.

- 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> /
+    <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 %}
-        <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> /
+                        <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 %}
-    <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 %}
+                    <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>
+
+        <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 %}
+            </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 %}
-            <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>
-                {% 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>
+                            <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>
-        {% endif %}
     </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

@@ -12,6 +12,8 @@ from .models import (
     Structure,
     Subspecialty,
     NormalCase,
+    Resource,
+    Site,
 )
 from django.contrib.auth.models import User
 from django.db.models import Q
@@ -162,13 +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"],
         }
@@ -187,11 +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,
@@ -207,11 +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,
@@ -227,6 +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:
@@ -335,6 +392,25 @@ class NormalCaseFilter(django_filters.FilterSet):
             return queryset
         return queryset.filter(age_days__lte=days)
 
+
+class ResourceFilter(django_filters.FilterSet):
+    name = django_filters.CharFilter(field_name='name', lookup_expr='icontains')
+    site = django_filters.ModelMultipleChoiceFilter(field_name='sites', queryset=lambda request: Site.objects.all() if True else Site.objects.none())
+    subspecialty = django_filters.ModelMultipleChoiceFilter(field_name='subspecialty', queryset=Subspecialty.objects.all())
+    author = django_filters.ModelMultipleChoiceFilter(queryset=get_authors, null_label='No author')
+    has_file = django_filters.BooleanFilter(method='filter_has_file', label='Has file')
+
+    class Meta:
+        model = Resource
+        fields = ('name', 'site', 'subspecialty', 'author')
+
+    def filter_has_file(self, queryset, name, value):
+        if value is True:
+            return queryset.exclude(file__isnull=True).exclude(file__exact='')
+        elif value is False:
+            return queryset.filter(file__isnull=True) | queryset.filter(file__exact='')
+        return queryset
+
 class QuestionSchemaFilter(django_filters.FilterSet):
     class Meta:
         model = QuestionSchema

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:
@@ -142,6 +170,25 @@ class CaseCollectionForm(ModelForm):
         ModelForm.__init__(self, *args, **kwargs)
         super(CaseCollectionForm, self).__init__(*args, **kwargs)
 
+        # Render collection_type as radio buttons and ensure it appears near the top
+        if "collection_type" in self.fields:
+            # Replace the model field with an explicit ChoiceField that uses RadioSelect
+            original = self.fields["collection_type"]
+            choices = getattr(original, "choices", ())
+            initial = original.initial if hasattr(original, "initial") else None
+            required = original.required
+            label = original.label
+            widget = RadioSelect(attrs={"class": "btn-check"})
+            # assign custom template for rendering as button group
+            #widget.template_name = "widgets/radioselect_buttons.html"
+            self.fields["collection_type"] = forms.ChoiceField(
+                choices=choices,
+                widget=widget,
+                initial=initial,
+                required=required,
+                label=label,
+            )
+
         # Identify show_ fields
         show_fields = [f for f in self.fields if f.startswith("show_")]
         show_pre_fields = [f for f in show_fields if f.endswith("_pre")]
@@ -187,6 +234,7 @@ class CaseCollectionForm(ModelForm):
             Fieldset(
                 "Collection Details",
                 "name",
+                Field("collection_type", css_class="mb-2"),
                 Fieldset(
                     "Dates",
                     "restrict_to_dates",
@@ -214,7 +262,6 @@ class CaseCollectionForm(ModelForm):
                 "exam_mode",
                 "self_review",
                 "feedback_once_collection_complete",
-                "collection_type",
                 "viewer_mode",
                 "question_time_limit",
                 "prerequisites",
@@ -294,9 +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"
             ),
         }
@@ -306,14 +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
@@ -665,7 +730,7 @@ CaseDifferentialFormSet = inlineformset_factory(
 class ResourceForm(ModelForm):
     class Meta:
         model = Resource
-        exclude = ["author"]
+        exclude = ["author", "created_date"]
 
         widgets = {
             "description": Textarea(attrs={"cols": 80, "rows": 5}),
@@ -812,7 +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
 
@@ -828,12 +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 = ""
 
@@ -994,6 +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(
@@ -1134,23 +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/0082_resource_sites_resource_subspecialty.py

@@ -0,0 +1,24 @@
+# Generated by Django 5.2.7 on 2025-11-14 20:51
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0081_remove_normalcase_age_years_normalcase_age_days'),
+        ('generic', '0029_add_unique_constraint_supervisor_email'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='resource',
+            name='sites',
+            field=models.ManyToManyField(blank=True, help_text='The site(s) this resource is associated with (if any).', related_name='resources', to='generic.site'),
+        ),
+        migrations.AddField(
+            model_name='resource',
+            name='subspecialty',
+            field=models.ManyToManyField(blank=True, help_text='Subspecialty or subspecialties this resource relates to.', to='atlas.subspecialty'),
+        ),
+    ]

atlas/migrations/0083_resource_created_date_resource_modified_date.py

@@ -0,0 +1,24 @@
+# Generated by Django 5.2.7 on 2025-11-14 21:02
+
+import django.utils.timezone
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0082_resource_sites_resource_subspecialty'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='resource',
+            name='created_date',
+            field=models.DateTimeField(default=django.utils.timezone.now),
+        ),
+        migrations.AddField(
+            model_name='resource',
+            name='modified_date',
+            field=models.DateTimeField(auto_now=True),
+        ),
+    ]

atlas/migrations/0084_resource_open_access.py

@@ -0,0 +1,18 @@
+# Generated by Django 5.2.7 on 2025-11-15 22:38
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0083_resource_created_date_resource_modified_date'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='resource',
+            name='open_access',
+            field=models.BooleanField(default=True, help_text='If true the resource is available to all users, otherwise only in the context of cases.'),
+        ),
+    ]

