Update app.py

app.py

@@ -780,32 +780,20 @@ def create_gradio_interface():
             title="🧬 Gene Analysis Pipeline (Error Mode)"
         )
 # --- Application Startup ---
-async def run_pipeline_from_file(fasta_file_obj, similarity_score, build_ml_tree):
-    temp_file_path = None
+def run_application():
     try:
-        if fasta_file_obj is None:
-            return "❌ No file provided", "", "", "", "", None, None, None, None, "No input", "No input", None, None
-        with tempfile.NamedTemporaryFile(delete=False, suffix=".fasta", dir="/tmp") as temp_file:
-            if isinstance(fasta_file_obj, UploadFile):
-                content = await fasta_file_obj.read()
-                temp_file.write(content)
-            else:
-                with open(fasta_file_obj, 'rb') as f:
-                    content = f.read()
-                temp_file.write(content)
-            temp_file_path = temp_file.name
-        dna_input = read_fasta_file(temp_file_path)
-        if not dna_input:
-            cleanup_file(temp_file_path)
-            return "❌ Failed to read FASTA file", "", "", "", "", None, None, None, None, "No input", "No input", None, None
-        result = run_pipeline(dna_input, similarity_score, build_ml_tree)
-        cleanup_file(temp_file_path)
-        return result
+        main_gradio_app = create_gradio_interface()
+        main_gradio_app = gr.mount_gradio_app(app, main_gradio_app, path="/gradio")
+        # ... (logging and uvicorn.run)
     except Exception as main_error:
-        logger.error(f"Pipeline from file error: {main_error}", exc_info=True)
-        cleanup_file(temp_file_path)
-        error_msg = f"❌ Error: {str(main_error)}"
-        return error_msg, "", "", "", "", None, None, None, None, error_msg, error_msg, None, None
+        logger.error(f"Application startup failed: {main_error}", exc_info=True)
+        try:
+            logger.info("🔄 Falling back to Gradio-only mode...")
+            fallback_gradio_app = create_gradio_interface()
+            # ... (launch fallback)
+        except Exception as fallback_error:
+            logger.error(f"Fallback failed: {fallback_error}", exc_info=True)
+            print("❌ Application failed to start. Check logs for details.")
 if __name__ == "__main__":
     print("🧬 Gene Analysis Pipeline Starting...")
     print("=" * 50)