="case_id" id="case-select" class="form-select" required>
+                                            {% for case in available_cases %}
+                                                <option value="{{ case.pk }}">{{ case.title }}</option>
+                                            {% endfor %}
+                                        </select>
+                                    </div>
+                                    <div class="d-flex gap-2">
+                                        <button type="submit" class="btn btn-primary btn-sm">Add to Case</button>
+                                        <button type="button" class="btn btn-outline-secondary btn-sm" onclick="document.getElementById('add-series-to-case-details').open = false">Close</button>
+                                    </div>
+                                </form>
+                            </details>
                         {% endif %}
                     </div>
                 </div>
+
+                <div class="card mb-3">
+                    <div class="card-header">Actions</div>
+                    <div class="card-body d-flex flex-column gap-2">
+                        <a class="btn btn-outline-primary btn-sm" href="{% url 'atlas:series_anonymise_dicom' pk=series.pk %}">Anonymise dicoms</a>
+                        <a class="btn btn-outline-primary btn-sm" href="{% url 'atlas:series_order_dicom' pk=series.pk %}">Order by slice location</a>
+                        <a class="btn btn-outline-primary btn-sm" href="{% url 'atlas:series_order_dicom_instance' pk=series.pk %}">Order by instance number</a>
+                        <a class="btn btn-outline-primary btn-sm" href="{% url 'atlas:series_order_dicom_SeriesInstanceUID' pk=series.pk %}">Order by SeriesInstanceUID</a>
+                        <a class="btn btn-outline-primary btn-sm" href="{% url 'atlas:series_order_upload_filename' pk=series.pk %}">Order by uploaded filename</a>
+                        <a class="btn btn-outline-warning btn-sm" href="{% url 'api-1:series_split_by_tag' series.pk 'ImageType' %}">Split by ImageType tag</a>
+                    </div>
+                </div>
+
+
+
+                {% if can_edit %}
+                    <div class="card">
+                        <div class="card-header">Truncate series</div>
+                        <div class="card-body">
+                            <p class="small">Limit the series to the selected bounds (the rest of the images will be deleted). This action is irreversible on site.</p>
+                            <div class="alert alert-warning"><strong>Warning:</strong> If you have reordered the series this may remove the wrong images.</div>
+                            <div class="mb-2">
+                                <label class="form-label">Start</label>
+                                <div class="input-group">
+                                    <input id="lower-truncation-bound-input" type="number" class="form-control form-control-sm" value="1">
+                                    <button id="set-lower-truncation-bound-button" class="btn btn-outline-secondary btn-sm">Set</button>
+                                </div>
+                            </div>
+                            <div class="mb-2">
+                                <label class="form-label">End</label>
+                                <div class="input-group">
+                                    <input id="upper-truncation-bound-input" type="number" class="form-control form-control-sm" value="{{image_url_array_and_count.1}}">
+                                    <button id="set-upper-truncation-bound-button" class="btn btn-outline-secondary btn-sm">Set</button>
+                                </div>
+                            </div>
+                            <div class="d-flex gap-2">
+                                <button id="truncate-test-button" class="btn btn-sm btn-outline-primary">Test truncate</button>
+                                <button id="truncate-button" class="btn btn-sm btn-danger">Truncate series</button>
+                            </div>
+                            <div id="truncate-output" class="mt-2"></div>
+                        </div>
+                    </div>
+                {% endif %}
             </div>
         </div>
     </div>
 
-    <div class="row">
-        <div class="col-md-8 mb-3">
-            <div class="card">
-                <div class="card-body p-2">
-                    {% with image_url_array_and_count=series.get_image_url_array_and_count %}
-                    <div id="root" class="dicom-viewer-root w-100" data-images="{{ image_url_array_and_count.0 }}"
-                             style="height: 600px; box-sizing: border-box; background: #222;" data-auto-cache-stack=false>
-                    </div>
-                    {% endwith %}
-                </div>
-                <div class="card-footer bg-white d-flex flex-wrap gap-2 align-items-center">
-                    {% if can_edit and editing_finding < 1 %}
-                        <button id="add-finding-button" class="btn btn-primary btn-sm">Add finding</button>
-                        <button id="clone-finding-button" class="btn btn-outline-primary btn-sm"
-                                        title="Clone an existing finding"
-                                        hx-get="{% url 'atlas:series_finding_related' series.pk %}"
-                                        hx-target="#clone-findings-modal"
-                                        hx-trigger="click"
-                                        data-bs-toggle="modal"
-                                        data-bs-target="#clone-findings-modal">Clone finding</button>
-                    {% endif %}
-                    <div class="ms-auto text-muted small">{{ series.get_image_count }} images</div>
-                </div>
-            </div>
 
-            <div class="mt-3">
-                <!-- Finding form moved below the viewport -->
-                <div class="card mt-3">
-                    <div class="card-header">Finding form</div>
-                    <div class="card-body">
-                        <div id="finding-form">
-                            <div class="hide" id="hidden-form">
-                                {% if editing_finding > 0 %}
-                                    <h5>Editing Finding</h5>
-                                    <p class="small">Editing finding with ID: {{editing_finding}}</p>
-                                {% else %}
-                                    <h5>Add Finding</h5>
-                                    <p class="small">Click the button below to add a new finding.</p>
-                                {% endif %}
-                                <form method="post" id="series_finding_form">
-                                    {% csrf_token %}
-                                    {{series_finding_form|crispy}}
-                                    <div class="d-flex gap-2 mt-2">
-                                        <input type="submit" value="Submit" class="btn btn-success btn-sm">
-                                        <button id="cancel-add-finding-button" class="btn btn-secondary btn-sm">Cancel</button>
-                                    </div>
-                                </form>
-                            </div>
-                        </div>
-                    </div>
-                </div>
-                <details class="styled-detail open">
-                    <summary>Findings</summary>
-                    <div class="mt-2">
-                        {% for finding in series.findings.all %}
-                            <div class="card mb-2">
-                                <div class="card-body d-flex flex-column flex-md-row justify-content-between gap-2">
-                                    <div>
-                                        <button id="finding-{{finding.pk}}-3d" class="btn btn-sm btn-outline-secondary view-finding-button-3d me-2"
-                                                        data-annotationjson3d='{{finding.annotation_json_3d}}' data-viewerstatejson='{{finding.viewer_state_3d}}' data-findingid='{{finding.pk}}'>View 3D</button>
-                                        <strong>Finding(s):</strong>
-                                        {% for f in finding.findings.all %}{{f.get_link}}{% endfor %}<br />
-                                        <strong>Structure(s):</strong> {% for s in finding.structures.all %}{{s.get_link}}{% endfor %}<br />
-                                        <strong>Condition(s):</strong> {% for s in finding.conditions.all %}{{s.get_link}}{% endfor %}<br />
-                                        <div class="mt-2">{{finding.description}}</div>
-                                    </div>
-                                    <div class="text-end">
-                                        {% if request.user.is_superuser %}
-                                            <button class="btn btn-sm btn-outline-dark mb-2" type="button" data-bs-toggle="collapse" data-bs-target="#extra-{{finding.pk}}">Raw JSON</button>
-                                            <div class="collapse" id="extra-{{finding.pk}}">
-                                                <pre class="small bg-light p-2">{{finding.annotation_json}}</pre>
-                                                <pre class="small bg-light p-2">{{finding.viewport_json}}</pre>
-                                            </div>
-                                        {% endif %}
-                                        {% if can_edit %}
-                                            <div class="d-flex flex-column">
-                                                <a href="{% url 'atlas:series_edit_finding' pk=series.pk finding_pk=finding.pk %}" class="btn btn-sm btn-outline-primary mb-1">Edit</a>
-                                                <a href="{% url 'atlas:delete_finding' pk=finding.pk %}" class="btn btn-sm btn-outline-danger">Delete</a>
-                                            </div>
-                                        {% endif %}
-                                    </div>
-                                </div>
-                            </div>
-                        {% empty %}
-                            <p class="text-muted">No findings available.</p>
-                        {% endfor %}
-                    </div>
-                </details>
-            </div>
-        </div>
-
-        <div class="col-md-4 mb-3">
-            <div class="card mb-3">
-                <div class="card-header">Cases</div>
-                <div class="card-body">
-                    <div id="cases-list">
-                        {% include 'atlas/partials/series_cases_list.html' %}
-                    </div>
-                    {% if can_edit %}
-                        <details id="add-series-to-case-details" class="mt-2">
-                            <summary>Add Series to Case</summary>
-                            <form hx-post="{% url 'atlas:add_series_to_case' series.pk %}" hx-target="#cases-list" hx-swap="innerHTML" class="mt-2">
-                                {% csrf_token %}
-                                <div class="mb-2">
-                                    <label for="case-select" class="form-label">Select Case</label>
-                                    <select name="case_id" id="case-select" class="form-select" required>
-                                        {% for case in available_cases %}
-                                            <option value="{{ case.pk }}">{{ case.title }}</option>
-                                        {% endfor %}
-                                    </select>
-                                </div>
-                                <div class="d-flex gap-2">
-                                    <button type="submit" class="btn btn-primary btn-sm">Add to Case</button>
-                                    <button type="button" class="btn btn-outline-secondary btn-sm" onclick="document.getElementById('add-series-to-case-details').open = false">Close</button>
-                                </div>
-                            </form>
-                        </details>
-                    {% endif %}
-                </div>
-            </div>
-
-            <div class="card mb-3">
-                <div class="card-header">Actions</div>
-                <div class="card-body d-flex flex-column gap-2">
-                    <a class="btn btn-outline-primary btn-sm" href="{% url 'atlas:series_anonymise_dicom' pk=series.pk %}">Anonymise dicoms</a>
-                    <a class="btn btn-outline-primary btn-sm" href="{% url 'atlas:series_order_dicom' pk=series.pk %}">Order by slice location</a>
-                    <a class="btn btn-outline-primary btn-sm" href="{% url 'atlas:series_order_dicom_instance' pk=series.pk %}">Order by instance number</a>
-                    <a class="btn btn-outline-primary btn-sm" href="{% url 'atlas:series_order_dicom_SeriesInstanceUID' pk=series.pk %}">Order by SeriesInstanceUID</a>
-                    <a class="btn btn-outline-primary btn-sm" href="{% url 'atlas:series_order_upload_filename' pk=series.pk %}">Order by uploaded filename</a>
-                    <a class="btn btn-outline-warning btn-sm" href="{% url 'api-1:series_split_by_tag' series.pk 'ImageType' %}">Split by ImageType tag</a>
-                </div>
-            </div>
-
-            
-
-            {% if can_edit %}
-                <div class="card">
-                    <div class="card-header">Truncate series</div>
-                    <div class="card-body">
-                        <p class="small">Limit the series to the selected bounds (the rest of the images will be deleted). This action is irreversible on site.</p>
-                        <div class="alert alert-warning"><strong>Warning:</strong> If you have reordered the series this may remove the wrong images.</div>
-                        <div class="mb-2">
-                            <label class="form-label">Start</label>
-                            <div class="input-group">
-                                <input id="lower-truncation-bound-input" type="number" class="form-control form-control-sm" value="1">
-                                <button id="set-lower-truncation-bound-button" class="btn btn-outline-secondary btn-sm">Set</button>
-                            </div>
-                        </div>
-                        <div class="mb-2">
-                            <label class="form-label">End</label>
-                            <div class="input-group">
-                                <input id="upper-truncation-bound-input" type="number" class="form-control form-control-sm" value="{{image_url_array_and_count.1}}">
-                                <button id="set-upper-truncation-bound-button" class="btn btn-outline-secondary btn-sm">Set</button>
-                            </div>
-                        </div>
-                        <div class="d-flex gap-2">
-                            <button id="truncate-test-button" class="btn btn-sm btn-outline-primary">Test truncate</button>
-                            <button id="truncate-button" class="btn btn-sm btn-danger">Truncate series</button>
-                        </div>
-                        <div id="truncate-output" class="mt-2"></div>
-                    </div>
-                </div>
-            {% endif %}
+    <div id="clone-findings-modal" class="modal modal-blur fade" tabindex="-1">
+        <div class="modal-dialog modal-dialog-centered related-finding-modal" style="max-width: 700px;">
+            <div class="modal-content"></div>
         </div>
     </div>
-</div>
 
 
-<div id="clone-findings-modal" class="modal modal-blur fade" tabindex="-1">
-    <div class="modal-dialog modal-dialog-centered related-finding-modal" style="max-width: 700px;">
-        <div class="modal-content"></div>
-    </div>
-</div>
+    <script>
+        $(document).ready(function () {
+            const apiKey = "root"
+
+            $("#set-lower-truncation-bound-button").click(() => {
+                $("#lower-truncation-bound-input").val(getCurrentStackPosition_root(0) + 1);
+            });
+            $("#set-upper-truncation-bound-button").click(() => {
+                $("#upper-truncation-bound-input").val(getCurrentStackPosition_root(0) + 1);
+            });
+            $("#truncate-test-button").click(() => {
+                const lower = parseInt($("#lower-truncation-bound-input").val()) - 1;
+                const upper = parseInt($("#upper-truncation-bound-input").val()) - 1;
+                const ok = window[`truncateStack_${apiKey}`](lower, upper);
+                if (ok) {
+                    $("#truncate-output").text("The truncated images are shown above.");
+                }
+            });
+            $("#truncate-button").click(() => {
+                lower_bound = parseInt($("#lower-truncation-bound-input").val()) - 1;
+                upper_bound = parseInt($("#upper-truncation-bound-input").val()) - 1;
+
+                if (lower_bound >= upper_bound) {
+                    alert("The lower bound must be less than the upper bound.");
+                    return;
+                }
+
+                if(confirm(`Trucated series. This will leave ${upper_bound - lower_bound + 1} images.`) == true) {
+                    htmx.ajax("GET", `{% url 'api-1:series_truncate' series.id '****' '++++' %}`.replace("****", lower_bound).replace("++++", upper_bound), "#truncate-output")
+
+                }
 
 
-<script>
-    $(document).ready(function () {
-        const apiKey = "root"
+            })
 
