Make prod deploys work from a clean checkout of main

README.md

@@ -59,9 +59,11 @@ ssh visitor@bdmap1.wse.jhu.edu
 ```
 
 #### 1. Pull latest changes
+Production must always deploy from `main`. Confirm the branch first, then pull.
 ```
 cd /home/visitor/PanTS-Viewer
 git fetch
+git checkout main
 git pull
 ```
 
@@ -72,8 +74,9 @@ cd /home/visitor/PanTS-Viewer/PanTS-Demo && npm ci && npm run build
 
 #### 3. Restart the backend
 ```
-# Kill the old gunicorn process
-kill $(pgrep -f "gunicorn.*app:app")
+# Stop the old gunicorn process and wait for the port to free
+pkill -f "gunicorn.*app:app"; sleep 2
+pgrep -f "gunicorn.*app:app" && echo "still running - rerun the line above" || echo "port clear"
 
 # Start a new gunicorn process
 nohup /home/visitor/.conda/envs/PanTS_backend/bin/gunicorn \
@@ -85,8 +88,13 @@ echo "PID: $!"
 ```
 
 #### 4. Verify the backend is running
+Give it a few seconds to load, then check the backend booted, the dataset loads, and masks serve (all three must succeed).
 ```
-sleep 3 && curl http://127.0.0.1:8000/api/ping
+sleep 8
+curl http://127.0.0.1:8000/api/ping
+curl -s "http://127.0.0.1:8000/api/search?limit=1" | head -c 120; echo
+curl -s -o /dev/null -w "segmentations: %{http_code}\n" "http://127.0.0.1:8000/api/get-segmentations/17.nii.gz"
 ```
+Expect `{"message":"pong"}`, a JSON object with `items`, and `segmentations: 200`. If the backend fails to boot, check the log for the traceback.
 
 Logs are written to `/tmp/gunicorn.log`.

flask-server/api/api_blueprint.py

@@ -760,10 +760,17 @@ async def get_segmentations(combined_labels_id):
     try:
         serve_path = nifti_path
         if img.get_data_dtype() != np.uint8:
-            # The source is a float label map; Cornerstone needs uint8. Write the
-            # converted copy to a sibling file and serve THAT — never overwrite the
-            # original ground-truth mask on disk (an HTTP GET must not mutate data).
-            converted_path = nifti_path.replace('.nii.gz', '_uint8.nii.gz')
+            # The source is a float label map; Cornerstone needs uint8. Cache the
+            # converted copy in a WRITABLE temp dir and serve THAT — never write
+            # into the dataset's mask_only/ (it is read-only on the server, and an
+            # HTTP GET must not mutate ground-truth data). Writing the sibling into
+            # mask_only/ 500'd the segmentation endpoint in production.
+            cache_dir = "/tmp/pants_uint8"
+            os.makedirs(cache_dir, exist_ok=True)
+            converted_path = os.path.join(
+                cache_dir,
+                f"{get_panTS_id(secure_filename(combined_labels_id))}_combined_labels_uint8.nii.gz",
+            )
             if not os.path.exists(converted_path):
                 print("⚠️ Detected float label map, converting to uint8 for Cornerstone compatibility...")
                 raw = np.asanyarray(img.dataobj)

flask-server/services/segmentation_metrics.py

@@ -0,0 +1,40 @@
+"""
+services/segmentation_metrics.py
+
+Per-session segmentation metrics for the AI assistant when a user is viewing
+an *uploaded* (session) case rather than a numeric dataset case.
+
+This module is intentionally defensive. Its only caller
+(``api_blueprint._ai_load_metrics``) treats a returned dict that contains an
+``"error"`` key as "no server metrics available" and falls back to
+frontend-supplied metrics. Therefore this function must NEVER raise and must
+always return a dict: a missing/undecodable session mask has to degrade
+gracefully to the frontend metrics instead of breaking AI chat -- or, as we
+learned the hard way, breaking the whole backend at import time when this
+module was referenced but never committed.
+
+Server-side computation of per-organ metrics for uploaded sessions is not
+implemented in this build, so we return a clean "unavailable" result. The
+public shape mirrors ``get_mask_data_internal`` ({"organ_metrics": [...]}).
+"""
+
+from __future__ import annotations
+
+
+def calculate_session_metrics(session_id, sessions_dir_name=None):
+    """Best-effort per-organ metrics for an uploaded session case.
+
+    Returns a dict shaped like ``get_mask_data_internal`` on success, or
+    ``{"error": ...}`` when the session's mask cannot be located/computed.
+    Never raises.
+    """
+    try:
+        identifier = str(session_id or "").strip()
+        if not identifier:
+            return {"error": "no session id", "organ_metrics": []}
+
+        # Session masks are not computed server-side in this build; signal
+        # "unavailable" so the caller falls back to frontend-supplied metrics.
+        return {"error": "session metrics unavailable", "organ_metrics": []}
+    except Exception as error:  # never let this break the import or the caller
+        return {"error": f"{type(error).__name__}: {error}", "organ_metrics": []}