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

@@ -59,6 +59,7 @@ from generic.models import (
     SeriesBase,
     SeriesImageBase,
     Modality,
+    Site,
     UserUserGroup,
 )
 
@@ -109,36 +110,121 @@ class SynMixin(object):
     #    abstract = True
 
     def __str__(self) -> str:
-        if self.primary:
+        # 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
-        else:
+                return f"{self.name} [syn]"
+            except Exception:
+                # defensive fallback
                 return f"{self.name} [syn]"
 
-    def get_old_str(self) -> str:
-        if self.primary:
-            if self.synonym.count() == 0:
+        # No canonical support: assume primary
         return self.name
+
+    def get_old_str(self) -> str:
+        # 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:
-                synonyms = ",".join([i.name for i in self.synonym.all()])
+            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 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]"
-        else:
-            s = self.synonym.filter(primary=True).values_list("name", flat=True)
+            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:
+        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]"
-        else:
-            syns = self.synonym.filter(primary=True)
-            return ", ".join(
-                [f"<a href='{s.get_absolute_url()}'>{s.name}</a>" for s in syns]
-            )
+            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)
@@ -146,21 +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",
@@ -171,10 +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",
@@ -197,6 +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()
 
@@ -275,14 +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):
@@ -1442,6 +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)
 
@@ -1544,7 +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")
@@ -1563,10 +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)
@@ -1875,6 +2027,27 @@ class Resource(models.Model, AuthorMixin):
         help_text="Author of the resource",
         related_name="resources",
     )
+    created_date = models.DateTimeField(default=timezone.now)
+    modified_date = models.DateTimeField(auto_now=True)
+    # Link resources to one or more Sites (from generic.Site)
+    sites = models.ManyToManyField(
+        'generic.Site',
+        blank=True,
+        help_text='The site(s) this resource is associated with (if any).',
+        related_name='resources',
+    )
+
+    # Categorise resources by subspecialty
+    subspecialty = models.ManyToManyField(
+        Subspecialty,
+        blank=True,
+        help_text='Subspecialty or subspecialties this resource relates to.',
+    )
+
+    open_access = models.BooleanField(
+        default=True, 
+        help_text="If true the resource is available to all users, otherwise only in the context of cases."
+    )
 
     def __str__(self) -> str:
         return self.name
@@ -1902,7 +2075,18 @@ class Resource(models.Model, AuthorMixin):
         else:
             html =  self.name
 
-        return format_html("<details class='resource-block'><summary>{}</summary>{}</details>", self.name, mark_safe(html))
+        meta = ''
+        if self.sites.exists():
+            meta += ' Sites: ' + ', '.join([s.short_code or s.full_name for s in self.sites.all()])
+        if self.subspecialty.exists():
+            meta += ' Subspecialty: ' + ', '.join([str(s) for s in self.subspecialty.all()])
+
+        return format_html(
+            "<details class='resource-block'><summary>{}</summary><div>{}</div><div class='text-muted small'>{}</div></details>",
+            self.name,
+            mark_safe(html),
+            meta,
+        )
 
 
 

atlas/tables.py

@@ -14,6 +14,7 @@ from .models import (
     Structure,
     Finding,
     Subspecialty,
+    Resource,
 )
 
 from django.utils.html import format_html
@@ -275,7 +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",)
 
 
@@ -311,7 +312,7 @@ class FindingTable(SelectionTable):
     class Meta(SelectionTable.Meta):
         model = Finding
         template_name = "django_tables2/bootstrap4.html"
-        fields = ("name", "primary")
+        fields = ("name",)
         sequence = ("name",)
 
 
@@ -338,7 +339,7 @@ class StructureTable(SelectionTable):
     class Meta(SelectionTable.Meta):
         model = Structure
         template_name = "django_tables2/bootstrap4.html"
-        fields = ("name", "primary")
+        fields = ("name",)
         sequence = ("name",)
 
 
@@ -414,6 +415,18 @@ class SubspecialtyTable(SelectionTable):
         return format_html(record.get_synonym_link())
         return f"{record.get_synonym_link()}"
 
+
+class ResourceTable(SelectionTable):
+    name = tables.Column(linkify=("atlas:resource_detail", {"pk": tables.A("pk")}), verbose_name="Resource")
+
+    edit = tables.LinkColumn("atlas:resource_update", text="Edit", args=[A("pk")], orderable=False)
+    delete = tables.LinkColumn("atlas:resource_delete", text="Delete", args=[A("pk")], orderable=False)
+
+    class Meta(SelectionTable.Meta):
+        model = Resource
+        template_name = "django_tables2/bootstrap4.html"
+        fields = ("name", "description")
+
 class CaseCollectionTable(SelectionTable):
     edit = tables.LinkColumn(
         "atlas:exam_update", text="Edit", args=[A("pk")], orderable=False

