From 2f9a198f045d6181a28c97d6784f4ea0ecd8cfe7 Mon Sep 17 00:00:00 2001
From: pmustonebi <muston@ebi.ac.uk>
Date: Wed, 26 Nov 2025 11:47:47 +0000
Subject: [PATCH] Updated to add sequenceCount and healthcheck

---
 .DS_Store | Bin 0 -> 6148 bytes
 app.py    |  24 +++++++++++++++++++++++-
 2 files changed, 23 insertions(+), 1 deletion(-)
 create mode 100644 .DS_Store

diff --git a/.DS_Store b/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5efd53fa377be31a6a3116f1c67080f22334e617
GIT binary patch
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diff --git a/app.py b/app.py
index 84f90ed..cc2501f 100644
--- a/app.py
+++ b/app.py
@@ -11,6 +11,19 @@
 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):
     """
@@ -18,6 +31,14 @@ def get_msa_data(identifier):
     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', []))
             }
         }