Update app.py

app.py

@@ -780,45 +780,32 @@ def create_gradio_interface():
             title="🧬 Gene Analysis Pipeline (Error Mode)"
         )
 # --- Application Startup ---
-def run_application():
+async def run_pipeline_from_file(fasta_file_obj, similarity_score, build_ml_tree):
+    temp_file_path = None
     try:
-        main_gradio_app = create_gradio_interface()
-        main_gradio_app = gr.mount_gradio_app(app, main_gradio_app, path="/gradio")
-        logger.info("🧬 Gene Analysis Pipeline Starting...")
-        logger.info("=" * 50)
-        logger.info("🔍 Checking system components...")
-        logger.info(f"🤖 Boundary Model: {'✅ Loaded' if boundary_model else '❌ Missing'}")
-        logger.info(f"🧠 Keras Model: {'✅ Loaded' if keras_model else '❌ Missing'}")
-        logger.info(f"🌳 Tree Analyzer: {'✅ Loaded' if analyzer else '❌ Missing'}")
-        mafft_available, iqtree_available = check_tool_availability()
-        logger.info(f"🧬 MAFFT: {'✅ Available' if mafft_available else '❌ Missing'}")
-        logger.info(f"🌲 IQ-TREE: {'✅ Available' if iqtree_available else '❌ Missing'}")
-        logger.info("=" * 50)
-        logger.info("🚀 Starting Gene Analysis Pipeline...")
-        logger.warning("⚠️ Running without request queuing. Concurrent requests may block.")
-        logger.info("📊 FastAPI docs available at: http://localhost:7860/docs")
-        logger.info("🧬 Gradio interface available at: http://localhost:7860/gradio")
-        uvicorn.run(
-            app,
-            host="0.0.0.0",
-            port=7860,
-            log_level="info",
-            access_log=True
-        )
+        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
     except Exception as main_error:
-        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()
-            logger.info("🧬 Gradio interface available at: http://localhost:7860")
-            fallback_gradio_app.launch(
-                server_name="0.0.0.0",
-                server_port=7860,
-                prevent_thread_lock=True
-            )
-        except Exception as fallback_error:
-            logger.error(f"Fallback failed: {fallback_error}", exc_info=True)
-            print("❌ Application failed to start. Check logs for details.")
+        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
 if __name__ == "__main__":
     print("🧬 Gene Analysis Pipeline Starting...")
     print("=" * 50)