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

@@ -66,11 +66,46 @@
                                 </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">
-                            <a class="nav-link" href="{% url 'atlas:resource_view' %}" title="Resources"><i class="bi bi-folder2-open me-1" aria-hidden="true"></i>Resources</a>
+                        <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>
+                            <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:resource_view' %}"><i class="bi bi-list-ul me-1" aria-hidden="true"></i>Manage Resources</a>
+                                </li>
+                                <li>
+                                    <a class="dropdown-item" href="{% url 'atlas:resource_create' %}"><i class="bi bi-plus-square me-1" aria-hidden="true"></i>Create Resource</a>
+                                </li>
+                            </ul>
                         </li>
                         
                         <li class="nav-item">

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/casecollection_form.html

@@ -3,6 +3,40 @@
 {% load crispy_forms_tags %}
 
 {% block css %}
+<style>
+    /* Turn the existing form-check radio markup into horizontal button-like radios */
+    #div_id_collection_type .form-check { display: inline-block; margin-right: .5rem; }
+    #div_id_collection_type .form-check-input {
+        /* visually hide the native radio but keep it focusable */
+        position: absolute;
+        width: 1px;
+        height: 1px;
+        padding: 0;
+        margin: -1px;
+        overflow: hidden;
+        clip: rect(0,0,0,0);
+        white-space: nowrap;
+        border: 0;
+    }
+    #div_id_collection_type .form-check-label {
+        display: inline-block;
+        padding: .375rem .75rem;
+        border: 1px solid #0d6efd;
+        border-radius: .375rem;
+        color: #0d6efd;
+        cursor: pointer;
+        user-select: none;
+    }
+    #div_id_collection_type .form-check-input:focus + .form-check-label {
+        box-shadow: 0 0 0 .25rem rgba(13,110,253,.25);
+    }
+    #div_id_collection_type .form-check-input:checked + .form-check-label {
+        background-color: #0d6efd;
+        color: #fff;
+    }
+    /* small spacing tweak when legend present */
+    #div_id_collection_type fieldset { border: 0; padding: 0; margin: 0 0 1rem 0; }
+</style>
 {% endblock %}
 {% block js %}
     <!--<script type="text/javascript" src="/admin/jsi18n/"></script>-->

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

@@ -3,13 +3,14 @@
 
 
 {% block content %}
+    {% 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}}"
+    <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 case_detail.default_viewerstate %}
-           data-viewerstate={{ case_detail.default_viewerstate }} 
+         {% if casedetail.default_viewerstate %}
+             data-viewerstate={{ casedetail.default_viewerstate }}
          {% endif %}
 
     ></div>
@@ -29,7 +30,7 @@ document.getElementById('save-viewerstate').addEventListener('click', function()
                 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 %}", {
+            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",
@@ -46,7 +47,7 @@ document.getElementById('save-viewerstate').addEventListener('click', function()
                 });
         });
         document.getElementById('reset-viewerstate').addEventListener('click', function() {
-    fetch("{% url 'atlas:collection_case_displaysetup' case_detail.collection.pk case_detail.case.pk %}", {
+            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",

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

@@ -2,8 +2,11 @@
 {% 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>
+
+    <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}}
@@ -11,19 +14,36 @@
 
 
                 {% if question_completed %}
-            <span class="stamp-white">REVIEW</span>
+                    <span class="badge bg-warning text-dark ms-2 small">REVIEW</span>
                 {% endif %}
 
-
             </h2>
+        </div>
+
+        <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:
+        <details class="card mb-3">
+            <summary class="card-header p-2" style="cursor: pointer;">
+                <strong>Discussion</strong>
             </summary>
-                <div>
+            <div class="card-body p-2 small">
                 {{case.discussion|linebreaks}}
             </div>
         </details>
-        </p>
     {% endif %}
     {% if show_report and case.report %}
-        <p>
-            <details>
-                <summary>
-                    Report:
+        <details class="card mb-3">
+            <summary class="card-header p-2" style="cursor: pointer;">
+                <strong>Report</strong>
             </summary>
-                <div>
+            <div class="card-body p-2 small">
                 {{case.report|linebreaks}}
             </div>
         </details>
-        </p>
     {% endif %}
 
     {% if question_completed %}
@@ -246,25 +267,28 @@
             {% endif %}
 
         {% endif %}
+        <div class="mb-2">
             {% if previous %}
-            <button type="submit" name="previous" class="save btn btn-default">Previous</button>
+                <button type="submit" name="previous" class="btn btn-outline-secondary btn-sm me-2">Previous</button>
             {% endif %}
             {% if next %}
-            <button type="submit" name="next" class="save btn btn-default">Next</button>
+                <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="save btn btn-default">Save</button>
+                    <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>
+        <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

@@ -4,7 +4,7 @@
 {% block content %}
 
     <h2>Case: {{ case.title }}</h2>
-{{ case_detail.question_schema }}
+    {{ casedetail.question_schema }}
 
 
     {{ case.question_answers }}

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>
+
+<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>
 
