Update app.py

app.py

@@ -239,7 +239,7 @@ def phylogenetic_placement(sequence: str, mafft_cmd: str, iqtree_cmd: str):
         logger.error(f"Phylogenetic placement failed: {e}", exc_info=True)
         return False, f"Error: {str(e)}", None, None
     finally:
-        # Fixed: Properly handle cleanup with specific exception handling
+        # FIXED: Properly handle cleanup with specific exception handling
         if query_fasta and os.path.exists(query_fasta):
             try:
                 os.unlink(query_fasta)
@@ -429,9 +429,8 @@ async def run_pipeline_from_file(fasta_file_obj, similarity_score, build_ml_tree
         if temp_file_path and os.path.exists(temp_file_path):
             try:
                 os.unlink(temp_file_path)
-            except Exception as e:
-                logger.warning(f"Failed to delete temp file {temp_file_path}: {e}")
-
+            except Exception as cleanup_error:  # FIXED: Use different variable name
+                logger.warning(f"Failed to delete temp file {temp_file_path}: {cleanup_error}")
 # --- Pydantic Models ---
 class AnalysisRequest(BaseModel):
     sequence: str
@@ -547,9 +546,9 @@ async def analyze_file(
         if temp_file_path and os.path.exists(temp_file_path):
             try:
                 os.unlink(temp_file_path)
-            except Exception as e:
-                logger.warning(f"Failed to clean up {temp_file_path}: {e}")
-
+            except Exception as cleanup_error:  # FIXED: Use different variable name
+                logger.warning(f"Failed to clean up {temp_file_path}: cleanup_error}")
+                
 @app.get("/download/{file_type}/{query_id}")
 async def download_file(file_type: str, query_id: str):
     try:
@@ -759,7 +758,6 @@ def create_gradio_interface():
 
 # --- Application Startup ---
 def run_application():
-    main_gradio_app = None  # Predefine for main app
     try:
         main_gradio_app = create_gradio_interface()
         main_gradio_app = gr.mount_gradio_app(app, main_gradio_app, path="/gradio")
@@ -787,8 +785,7 @@ def run_application():
             )
         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("❌ Application failed to start. Check logs for details.")if __name__ == "__main__":
     print("🧬 Gene Analysis Pipeline Starting...")
     print("=" * 50)
     print("🔍 Checking system components...")