Update app.py

app.py

@@ -713,21 +713,30 @@ def create_gradio_interface():
                         value="<div style='text-align: center; color: #666; padding: 20px;'>No report generated yet. Run analysis to see results.</div>"
                     )
 
-            # Event handlers
+            # Event handlers with enhanced logging
             def handle_analysis_output(*outputs):
-                boundary_output, keras_output, ml_tree_output, simplified_ml_output, summary_output, aligned_file, phy_file, _, _, tree_html_content, report_html_content, tree_html_path, report_html_path = outputs
-                return (
-                    boundary_output, keras_output, ml_tree_output, simplified_ml_output, summary_output,
-                    gr.File.update(value=aligned_file, visible=aligned_file is not None),
-                    gr.File.update(value=phy_file, visible=phy_file is not None),
-                    gr.File.update(value=tree_html_path, visible=tree_html_path is not None),
-                    gr.File.update(value=report_html_path, visible=report_html_path is not None),
-                    tree_html_content,
-                    report_html_content
-                )
+                try:
+                    boundary_output, keras_output, ml_tree_output, simplified_ml_output, summary_output, aligned_file, phy_file, _, _, tree_html_content, report_html_content, tree_html_path, report_html_path = outputs
+                    return (
+                        boundary_output, keras_output, ml_tree_output, simplified_ml_output, summary_output,
+                        gr.File.update(value=aligned_file, visible=aligned_file is not None),
+                        gr.File.update(value=phy_file, visible=phy_file is not None),
+                        gr.File.update(value=tree_html_path, visible=tree_html_path is not None),
+                        gr.File.update(value=report_html_path, visible=report_html_path is not None),
+                        tree_html_content,
+                        report_html_content
+                    )
+                except Exception as handler_error:
+                    logger.error(f"Error in handle_analysis_output: {handler_error}", exc_info=True)
+                    return (
+                        f"Error: {str(handler_error)}", "", "", "", "",
+                        gr.File.update(visible=False), gr.File.update(visible=False),
+                        gr.File.update(visible=False), gr.File.update(visible=False),
+                        "", ""
+                    )
 
             analyze_btn.click(
-                fn=run_pipeline,
+                fn=lambda *args: handle_analysis_output(run_pipeline(*args)),
                 inputs=[dna_input, similarity_score, build_ml_tree],
                 outputs=[
                     boundary_output, keras_output, ml_tree_output, tree_analysis_output, summary_output,
@@ -736,7 +745,7 @@ def create_gradio_interface():
             )
 
             analyze_file_btn.click(
-                fn=run_pipeline_from_file,
+                fn=lambda *args: handle_analysis_output(run_pipeline_from_file(*args)),
                 inputs=[file_input, file_similarity_score, file_build_ml_tree],
                 outputs=[
                     boundary_output, keras_output, ml_tree_output, tree_analysis_output, summary_output,
@@ -784,6 +793,16 @@ def run_application():
     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")
@@ -792,24 +811,23 @@ def run_application():
             app,
             host="0.0.0.0",
             port=7860,
-            log_level="info"
+            log_level="info",
+            access_log=True
         )
     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.warning("⚠️ Running without request queuing in fallback mode.")
+            logger.info("🧬 Gradio interface available at: http://localhost:7860")
             fallback_gradio_app.launch(
                 server_name="0.0.0.0",
                 server_port=7860,
-                share=False,
-                debug=False
+                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.")
-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...")