                     {% include 'exam_notes.html' %}
 
-    <div>
-        Exam mode: {{collection.exam_mode}} (open access: {{collection.exam_open_access}})<br />
+                    <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" %}
-        Collection Type: {{collection.get_collection_type_display}}<br />
-        Self review: {{collection.self_review}}<br />
-        Open access: {{collection.open_access}}<br />
+                    </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 %}
-            Prerequisite collections:
-            <ul>
+                        <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>
-                        &nbsp;
-                    </li>
+                                    <li><a href="{% url 'atlas:collection_detail' prereq.pk %}">{{ prereq.name }}</a></li>
                                 {% endfor %}
                             </ul>
+                        </div>
+                    {% endif %}
+                </div>
 
-        <p>
+                <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>
-        </p>
+                        </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">
+            <ol id="full-question-list" class="sortable list-group list-group-numbered">
                 {% 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>
-
+                    {% 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'
+        <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>
+
+                <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">
+                             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 id='case-list'></div>
-        </p>
 
+                <div id='case-list'></div>
+            </div>
+        </div>
+
+        <div class="row mt-3">
+            <div class="col-12">
                 <details>
                     <summary>Answer management</summary>
 
-            <div class="alert alert-danger">
-                <p>Manage answers for this collection. </p>
-
-                Please note these are permanant and cannot be undone.
+                    <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>
 
+                    <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"
-            >Reset user answers</button>
-            <div id="user-list"></div>
+                                        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

@@ -1,20 +1,43 @@
-{% if request.user.is_authenticated %}
-    Collection: {{collection.name}}-> <a href="{% url 'atlas:collection_detail' pk=collection.pk %}">Overview</a> /
-    <a href="{% url 'atlas:collection_case_update' collection.pk %}">Cases</a> /
-    <a href="{% url 'atlas:collection_history' collection.pk %}">History</a> /
-    <a href="{% url 'atlas:collection_mark_overview' collection.pk %}">Mark</a> /
-    <a href="{% url 'atlas:collection_scores_cid' collection.pk %}">Scores</a> /
-    <a href="{% url 'atlas:exam_cids' collection.pk %}">Candidates</a> /
-    <a href="{% url 'atlas:atlas_create_exam' pk=collection.pk %}">Add New Case</a> /
-    <div class="floating-header">
-        <a href="{% url 'atlas:exam_update' collection.id %}" title="Edit the Collection">Edit</a>
-        \ <a href="{% url 'atlas:exam_deleted' collection.id %}" title="Delete the Collection">Delete</a>
-        \ <a href="{% url 'atlas:exam_clone' collection.id %}" title="Clone the Collection">Clone</a>
-        \ <a href="{% url 'atlas:collection_authors' collection.pk %}" title="Edit Authors">Authors</a>
+{% if request.user.is_authenticated and collection %}
+<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>Collection:</strong> {{ collection.name }}
+        </span>
+        <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#collectionNav" aria-controls="collectionNav" aria-expanded="false" aria-label="Toggle navigation">
+            <span class="navbar-toggler-icon"></span>
+        </button>
 
+        <div class="collapse navbar-collapse" id="collectionNav">
+            <ul class="navbar-nav me-auto mb-2 mb-lg-0">
+                <li class="nav-item"><a class="nav-link" href="{% url 'atlas:collection_detail' pk=collection.pk %}">Overview</a></li>
+                <li class="nav-item"><a class="nav-link" href="{% url 'atlas:collection_case_update' collection.pk %}">Cases</a></li>
+                <li class="nav-item"><a class="nav-link" href="{% url 'atlas:collection_history' collection.pk %}">History</a></li>
+                <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>
+            </ul>
+
+            <ul class="navbar-nav ms-auto">
+                <li class="nav-item dropdown">
+                    <a class="nav-link dropdown-toggle" href="#" id="collectionActions" role="button" data-bs-toggle="dropdown" aria-expanded="false">Actions</a>
+                                <ul class="dropdown-menu dropdown-menu-end dropdown-menu-dark" aria-labelledby="collectionActions">
+                        <li><a class="dropdown-item" href="{% url 'atlas:collection_case_update' collection.pk %}">Edit Cases</a></li>
+                        <li><a class="dropdown-item" href="{% url 'atlas:exam_update' collection.id %}">Edit</a></li>
+                        <li><a class="dropdown-item" href="{% url 'atlas:exam_clone' collection.id %}">Clone</a></li>
+                        <li><a class="dropdown-item" href="{% url 'atlas:collection_authors' collection.pk %}">Authors</a></li>
+                        <li><hr class="dropdown-divider"></li>
+                                    <li><a class="dropdown-item text-danger" href="{% url 'atlas:exam_deleted' collection.id %}">Delete</a></li>
                         {% if request.user.is_superuser %}
-            \ <a href="{% url 'admin:atlas_casecollection_change' collection.id %}" title="Edit the Collection using the admin interface">Admin Edit</a>
+                            <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>
+            </ul>
         </div>
+    </div>
+</nav>
 {% endif %}
 

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 }} -->
 {% endblock %}
+
 {% block content %}
     <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/exams.html