-        $("#set-lower-truncation-bound-button").click(() => {
-            $("#lower-truncation-bound-input").val(getCurrentStackPosition_root(0) + 1);
-        });
-        $("#set-upper-truncation-bound-button").click(() => {
-            $("#upper-truncation-bound-input").val(getCurrentStackPosition_root(0) + 1);
-        });
-        $("#truncate-test-button").click(() => {
-            const lower = parseInt($("#lower-truncation-bound-input").val()) - 1;
-            const upper = parseInt($("#upper-truncation-bound-input").val()) - 1;
-            const ok = window[`truncateStack_${apiKey}`](lower, upper);
-            if (ok) {
-                $("#truncate-output").text("The truncated images are shown above.");
-            }
-        });
-        $("#truncate-button").click(() => {
-            lower_bound = parseInt($("#lower-truncation-bound-input").val()) - 1;
-            upper_bound = parseInt($("#upper-truncation-bound-input").val()) - 1;
-
-            if (lower_bound >= upper_bound) {
-                alert("The lower bound must be less than the upper bound.");
-                return;
-            }
-
-            if(confirm(`Trucated series. This will leave ${upper_bound - lower_bound + 1} images.`) == true) {
-                htmx.ajax("GET", `{% url 'api-1:series_truncate' series.id '****' '++++' %}`.replace("****", lower_bound).replace("++++", upper_bound), "#truncate-output")
-
-            }
-
-
-        })
-
-        $("#add-finding-button").click(() => {
-            $("#hidden-form").show()
+            $("#add-finding-button").click(() => {
+                $("#hidden-form").show()
             //dicom_element = $(".cornerstone-element").get(0);
             //cornerstoneTools.globalImageIdSpecificToolStateManager.clear(dicom_element);
             //cornerstone.reset(dicom_element);
             ////cornerstone.resize(dicom_element, true);
-            $("#add-finding-button").hide()
-            $("#clone-finding-button").hide()
+                $("#add-finding-button").hide()
+                $("#clone-finding-button").hide()
             //$("#finding-form").empty().append(
             //    $("#hidden-form form").clone()
             //);
 
+            });
+            $("#cancel-add-finding-button").click((e) => {
+                $("#hidden-form").hide()
+                $("#add-finding-button").show()
+                $("#clone-finding-button").show()
+                e.preventDefault();
+            });
+
+
+            $("#reset-viewport-button").click(() => {
+                resetViewer_root();
+
+            });
+            $(".view-finding-button-3d").each((n, el) => {
+                $(el).click((e) => {
+                    dicom_element = $(".cornerstone-element").get(0);
+                    annotationjson3d = JSON.parse(e.currentTarget.dataset.annotationjson3d);
+                    viewer_state_json = JSON.parse(e.currentTarget.dataset.viewerstatejson);
+                    console.log("Loading 3D annotation and viewer state", annotationjson3d, viewer_state_json);
+                    importAnnotations_root(annotationjson3d);
+                    importViewerState_root(viewer_state_json);
+                    $(el).addClass("active");
+                });
+            });
+
+
+            {% if editing_finding > 0 %}
+                $("#hidden-form").show()
+                setTimeout(function() {
+                    $(".view-finding-button-3d[data-findingid={{editing_finding}}]").trigger("click");
+                }, 1000)
+
+            {% endif %}
+
+
+            {% if request.GET.show_finding %}
+                function show_finding() {
+                    console.log("show finding")
+                    $("#finding-{{ request.GET.show_finding }}").trigger("click");
+                }
+                setTimeout(show_finding, 500);
+            {% endif %}
         });
-        $("#cancel-add-finding-button").click((e) => {
-            $("#hidden-form").hide()
-            $("#add-finding-button").show()
-            $("#clone-finding-button").show()
+
+        $(document).on('submit', '#series_finding_form', function (e) {
             e.preventDefault();
-        });
 
-
-        $("#reset-viewport-button").click(() => {
-            resetViewer_root();
-
-        });
-        $(".view-finding-button-3d").each((n, el) => {
-            $(el).click((e) => {
-                dicom_element = $(".cornerstone-element").get(0);
-                annotationjson3d = JSON.parse(e.currentTarget.dataset.annotationjson3d);
-                viewer_state_json = JSON.parse(e.currentTarget.dataset.viewerstatejson);
-                console.log("Loading 3D annotation and viewer state", annotationjson3d, viewer_state_json);
-                importAnnotations_root(annotationjson3d);
-                importViewerState_root(viewer_state_json);
-                $(el).addClass("active");
+            $.ajax({
+                type: 'POST',
+                url: '{% url "atlas:add_finding" %}',
+                data: {
+                    series_finding_id: {{ editing_finding }},
+                    description: $('#id_description').val(),
+                    series: {{ series.pk }},
+                    annotation_json_3d: window.exportAnnotations_root(),
+                    viewer_state_3d: window.exportViewerState_root(),
+                    findings: JSON.stringify($('#finding-form select[name="findings"]').find(":selected")
+                            .map((i, el) => {
+                                return $(el).val()
+                            }).toArray()),
+                    structures: JSON.stringify($('#finding-form select[name="structures"]').find(
+                        ":selected")
+                            .map((i, el) => {
+                                return $(el).val()
+                            }).toArray()),
+                    conditions: JSON.stringify($('#finding-form select[name="conditions"]').find(
+                        ":selected")
+                            .map((i, el) => {
+                                return $(el).val()
+                            }).toArray()),
+                    csrfmiddlewaretoken: $('input[name=csrfmiddlewaretoken]').val(),
+                    action: 'post'
+                },
+                success: function (json) {
+                    $("#finding-form").empty();
+                    toastr.info('Finding added.');
+                    location.href='{{series.get_absolute_url}}';
+                },
+                error: function (xhr, errmsg, err) {
+                    console.log(xhr.status + ": " + xhr
+                            .responseText); // provide a bit more info about the error to the console
+                }
             });
         });
-
-
-        {% if editing_finding > 0 %}
-            $("#hidden-form").show()
-            setTimeout(function() {
-                $(".view-finding-button-3d[data-findingid={{editing_finding}}]").trigger("click");
-            }, 1000)
-
-        {% endif %}
-
-
-        {% if request.GET.show_finding %}
-            function show_finding() {
-                console.log("show finding")
-                $("#finding-{{ request.GET.show_finding }}").trigger("click");
-            }
-            setTimeout(show_finding, 500);
-        {% endif %}
-    });
-
-    $(document).on('submit', '#series_finding_form', function (e) {
-        e.preventDefault();
-
-        $.ajax({
-            type: 'POST',
-            url: '{% url "atlas:add_finding" %}',
-            data: {
-                series_finding_id: {{ editing_finding }},
-                description: $('#id_description').val(),
-                series: {{ series.pk }},
-                annotation_json_3d: window.exportAnnotations_root(),
-                viewer_state_3d: window.exportViewerState_root(),
-                findings: JSON.stringify($('#finding-form select[name="findings"]').find(":selected")
-                        .map((i, el) => {
-                            return $(el).val()
-                        }).toArray()),
-                structures: JSON.stringify($('#finding-form select[name="structures"]').find(
-                    ":selected")
-                        .map((i, el) => {
-                            return $(el).val()
-                        }).toArray()),
-                conditions: JSON.stringify($('#finding-form select[name="conditions"]').find(
-                    ":selected")
-                        .map((i, el) => {
-                            return $(el).val()
-                        }).toArray()),
-                csrfmiddlewaretoken: $('input[name=csrfmiddlewaretoken]').val(),
-                action: 'post'
-            },
-            success: function (json) {
-                $("#finding-form").empty();
-                toastr.info('Finding added.');
-                location.href='{{series.get_absolute_url}}';
-            },
-            error: function (xhr, errmsg, err) {
-                console.log(xhr.status + ": " + xhr
-                        .responseText); // provide a bit more info about the error to the console
-            }
-        });
-    });
-</script>
+    </script>
 
 {% endwith %}
 
@@ -402,14 +426,14 @@
         transition: background 0.2s, font-size 0.2s;
     }
 
-details.styled-detail:not([open]) {
-    padding-bottom: 0;
-    min-height: 0;
-}
+    details.styled-detail:not([open]) {
+        padding-bottom: 0;
+        min-height: 0;
+    }
 
-details.styled-detail:not([open]) > *:not(summary) {
-    display: none;
-}
+    details.styled-detail:not([open]) > *:not(summary) {
+        display: none;
+    }
 
     details.styled-detail:not([open]) > summary {
         padding: 0.7em 1.2em 0.3em 1.2em;

atlas/templates/atlas/structure_detail.html

@@ -14,8 +14,8 @@
     </div>
     <div>
         <h3>Name: {{structure.name}}</h3>
-        Primary name: {{structure.primary}}<br />
-        Synonyms: {{structure.synonym.all|join:", "}}<br />
+    Primary name: {% if structure.canonical %}No (alias of <a href="{{ structure.canonical.get_absolute_url }}">{{ structure.canonical.name }}</a>){% else %}Yes{% endif %}<br />
+    Synonyms: {{ structure.get_synonym_link|safe }}<br />
     </div>
     <h4>Associated Cases</h4>
     <ul>

atlas/templates/atlas/subspecialty_form.html

@@ -0,0 +1,23 @@
+{% extends "atlas/base.html" %}
+{% load crispy_forms_tags %}
+
+{% block js %}
+    {{ form.media }}
+{% endblock %}
+
+{% block content %}
+    <h2>Add / Edit Subspecialty</h2>
+    <p>Use this form to create or edit a subspecialty.</p>
+    <p>Please check if it already <a href='{% url "atlas:subspecialty_view" %}'>exists</a> before doing so!</p>
+
+    <form action="" method="post" enctype="multipart/form-data" id="subspecialty-form">
+        {% csrf_token %}
+        {% crispy form %}
+
+        <div class="mt-3">
+            <button type="submit" class="btn btn-primary">Submit</button>
+            <a class="btn btn-secondary ms-2" href="{% url 'atlas:subspecialty_view' %}">Cancel</a>
+        </div>
+    </form>
+
+{% endblock %}

atlas/templates/atlas/view.html

@@ -7,7 +7,14 @@
 {% block content %}
 
     <div class="container-fluid">
-        <h2>My Collections</h2>
+        <div class="d-flex align-items-start justify-content-between">
+            <h2 class="mb-0">{{ model_verbose_name_plural|capfirst }}</h2>
+            {% if request.user.is_staff and create_url %}
+                <div>
+                    <a class="btn btn-sm btn-primary" href="{{ create_url }}">Add new {{ model_verbose_name }}</a>
+                </div>
+            {% endif %}
+        </div>
 {% comment %}         <details>
             <summary>
                 <h4>Filter</h4>
@@ -19,7 +26,6 @@
                 </form>
             </div>
         </details> {% endcomment %}
-            View my <a href='{% url "atlas:case_view" %}?author={{request.user.id}}'>cases</a>.
         {% render_table table %}
         {% include "generic/partials/filter_bar.html" with filter=filter app_name=app_name collapse_id="bottom-filter-body" %}
     </div>

atlas/urls.py

@@ -34,6 +34,7 @@ urlpatterns = [
     path("author/", views.author_list, name="author_list"),
     path("case/", views.CaseView.as_view(), name="case_view"),
     path("collection/<int:collection_id>/add_case", views.add_case_to_collection, name="add_case_to_collection"),
+    path("collection/case_search", views.case_search, name="case_search"),
     path("collection/", views.CollectionView.as_view(), name="collection_view"),
     path("collection/user", views.user_collections, name="user_collections"),
     path("uploads", views.user_uploads, name="user_uploads"),
@@ -111,6 +112,11 @@ urlpatterns = [
         views.CollectionCaseUpdate.as_view(),
         name="collection_case_update",
     ),
+    path(
+        "collection/<int:pk>/case_jump",
+        views.collection_case_jump_partial,
+        name="collection_case_jump_partial",
+    ),
     path(
         "collection/add_cases",
         views.add_cases_to_collection,
@@ -167,30 +173,56 @@ urlpatterns = [
     ),
     path("exam/<int:pk>/groups", views.ExamGroupsUpdate.as_view(), name="exam_groups_edit"),
     path(
-        "collection/<int:exam_id>/case/<int:case_id>/details",
+        "collection/<int:exam_id>/case/<int:case_number>/details",
         views.collection_case_details,
         name="collection_case_details",
     ),
+    # Backwards-compatible redirect from legacy case_id-style URLs
     path(
-        "collection/<int:exam_id>/case/<int:case_id>/questions",
+        "collection/<int:exam_id>/case/id/<int:case_id>/details",
+        views.redirect_collection_case_details_by_id,
+        name="collection_case_details_legacy",
+    ),
+    path(
+        "collection/<int:exam_id>/case/<int:case_number>/questions",
         views.collection_case_questions,
         name="collection_case_questions",
     ),
     path(
-        "collection/<int:exam_id>/case/<int:case_id>/priors",
+        "collection/<int:exam_id>/case/id/<int:case_id>/questions",
+        views.redirect_collection_case_questions_by_id,
+        name="collection_case_questions_legacy",
+    ),
+    path(
+        "collection/<int:exam_id>/case/<int:case_number>/priors",
         views.collection_case_priors,
         name="collection_case_priors",
     ),
     path(
-        "collection/<int:exam_id>/case/<int:case_id>/dicom_json",
+        "collection/<int:exam_id>/case/id/<int:case_id>/priors",
+        views.redirect_collection_case_priors_by_id,
+        name="collection_case_priors_legacy",
+    ),
+    path(
+        "collection/<int:exam_id>/case/<int:case_number>/dicom_json",
         views.collection_case_dicom_json,
         name="collection_case_dicom_json",
     ),
     path(
-        "collection/<int:exam_id>/case/<int:case_id>/dicom_json/review",
+        "collection/<int:exam_id>/case/id/<int:case_id>/dicom_json",
+        views.redirect_collection_case_dicom_json_by_id,
+        name="collection_case_dicom_json_legacy",
+    ),
+    path(
+        "collection/<int:exam_id>/case/<int:case_number>/dicom_json/review",
         views.collection_case_dicom_json_review,
         name="collection_case_dicom_json_review",
     ),
+    path(
+        "collection/<int:exam_id>/case/id/<int:case_id>/dicom_json/review",
+        views.redirect_collection_case_dicom_json_review_by_id,
+        name="collection_case_dicom_json_review_legacy",
+    ),
     path(
         "collection/<int:exam_id>/question_schemas",
         views.collection_question_schemas,
@@ -271,26 +303,52 @@ urlpatterns = [
         views.collection_case_view,
         name="collection_case_view",
     ),
+    # legacy path that used case PK; redirect to canonical case_number URL
     path(
-        "collection/<int:collection_id>/<int:case_id>/display_setup",
+        "collection/<int:pk>/id/<int:case_id>",
+        views.redirect_collection_case_view_by_id,
+        name="collection_case_view_legacy",
+    ),
+    path(
+        "collection/<int:collection_id>/<int:case_number>/display_setup",
         views.collection_case_displaysetup,
         name="collection_case_displaysetup",
     ),
+    path(
+        "collection/<int:collection_id>/id/<int:case_id>/display_setup",
+        views.redirect_collection_case_displaysetup_by_id,
+        name="collection_case_displaysetup_legacy",
+    ),
     path(
         "collection/<int:pk>/<int:case_number>/take/<int:cid>/<str:passcode>",
         views.collection_case_view_take,
         name="collection_case_view_take",
     ),
+    path(
+        "collection/<int:pk>/id/<int:case_id>/take/<int:cid>/<str:passcode>",
+        views.redirect_collection_case_view_take_by_id,
+        name="collection_case_view_take_legacy",
+    ),
     path(
         "collection/<int:pk>/<int:case_number>/take/",
         views.collection_case_view_take_user,
         name="collection_case_view_take_user",
     ),
+    path(
+        "collection/<int:pk>/id/<int:case_id>/take/",
+        views.redirect_collection_case_view_take_user_by_id,
+        name="collection_case_view_take_user_legacy",
+    ),
     path(
         "collection/<int:pk>/<int:case_number>/take/answers",
         views.collection_case_view_take_user_answers,
         name="collection_case_view_take_user_answers",
     ),
+    path(
+        "collection/<int:pk>/id/<int:case_id>/take/answers",
+        views.redirect_collection_case_view_take_user_answers_by_id,
+        name="collection_case_view_take_user_answers_legacy",
+    ),
     path(
         "collection/<int:pk>/json_edit",
         views.GenericExamViews.exam_json_edit,
@@ -370,6 +428,7 @@ urlpatterns = [
     path(
         "subspecialty/<int:pk>", views.subspecialty_detail, name="subspecialty_detail"
     ),
+    path("subspecialty/create", views.SubspecialtyCreate.as_view(), name="subspecialty_create"),
     path("condition/create", views.ConditionCreate.as_view(), name="condition_create"),
     path("finding/", views.FindingView.as_view(), name="finding_view"),
     path("finding/<int:pk>", views.finding_detail, name="finding_detail"),
@@ -398,6 +457,7 @@ urlpatterns = [
     # TODO: case context series viewing (so that we can view series in the context of a case)
     path("series/<int:pk>", views.series_detail, name="series_detail"),
     path("series/<int:pk>/viewer", views.series_viewer, name="series_viewer"),
+    path("series/<int:pk>/images/", views.series_images_partial, name="series_images"),
     path("series/<int:pk>/authors", views.SeriesAuthorUpdate.as_view(), name="series_authors"),
     path("series/<int:series_id>/finding/related", views.series_finding_related, name="series_finding_related"),
     path("series/", views.SeriesView.as_view(), name="series_view"),
@@ -543,6 +603,7 @@ urlpatterns = [
     path(
         "presentation/<int:pk>", views.presentation_detail, name="presentation_detail"
     ),
+    path("presentation/create", views.PresentationCreate.as_view(), name="presentation_create"),
     path(
         "process/",
         views.PathologicalProcessView.as_view(),
@@ -553,6 +614,7 @@ urlpatterns = [
         views.pathological_process_detail,
         name="pathological_process_detail",
     ),
+    path("process/create", views.PathologicalProcessCreate.as_view(), name="pathological_process_create"),
     path("combine_series/", views.combine_series, name="combine_series"),
     path(
         "case/<int:case_id>/linked/",

