fix socketIO connection and Log placeholder

app.py

@@ -28,7 +28,7 @@ app.config["SECRET_KEY"] = "dev-key"
 app.wsgi_app = ProxyFix(app.wsgi_app, x_for=1, x_proto=1, x_host=1, x_prefix=1)
 
 # # Socket.IO (logs on for debugging)
-# socketio = SocketIO(app, async_mode="eventlet", cors_allowed_origins="*")
+socketio = SocketIO(app, async_mode="eventlet", cors_allowed_origins="*")
 
 
 # --- job registry for cancel flags ---
@@ -171,7 +171,7 @@ def run_job(job_id, accessions):
             sources                   = out.get("Sources", "No Links")
             time_cost                 = out.get("Time cost") or f"{dt:.2f}s"
 
-            send_row = {
+            send = {
                 "idx": i,
                 "sample_id": sample_id,
                 "predicted_country": predicted_country,
@@ -182,7 +182,7 @@ def run_job(job_id, accessions):
                 "time_cost": time_cost,
             }
 
-            socketio.emit("row", send_row, room=room)
+            socketio.emit("row", send, room=room)
             socketio.sleep(0)  # <- correct spelling; yield so the emit flushes
             send_log(f"Processed {acc} in {dt:.2f}s")
 
@@ -202,39 +202,39 @@ def run_job(job_id, accessions):
         CANCEL_FLAGS.pop(job_id, None)
         JOBS.pop(job_id, None)  # <— tidy queued job
 
-# # ---- Socket.IO events ----
-# @socketio.on("connect")
-# def on_connect():
-#     emit("connected", {"ok": True})
-
-# @socketio.on("join")
-# def on_join(data):
-#     job_id = data.get("job_id")
-#     if job_id:
-#         join_room(job_id)
-#         emit("joined", {"room": job_id})
-
-#         # Start the job once the client is in the room
-#         job = JOBS.get(job_id)
-#         if job and not job["started"]:
-#             job["started"] = True
-#             total = len(job["accs"])
-#             # Send an initial queued/total status so the UI can set progress denominator
-#             socketio.emit("status", {"state": "queued", "total": total}, room=job_id)
-#             socketio.start_background_task(run_job, job_id, job["accs"])
-
-# @socketio.on("leave")
-# def on_leave(data):
-#     job_id = data.get("job_id")
-#     if job_id:
-#         leave_room(job_id)
-
-# @socketio.on("cancel")
-# def on_cancel(data):
-#     job_id = data.get("job_id")
-#     if job_id in CANCEL_FLAGS:
-#         CANCEL_FLAGS[job_id] = True  # flip the flag
-#         emit("status", {"state": "cancelling"}, room=job_id)
+# ---- Socket.IO events ----
+@socketio.on("connect")
+def on_connect():
+    emit("connected", {"ok": True})
+
+@socketio.on("join")
+def on_join(data):
+    job_id = data.get("job_id")
+    if job_id:
+        join_room(job_id)
+        emit("joined", {"room": job_id})
+
+        # Start the job once the client is in the room
+        job = JOBS.get(job_id)
+        if job and not job["started"]:
+            job["started"] = True
+            total = len(job["accs"])
+            # Send an initial queued/total status so the UI can set progress denominator
+            socketio.emit("status", {"state": "queued", "total": total}, room=job_id)
+            socketio.start_background_task(run_job, job_id, job["accs"])
+
+@socketio.on("leave")
+def on_leave(data):
+    job_id = data.get("job_id")
+    if job_id:
+        leave_room(job_id)
+
+@socketio.on("cancel")
+def on_cancel(data):
+    job_id = data.get("job_id")
+    if job_id in CANCEL_FLAGS:
+        CANCEL_FLAGS[job_id] = True  # flip the flag
+        emit("status", {"state": "cancelling"}, room=job_id)
 
 @app.route("/about")
 def about():

templates/Output.html

@@ -75,7 +75,7 @@
 
         <h3>Live log</h3>
         <pre id="live-log" class="log mono" aria-live="polite" aria-atomic="false">
-          <span class="logline muted">Waiting for messages…</span>
+          <span id="log-placeholder" class="logline muted">Waiting for messages…</span>
         </pre>
       </div>
 
@@ -209,6 +209,10 @@
     }
     function appendLog(line) {
       if (!els.log) return;
+
+      const ph = document.getElementById('log-placeholder');
+      if (ph) ph.remove(); // drop the placeholder once
+
       const span = document.createElement('span');
       span.className = 'logline';
       span.textContent = line;