Merge branch 'dockerprod' into master

.env.dev

@@ -0,0 +1,23 @@
+# 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=8080
+# Pick a non-privileged HTTPS port to avoid conflicts with host installs
+NGINX_HTTPS_PORT=8444

.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

@@ -11,4 +11,10 @@ venv
 
 *.log
 
-temp/
+temp/
+
+# Loki runtime data
+/docker/loki-data/
+/docker/loki-wal/
+# Local runtime logs collected by Promtail
+/logs/

README.md

@@ -0,0 +1,55 @@
+README
+======
+
+Quick notes for running this repository (development & observability)
+
+Running locally (development)
+- Use the included compose files. To run the dev stack (overrides) set `COMPOSE_ENV=dev` so the correct env file is loaded:
+
+  ```sh
+  # run nginx on non-privileged ports (see .env.dev)
+  COMPOSE_ENV=dev docker compose -f docker/docker-compose.prod.yml -f docker/docker-compose.dev.yml up -d --build
+  ```
+
+- By default the development nginx ports are set in `.env.dev` to avoid colliding with a host nginx. The defaults now are:
+  - `NGINX_HTTP_PORT=8080`
+  - `NGINX_HTTPS_PORT=8444`
+
+Logging & observability (Loki + Promtail + Grafana)
+- Promtail is configured to scrape `/var/log/rad/*.log` and push to Loki. Promtail's config is at `docker/promtail-config.yml` and the Loki config is at `docker/loki-config/local-config.yaml`.
+- The nginx configs (both `deploy/nginx/prod.conf` and `deploy/nginx/dev.conf`) are configured to write access and error logs to `/var/log/rad/nginx.access.log` and `/var/log/rad/nginx.error.log` respectively.
+- The compose files mount a host `logs/` folder into `/var/log/rad` so both nginx (write) and promtail (read) can access the same files:
+  - `../logs:/var/log/rad:rw` (nginx)
+  - `../logs:/var/log/rad:ro` (promtail)
+
+Host setup for logs
+- Create the host logs folder at the repo root (this repo's `logs/`). In development you can use permissive permissions so containers can write to it quickly:
+
+  ```sh
+  mkdir -p logs
+  # development: make writable by all (change this for production)
+  sudo chown $USER:$USER logs
+  chmod 0777 logs
+  ```
+
+- In production prefer setting the folder owner to the nginx worker UID (or run nginx under a specific user) and use `0755` or `0750` as appropriate. Example:
+
+  ```sh
+  # run on the host (determine nginx UID as needed)
+  sudo chown -R 101:101 /srv/rad/logs
+  sudo chmod 0755 /srv/rad/logs
+  ```
+
+Viewing logs in Grafana
+- Grafana is available on the port exposed by compose (default `3000`).
+- The Loki datasource is configured to use `http://loki:3100` (see compose). In Grafana Explore choose the Loki datasource and run queries such as:
+
+  - `{job="rad_app"}`  (all collected logs)
+  - `{job="rad_app", filename="/var/log/rad/nginx.access.log"}`
+
+Notes & recommendations
+- In development the `logs/` folder is ignored by git (`/.gitignore` updated). Do not commit runtime logs.
+- Consider a log rotation/retention policy for production (e.g., `logrotate` or use Loki retention policies).
+- If you need nginx to re-resolve the backend service IP without restarting, consider using `resolver` and variable-based upstreams in the nginx config. For many development workflows restarting nginx after web restarts is the simplest approach.
+
+If you want, I can also add a short `docs/OBSERVABILITY.md` with more details and recommended production settings (TLS/auth for Loki, retention, log rotation).

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):

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/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/series_viewer.html

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

atlas/urls.py

@@ -457,6 +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"),

atlas/views.py

@@ -796,6 +796,17 @@ def series_detail(request, pk, finding_pk=None):
     )
 