deploy/nginx/dev.conf

@@ -0,0 +1,30 @@
+upstream app_server {
+    server web:8000;
+}
+
+server {
+    listen 80;
+    listen [::]:80;
+    server_name _;
+
+    client_max_body_size 100M;
+
+    location /static/ {
+        alias /usr/src/app/static/;
+        expires 30d;
+        add_header Cache-Control "public, max-age=2592000";
+    }
+
+    location /media {
+        alias /usr/src/app/media;
+    }
+
+    location / {
+        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+        proxy_set_header X-Forwarded-Proto $scheme;
+        proxy_set_header Host $host;
+        proxy_redirect off;
+        proxy_buffering off;
+        proxy_pass http://app_server;
+    }
+}

deploy/nginx/prod.conf

@@ -0,0 +1,127 @@
+upstream app_server {
+    # In production we proxy to the 'web' service (gunicorn) listening on 8000
+    server web:8000;
+}
+
+server {
+    listen 80;
+    listen [::]:80;
+    server_name _;
+
+    client_max_body_size 100M;
+
+    # Serve static files from the static volume
+    location /static/ {
+        alias /usr/src/app/static/;
+        expires 30d;
+        add_header Cache-Control "public, max-age=2592000";
+    }
+
+    # Serve media files from the media volume. CORS handling preserved.
+    set $cors "";
+    if ($http_origin ~* (https?://(localhost:5173|viewer\.penracourses\.org\.uk))) {
+        set $cors $http_origin;
+    }
+
+    location /media {
+        if ($request_method = OPTIONS ) {
+            add_header 'Access-Control-Allow-Origin' $cors always;
+            add_header 'Access-Control-Allow-Credentials' 'true' always;
+            add_header 'Access-Control-Allow-Headers' "Origin, X-Requested-With, Content-Type, Accept" always;
+            add_header 'Access-Control-Allow-Methods' 'GET, POST, OPTIONS';
+            add_header 'Access-Control-Max-Age' 1728000;
+            add_header 'Content-Type' 'text/plain; charset=utf-8';
+            add_header 'Content-Length' 0;
+            return 200;
+        }
+        add_header 'Access-Control-Allow-Origin' $cors always;
+        alias /usr/src/app/media;
+    }
+
+    # Viewer / OHIF / other static frontends - mount these into the nginx container at deploy time
+    location /viewer {
+        alias /srv/www/viewer;
+        index index.html;
+        try_files $uri $uri/ /viewer/index.html;
+        add_header Cache-Control "no-store, no-cache, must-revalidate";
+        add_header 'Cross-Origin-Resource-Policy' 'cross-origin';
+    }
+
+    location /ohif {
+        add_header 'Cross-Origin-Opener-Policy' 'same-origin' always;
+        add_header 'Cross-Origin-Embedder-Policy' 'require-corp' always;
+        add_header 'Cross-Origin-Resource-Policy' 'same-site' always;
+        alias /srv/www/ohif;
+        try_files $uri /ohif/index.html;
+    }
+
+    # rts and other host-mounted folders
+    location /rts {
+        alias /srv/www/rts;
+    }
+
+    location /rota {
+        alias /srv/proc/rota;
+        autoindex on;
+    }
+
+    location /uploader {
+        alias /srv/uploader;
+        autoindex on;
+    }
+
+    # Reporter proxy - if you run a reporter service, set it up on the 'reporter' network name
+    location ~ ^/reporter/(.*)$ {
+        proxy_http_version 1.1;
+        proxy_set_header Upgrade $http_upgrade;
+        proxy_set_header Connection $connection_upgrade;
+        proxy_set_header Authorization $http_authorization;
+        proxy_pass_header Authorization;
+
+        proxy_pass http://reporter:5129/$1?$args;
+        proxy_set_header X-Forwarded-Prefix /reporter;
+        proxy_redirect http://reporter:5129/ /reporter/;
+    }
+
+    # Default proxy to the Django/gunicorn upstream
+    location / {
+        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+        proxy_set_header X-Forwarded-Proto $scheme;
+        proxy_set_header Host $host;
+        proxy_redirect off;
+        proxy_buffering off;
+        add_header 'Cross-Origin-Embedder-Policy' 'require-corp' always;
+        add_header 'Cross-Origin-Resource-Policy' 'same-site' always;
+
+        proxy_pass http://app_server;
+    }
+
+    # Default dev / health server block; keep 443 managed outside of docker unless you mount certs
+}
+
+# A minimal HTTPS server block that expects certs to be mounted at /etc/letsencrypt
+server {
+    listen 443 ssl;
+    listen [::]:443 ssl;
+    server_name www.penracourses.org.uk penracourses.org.uk viewer.penracourses.org.uk;
+
+    ssl_certificate /etc/letsencrypt/live/www.penracourses.org.uk/fullchain.pem;
+    ssl_certificate_key /etc/letsencrypt/live/www.penracourses.org.uk/privkey.pem;
+    include /etc/letsencrypt/options-ssl-nginx.conf;
+    ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem;
+
+    client_max_body_size 4G;
+
+    # Same static/media handling as above
+    location /static/ { alias /usr/src/app/static/; }
+    location /media { alias /usr/src/app/media; }
+
+    location / {
+        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+        proxy_set_header X-Forwarded-Proto $scheme;
+        proxy_set_header Host $host;
+        proxy_redirect off;
+        proxy_buffering off;
+        proxy_pass http://app_server;
+    }
+}

deploy/settings_local.py

@@ -0,0 +1,122 @@
+"""
+Example `settings_local.py` derived from the production server file.
+This file is a template only — DO NOT commit real secrets. Copy it to
+`rad/deploy/settings_local.py` on your server (or provide your own) and
+ensure the real file is excluded from git.
+"""
+import os
+
+DEBUG = True
+
+INTERNAL_IPS = ["82.69.88.125", "217.155.198.96", "localhost", "127.0.0.1"]
+
+# When running in Docker (dev), requests will often come from an internal
+# container/network address. Add any discovered host/container IPs (and a
+# likely gateway address) to INTERNAL_IPS so the debug toolbar can render.
+if DEBUG:
+    try:
+        import socket
+
+        hostname, _, ips = socket.gethostbyname_ex(socket.gethostname())
+        for ip in ips:
+            if ip not in INTERNAL_IPS:
+                INTERNAL_IPS.append(ip)
+            # common docker gateway pattern: replace last octet with '1'
+            parts = ip.split('.')
+            if len(parts) == 4:
+                parts[-1] = '1'
+                gw = '.'.join(parts)
+                if gw not in INTERNAL_IPS:
+                    INTERNAL_IPS.append(gw)
+    except Exception:
+        # best-effort only; don't fail startup if this lookup doesn't work
+        pass
+
+# In local/dev enable the toolbar unconditionally to avoid IP/proxy
+# headaches while developing inside Docker/behind nginx.
+DEBUG_TOOLBAR_CONFIG = {
+    "SHOW_TOOLBAR_CALLBACK": lambda request: True,
+}
+
+# Paths inside the nginx container / host-mounted deploy directories.
+# On the server, these paths are mounted into nginx as described in the
+# deployment README. Adjust as needed.
+STATIC_ROOT = '/usr/src/app/static/'
+
+EMAIL_BACKEND = "django.core.mail.backends.smtp.EmailBackend"
+
+if not DEBUG:
+    LOGGING = {
+        'version': 1,
+        'disable_existing_loggers': False,
+        'formatters': {
+            'verbose': {
+                'format': "[%(asctime)s] %(levelname)s [%(name)s:%(lineno)s] %(message)s",
+                'datefmt': "%d/%b/%Y %H:%M:%S",
+            },
+            'simple': {
+                'format': '%(levelname)s %(message)s',
+            },
+        },
+        'handlers': {
+            'file': {
+                'level': 'DEBUG',
+                'class': 'logging.FileHandler',
+                'filename': 'log.txt',
+                'formatter': 'verbose',
+            },
+        },
+        'loggers': {
+            'django': {
+                'handlers': ['file'],
+                'propagate': True,
+                'level': 'DEBUG',
+            },
+            'atlas': {
+                'handlers': ['file'],
+                'level': 'DEBUG',
+            },
+        }
+    }
+
+# External service credentials (placeholders)
+CIMAR_USERNAME = "your.username@example.com"
+CIMAR_PASSWORD = "<REPLACE-WITH-SECRET>"
+
+# Celery settings — when running in docker the redis service is
+# reachable at the `redis` hostname provided by docker compose.
+CELERY_BROKER_URL = "redis://redis:6379"
+CELERY_RESULT_BACKEND = "redis://redis:6379"
+
+DATABASES = {
+    "default": {
+        "ENGINE": "django.db.backends.postgresql_psycopg2",
+        "NAME": os.environ.get("DB_NAME", "django"),
+        "USER": os.environ.get("DB_USER", "django"),
+        "PASSWORD": os.environ.get("DB_PASSWORD", "AVNS_NG_s4i7SMMobWLO"),
+        #"HOST": os.environ.get("DB_HOST", "db-postgresql-lon1-05515-do-user-8165014-0.b.db.ondigitalocean.com"),
+        "HOST": os.environ.get("DB_HOST", "db-postgresql-lon1-05515-jan-22-backup-do-user-8165014-0.c.db.ondigitalocean.com"),
+        "PORT": os.environ.get("DB_PORT", "25060"),
+        #"NAME": os.environ.get("DB_NAME", "django"),
+        #"USER": os.environ.get("DB_USER", "django"),
+        #"PASSWORD": os.environ.get("DB_PASSWORD", "f7bf31dc9bda1256ea827953480d1917"),
+        #"HOST": os.environ.get("DB_HOST", "161.35.163.87"),
+        #"PORT": os.environ.get("DB_PORT", "5432"),
+    }
+}
+
+# Development overrides to avoid forcing HTTPS and secure cookies in local dev
+# (production should keep these True).
+SECURE_SSL_REDIRECT = False
+SESSION_COOKIE_SECURE = False
+CSRF_COOKIE_SECURE = False
+SECURE_HSTS_SECONDS = 0
+
+# Allow requests from the local dev nginx/dev server and direct runserver
+# (include scheme+host+port for Django's origin checking).
+CSRF_TRUSTED_ORIGINS = [
+    "http://127.0.0.1:8000",
+    "http://localhost:8000",
+]
+
+REMOTE_URL = "http://127.0.0.1:8000"

deploy/settings_local.py.example

@@ -0,0 +1,60 @@
+"""
+Example `settings_local.py` derived from the production server file.
+This file is a template only — DO NOT commit real secrets. Copy it to
+`rad/deploy/settings_local.py` on your server (or provide your own) and
+ensure the real file is excluded from git.
+"""
+
+DEBUG = False
+
+INTERNAL_IPS = ["82.69.88.125", "217.155.198.96"]
+
+# Paths inside the nginx container / host-mounted deploy directories.
+# On the server, these paths are mounted into nginx as described in the
+# deployment README. Adjust as needed.
+STATIC_ROOT = '/usr/src/app/static/'
+
+EMAIL_BACKEND = "django.core.mail.backends.smtp.EmailBackend"
+
+if not DEBUG:
+    LOGGING = {
+        'version': 1,
+        'disable_existing_loggers': False,
+        'formatters': {
+            'verbose': {
+                'format': "[%(asctime)s] %(levelname)s [%(name)s:%(lineno)s] %(message)s",
+                'datefmt': "%d/%b/%Y %H:%M:%S",
+            },
+            'simple': {
+                'format': '%(levelname)s %(message)s',
+            },
+        },
+        'handlers': {
+            'file': {
+                'level': 'DEBUG',
+                'class': 'logging.FileHandler',
+                'filename': 'log.txt',
+                'formatter': 'verbose',
+            },
+        },
+        'loggers': {
+            'django': {
+                'handlers': ['file'],
+                'propagate': True,
+                'level': 'DEBUG',
+            },
+            'atlas': {
+                'handlers': ['file'],
+                'level': 'DEBUG',
+            },
+        }
+    }
+
+# External service credentials (placeholders)
+CIMAR_USERNAME = "your.username@example.com"
+CIMAR_PASSWORD = "<REPLACE-WITH-SECRET>"
+
+# Celery settings — when running in docker the redis service is
+# reachable at the `redis` hostname provided by docker compose.
+CELERY_BROKER_URL = "redis://redis:6379"
+CELERY_RESULT_BACKEND = "redis://redis:6379"