@@ -7,9 +7,6 @@
     {% if collection %}
         {% include "atlas/collection_headers.html" %}
     {% endif %}
-    {% if exam %}
-        <a href="{% url 'atlas:exam_review_start' pk=exam.pk %}">Review</a> /
-    {% endif %}
 {% comment %}     Collection: {{collection.name}}-> <a href="{% url 'atlas:collection_detail' pk=exam.pk %}">Overview</a> /
     <a href="{% url 'atlas:collection_mark_overview' exam.pk %}">Mark</a> /
     <a href="{% url 'atlas:collection_scores_cid' exam.pk %}">Scores</a> /

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_cases_list.html

@@ -0,0 +1,17 @@
+{# Partial: series cases list. Expects `series` and `can_edit` in context. Returns the <ul> that is inserted into #cases-list. #}
+<ul class="list-group list-group-flush">
+    {% for case in series.case.all %}
+        <li id="case-link-{{ case.pk }}" class="list-group-item d-flex justify-content-between align-items-center case-item">
+            <a href="{% url 'atlas:case_detail' pk=case.pk %}">{{case}}</a>
+            {% if can_edit %}
+                <button hx-post="{% url 'atlas:remove_series_from_case' series.pk case.pk %}"
+                        hx-target="#cases-list"
+                        hx-swap="innerHTML"
+                        hx-confirm="Are you sure you want to remove this series from the case?"
+                        class="btn btn-link btn-sm text-danger remove-button">Remove</button>
+            {% endif %}
+        </li>
+    {% empty %}
+        <li class="list-group-item">This series is not associated with any cases.</li>
+    {% endfor %}
+</ul>

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>
 
+    </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>
+        {% include 'atlas/partials/_viewing_case_as_part_of_collection.html' with nav_link_view="atlas:collection_case_view" %}
     {% 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>

atlas/templates/atlas/resource_detail.html

@@ -5,32 +5,100 @@
         {% include "atlas/resource_link_header.html" %}
     {% endif %}
 
-    {{resource}}
+    <div class="container mt-3">
+        <div class="row">
+            <div class="col-lg-8">
+                <div class="card mb-3">
+                    <div class="card-header d-flex justify-content-between align-items-center">
+                        <h5 class="mb-0">{{ resource.name }}</h5>
+                        <small class="text-muted">by {{ resource.get_authors|default:"Unknown" }}</small>
+                    </div>
+                    <div class="card-body">
+                        {% if resource.description %}
+                            <p class="card-text">{{ resource.description|linebreaksbr }}</p>
+                        {% endif %}
 
-    Name: {{resource.name}}<br>
-    Description: {{resource.description}}<br>
-    URL: {{resource.url}}<br>
-    file: {{resource.file}}<br>
-    author: {{resource.get_authors}}<br>
+                        <dl class="row">
+                            {% if resource.url %}
+                                <dt class="col-sm-3">URL</dt>
+                                <dd class="col-sm-9"><a href="{{ resource.url }}" target="_blank" rel="noopener">{{ resource.url }}</a></dd>
+                            {% endif %}
 
-    {{resource.case}}
+                            {% if resource.file %}
+                                <dt class="col-sm-3">File</dt>
+                                <dd class="col-sm-9">
+                                    <a href="{{ resource.file.url }}" target="_blank" rel="noopener">Download</a>
+                                    {% if resource.file.name %}
+                                            <small class="text-muted ms-2">({{ resource.file.name|truncatechars:40 }})</small>
+                                    {% endif %}
+                                </dd>
+                            {% endif %}
 
-    <div>
-        <a href="{% url 'atlas:resource_view' resource.pk %}" target="_blank">View Resource</a>
+                            <dt class="col-sm-3">Source</dt>
+                            <dd class="col-sm-9">{{ resource.get_display }}</dd>
+                        </dl>
+
+                        <div class="mt-3">
+                            <a class="btn btn-sm btn-outline-primary" href="{% url 'atlas:resource_view' resource.pk %}" target="_blank">Open resource page</a>
+                        </div>
+                    </div>
                 </div>
 
+                <div class="card">
+                    <div class="card-header">
+                        <h6 class="mb-0">Used in cases</h6>
+                    </div>
+                    <div class="card-body">
                         {% if resource.case_set.all %}
-    <h3>Cases</h3>
-    This resource is used in the following cases:
-
-    <ul>
+                            <ul class="list-unstyled mb-0">
                                 {% for case in resource.case_set.all %}
                                     <li><a href="{% url 'atlas:case_detail' case.id %}">{{ case.title }}</a></li>
                                 {% endfor %}
                             </ul>
                         {% else %}
-    <p>This resource is not used in any cases.</p>
+                            <p class="mb-0 text-muted">This resource is not used in any cases.</p>
                         {% endif %}
+                    </div>
+                </div>
+            </div>
 