 
+@login_required
+@user_is_author_or_atlas_series_checker_or_atlas_marker_or_open_access
+def series_images_partial(request, pk):
+    """Return a small fragment that lists images for a series. Intended for HTMX."""
+    series = get_object_or_404(Series, pk=pk)
+    logger.debug(series)
+    images = series.images.filter(removed=False).order_by("pk")
+    logger.debug(images)
+    return render(request, "atlas/partials/series_images.html", {"series": series, "images": images})
+
+
 @login_required
 # @user_is_atlas_editor
 def question_schema_detail(request, pk: int):

deploy/nginx/dev.conf

@@ -0,0 +1,34 @@
+upstream app_server {
+    server web:8000;
+}
+
+server {
+    listen 80;
+    listen [::]:80;
+    server_name _;
+
+    # Write logs to the host-mounted folder so Promtail can scrape them
+    access_log /var/log/rad/nginx.access.log combined;
+    error_log  /var/log/rad/nginx.error.log warn;
+
+    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 +1,135 @@
+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 _;
+
+    # Write logs to the host-mounted folder so Promtail can scrape them
+    access_log /var/log/rad/nginx.access.log combined;
+    error_log  /var/log/rad/nginx.error.log warn;
+
+    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;
+
+    # Write logs to the host-mounted folder so Promtail can scrape them
+    access_log /var/log/rad/nginx.access.log combined;
+    error_log  /var/log/rad/nginx.error.log warn;
+
+    # 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 +1,70 @@
+# 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
+      - ../logs:/var/log/rad:rw
+
+  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 +1,120 @@
+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
+      - ../logs:/var/log/rad:rw
+      - 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/mixins.py

@@ -65,6 +65,9 @@ class AuthorMixin():
 
     def is_author(self, user: User) -> bool:
         """Returns True if the user is an author of the object"""
+        if user.is_superuser:
+            return True
+
         return self.author.filter(id=user.id).exists()
 
 

generic/templates/generic/exam_overview_headers.html

@@ -93,7 +93,7 @@
                 <div class="card">
                     <div class="card-body p-2">
                         <div class="d-flex justify-content-between align-items-center">
-                            <div>
+                            <div title="Defines if this exam is freely available to all users.">
                                 Open access:
                                 <span class="fw-bold">{{ exam.open_access }}</span>
                             </div>
@@ -121,10 +121,10 @@
                     </div>
                 </div>
                 <div class="card">
-                    <div class="card-header p-2">
+                    <div class="card-header p-2" title="Allow bulk setting of question open access status. Note: questions and exams have different open access settings.">
                         {# Use d-block on small screens so the summary text wraps nicely; md uses flex for spacing #}
-                        <a class="d-block d-md-flex justify-content-between align-items-center" data-bs-toggle="collapse" data-bs-target="#open-access-bulk" role="button" aria-expanded="false" aria-controls="open-access-bulk">
-                            <span>Open access (questions)</span>
+                        <a class="d-block d-md-flex justify-content-between align-items-center text-decoration-none text-reset" data-bs-toggle="collapse" data-bs-target="#open-access-bulk" role="button" aria-expanded="false" aria-controls="open-access-bulk">
+                            <small>Open access (questions)</small>
                             <small class="text-muted">Expand to change selected questions open access status</small>
                         </a>
                     </div>
@@ -133,7 +133,6 @@
                             <form hx-post="{% url 'generic:generic_exam_set_open_access' %}" hx-target="#action-result" hx-swap="innerHTML" class="row g-2 align-items-center">
                                 <input type="hidden" name="type" value="sbas" />
                                 <input type="hidden" name="exam_id" value="{{ exam.pk }}" />
-                                <div class="col-12 small text-muted">Select questions on the list above (checkboxes) then click one of the actions below.</div>
                                 <div class="col-12 d-flex flex-column flex-md-row gap-2 justify-content-md-end">
                                     <button class="btn btn-sm btn-outline-success" type="submit" name="set_open_access" value="true" hx-include="input[name='selection']:checked">Set Open Access = True</button>
                                     <button class="btn btn-sm btn-outline-danger" type="submit" name="set_open_access" value="false" hx-include="input[name='selection']:checked">Set Open Access = False</button>

generic/views.py

@@ -1774,7 +1774,7 @@ class ExamViews(View, LoginRequiredMixin):
     def exam_list_collection(self, request, collection_id):
         collection = get_object_or_404(ExamCollection, pk=collection_id)
 
-        if not request.user in collection.author.all():
+        if not collection.is_author(request.user):
             raise PermissionDenied
 
         return self.exam_list(request, all=True, collection=collection)

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):

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):

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):

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):

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):

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"