docker/docker-compose.dev.yml

@@ -0,0 +1,69 @@
+# Development override: point the web service to rad/.env.dev and map nginx to
+# non-privileged host ports so you can run without sudo.
+
+services:
+  web:
+    env_file:
+      - ../.env.dev
+    # Development: run Django's autoreloading development server instead of
+    # the production entrypoint/gunicorn. Mount the repository into the
+    # container so code edits on the host trigger Django's autoreload.
+    entrypoint: ["python", "manage.py", "runserver", "0.0.0.0:8000"]
+    # Clear any command set by the prod compose file (which would be passed
+    # as an extra argument to manage.py). Setting an empty command prevents
+    # the image `command` from being appended to the entrypoint.
+    command: []
+    volumes:
+      - ../:/usr/src/app:cached
+      # Mount the app log directory so logs are visible on the host at ./logs
+      - ../logs:/var/log/rad
+  nginx:
+    # Development nginx override: mount a simplified config that does not
+    # reference LetsEncrypt certs so the container can start without real
+    # certificates present on the host.
+    image: nginx:1.25-alpine
+    volumes:
+      - ../deploy/nginx/dev.conf:/etc/nginx/conf.d/default.conf:ro
+
+  loki:
+    image: grafana/loki:2.8.2
+    command: -config.file=/etc/loki/local-config.yaml
+    ports:
+      - "3100:3100"
+    volumes:
+      - ./loki-config/local-config.yaml:/etc/loki/local-config.yaml:ro
+      - ./loki-data:/loki
+    restart: unless-stopped
+    healthcheck:
+      test: ["CMD-SHELL", "wget -qO- http://localhost:3100/ready || exit 1"]
+      interval: 5s
+      timeout: 3s
+      retries: 6
+
+  promtail:
+    image: grafana/promtail:2.8.2
+    volumes:
+      - ../logs:/var/log/rad:ro
+      - ./promtail-config.yml:/etc/promtail/promtail-config.yml:ro
+    command: -config.file=/etc/promtail/promtail-config.yml
+    depends_on:
+      - loki
+    restart: unless-stopped
+
+  grafana:
+    image: grafana/grafana:10.2.0
+    ports:
+      - "3000:3000"
+    environment:
+      - GF_SECURITY_ADMIN_PASSWORD=admin
+    volumes:
+      - grafana-data:/var/lib/grafana
+    depends_on:
+      loki:
+        condition: service_healthy
+    restart: unless-stopped
+
+volumes:
+  grafana-data:
+  loki-data:
+

docker/docker-compose.local.yml

@@ -29,7 +29,7 @@ services:
       - 8000:8000
       - 3459:3459
     env_file:
-      - ./.env.dev
+      - ./.env.dev.local
   db:
     image: postgres:14.2-alpine
     volumes:

docker/docker-compose.prod.yml

@@ -0,0 +1,119 @@
+services:
+  redis:
+    image: redis:7.4.2-alpine
+    restart: always
+    volumes:
+      - redis_data:/data
+    healthcheck:
+      test: ["CMD","redis-cli","ping"]
+      interval: 10s
+      timeout: 5s
+      retries: 5
+
+  web:
+    build:
+      # build context is the repository root (one level up from this file)
+      context: ..
+      dockerfile: rad/Dockerfile.prod
+    restart: always
+    # Use COMPOSE_ENV to select which env file to load (defaults to 'prod').
+    # Example: COMPOSE_ENV=dev docker compose -f rad/docker/docker-compose.prod.yml -f rad/docker/docker-compose.dev.yml up -d
+    env_file:
+      - ../.env.${COMPOSE_ENV:-prod}
+    environment:
+      - DJANGO_SETTINGS_MODULE=rad.settings
+    depends_on:
+      redis:
+        condition: service_healthy
+    volumes:
+      - static_volume:/usr/src/app/static
+      - media_volume:/usr/src/app/media
+      # Mount the server-specific local settings if present (DO NOT commit secrets).
+      # On the server create: rad/deploy/settings_local.py and it will be mounted into the container.
+      - ../deploy/settings_local.py:/usr/src/app/rad/settings_local.py:ro
+    expose:
+      - "8000"
+    command: ["/usr/src/app/entrypoint.sh"]
+
+  nginx:
+    image: nginx:stable-alpine
+    restart: always
+    ports:
+      - "${NGINX_HTTP_PORT:-80}:80"
+      - "${NGINX_HTTPS_PORT:-443}:443"
+    depends_on:
+      - web
+    volumes:
+      - ../deploy/nginx/prod.conf:/etc/nginx/conf.d/default.conf:ro
+      - static_volume:/usr/src/app/static:ro
+      - media_volume:/usr/src/app/media:ro
+      - ../deploy/nginx/certs:/etc/letsencrypt:ro
+      # Host-provided front-end bundles and static folders. Populate these under rad/deploy on the server
+      - ../deploy/www/viewer:/srv/www/viewer:ro
+      - ../deploy/www/ohif:/srv/www/ohif:ro
+      - ../deploy/www/rts:/srv/www/rts:ro
+      - ../deploy/nicereporter:/srv/nicereporter:rw
+      - ../deploy/proc-rota:/srv/proc/rota:ro
+      - ../deploy/uploader:/srv/uploader:ro
+    healthcheck:
+      test: ["CMD-SHELL","nginx -t" ]
+      interval: 30s
+      timeout: 10s
+      retries: 3
+
+  # Optional local observability stack (can be enabled on servers that
+  # should run Loki/Grafana). These services use configs found under
+  # the repository `docker/` directory so the same config works in dev.
+  loki:
+    image: grafana/loki:2.8.2
+    command: -config.file=/etc/loki/local-config.yaml
+    ports:
+      - "3100:3100"
+    volumes:
+      - ./loki-config/local-config.yaml:/etc/loki/local-config.yaml:ro
+      - ../docker/loki-data:/loki
+      # WAL directory: map a host folder so Loki (running as UID 10001)
+      # can create the write-ahead log. Host folder created under
+      # `docker/loki-wal` and owned by UID 10001.
+      - ../docker/loki-wal:/wal
+    restart: unless-stopped
+    healthcheck:
+      test: ["CMD-SHELL", "wget -qO- http://localhost:3100/ready || exit 1"]
+      interval: 10s
+      timeout: 5s
+      retries: 6
+
+  promtail:
+    image: grafana/promtail:2.8.2
+    volumes:
+      # In prod you may want to point this at the host system log directory.
+      - ../logs:/var/log/rad:ro
+      - ./promtail-config.yml:/etc/promtail/promtail-config.yml:ro
+    command: -config.file=/etc/promtail/promtail-config.yml
+    depends_on:
+      - loki
+    restart: unless-stopped
+
+  grafana:
+    image: grafana/grafana:10.2.0
+    ports:
+      - "3000:3000"
+    environment:
+      - GF_SECURITY_ADMIN_PASSWORD=admin
+    volumes:
+      - grafana-data:/var/lib/grafana
+    depends_on:
+      loki:
+        condition: service_healthy
+    restart: unless-stopped
+
+volumes:
+  postgres_data:
+  redis_data:
+  static_volume:
+  media_volume:
+  grafana-data:
+
+networks:
+  default:
+    driver: bridge

docker/docker-compose.test.yml

@@ -0,0 +1,26 @@
+version: "3.8"
+
+# Local test compose overlay — adds a Postgres service so you can run the
+# full stack locally without an external DB. Use it together with
+# docker-compose.prod.yml:
+#
+# docker compose -f rad/docker/docker-compose.prod.yml -f rad/docker/docker-compose.test.yml up -d --build
+
+services:
+  db:
+    image: postgres:14-alpine
+    restart: always
+    environment:
+      POSTGRES_USER: ${POSTGRES_USER:-django}
+      POSTGRES_PASSWORD: ${POSTGRES_PASSWORD:-postgres}
+      POSTGRES_DB: ${POSTGRES_DB:-rad}
+    volumes:
+      - postgres_test_data:/var/lib/postgresql/data
+    healthcheck:
+      test: ["CMD-SHELL","pg_isready -U ${POSTGRES_USER:-django}" ]
+      interval: 10s
+      timeout: 5s
+      retries: 5
+
+volumes:
+  postgres_test_data:

docker/loki-config/local-config.yaml

@@ -0,0 +1,43 @@
+server:
+  http_listen_port: 3100
+  grpc_listen_port: 9095
+
+ingester:
+  lifecycler:
+    address: 127.0.0.1
+    ring:
+      kvstore:
+        store: inmemory
+      replication_factor: 1
+  chunk_idle_period: 5m
+  chunk_retain_period: 30s
+  max_transfer_retries: 0
+
+schema_config:
+  configs:
+    - from: 2020-10-24
+      store: boltdb-shipper
+      object_store: filesystem
+      schema: v11
+      index:
+        prefix: index_
+        period: 24h
+
+storage_config:
+  boltdb_shipper:
+    active_index_directory: /loki/index
+    cache_location: /loki/cache
+    shared_store: filesystem
+  filesystem:
+    directory: /loki/chunks
+
+# Compactor settings: ensure compactor working directory is inside the mounted
+# `/loki` path so the process (running as UID 10001) can create files.
+compactor:
+  working_directory: /loki/compactor
+  shared_store: filesystem
+
+limits_config:
+  enforce_metric_name: false
+
+auth_enabled: false

docker/loki-data/chunks/loki_cluster_seed.json

@@ -0,0 +1 @@
+{"UID":"f8cade59-3cf9-4ae3-965d-8b0a57007d58","created_at":"2025-12-01T17:14:05.101735276Z","version":{"version":"2.8.2","revision":"9f809eda7","branch":"HEAD","buildUser":"root@e401cfcb874f","buildDate":"2023-05-03T11:07:54Z","goVersion":"go1.20.4"}}

docker/promtail-config.yml

@@ -0,0 +1,18 @@
+server:
+  http_listen_port: 9080
+  grpc_listen_port: 0
+
+positions:
+  filename: /tmp/positions.yaml
+
+clients:
+  - url: http://loki:3100/loki/api/v1/push
+
+scrape_configs:
+  - job_name: rad_app_logs
+    static_configs:
+      - targets:
+          - localhost
+        labels:
+          job: rad_app
+          __path__: /var/log/rad/*.log

entrypoint.sh

@@ -0,0 +1,25 @@
+#!/bin/sh
+set -e
+
+# Lightweight wait-for-postgres using nc (expects DATABASE_HOST and DATABASE_PORT env vars)
+if [ -n "${DATABASE_HOST}" ]; then
+  host="$DATABASE_HOST"
+  port="${DATABASE_PORT:-5432}"
+  echo "Waiting for database at ${host}:${port}..."
+  while ! nc -z "$host" "$port"; do
+    sleep 1
+  done
+fi
+
+echo "Applying database migrations..."
+python manage.py migrate --noinput
+
+echo "Collecting static files..."
+python manage.py collectstatic --noinput
+
+echo "Starting gunicorn..."
+exec gunicorn rad.wsgi:application \
+    --name rad_gunicorn \
+    --bind 0.0.0.0:8000 \
+    --workers ${GUNICORN_WORKERS:-3} \
+    --log-level ${GUNICORN_LOGLEVEL:-info}

generic/templates/generic/exam_overview_headers.html

@@ -7,9 +7,9 @@
                 <div>
                     <h1 class="h4 mb-1">Exam: {{ exam }}</h1>
                 </div>
-                <div class="mt-2 mt-md-0">
+{% comment %}                 <div class="mt-2 mt-md-0">
                     {% include "generic/exam_link_headers.html" %}
-                </div>
+                </div> {% endcomment %}
             </div>
             {% include 'exam_notes.html' %}
 
@@ -44,6 +44,8 @@
                 Time limit: <strong>{{ exam.time_limit }}</strong> seconds (<span title="Time per question: {% widthratio exam.time_limit question_number 1 %} seconds">per question</span>)
             </div>
 
+            <div class="mt-2 small text-muted">Author(s): {% for author in exam.author.all %}{{ author }}{% if not forloop.last %}, {% endif %}{% endfor %}</div>
+
             <div class="mt-2">
                 Exam mode: <strong>{{ exam.exam_mode }}</strong>
                 {% if exam.exam_mode %}
@@ -178,17 +180,7 @@
         </div>
     </div>
 
-    <div class="row">
-        <div class="col-12 col-md-6">
-            {% if exam.examcollection %}
-                <div class="small">Exam Collection: <a href="{{ exam.examcollection.get_absolute_url }}">{{ exam.examcollection }}</a></div>
-            {% endif %}
-            <div class="small mt-1">Author(s): {% for author in exam.author.all %}{{ author }}{% if not forloop.last %}, {% endif %}{% endfor %}</div>
-        </div>
-        <div class="col-12 col-md-6 text-md-end small mt-2 mt-md-0">
-            <span title="If true the results from this exam will be visible to supervisors automatically.">Supervisor visible: {{ exam.results_supervisor_visible }}</span>
-        </div>
-    </div>
+    {# Authors and supervisor visibility moved earlier in the header; duplicate block removed #}
 </div>
 
 {% block css %}

generic/templates/generic/partials/exams/dropdown_menu.html

@@ -0,0 +1,58 @@
+
+<ul class="navbar-nav ms-auto">
+    <li class="nav-item dropdown">
+        <a class="nav-link dropdown-toggle" href="#" id="examActions" role="button" data-bs-toggle="dropdown" aria-expanded="false">Actions</a>
+        <ul class="dropdown-menu dropdown-menu-end dropdown-menu-dark" aria-labelledby="examActions">
+            {# Primary action: add question #}
+            <li>
+                <a class="dropdown-item text-primary" href="{% url exam.get_app_name|add:':question_create' %}">
+                    <i class="bi bi-plus-lg me-2"></i> Add Question
+                </a>
+            </li>
+
+            {# Edit / Clone group #}
+            <li>
+                <a class="dropdown-item text-white" href="{% url exam.get_app_name|add:':exam_update' exam.pk %}">
+                    <i class="bi bi-pencil-square me-2"></i> Edit Exam
+                </a>
+            </li>
+            <li>
+                <a class="dropdown-item text-white" href="{% url exam.get_app_name|add:':exam_clone' exam.pk %}">
+                    <i class="bi bi-files me-2"></i> Clone
+                </a>
+            </li>
+
+            <li><hr class="dropdown-divider"></li>
+
+            {# Authors / Markers (informational) #}
+            <li>
+                <a class="dropdown-item text-info" href="{% url exam.get_app_name|add:':exam_authors' exam.id %}">
+                    <i class="bi bi-people me-2"></i> Authors
+                </a>
+            </li>
+            <li>
+                <a class="dropdown-item text-info" href="{% url exam.get_app_name|add:':exam_markers' exam.id %}">
+                    <i class="bi bi-person-badge me-2"></i> Markers
+                </a>
+            </li>
+
+            <li><hr class="dropdown-divider"></li>
+
+            {# Delete is destructive - show in red #}
+            <li>
+                <a class="dropdown-item text-danger" href="{% url exam.get_app_name|add:':exam_delete' exam.id %}">
+                    <i class="bi bi-trash me-2"></i> Delete
+                </a>
+            </li>
+
+            {% if request.user.is_superuser %}
+                <li><hr class="dropdown-divider"></li>
+                <li>
+                    <a class="dropdown-item text-warning" href="{% url 'admin:anatomy_exam_change' exam.pk %}">
+                        <i class="bi bi-tools me-2"></i> Admin Edit
+                    </a>
+                </li>
+            {% endif %}
+        </ul>
+    </li>
+</ul>

longs/api.py

@@ -14,19 +14,20 @@ router = Router()
 
 
 class QuestionSchema(ModelSchema):
-    class Config:
+    class Meta:
         model = Question
 