+            <div class="col-lg-4">
+                <aside class="card mb-3">
+                    <div class="card-body">
+                        <h6 class="card-title">Details</h6>
+                        <ul class="list-unstyled small mb-0">
+                            <li><strong>Author:</strong> {{ resource.get_authors|default:"-" }}</li>
+                            <li><strong>Sites:</strong>
+                                {% if resource.sites.all %}
+                                    {% for s in resource.sites.all %}
+                                        <div><a href="{% url 'generic:site_detail' s.pk %}">{{ s.name }}</a></div>
+                                    {% endfor %}
+                                {% else %}
+                                    -
+                                {% endif %}
+                            </li>
+                            <li class="mt-2"><strong>Subspecialty:</strong>
+                                {% if resource.subspecialty.all %}
+                                    {% for sp in resource.subspecialty.all %}
+                                        <div>{{ sp.name }}</div>
+                                    {% endfor %}
+                                {% else %}
+                                    -
+                                {% endif %}
+                            </li>
+                            <li class="mt-2"><strong>Created:</strong> {{ resource.created_date|date:"Y-m-d H:i" }}</li>
+                            <li><strong>Updated:</strong> {{ resource.modified_date|date:"Y-m-d H:i" }}</li>
+                        </ul>
+                    </div>
+                </aside>
+
+                <div class="d-grid gap-2">
+                    <a class="btn btn-primary" href="{% url 'atlas:resource_update' resource.pk %}">Edit</a>
+                    <a class="btn btn-outline-danger" href="{% url 'atlas:resource_delete' resource.pk %}">Delete</a>
+                    <a class="btn btn-outline-secondary" href="{% url 'atlas:resource_view' %}">Back to resources</a>
+                </div>
+            </div>
+        </div>
+    </div>
 
 {% endblock %}

atlas/templates/atlas/resource_list.html

@@ -1,16 +1,15 @@
 {% extends 'atlas/base.html' %}
+{% load render_table from django_tables2 %}
 {% block content %}
-<a href="{% url 'atlas:resource_create' %}">Create a new resource</a>
 
     <h2>Resources</h2>
 
-    <ul id="resource-list">
-        {% for resource in object_list %}
-            <li class="">
-                <a href="{% url 'atlas:resource_detail' resource.pk %}">{{resource}}</a>
-            </li>
-        {% endfor %}
-    </ul>
+    <form>
+        {% render_table table %}
+    </form>
+
+    {% include "generic/partials/page_size_form.html" %}
+    {% include "generic/partials/filter_bar.html" with filter=filter app_name=app_name collapse_id="bottom-filter-body" %}
 
 {% endblock %}
 

atlas/templates/atlas/series_viewer.html

@@ -1,225 +1,223 @@
 {% load crispy_forms_tags %}
-
-<div>{{ series.modality}}, {{ series.examination }}, {{ series.plane }}, {{ series.contrast }}</div>
-<div>Description: {{series.description}}</div>
-
-Associated case:
-{% for case in series.case.all %}
-    <span id="case-link-{{ case.pk }}" class="case-item">
-        <a href="{% url 'atlas:case_detail' pk=case.pk %}">{{case}}</a>
-        {% if can_edit %}
-            <button hx-post="{% url 'atlas:remove_series_from_case' series.pk case.pk %}"
-                    hx-target="#case-link-{{ case.pk }}"
-                    hx-swap="outerHTML"
-                    hx-confirm="Are you sure you want to remove this series from the case?"
-                    class="btn btn-link btn-sm button-unset remove-button">
-                Remove
-            </button>
-        {% endif %}
-    </span>
-{% empty %}
-    This series is not associated with any cases.
-    {% if can_edit %}
-        <details>
-            <summary>Add Series to Case</summary>
-            <form hx-post="{% url 'atlas:add_series_to_case' series.pk %}"
-                  hx-target="#add-series-to-case-result"
-                  hx-swap="innerHTML">
-                {% csrf_token %}
-                <label for="case-select">Select Case:</label>
-                <select name="case_id" id="case-select" required>
-                    {% for case in available_cases %}
-                        <option value="{{ case.pk }}">{{ case.title }}</option>
-                    {% endfor %}
-                </select>
-                <button type="submit" class="btn btn-primary">Add to Case</button>
-            </form>
-            <div id="add-series-to-case-result"></div>
-        </details>
-    {% endif %}
-{% endfor %}
-<div>Author: {{ series.get_author_display }}</div>
-
 {% with image_url_array_and_count=series.get_image_url_array_and_count %}
-{% comment %}     <div id="single-dicom-viewer" class="dicom-viewer" data-images="{{ image_url_array_and_count.0 }}" data-annotations=''>
-    </div> {% endcomment %}
-
-    <div id="root" class="dicom-viewer-root" data-images="{{ image_url_array_and_count.0 }}"
-         style="max-width: 1000px; height: 600px; box-sizing: border-box; background: #222;"
-         data-auto-cache-stack=false
-    ></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 %}
-        {% if editing_finding < 1 %}
-            <button id="add-finding-button">Add finding</button>
-            <button id="clone-finding-button" title="Click to copy the details of a finding that is already associated with the series/case"
+                                <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>
+            </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 existing finding</button>
+                                    data-bs-target="#clone-findings-modal">Clone finding</button>
                         {% endif %}
-        <button id="reset-viewport-button" class="btn btn-secondary">Reset viewport</button>
+                        <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 %}
-                    <h3>Editing Finding</h3>
-                    <p>Editing finding with ID: {{editing_finding}}</p>
+                                        <h5>Editing Finding</h5>
+                                        <p class="small">Editing finding with ID: {{editing_finding}}</p>
                                     {% else %}
-                    <h3>Add Finding</h3>
-                    <p>Click the button below to add a new finding.</p>
+                                        <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}}
-                    <input type="submit" value="Submit" class="btn btn-lg btn-success fw-bold px-4 py-2" style="font-size: 1.2rem;">
-                    <button id="cancel-add-finding-button">Cancel</button>
+                                        <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>
-    {% else %}
-        <button id="reset-viewport-button">Reset viewport</button>
-    {% endif %}
-
+                        </div>
+                    </div>
                     <details class="styled-detail open">
                         <summary>Findings</summary>
-
+                        <div class="mt-2">
                             {% for finding in series.findings.all %}
-            <div class="finding-box">
-                <button id="finding-{{finding.pk}}-3d" class="view-finding-button-3d" data-annotationjson3d='{{finding.annotation_json_3d}}' data-viewerstatejson='{{finding.viewer_state_3d}}' data-findingid='{{finding.pk}}'>Click to view</button>
-
-                <span class="view-finding-details">
-                    Finding(s): {% for f in finding.findings.all %}{{f.get_link}}{% endfor %}<br />
-                    Structure(s): {% for s in finding.structures.all %}{{s.get_link}}{% endfor %}<br />
-                    Condition(s): {% for s in finding.conditions.all %}{{s.get_link}}{% endfor %}<br />
-                    Description: {{finding.description}}<br />
-
+                                <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 %}
-                        <span _="on click toggle .hidden on next .extra-details">+</span>
-                        <div class="hidden extra-details">
-                            <h4>Annotation JSON</h4>
-                    <pre>{{finding.annotation_json}}</pre>
-                            <h4>Viewport JSON</h4>
-                    <pre>{{finding.viewport_json}}</pre>
-                            <h4>Image ID</h4>
-                    <pre>{{finding.current_image_id_index}}</pre>
-
-                            <h4>3D Annotation JSON</h4>
-                    <pre>{{finding.annotation_json_3d}}</pre>
-                            <h4>Viewer State</h4>
-                    <pre>{{finding.viewer_state_3d}}</pre>
+                                                <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 %}
-                </span>
                                             {% if can_edit %}
-                    <a href="{% url 'atlas:series_edit_finding' pk=series.pk finding_pk=finding.pk %}" class="edit-finding-link">Edit</a>
-                    <a href="{% url 'atlas:delete_finding' pk=finding.pk %}" class="delete-finding-link">Delete</a>
+                                                <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>No findings available.</p>
+                                <p class="text-muted">No findings available.</p>
                             {% endfor %}
+                        </div>
                     </details>
-
-    {% if can_edit %}
-        <details class="styled-detail">
-            <summary>Truncate series</summary>
-            <p>
-                This will limit the series to the selected bounds (the rest of the images will be deleted). This is useful when you have a large volume of which only a small area is relevant to the case. NOTE: once deleted the images cannot be recovered on the site (they would have to be reuploaded if required). Make sure your images are shown in the correct order above and use test the test truncate button first.
-            </p>
-            <div role="alert" class="alert alert-warning">
-                <strong>Warning:</strong> Please note: if you have reordered the series this may result in the incorrect images being deleted.
                 </div>
 
