Add Sequence Count

app.py

@@ -11,13 +11,34 @@
 app = Flask(__name__)
 CORS(app)  # Enable CORS for all routes
 
+@app.route('/', methods=['GET'])
+def health_check():
+    """
+    Health check endpoint for Kubernetes liveness/readiness probes.
+    Returns: JSON with service status
+    """
+    return jsonify({
+        'status': 'healthy',
+        'service': 'RNA Alignment API',
+        'environment': os.getenv('ENVIRONMENT', 'unknown')
+    }), 200
+
+
 @app.route('/<identifier>', methods=['GET'])
 def get_msa_data(identifier):
     """
     Get MSA data by identifier from S3, parsed and formatted for the MSA viewer.
     URL pattern: /{identifier}
     Returns: JSON data structure ready for MSA viewer consumption
     """
+    # Prevent health check route from being treated as an identifier
+    if identifier in ['health', 'favicon.ico']:
+        return jsonify({
+            'status': 'error',
+            'message': 'Invalid identifier',
+            'data': None
+        }), 400
+
     try:
         # Get .sto file content from S3
         sto_content = get_seed_file_from_s3(identifier)
@@ -40,7 +61,8 @@ def get_msa_data(identifier):
                 'identifier': identifier,
                 'consensus': msa_data['consensus'],
                 'notation': msa_data.get('notation'),
-                'sequences': msa_data.get('sequences')
+                'sequences': msa_data.get('sequences'),
+                'sequenceCount': len(msa_data.get('sequences', []))
             }
         }