-        #model_fields = ["question", "history", "feedback", "normal", "laterality"]
-        model_fields = "__all__"
+        # Use `fields` per newer ninja ModelSchema API
+        #fields = ["question", "history", "feedback", "normal", "laterality"]
+        fields = "__all__"
 
-        #model_exclude = ["answers"]
+        #exclude = ["answers"]
 
 class ExamSchema(ModelSchema):
-    class Config:
+    class Meta:
         model = Exam
 
-        model_fields = ["id", "name", "active", "publish_results"]
+        fields = ["id", "name", "active", "publish_results"]
 
 @router.get('/')
 def list_questions(request):

longs/templates/longs/exams.html

@@ -2,12 +2,27 @@
 
 {% block navigation %}
     {{block.super}}
-    <br/>
-    Exams: {{exam}}-> 
-    <a href="{% url 'longs:exam_overview' pk=exam.pk %}">Overview</a> / 
-    <a href="{% url 'longs:mark_overview' pk=exam.pk %}">Mark</a> / 
-    <a href="{% url 'longs:exam_scores_all' pk=exam.pk %}">Scores</a> /
-    <a href="{% url 'longs:exam_cids' exam_id=exam.pk %}">Candidates</a> /
-    <a href="{% url 'longs:exam_stats' exam_id=exam.pk %}">Stats</a> /
-    <a href="{% url 'longs:exam_review_start' pk=exam.pk %}">Review</a> /
+    <nav class="navbar navbar-expand-lg navbar-dark bg-dark mt-2 rounded">
+        <div class="container-fluid px-3">
+            <span class="navbar-text me-3 text-white">
+                <strong>Exam:</strong> {{ exam.title|default:exam.name|default:exam }}
+            </span>
+            <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#examNav" aria-controls="examNav" aria-expanded="false" aria-label="Toggle navigation">
+                <span class="navbar-toggler-icon"></span>
+            </button>
+
+            <div class="collapse navbar-collapse" id="examNav">
+                <ul class="navbar-nav me-auto mb-2 mb-lg-0">
+                    <li class="nav-item"><a class="nav-link" href="{% url 'longs:exam_overview' pk=exam.pk %}">Overview</a></li>
+                    <li class="nav-item"><a class="nav-link" href="{% url 'longs:mark_overview' pk=exam.pk %}">Mark</a></li>
+                    <li class="nav-item"><a class="nav-link" href="{% url 'longs:exam_scores_all' pk=exam.pk %}">Scores</a></li>
+                    <li class="nav-item"><a class="nav-link" href="{% url 'longs:exam_cids' exam_id=exam.pk %}">Candidates</a></li>
+                    <li class="nav-item"><a class="nav-link" href="{% url 'longs:exam_stats' exam_id=exam.pk %}">Stats</a></li>
+                    <li class="nav-item"><a class="nav-link" href="{% url 'longs:exam_review_start' pk=exam.pk %}">Review</a></li>
+                </ul>
+
+                {% include 'generic/partials/exams/dropdown_menu.html'%}
+            </div>
+        </div>
+    </nav>
 {% endblock %}

physics/api.py

@@ -15,19 +15,19 @@ router = Router()
 
 
 class QuestionSchema(ModelSchema):
-    class Config:
+    class Meta:
         model = Question
 
-        #model_fields = ["question", "history", "feedback", "normal", "laterality"]
-        model_fields = "__all__"
+        # Use `fields` per newer ninja ModelSchema API
+        fields = "__all__"
 
-        #model_exclude = ["answers"]
+        #exclude = ["answers"]
 
 class ExamSchema(ModelSchema):
-    class Config:
+    class Meta:
         model = Exam
 
-        model_fields = ["id", "name", "active", "publish_results"]
+        fields = ["id", "name", "active", "publish_results"]
 
 @router.get('/')
 def list_questions(request):

physics/forms.py

@@ -48,3 +48,32 @@ class ExamMarkerForm(ExamMarkerFormMixin):
 class ExamGroupsForm(ExamGroupsFormMixin):
     class Meta(ExamGroupsFormMixin.Meta):
         model = Exam
+
+
+class QuestionForm(ModelForm):
+    class Meta:
+        model = Question
+        fields = [
+            "stem",
+            "a",
+            "a_answer",
+            "a_feedback",
+            "b",
+            "b_answer",
+            "b_feedback",
+            "c",
+            "c_answer",
+            "c_feedback",
+            "d",
+            "d_answer",
+            "d_feedback",
+            "e",
+            "e_answer",
+            "e_feedback",
+            "category",
+        ]
+
+    def __init__(self, *args, **kwargs):
+        # accept an optional user kwarg for parity with other apps
+        self.user = kwargs.pop("user", None)
+        super().__init__(*args, **kwargs)

physics/templates/physics/exam_overview.html

@@ -7,70 +7,101 @@
 {% block content %}
 
     {% load thumbnail %}
-    <div class="physics">
+    <div class="container physics my-3">
 
-        This exam will be available to take <a href="{% url 'physics:exam_start' pk=exam.pk %}">here</a> (when active).
+        <p class="mb-3">This exam will be available to take <a href="{% url 'physics:exam_start' pk=exam.pk %}">here</a> (when active).</p>
 
-        {% autoescape off %}
-            <ol id="full-question-list-physics">
+        <div class="card">
+            <div class="card-header d-flex justify-content-between align-items-center">
+                <h5 class="mb-0">Questions <small class="text-muted">({{ questions.count }})</small></h5>
+                <div class="text-muted small">Exam: {{ exam.title }}</div>
+            </div>
+
+            <ul class="list-group list-group-flush" id="full-question-list-physics">
                 {% for question in questions.all %}
+                    <li class="list-group-item">
+                        <div class="d-flex align-items-start">
+                            <div class="me-3">
+                                <span class="badge bg-secondary">{{ forloop.counter }}</span>
+                            </div>
+                            <div class="flex-grow-1">
+                                <div class="fw-bold mb-2">{{ question.stem|safe }}</div>
 
-                    <li>
-                        {{ question.stem }}
-                        <ol type="a" class="abcde">
-                            <li class="question-a">
-                                <span class="question-text">{{ question.a }}</span>: <span class="question-answer">{{ question.a_answer }}</span>
-                                {% if question.a_feedback %}
-                                    <span class="question-feedback">{{question.a_feedback}}</span>
-                                {% endif %}
-                            </li>
-                            <li class="question-b">
-                                <span class="question-text">{{ question.b }}</span>: <span class="question-answer">{{ question.b_answer }}</span>
-                                {% if question.b_feedback %}
-                                    <span class="question-feedback">{{question.b_feedback}}</span>
-                                {% endif %}
-                            </li>
-                            <li class="question-c">
-                                <span class="question-text">{{ question.c }}</span>: <span class="question-answer">{{ question.c_answer }}</span>
-                                {% if question.c_feedback %}
-                                    <span class="question-feedback">{{question.c_feedback}}</span>
-                                {% endif %}
-                            </li>
-                            <li class="question-d">
-                                <span class="question-text">{{ question.d }}</span>: <span class="question-answer">{{ question.d_answer }}</span>
-                                {% if question.d_feedback %}
-                                    <span class="question-feedback">{{question.d_feedback}}</span>
-                                {% endif %}
-                            </li>
-                            <li class="question-e">
-                                <span class="question-text">{{ question.e }}</span>: <span class="question-answer">{{ question.e_answer }}</span>
-                                {% if question.e_feedback %}
-                                    <span class="question-feedback">{{question.e_feedback}}</span>
-                                {% endif %}
-                            </li>
-                        </ol>
-                        Category: {{ question.category }}, <a href="{% url 'physics:question_detail' pk=question.pk %}">View [id: {{question.pk}}]</a> <a
-                            href="{% url 'admin:physics_question_change' question.id %}">Edit</a>
+                                <div class="mb-2">
+                                    <ol type="a" class="mb-0">
+                                        <li class="d-flex justify-content-between align-items-start py-1">
+                                            <div><span class="me-2">a)</span><span>{{ question.a }}</span></div>
+                                            <div class="text-end">
+                                                <div class="text-primary fw-semibold">{{ question.a_answer }}</div>
+                                                {% if question.a_feedback %}
+                                                    <div class="text-muted small">Feedback: {{ question.a_feedback }}</div>
+                                                {% endif %}
+                                            </div>
+                                        </li>
+                                        <li class="d-flex justify-content-between align-items-start py-1">
+                                            <div><span class="me-2">b)</span><span>{{ question.b }}</span></div>
+                                            <div class="text-end">
+                                                <div class="text-primary fw-semibold">{{ question.b_answer }}</div>
+                                                {% if question.b_feedback %}
+                                                    <div class="text-muted small">Feedback: {{ question.b_feedback }}</div>
+                                                {% endif %}
+                                            </div>
+                                        </li>
+                                        <li class="d-flex justify-content-between align-items-start py-1">
+                                            <div><span class="me-2">c)</span><span>{{ question.c }}</span></div>
+                                            <div class="text-end">
+                                                <div class="text-primary fw-semibold">{{ question.c_answer }}</div>
+                                                {% if question.c_feedback %}
+                                                    <div class="text-muted small">Feedback: {{ question.c_feedback }}</div>
+                                                {% endif %}
+                                            </div>
+                                        </li>
+                                        <li class="d-flex justify-content-between align-items-start py-1">
+                                            <div><span class="me-2">d)</span><span>{{ question.d }}</span></div>
+                                            <div class="text-end">
+                                                <div class="text-primary fw-semibold">{{ question.d_answer }}</div>
+                                                {% if question.d_feedback %}
+                                                    <div class="text-muted small">Feedback: {{ question.d_feedback }}</div>
+                                                {% endif %}
+                                            </div>
+                                        </li>
+                                        <li class="d-flex justify-content-between align-items-start py-1">
+                                            <div><span class="me-2">e)</span><span>{{ question.e }}</span></div>
+                                            <div class="text-end">
+                                                <div class="text-primary fw-semibold">{{ question.e_answer }}</div>
+                                                {% if question.e_feedback %}
+                                                    <div class="text-muted small">Feedback: {{ question.e_feedback }}</div>
+                                                {% endif %}
+                                            </div>
+                                        </li>
+                                    </ol>
+                                </div>
 
+                                <div class="small text-muted">
+                                    Category: {{ question.category }}
+                                    — <a href="{% url 'physics:question_detail' pk=question.pk %}">View</a>
+                                    <a href="{% url 'admin:physics_question_change' question.id %}" class="ms-2">Edit</a>
+                                </div>
+                            </div>
+                        </div>
                     </li>
+                {% empty %}
+                    <li class="list-group-item text-muted">No questions available.</li>
                 {% endfor %}
-            </ol>
-        {% endautoescape %}
+            </ul>
+        </div>
 
     </div>
+
     {% include 'exam_overview_js.html' %}
+
 {% endblock %}
+
 {% block css %}
     <style>
-        .question-answer {
-            font-weight: bolder;
-        }
-        .question-feedback {
-            opacity: 50%;
-            float: right
-        }
-        .question-feedback::before {
-            content: "Feedback: ";
-        }
+        /* Small visual tweaks on top of Bootstrap */
+        .question-feedback { opacity: 0.7; }
+        .list-group-item ol { margin: 0; padding-left: 1.4rem; }
+        .list-group-item li { list-style-position: inside; }
     </style>
 {% endblock %}

physics/templates/physics/exam_take.html

@@ -58,35 +58,20 @@
            - Also supports a manual `.dark-mode` class on body or a parent
         */
 
-        :root {
-            --bg: #ffffff;
-            --text: #212529;
-            --muted: #6c757d;
-            --secondary: #6c757d;
-            --card-bg: #ffffff;
-            --card-border: #e9ecef;
-            --primary: #0d6efd;
-            --success: #198754;
-            --danger: #dc3545;
-            --feedback-bg: #f8f9fa;
-            --shadow: 0 1px 2px rgba(0,0,0,0.03);
-        }
 
-        @media (prefers-color-scheme: dark) {
-            :root {
-                --bg: #050607;
-                --text: #e6eef6;
-                --muted: #9aa4ad;
-                --card-bg: #0f1720;
-                --card-border: #1f2a33;
-                --primary: #6ea8ff;
-                --success: #36d07a;
-                --danger: #ff6b6b;
-                --feedback-bg: #071322;
-                --shadow: 0 2px 6px rgba(0,0,0,0.6);
-            }
-            body, .exam-take-container { background: var(--bg); color: var(--text); }
+        :root {
+            --bg: #050607;
+            --text: #e6eef6;
+            --muted: #9aa4ad;
+            --card-bg: #0f1720;
+            --card-border: #1f2a33;
+            --primary: #6ea8ff;
+            --success: #36d07a;
+            --danger: #ff6b6b;
+            --feedback-bg: #071322;
+            --shadow: 0 2px 6px rgba(0,0,0,0.6);
         }
+        body, .exam-take-container { background: var(--bg); color: var(--text); }
 