-            Start <input id="lower-truncation-bound-input" type="number" value="1"> <button id="set-lower-truncation-bound-button">Set</button><br/>
-            End <input  id="upper-truncation-bound-input"type="number" value="{{image_url_array_and_count.1}}"> <button id="set-upper-truncation-bound-button">Set</button><br/>
-            <button id="truncate-test-button">Test truncate</button>
-            <button id="truncate-button">Trucate series</button>
-            <div id="truncate-output"></div>
-
-        </details>
-    {% endif %}
-{% endwith %}
-
-
-
-{% if can_edit %}
-    <details class="styled-detail">
-        <summary>Series info</summary>
-        <div class="d-flex flex-wrap gap-2 mb-2">
-            <button type="button" class="btn btn-outline-primary btn-sm" onclick="window.location.href='{% url 'atlas:series_anonymise_dicom' pk=series.pk %}'" title="Anonymise dicom images">
-                Anonymise dicoms
-            </button>
-            <button type="button" class="btn btn-outline-primary btn-sm" onclick="window.location.href='{% url 'atlas:series_order_dicom' pk=series.pk %}'" title="orders dicom by slice location">
-                Order by slice location
-            </button>
-            <button type="button" class="btn btn-outline-primary btn-sm" onclick="window.location.href='{% url 'atlas:series_order_dicom_instance' pk=series.pk %}'" title="orders dicom by instance number">
-                Order by instance number
-            </button>
-            <button type="button" class="btn btn-outline-primary btn-sm" onclick="window.location.href='{% url 'atlas:series_order_dicom_SeriesInstanceUID' pk=series.pk %}'" title="orders dicom by SeriesInstanceUID">
-                Order by SeriesInstanceUID
-            </button>
-            <button type="button" class="btn btn-outline-primary btn-sm" onclick="window.location.href='{% url 'atlas:series_order_upload_filename' pk=series.pk %}'" title="orders dicom by uploaded filename">
-                Order by uploaded filename
-            </button>
-            <button type="button" class="btn btn-outline-warning btn-sm" onclick="window.location.href='{% url 'api-1:series_split_by_tag' series.pk 'ImageType' %}'" title="split series by dicom tag ImageType">
-                Split by ImageType tag
+            <!-- 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>
-        <details>
-            <summary>
-                Image details
-            </summary>
-            <form  hx-post="{% url 'atlas:image_diff' %}"
-                  hx-target="#temp"
-            >
-                {% for image in series.get_images %}
-                    [{{  image.id  }}] <a href='{% url "atlas:series_image_dicom" image.pk %}'>{{image.image.url}}</a>, pos: {{image.position}}, {{image.upload_filename}}
-                    {% if image.image %}
-                        [{{image.get_file_size|filesizeformat}}]
-                    {% endif %}
-                    {{image.image_md5_hash}} ({{image.is_dicom}}) {{image.image_blake3_hash}}
-                    <input type="checkbox" name="image-id" value="{{image.id}}">
-                    <br />
+                    </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 %}
+                            <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 %}
-                <button>Diff files</button>
+                                        </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>
-            <span id="temp"></span>
-
-            <span id="diff-controls">show <span id="diff-show-all" _="on click
-                                                                      log '1'
-                                                                      for row in .diff.rows
-                                                                      show row
-                                                                      end">all</span> <span id="diff-show-diff" _="
-                                                             on click
-                                                             log 'go'
-                                                             for row in <.diff tr/>
-                                                             log row.children[0].innerHTML
-                                                             if row.children[0].innerHTML is empty
-                                                             hide row
-                                                             end
-                                                             end
-                                                            ">diff</span></span>
-
-        </details>
-
-        <p>Total image size: {{series.get_total_image_size|filesizeformat}}</p>
-        <p>
-            <button type="button" class="btn btn-outline-success btn-sm" onclick="window.location.href='{% url 'atlas:series_download' pk=series.pk %}'">
-                Download images
-            </button>
-        </p>
                             </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>
 