         /* Manual override: add `dark-mode` to body or a parent to force dark theme */
         body.dark-mode, .dark-mode { color: var(--text); background: var(--bg); }

physics/templates/physics/exams.html

@@ -1,11 +1,27 @@
 {% extends 'physics/base.html' %}
 
 {% block navigation %}
-{{block.super}}
-<br/>
-Exams: {{exam}}-> <a href="{% url 'physics:exam_overview' pk=exam.pk %}">Overview</a> / 
-<a href="{% url 'physics:exam_scores_all' pk=exam.pk %}">Scores</a> /
-<a href="{% url 'physics:exam_cids' exam_id=exam.pk %}">Candidates</a> /
-    <a href="{% url 'physics:exam_stats' exam_id=exam.pk %}">Stats</a> /
-    <a href="{% url 'physics:exam_review_start' pk=exam.pk %}">Review</a> /
+    {{block.super}}
+    <nav class="navbar navbar-expand-lg navbar-dark bg-dark mt-2 rounded">
+        <div class="container-fluid px-3">
+            <span class="navbar-text me-3 text-white">
+                <strong>Exam:</strong> {{ exam.title|default:exam.name|default:exam }}
+            </span>
+            <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#examNav" aria-controls="examNav" aria-expanded="false" aria-label="Toggle navigation">
+                <span class="navbar-toggler-icon"></span>
+            </button>
+
+            <div class="collapse navbar-collapse" id="examNav">
+                <ul class="navbar-nav me-auto mb-2 mb-lg-0">
+                    <li class="nav-item"><a class="nav-link" href="{% url 'physics:exam_overview' pk=exam.pk %}">Overview</a></li>
+                    <li class="nav-item"><a class="nav-link" href="{% url 'physics:exam_scores_all' pk=exam.pk %}">Scores</a></li>
+                    <li class="nav-item"><a class="nav-link" href="{% url 'physics:exam_cids' exam_id=exam.pk %}">Candidates</a></li>
+                    <li class="nav-item"><a class="nav-link" href="{% url 'physics:exam_stats' exam_id=exam.pk %}">Stats</a></li>
+                    <li class="nav-item"><a class="nav-link" href="{% url 'physics:exam_review_start' pk=exam.pk %}">Review</a></li>
+                </ul>
+
+                {% include 'generic/partials/exams/dropdown_menu.html'%}
+            </div>
+        </div>
+    </nav>
 {% endblock %}

physics/templates/physics/question_form.html

@@ -0,0 +1,40 @@
+{% extends "physics/base.html" %}
+{% load crispy_forms_tags %}
+
+{% block content %}
+  <div class="container py-3">
+    <div class="row">
+      <div class="col-12">
+        <h1>Add question</h1>
+        <form method="post" novalidate>
+          {% csrf_token %}
+          {{ form.media }}
+
+          {% if form.non_field_errors %}
+            <div class="alert alert-danger">{{ form.non_field_errors }}</div>
+          {% endif %}
+
+          {% if form.helper %}
+            {% crispy form form.helper %}
+          {% else %}
+            {% for field in form %}
+              <div class="mb-3">
+                {{ field.label_tag }}
+                {{ field }}
+                {% if field.help_text %}
+                  <div class="form-text">{{ field.help_text }}</div>
+                {% endif %}
+                {% for error in field.errors %}
+                  <div class="text-danger small">{{ error }}</div>
+                {% endfor %}
+              </div>
+            {% endfor %}
+          {% endif %}
+
+          <button type="submit" class="btn btn-primary">Save</button>
+          <a href="javascript:history.back()" class="btn btn-secondary">Cancel</a>
+        </form>
+      </div>
+    </div>
+  </div>
+{% endblock %}

physics/urls.py

@@ -10,6 +10,8 @@ urlpatterns = []
 urlpatterns.extend(
     [
         path("question/", views.QuestionView.as_view(), name="question_view"),
+        path("question/create/", views.QuestionCreate.as_view(), name="question_create"),
+        path("question/create/exam/<int:pk>", views.QuestionCreate.as_view(), name="question_create_exam"),
         path("question/<int:pk>/", views.question_detail, name="question_detail"),
         path("exam/<int:pk>/take_old", views.exam_take_old, name="exam_take_old"),
         path(

physics/views.py

@@ -56,7 +56,14 @@ from generic.views import (
 
 from django.core.exceptions import PermissionDenied
 
-from .forms import ExamGroupsForm, ExamMarkerForm, UserAnswerForm, ExamAuthorForm, ExamForm
+from .forms import (
+    ExamGroupsForm,
+    ExamMarkerForm,
+    UserAnswerForm,
+    ExamAuthorForm,
+    ExamForm,
+    QuestionForm,
+)
 from .decorators import (
     user_is_author_or_physics_checker,
     user_is_exam_author_or_physics_checker,
@@ -534,6 +541,55 @@ class QuestionView(
         return context
 
 
+class QuestionCreateBase(RevisionMixin, LoginRequiredMixin, CreateView):
+    model = Question
+    form_class = QuestionForm
+
+    def get_form_kwargs(self):
+        kwargs = super(QuestionCreateBase, self).get_form_kwargs()
+        kwargs.update({"user": self.request.user})
+        return kwargs
+
+    def form_valid(self, form):
+        self.object = form.save(commit=False)
+        self.object.save()
+
+        # add the current user as an author
+        form.instance.author.add(self.request.user.id)
+
+        response = super().form_valid(form)
+        return response
+
+
+class QuestionCreate(QuestionCreateBase):
+    def get_initial(self):
+        if "pk" in self.kwargs:
+            initial = super().get_initial()
+            exam = get_object_or_404(Exam, pk=self.kwargs["pk"])
+            # When creating a question from an exam context we don't have an
+            # 'exams' field on the ModelForm (exams is a reverse relation).
+            # Store nothing in the initial data here; attachment is handled
+            # in form_valid below.
+            return initial
+
+    def form_valid(self, form):
+        # Let the base class save the object and set the author
+        response = super().form_valid(form)
+
+        # If the create URL included an exam pk, add the new question to that exam
+        if "pk" in self.kwargs:
+            try:
+                exam = get_object_or_404(Exam, pk=self.kwargs["pk"])
+                # exam.exam_questions is a ManyToMany through relation; add is fine
+                exam.exam_questions.add(self.object)
+            except Exception:
+                # Don't fail the whole request if attaching to the exam fails;
+                # the question has already been created and author set.
+                pass
+
+        return response
+
+
 class UserAnswerView(AuthorOrCheckerRequiredMixin, LoginRequiredMixin, DetailView):
     model = UserAnswer
 

rad.code-workspace

@@ -0,0 +1,15 @@
+{
+	"folders": [
+		{
+			"name": "rad",
+			"path": "."
+		}
+	],
+	"settings": {
+		"python.testing.pytestArgs": [
+			"."
+		],
+		"python.testing.unittestEnabled": false,
+		"python.testing.pytestEnabled": true
+	}
+}

rad/Dockerfile.prod

@@ -0,0 +1,79 @@
+FROM python:3.14-slim
+
+# Copy uv helper binary from the uv image so we can manage venvs and pip
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
+
+ENV PYTHONDONTWRITEBYTECODE=1
+ENV PYTHONUNBUFFERED=1
+
+# Install build deps required for common Python packages and netcat for health wait
+RUN apt-get update \
+     && apt-get install -y --no-install-recommends \
+         build-essential \
+         gcc \
+         git \
+         libpq-dev \
+         pkg-config \
+         libcairo2-dev \
+         # some distributions provide libgdk-pixbuf under the xlib name
+         libgdk-pixbuf-xlib-2.0-0 \
+         libgdk-pixbuf-xlib-2.0-dev \
+         libjpeg-dev \
+         zlib1g-dev \
+         wget \
+         ca-certificates \
+         netcat-openbsd \
+     && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /usr/src/app
+
+# Install python deps into a uv-managed venv for reproducible builds
+COPY requirements.txt /usr/src/app/
+# Prebuild wheels into /wheels so compiled artifacts are cached in a layer.
+# This speeds rebuilds when `requirements.txt` hasn't changed. The first build
+# still needs to compile any packages without prebuilt wheels.
+RUN mkdir -p /wheels \
+    && python -m venv /tmp/venvbuild \
+    && /tmp/venvbuild/bin/pip install --upgrade pip setuptools wheel \
+    && /tmp/venvbuild/bin/pip wheel --wheel-dir=/wheels -r requirements.txt \
+    && rm -rf /tmp/venvbuild
+
+# Create the final uv-managed venv and install from the cached wheels where
+# possible. Using `--no-index --find-links=/wheels` makes pip prefer the
+# prebuilt wheels, avoiding recompilation.
+RUN uv venv /opt/venv \
+    && export VIRTUAL_ENV=/opt/venv \
+    && export PATH="/opt/venv/bin:$PATH" \
+    && uv pip install --upgrade pip setuptools wheel \
+    && uv pip install --no-index --find-links=/wheels -r requirements.txt
+
+# Ensure the runtime environment uses the uv-managed venv by default.
+# This persists the venv into image ENV so `python` and `gunicorn` point
+# to the venv-installed binaries at container start.
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH="/opt/venv/bin:$PATH"
+
+# Create non-root user before copying files so we can use Docker's
+# `--chown` flag during COPY and avoid an expensive recursive `chown -R`.
+RUN useradd -m appuser
+
+# Create directory for application logs and ensure ownership is correct.
+# Do this as root before switching to `appuser` so the directory exists
+# and can be mounted by the dev compose override.
+RUN mkdir -p /var/log/rad \
+    && chown -R appuser:appuser /var/log/rad
+
+# Copy project files into image and set ownership during copy (faster than
+# a separate `chown -R` step). This keeps layer reuse efficient.
+COPY --chown=appuser:appuser . /usr/src/app
+
+# Ensure the venv is usable by the non-root user; chown only the venv path
+# (much smaller than the whole project tree) to avoid a long recursive chown.
+RUN chown -R appuser:appuser /opt/venv
+
+# Make the entrypoint executable (some files in the repo may not have the
+# executable bit set). Do this as root before switching to the app user.
+RUN [ -f /usr/src/app/entrypoint.sh ] && chmod +x /usr/src/app/entrypoint.sh || true
+USER appuser
+
+ENTRYPOINT ["/usr/src/app/entrypoint.sh"]

rad/wsgi.py

@@ -10,6 +10,36 @@ https://docs.djangoproject.com/en/1.11/howto/deployment/wsgi/
 import os
 
 from django.core.wsgi import get_wsgi_application
+from loguru import logger
+import sys
+from pathlib import Path
+
+# Configure Loguru sinks early so app imports see consistent logging.
+# Log to stdout (so `docker logs` shows messages) and to a file at
+# `/var/log/rad/app.log` for persistent collection / host tailing.
+try:
+	# ensure directory exists
+	log_dir = Path("/var/log/rad")
+	log_dir.mkdir(parents=True, exist_ok=True)
+	# Add stdout sink (if not already added by other code)
+	logger.remove()  # remove default handlers to avoid duplicate lines
+	logger.add(sys.stdout, level="INFO", enqueue=True, backtrace=False, diagnose=False)
+	# Add rotating file sink for persistence in container. Use JSON lines
+	# (serialize=True) to make logs easy to query in Loki/Grafana.
+	logger.add(
+		str(log_dir / "app.log"),
+		rotation="10 MB",
+		retention="10 days",
+		level="DEBUG",
+		enqueue=True,
+		serialize=True,
+	)
+except Exception:
+	# Best-effort only — don't crash WSGI startup if logging can't be configured
+	try:
+		logger.add(sys.stderr)
+	except Exception:
+		pass
 
 os.environ.setdefault("DJANGO_SETTINGS_MODULE", "rad.settings")
 

rapids/api.py

@@ -15,19 +15,19 @@ router = Router()
 
 
 class RapidSchema(ModelSchema):
-    class Config:
+    # `ninja` newer versions require an inner `Meta` class instead of `Config`
+    # for ModelSchema. Replace `Config` with `Meta` to be compatible.
+    class Meta:
         model = Rapid
-
-        #model_fields = ["question", "history", "feedback", "normal", "laterality"]
-        model_fields = "__all__"
-
-        #model_exclude = ["answers"]
+        #model_fields (old API) -> use `fields` per newer ninja ModelSchema API
+        #fields can be a list of field names or the string "__all__".
+        #fields = ["question", "history", "feedback", "normal", "laterality"]
+        fields = "__all__"
 
 class ExamSchema(ModelSchema):
-    class Config:
+    class Meta:
         model = Exam
-
-        model_fields = ["id", "name", "active", "publish_results"]
+        fields = ["id", "name", "active", "publish_results"]
 
 @router.get('/')
 def list_rapids(request):

rapids/templates/rapids/exams.html

@@ -2,15 +2,30 @@
 
 {% block navigation %}
     {{block.super}}
-    <br/>
-    Exams: {{exam}}->
-    <a href="{% url 'rapids:exam_overview' pk=exam.pk %}">Overview</a> /
-    {% if exam.exam_mode %}
-        <a href="{% url 'rapids:mark_overview' pk=exam.pk %}">Mark</a> /
-        <a href="{% url 'rapids:exam_scores_all' pk=exam.pk %}">Scores</a> /
-        <a href="{% url 'rapids:exam_cids' exam_id=exam.pk %}">Candidates</a> /
-        <a href="{% url 'rapids:exam_stats' exam_id=exam.pk %}">Stats</a> /
-    {% endif %}
-    <a href="{% url 'rapids:question_create_exam' pk=exam.pk %}">Add New Question</a>
-    <a href="{% url 'rapids:exam_review_start' pk=exam.pk %}">Review</a>
+    <nav class="navbar navbar-expand-lg navbar-dark bg-dark mt-2 rounded">
+        <div class="container-fluid px-3">
+            <span class="navbar-text me-3 text-white">
+                <strong>Exam:</strong> {{ exam.title|default:exam.name|default:exam }}
+            </span>
+            <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#examNav" aria-controls="examNav" aria-expanded="false" aria-label="Toggle navigation">
+                <span class="navbar-toggler-icon"></span>
+            </button>
+
+            <div class="collapse navbar-collapse" id="examNav">
+                <ul class="navbar-nav me-auto mb-2 mb-lg-0">
+                    <li class="nav-item"><a class="nav-link" href="{% url 'rapids:exam_overview' pk=exam.pk %}">Overview</a></li>
+                    {% if exam.exam_mode %}
+                        <li class="nav-item"><a class="nav-link" href="{% url 'rapids:mark_overview' pk=exam.pk %}">Mark</a></li>
+                        <li class="nav-item"><a class="nav-link" href="{% url 'rapids:exam_scores_all' pk=exam.pk %}">Scores</a></li>
+                        <li class="nav-item"><a class="nav-link" href="{% url 'rapids:exam_cids' exam_id=exam.pk %}">Candidates</a></li>
+                        <li class="nav-item"><a class="nav-link" href="{% url 'rapids:exam_stats' exam_id=exam.pk %}">Stats</a></li>
+                    {% endif %}
+                    <li class="nav-item"><a class="nav-link" href="{% url 'rapids:question_create_exam' pk=exam.pk %}">Add Question</a></li>
+                    <li class="nav-item"><a class="nav-link" href="{% url 'rapids:exam_review_start' pk=exam.pk %}">Review</a></li>
+                </ul>
+
+                {% include 'generic/partials/exams/dropdown_menu.html'%}
+            </div>
+        </div>
+    </nav>
 {% endblock %}

sbas/api.py

@@ -15,19 +15,18 @@ router = Router()
 
 
 class QuestionSchema(ModelSchema):
-    class Config:
+    class Meta:
         model = Question
 
-        #model_fields = ["question", "history", "feedback", "normal", "laterality"]
-        model_fields = "__all__"
+        fields = "__all__"
 
-        #model_exclude = ["answers"]
+        #exclude = ["answers"]
 
 class ExamSchema(ModelSchema):
-    class Config:
+    class Meta:
         model = Exam
 
-        model_fields = ["id", "name", "active", "publish_results"]
+        fields = ["id", "name", "active", "publish_results"]
 
 @router.get('/')
 def list_questions(request):

sbas/templates/sbas/exams.html

@@ -2,11 +2,26 @@
 
 {% block navigation %}
     {{block.super}}
-    <br/>
-    Exams: {{exam}}->
-    <a href="{% url 'sbas:exam_overview' pk=exam.pk %}">Overview</a> /
-    <a href="{% url 'sbas:exam_scores_all' pk=exam.pk %}">Scores</a> /
-    <a href="{% url 'sbas:exam_cids' exam_id=exam.pk %}">Candidates</a> /
-    <a href="{% url 'sbas:exam_stats' exam_id=exam.pk %}">Stats</a> /
-    <a href="{% url 'sbas:exam_review_start' pk=exam.pk %}">Review</a> /
+    <nav class="navbar navbar-expand-lg navbar-dark bg-dark mt-2 rounded">
+        <div class="container-fluid px-3">
+            <span class="navbar-text me-3 text-white">
+                <strong>Exam:</strong> {{ exam.title|default:exam.name|default:exam }}
+            </span>
+            <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#examNav" aria-controls="examNav" aria-expanded="false" aria-label="Toggle navigation">
+                <span class="navbar-toggler-icon"></span>
+            </button>
+
+            <div class="collapse navbar-collapse" id="examNav">
+                <ul class="navbar-nav me-auto mb-2 mb-lg-0">
+                    <li class="nav-item"><a class="nav-link" href="{% url 'sbas:exam_overview' pk=exam.pk %}">Overview</a></li>
+                    <li class="nav-item"><a class="nav-link" href="{% url 'sbas:exam_scores_all' pk=exam.pk %}">Scores</a></li>
+                    <li class="nav-item"><a class="nav-link" href="{% url 'sbas:exam_cids' exam_id=exam.pk %}">Candidates</a></li>
+                    <li class="nav-item"><a class="nav-link" href="{% url 'sbas:exam_stats' exam_id=exam.pk %}">Stats</a></li>
+                    <li class="nav-item"><a class="nav-link" href="{% url 'sbas:exam_review_start' pk=exam.pk %}">Review</a></li>
+                </ul>
+
+                {% include 'generic/partials/exams/dropdown_menu.html'%}
+            </div>
+        </div>
+    </nav>
 {% endblock %}

scripts/local-down.sh

@@ -0,0 +1,7 @@
+#!/bin/sh
+set -e
+
+REPO_ROOT="$(cd "$(dirname "$0")/.." && pwd)"
+cd "$REPO_ROOT"
+
+docker compose -f docker/docker-compose.prod.yml -f docker/docker-compose.test.yml -f docker/docker-compose.dev.yml down --volumes --remove-orphans

scripts/local-up.sh

@@ -0,0 +1,44 @@
+#!/bin/sh
+set -e
+
+# Simple local bring-up helper. Usage:
+#   ./rad/scripts/local-up.sh
+# It requires rad/.env.dev to exist (do NOT auto-create from examples) and then
+# runs the prod+dev compose stack using COMPOSE_ENV to select the env file.
+
+REPO_ROOT="$(cd "$(dirname "$0")/.." && pwd)"
+cd "$REPO_ROOT"
+
+if [ ! -f .env.dev ]; then
+  echo ".env.dev not found. Create .env.dev with your development values (pointing to the external dev DB) and re-run."
+  echo "You can copy .env.prod.example to start from a template, but DO NOT commit secrets."
+  exit 1
+fi
+
+# Default to 'dev' but allow overriding with COMPOSE_ENV environment variable
+COMPOSE_ENV=${COMPOSE_ENV:-dev}
+
+echo "Starting compose with COMPOSE_ENV=$COMPOSE_ENV (using .env.$COMPOSE_ENV)"
+# Load variables from .env.<env> into the environment so Compose variable
+# substitution (e.g. ${NGINX_HTTP_PORT}) works. We export all variables from
+# the file for the duration of the command.
+ENV_FILE="$REPO_ROOT/.env.$COMPOSE_ENV"
+if [ -f "$ENV_FILE" ]; then
+  # Export variables from the .env file safely without sourcing it. Some
+  # values include characters (parentheses, ampersands) that break POSIX
+  # shell parsing if the file is sourced directly. Read line-by-line,
+  # ignore comments/empty lines and export KEY=VALUE pairs.
+  while IFS= read -r _line || [ -n "$_line" ]; do
+    line="$_line"
+    case "$line" in
+      ''|\#*) continue ;;
+    esac
+    # Split on first '=' into key and value
+    key=${line%%=*}
+    val=${line#*=}
+    # Export directly (preserves special characters in the value)
+    export "$key=$val"
+  done < "$ENV_FILE"
+fi
+
+COMPOSE_ENV=$COMPOSE_ENV docker compose -f docker/docker-compose.prod.yml -f docker/docker-compose.dev.yml up --build

shorts/api.py

@@ -15,19 +15,19 @@ router = Router()
 
 
 class QuestionSchema(ModelSchema):
-    class Config:
+    class Meta:
         model = Question
 
-        #model_fields = ["question", "history", "feedback", "normal", "laterality"]
-        model_fields = "__all__"
+        # Use `fields` per newer ninja ModelSchema API
+        fields = "__all__"
 
-        #model_exclude = ["answers"]
+        #exclude = ["answers"]
 
 class ExamSchema(ModelSchema):
-    class Config:
+    class Meta:
         model = Exam
 
-        model_fields = ["id", "name", "active", "publish_results"]
+        fields = ["id", "name", "active", "publish_results"]
 
 @router.get('/')
 def list_questions(request):

shorts/templates/shorts/exams.html

@@ -2,15 +2,30 @@
 
 {% block navigation %}
     {{block.super}}
-    <br/>
-    Exams: {{exam}}->
-    <a href="{% url 'shorts:exam_overview' pk=exam.pk %}">Overview</a> /
-    {% if exam.exam_mode %}
-        <a href="{% url 'shorts:mark_overview' pk=exam.pk %}">Mark</a> /
-        <a href="{% url 'shorts:exam_scores_all' pk=exam.pk %}">Scores</a> /
-        <a href="{% url 'shorts:exam_cids' exam_id=exam.pk %}">Candidates</a> /
-        <a href="{% url 'shorts:exam_stats' exam_id=exam.pk %}">Stats</a> /
-    {% endif %}
-    <a href="{% url 'shorts:question_create_exam' pk=exam.pk %}">Add New Question</a>
-    <a href="{% url 'shorts:exam_review_start' pk=exam.pk %}">Review</a>
+    <nav class="navbar navbar-expand-lg navbar-dark bg-dark mt-2 rounded">
+        <div class="container-fluid px-3">
+            <span class="navbar-text me-3 text-white">
+                <strong>Exam:</strong> {{ exam.title|default:exam.name|default:exam }}
+            </span>
+            <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#examNav" aria-controls="examNav" aria-expanded="false" aria-label="Toggle navigation">
+                <span class="navbar-toggler-icon"></span>
+            </button>
+
+            <div class="collapse navbar-collapse" id="examNav">
+                <ul class="navbar-nav me-auto mb-2 mb-lg-0">
+                    <li class="nav-item"><a class="nav-link" href="{% url 'shorts:exam_overview' pk=exam.pk %}">Overview</a></li>
+                    {% if exam.exam_mode %}
+                        <li class="nav-item"><a class="nav-link" href="{% url 'shorts:mark_overview' pk=exam.pk %}">Mark</a></li>
+                        <li class="nav-item"><a class="nav-link" href="{% url 'shorts:exam_scores_all' pk=exam.pk %}">Scores</a></li>
+                        <li class="nav-item"><a class="nav-link" href="{% url 'shorts:exam_cids' exam_id=exam.pk %}">Candidates</a></li>
+                        <li class="nav-item"><a class="nav-link" href="{% url 'shorts:exam_stats' exam_id=exam.pk %}">Stats</a></li>
+                    {% endif %}
+                    <li class="nav-item"><a class="nav-link" href="{% url 'shorts:question_create_exam' pk=exam.pk %}">Add Question</a></li>
+                    <li class="nav-item"><a class="nav-link" href="{% url 'shorts:exam_review_start' pk=exam.pk %}">Review</a></li>
+                </ul>
+
+                {% include 'generic/partials/exams/dropdown_menu.html'%}
+            </div>
+        </div>
+    </nav>
 {% endblock %}