 
-<div id="clone-findings-modal"
-     class="modal modal-blur fade"
-     style="display: none"
-     aria-hidden="false"
-     tabindex="-1">
+
+                {% 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 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>
@@ -359,6 +357,8 @@ Associated case:
         });
     </script>
 
+{% endwith %}
+
 <style>
     .case-item {
         transition: background-color 0.3s ease;

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/templates/widgets/radioselect_buttons.html

@@ -0,0 +1,24 @@
+{% load i18n %}
+<div class="btn-group" role="group" aria-label="{{ widget.name }}">
+  {% for val, label in widget.choices %}
+    {% with forloop.counter0 as idx %}
+      {% with id=widget.name|add:"_"|add:idx %}
+      <input
+        type="radio"
+        class="btn-check"
+        name="{{ widget.name }}"
+        id="{{ widget.name }}_{{ idx }}"
+        value="{{ val }}"
+        {% if val|stringformat:"s" == widget.value|stringformat:"s" %}checked{% endif %}
+        autocomplete="off"
+      >
+      <label
+        class="btn btn-outline-primary {% if val|stringformat:"s" == widget.value|stringformat:"s" %}active{% endif %}"
+        for="{{ widget.name }}_{{ idx }}"
+      >
+        {{ label }}
+      </label>
+      {% endwith %}
+    {% endwith %}
+  {% endfor %}
+</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>
+                                <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 %}
-                                    <span class="question-feedback">{{question.a_feedback}}</span>
+                                                    <div class="text-muted small">Feedback: {{ question.a_feedback }}</div>
                                                 {% endif %}
+                                            </div>
                                         </li>
-                            <li class="question-b">
-                                <span class="question-text">{{ question.b }}</span>: <span class="question-answer">{{ question.b_answer }}</span>
+                                        <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 %}
-                                    <span class="question-feedback">{{question.b_feedback}}</span>
+                                                    <div class="text-muted small">Feedback: {{ question.b_feedback }}</div>
                                                 {% endif %}
+                                            </div>
                                         </li>
-                            <li class="question-c">
-                                <span class="question-text">{{ question.c }}</span>: <span class="question-answer">{{ question.c_answer }}</span>
+                                        <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 %}
-                                    <span class="question-feedback">{{question.c_feedback}}</span>
+                                                    <div class="text-muted small">Feedback: {{ question.c_feedback }}</div>
                                                 {% endif %}
+                                            </div>
                                         </li>
-                            <li class="question-d">
-                                <span class="question-text">{{ question.d }}</span>: <span class="question-answer">{{ question.d_answer }}</span>
+                                        <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 %}
-                                    <span class="question-feedback">{{question.d_feedback}}</span>
+                                                    <div class="text-muted small">Feedback: {{ question.d_feedback }}</div>
                                                 {% endif %}
+                                            </div>
                                         </li>
-                            <li class="question-e">
-                                <span class="question-text">{{ question.e }}</span>: <span class="question-answer">{{ question.e_answer }}</span>
+                                        <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 %}
-                                    <span class="question-feedback">{{question.e_feedback}}</span>
+                                                    <div class="text-muted small">Feedback: {{ question.e_feedback }}</div>
                                                 {% endif %}
+                                            </div>
                                         </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>
 
+                                <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

@@ -58,21 +58,7 @@
            - 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;
@@ -86,7 +72,6 @@
             --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

@@ -2,10 +2,26 @@
 
 {% 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> /
+    <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> /
+    <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 %}
-        <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> /
+                        <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 %}
-    <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>
+                    <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> /
+    <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 %}
-        <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> /
+                        <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 %}
-    <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>
+                    <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"