temp1/default

@@ -0,0 +1,402 @@
+upstream app_server {
+	server unix:/run/gunicorn.sock fail_timeout=0;
+}
+
+server {
+	#listen 80;
+
+	root /home/ross/web/viewer;
+	#index index.html index.htm;
+
+
+	server_name viewer.penracourses.org.uk;
+
+	location / {
+
+
+		#if ($request_method = 'OPTIONS') {
+		#	add_header 'Access-Control-Allow-Origin' * always;
+		#	add_header 'Access-Control-Allow-Credentials' 'true' always;
+		#	add_header 'Access-Control-Allow-Headers' "Origin, X-Requested-With, Content-Type, Accept" always;
+		#	add_header 'Access-Control-Allow-Methods' 'GET, POST, OPTIONS';
+		#	add_header 'Access-Control-Max-Age' 1728000;
+		#	add_header 'Content-Type' 'text/plain; charset=utf-8';
+		#	add_header 'Content-Length' 0;
+		#	return 204;
+		#}
+
+		#alias /home/ross/web/viewer;
+
+		#add_header Cross-Origin-Opener-Policy same-origin;
+		#add_header Cross-Origin-Embedder-Policy require-corp;
+
+		#add_header 'Cross-Origin-Opener-Policy' 'cross-origin' always;
+		#add_header 'Cross-Origin-Embedder-Policy' 'credentialless' always;
+
+		index index.html;
+
+		try_files $uri $uri/ /index.html;
+		add_header Cache-Control "no-store, no-cache, must-revalidate";
+		add_header 'Cross-Origin-Resource-Policy' 'cross-origin';
+	}
+
+
+
+	listen 443 ssl; # managed by Certbot
+		ssl_certificate /etc/letsencrypt/live/viewer.penracourses.org.uk/fullchain.pem; # managed by Certbot
+		ssl_certificate_key /etc/letsencrypt/live/viewer.penracourses.org.uk/privkey.pem; # managed by Certbot
+		include /etc/letsencrypt/options-ssl-nginx.conf; # managed by Certbot
+		ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem; # managed by Certbot
+
+}
+
+
+server {
+	listen 80;
+	server_name penracourses.org.uk;
+
+	return 301 https://www.penracourses.org.uk$request_uri;
+}
+
+server {
+	listen [::]:443 ssl; # managed by Certbot
+		server_name penracourses.org.uk;
+	listen 443 ssl; # managed by Certbot
+		ssl_certificate /etc/letsencrypt/live/penracourses.org.uk/fullchain.pem; # managed by Certbot
+		ssl_certificate_key /etc/letsencrypt/live/penracourses.org.uk/privkey.pem; # managed by Certbot
+		include /etc/letsencrypt/options-ssl-nginx.conf; # managed by Certbot
+		ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem; # managed by Certbot
+
+		return 301 https://www.penracourses.org.uk$request_uri;
+}
+
+
+server {
+	#listen 80;
+
+	root /usr/share/nginx/html;
+	index index.html index.htm;
+
+	client_max_body_size 4G;
+	#server_name _;
+	server_name www.penracourses.org.uk;
+	resolver 127.0.0.11;
+
+	keepalive_timeout 20;
+
+	set $cors "";
+if ($http_origin ~* (https?://(localhost:5173|viewer\.penracourses\.org\.uk))) {
+    set $cors $http_origin;
+}
+
+
+	# Your Django project's media files - amend as required
+	location /media  {
+		if ($request_method = OPTIONS ) {
+        add_header 'Access-Control-Allow-Origin' $cors always;
+			#add_header 'Access-Control-Allow-Origin' 'https://viewer.penracourses.org.uk' always;
+			add_header 'Access-Control-Allow-Credentials' 'true' always;
+			add_header 'Access-Control-Allow-Headers' "Origin, X-Requested-With, Content-Type, Accept" always;
+			add_header 'Access-Control-Allow-Methods' 'GET, POST, OPTIONS';
+			add_header 'Access-Control-Max-Age' 1728000;
+			add_header 'Content-Type' 'text/plain; charset=utf-8';
+			add_header 'Content-Length' 0;
+			return 200;
+		}
+		#add_header 'Access-Control-Allow-Origin' 'https://viewer.penracourses.org.uk' always;
+        add_header 'Access-Control-Allow-Origin' $cors always;
+
+
+		alias /home/ross/web/rad/media;
+		#add_header Access-Control-Allow-Origin *;
+		#add_header Access-Control-Allow-Origin http://localhost:8000;
+		#add_header Vary Origin;
+	}
+
+	# your Django project's static files - amend as required
+	location /static {
+		alias /home/ross/web/static;
+	}
+
+	# rts
+	location /rts {
+		alias /home/ross/web/rts;
+	}
+	# OHIF
+	location /viewer {
+		#add_header 'Cross-Origin-Opener-Policy' 'cross-origin' always;
+		#add_header 'Cross-Origin-Embedder-Policy' 'credentialless' always;
+		#add_header 'Cross-Origin-Resource-Policy' 'cross-origin' always;
+		alias /home/ross/web/viewer;
+	}
+	location /ohif {
+		add_header 'Cross-Origin-Opener-Policy' 'same-origin' always;
+		add_header 'Cross-Origin-Embedder-Policy' 'require-corp' always;
+		add_header 'Cross-Origin-Resource-Policy' 'same-site' always;
+		alias /home/ross/web/ohif;
+		try_files $uri /ohif/index.html;
+		#autoindex on;
+	}
+
+
+	# # Proxy the static assests for the Django Admin panel
+	# location /static/admin {
+		#    alias /usr/lib/python3/dist-packages/django/contrib/admin/static/admin/;
+		# }
+	location /rota {
+		alias /home/ross/proc/proc-rota;
+		autoindex on;
+	}
+
+	location /uploader {
+		alias /home/ross/uploader;
+		autoindex on;
+	}
+
+	location ~ ^/reporter/(.*)$ {
+		alias /home/ross/web/nicereporter;
+            proxy_http_version 1.1;
+            proxy_set_header Upgrade $http_upgrade;
+            proxy_set_header Connection $connection_upgrade;
+            proxy_set_header Authorization $http_authorization;
+            proxy_pass_header Authorization;
+
+            proxy_pass http://127.0.0.1:5129/$1?$args;
+            proxy_set_header X-Forwarded-Prefix /reporter;
+            proxy_redirect http://127.0.0.1:5129/ /reporter/;
+        }
+
+	location / {
+		proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+		proxy_set_header X-Forwarded-Proto $scheme;
+		proxy_set_header Host $host;
+		proxy_redirect off;
+		proxy_buffering off;
+		#add_header 'Cross-Origin-Opener-Policy' 'single-origin' always;
+		#add_header 'Cross-Origin-Embedder-Policy' 'require-corp' always;
+		#add_header 'Cross-Origin-Resource-Policy' 'same-site' always;
+		#add_header 'Cross-Origin-Opener-Policy' 'same-origin' always;
+		add_header 'Cross-Origin-Embedder-Policy' 'require-corp' always;
+		add_header 'Cross-Origin-Resource-Policy' 'same-site' always;
+		#add_header 'Access-Control-Allow-Origin' $cors always;
+
+		proxy_pass http://app_server;
+		#add_header Access-Control-Allow-Origin *;
+		#add_header Vary Origin;
+	}
+
+	#location ~* \.(jpg|jpeg|png|dicom)$ {
+		#    add_header Access-Control-Allow-Origin *;
+		#}
+	# rota
+
+
+	listen [::]:443 ssl; # managed by Certbot
+		listen 443 ssl; # managed by Certbot
+		ssl_certificate /etc/letsencrypt/live/penracourses.org.uk/fullchain.pem; # managed by Certbot
+		ssl_certificate_key /etc/letsencrypt/live/penracourses.org.uk/privkey.pem; # managed by Certbot
+		include /etc/letsencrypt/options-ssl-nginx.conf; # managed by Certbot
+		ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem; # managed by Certbot
+
+}
+
+#server {
+#server_name 161.35.163.87;
+#add_header X-Frame-Options "SAMEORIGIN";
+#
+#return 301 $scheme://penracourses.org.uk$request_uri;
+#}
+
+
+#server {
+#    #listen 80;
+#    #server_name penracoureses.org.uk www.penracourses.org.uk;
+#
+#    root /usr/share/nginx/html;
+#    index index.html index.htm;
+#
+#    client_max_body_size 4G;
+#    #server_name _;
+#    server_name penracourses.org.uk; # managed by Certbot
+#
+#    keepalive_timeout 5;
+#
+#    # Your Django project's media files - amend as required
+#    location /media  {
+#        alias /home/ross/web/rad/media;
+#        #add_header Access-Control-Allow-Origin *;
+#        #add_header Access-Control-Allow-Origin http://localhost:8000;
+#	#add_header Vary Origin;
+#    }
+#
+#    # your Django project's static files - amend as required
+#    location /static {
+#        alias /home/ross/web/rad/static;
+#    }
+#
+#    # rts
+#    location /rts {
+#        alias /home/ross/web/rts;
+#    }
+#
+#   # # Proxy the static assests for the Django Admin panel
+#   # location /static/admin {
+#   #    alias /usr/lib/python3/dist-packages/django/contrib/admin/static/admin/;
+#   # }
+#
+#    location / {
+#            proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+#            proxy_set_header Host $host;
+#            proxy_redirect off;
+#            proxy_buffering off;
+#
+#            proxy_pass http://app_server;
+#    }
+#
+#    #location ~* \.(jpg|jpeg|png|dicom)$ {
+#    #    add_header Access-Control-Allow-Origin *;
+#    #}
+#
+#    # rota
+#    location /rota {
+#        alias /home/ross/proc-rota;
+#    }
+#
+#    location /rota2 {
+#        alias /home/ross/neos;
+#    }
+#
+#
+#
+#
+#
+#    listen [::]:443 ssl ipv6only=on; # managed by Certbot
+#    listen 443 ssl; # managed by Certbot
+#    ssl_certificate /etc/letsencrypt/live/penracourses.org.uk/fullchain.pem; # managed by Certbot
+#    ssl_certificate_key /etc/letsencrypt/live/penracourses.org.uk/privkey.pem; # managed by Certbot
+#    include /etc/letsencrypt/options-ssl-nginx.conf; # managed by Certbot
+#    ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem; # managed by Certbot
+#
+#}
+
+
+
+server {
+	root /home/ross/web/rts;
+	index index.html index.htm;
+
+	client_max_body_size 4G;
+	#server_name _;
+	server_name dev.penracourses.org.uk www.dev.penracourses.org.uk;
+
+	keepalive_timeout 5;
+
+	# Your Django project's media files - amend as required
+	location /media  {
+		# Simple requests
+		if ($request_method ~* "(GET|POST)") {
+			add_header "Access-Control-Allow-Origin"  *;
+		}
+
+		# Preflighted requests
+		if ($request_method = OPTIONS ) {
+			add_header "Access-Control-Allow-Origin"  *;
+			add_header "Access-Control-Allow-Methods" "GET, POST, OPTIONS, HEAD";
+			add_header "Access-Control-Allow-Headers" "Authorization, Origin, X-Requested-With, Content-Type, Accept";
+			return 200;
+		}
+		alias /home/ross/web/rad/media;
+		#add_header Access-Control-Allow-Origin *;
+		#add_header Access-Control-Allow-Origin http://localhost:8000;
+		#add_header Vary Origin;
+	}
+
+	# your Django project's static files - amend as required
+	location /static {
+		alias /home/ross/web/rad/static;
+	}
+
+	# rts
+	location /rts {
+		alias /home/ross/web/rts;
+	}
+
+	# # Proxy the static assests for the Django Admin panel
+	# location /static/admin {
+		#    alias /usr/lib/python3/dist-packages/django/contrib/admin/static/admin/;
+		# }
+
+	location / {
+		add_header 'Access-Control-Allow-Origin' '*' always;
+		try_files $uri $uri/ =404;
+		#proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+		#proxy_set_header X-Forwarded-Proto $scheme;
+		#proxy_set_header Host $host;
+		#proxy_redirect off;
+		#proxy_buffering off;
+
+		#proxy_pass http://app_server;
+		#add_header Access-Control-Allow-Origin *;
+		#add_header Vary Origin;
+	}
+
+	#location ~* \.(jpg|jpeg|png|dicom)$ {
+		#    add_header Access-Control-Allow-Origin *;
+		#}
+
+
+
+
+	#listen [::]:443 ssl; # managed by Certbot
+	#listen 443 ssl; # managed by Certbot
+	#ssl_certificate /etc/letsencrypt/live/penracourses.org.uk/fullchain.pem; # managed by Certbot
+	#ssl_certificate_key /etc/letsencrypt/live/penracourses.org.uk/privkey.pem; # managed by Certbot
+	#include /etc/letsencrypt/options-ssl-nginx.conf; # managed by Certbot
+	#ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem; # managed by Certbot
+
+}
+
+
+server {
+	if ($host = penracourses.org.uk) {
+		return 301 https://www.$host$request_uri;
+	} # managed by Certbot
+
+
+	listen 80 ;
+	listen [::]:80  ;
+	server_name penracourses.org.uk;
+	return 404; # managed by Certbot
+
+
+}
+
+server {
+	if ($host = www.penracourses.org.uk) {
+		return 301 https://$host$request_uri;
+	} # managed by Certbot
+
+
+	listen 80 default_server;
+	listen [::]:80 default_server ipv6only=on;
+	server_name www.penracourses.org.uk;
+	return 404; # managed by Certbot
+
+
+}
+
+
+
+server {
+	if ($host = viewer.penracourses.org.uk) {
+		return 301 https://$host$request_uri;
+	} # managed by Certbot
+
+
+
+	server_name viewer.penracourses.org.uk;
+	listen 80;
+	return 404; # managed by Certbot
+
+
+}

temp1/settings_local.py

@@ -0,0 +1,54 @@
+DEBUG = False
+INTERNAL_IPS = ["82.69.88.125", "217.155.198.96"]
+#SECURE_SSL_REDIRECT = False
+#SECURE_PROXY_SSL_HEADER = ('HTTP_X_FORWARDED_PROTO', 'http')
+#REMOTE_URL = "http://46.101.13.46:8123"
+#
+#MEDIA_ROOT = '/home/django/rad/media/'
+STATIC_ROOT = '/home/ross/web/static/'
+
+#EMAIL_BACKEND = 'django.core.mail.backends.console.EmailBackend'
+EMAIL_BACKEND = "django.core.mail.backends.smtp.EmailBackend"
+
+if not DEBUG:
+  LOGGING = {
+      'version': 1,
+      'disable_existing_loggers': False,
+      'formatters': {
+          'verbose': {
+              'format' : "[%(asctime)s] %(levelname)s [%(name)s:%(lineno)s] %(message)s",
+              'datefmt' : "%d/%b/%Y %H:%M:%S"
+          },
+          'simple': {
+              'format': '%(levelname)s %(message)s'
+          },
+      },
+      'handlers': {
+          'file': {
+              'level': 'DEBUG',
+              'class': 'logging.FileHandler',
+              'filename': 'log.txt',
+              'formatter': 'verbose'
+          },
+      },
+      'loggers': {
+          'django': {
+              'handlers':['file'],
+              'propagate': True,
+              'level':'DEBUG',
+          },
+          'atlas': {
+              'handlers': ['file'],
+              'level': 'DEBUG',
+          },
+        #"django.core.mail": {"handlers": ["console"], "level": "DEBUG", "propagate": False},
+        #"smtplib": {"handlers": ["console"], "level": "DEBUG", "propagate": False},
+      }
+  }
+
+CIMAR_USERNAME = "ross.kruger@nhs.net"
+CIMAR_PASSWORD = "[prdr32@cimar]"
+
+# Celery settings
+CELERY_BROKER_URL = "redis://localhost:6379"
+CELERY_RESULT_BACKEND = "redis://localhost:6379"

templates/exam_overview_js.html

@@ -143,7 +143,8 @@
                 })
         })
         $("#button-edit-order").click(function (evt) {
-            $(this).remove();
+        // hide the edit button while in edit mode so we can restore it after saving
+        $(this).addClass('d-none').prop('disabled', true);
             sortable('.sortable');
             $("#full-question-list").addClass('sorting');
 
@@ -155,17 +156,38 @@
             for (var i = ul.children.length; i >= 0; i--) {
                 ul.appendChild(ul.children[Math.random() * i | 0]);
             }
+            renumber();
             }))
 
 
+            // helper to renumber visible cases and update links
+            function renumber() {
+                $("#full-question-list li").each((i, e) => {
+                    // update Case N label
+                    $(e).find('.case-number').text('Case ' + (i + 1));
+
+                    // update link href based on data-case-base-href (replace trailing 0)
+                    const a = $(e).find('.case-link');
+                    if (a.length) {
+                        const base = a.attr('data-case-base-href');
+                        if (base) {
+                            // replace trailing '/0' with new index
+                            const newHref = base.replace(/\/0$/, '/' + i);
+                            a.attr('href', newHref);
+                        }
+                    }
+                });
+            }
+
             $("#full-question-list li").each((n, el) => {
-    // Add up/down arrows at the start of each <li>
+                // Add up/down arrows at the start of each <li>
                 const upBtn = $("<button class='move-up btn btn-sm' title='Move up'>&#8593;</button>").click(function(e){
                     e.preventDefault();
                     const li = $(this).closest("li");
                     const prev = li.prev();
                     if (prev.length) {
                         prev.before(li);
+                        renumber();
                     }
                 });
                 const downBtn = $("<button class='move-down btn btn-sm' title='Move down'>&#8595;</button>").click(function(e){
@@ -174,20 +196,27 @@
                     const next = li.next();
                     if (next.length) {
                         next.after(li);
+                        renumber();
                     }
                 });
                 $(el).prepend(downBtn).prepend(upBtn);
 
-    // Existing delete button logic
-                $(el).append($(
-                    "<span class='exam-question-delete flex-col'><button title='Remove this question from the exam/collection'>Remove</button></span>"
-                ).click(() => {
-                    el.remove();
-                }));
+                // Prefer server-side HTMX remove button when present; otherwise keep a fallback
+                if ($(el).find('.case-remove').length === 0) {
+                    // fallback: append an inline client-side remove button (for contexts without server-side remove)
+                    $(el).append($(
+                        "<span class='exam-question-delete flex-col'><button title='Remove this question from the exam/collection'>Remove</button></span>"
+                    ).click(() => {
+                        el.remove();
+                        renumber();
+                    }));
+                } else {
+                    // If HTMX remove exists it will handle the server call and swap; renumber after swap via htmx:afterSwap
+                }
             });
 
             $("#full-question-list").after($(
-                "<button title='click and drag questions to change order'>Save exam order</button>"
+                "<button id='save-order-button' class='btn btn-primary btn-sm' title='click and drag questions to change order'>Save exam order</button>"
             ).click(() => {
                 new_order = [];
                 $("#full-question-list li").each((n, el) => {
@@ -208,6 +237,21 @@
 
                         if (data.status == "success") {
                             toastr.info('Exam order changed.')
+                            renumber();
+
+                            // cleanup ordering controls and restore edit button
+                            $('#random-order-button').remove();
+                            $('#save-order-button').remove();
+                            $('#cancel-order-button').remove();
+                            // remove per-item move controls
+                            $('#full-question-list .move-up, #full-question-list .move-down').remove();
+                            // remove fallback delete buttons if desired (keep server-side removes intact)
+                            $('#full-question-list .exam-question-delete').remove();
+                            // remove visual sorting state
+                            $('#full-question-list').removeClass('sorting');
+
+                            // restore the edit button so the user can re-enter edit mode
+                            $('#button-edit-order').removeClass('d-none').prop('disabled', false);
                         }
                     })
                     .always(function () {
@@ -220,6 +264,20 @@
             ).click(() => {
                 location.reload();
             }));
+            // Keep list numbering in sync after HTMX swaps that affect the case list
+            document.body.addEventListener('htmx:afterSwap', function(evt){
+                try {
+                    const target = evt.detail && evt.detail.target ? evt.detail.target : null;
+                    if (!target) return;
+                    if (target.id === 'full-question-list' || (target.closest && target.closest('#full-question-list'))) {
+                        setTimeout(function(){
+                            if (typeof renumber === 'function') renumber();
+                        }, 10);
+                    }
+                } catch(e) {
+                    console.error('htmx afterSwap renumber error', e);
+                }
+            });
         });