Update app.py

app.py

@@ -512,17 +512,50 @@ with gr.Blocks() as interface:
                     "\n".join(log_lines)
                 )
         
-                try:
-                    print("📄 Processing accession:", acc)
-                    rows = summarize_results(acc)
+                # try:
+                #     print("📄 Processing accession:", acc)
+                #     rows = summarize_results(acc)
+                #     all_rows.extend(rows)
+                #     processed_accessions += 1  # ✅ only count success
+                #     if email.strip():
+                #         save_to_excel(all_rows, "", "", output_file_path, is_resume=False)
+                #     log_lines.append(f"✅ Processed {acc} ({i+1}/{total})")
+                print("📄 Processing accession:", acc)
+
+                # Run summarize_results in a separate process with stop flag support
+                success, rows = run_with_timeout(
+                    summarize_results,
+                    args=(acc,),
+                    timeout=None,              # or set max seconds per sample if you want
+                    stop_value=global_stop_flag
+                )
+                
+                # If stop was pressed during this accession
+                if not success and global_stop_flag.value:
+                    log_lines.append(f"🛑 Cancelled {acc} before completion")
+                    yield (
+                        make_html_table(all_rows),
+                        gr.update(visible=True),
+                        gr.update(visible=False),
+                        "",
+                        "🛑 Stopped",
+                        "\n".join(log_lines)
+                    )
+                    break  # stop processing entirely
+                
+                # If it finished normally
+                if success and rows:
                     all_rows.extend(rows)
-                    processed_accessions += 1  # ✅ only count success
+                    processed_accessions += 1
                     if email.strip():
                         save_to_excel(all_rows, "", "", output_file_path, is_resume=False)
                     log_lines.append(f"✅ Processed {acc} ({i+1}/{total})")
-                except Exception as e:
-                    log_lines.append(f"❌ Failed to process {acc}: {e}")
-        
+                else:
+                    # If it failed due to timeout or other error
+                    if not global_stop_flag.value:
+                        log_lines.append(f"⚠️ Skipped {acc} due to timeout or error")
+                
+                # Always yield updated logs after each attempt
                 yield (
                     make_html_table(all_rows),
                     gr.update(visible=True),
@@ -531,6 +564,18 @@ with gr.Blocks() as interface:
                     "⏳ Processing...",
                     "\n".join(log_lines)
                 )
+
+                # except Exception as e:
+                #     log_lines.append(f"❌ Failed to process {acc}: {e}")
+        
+                # yield (
+                #     make_html_table(all_rows),
+                #     gr.update(visible=True),
+                #     gr.update(visible=False),
+                #     "",
+                #     "⏳ Processing...",
+                #     "\n".join(log_lines)
+                # )
         
             # Step 3: Final usage update
             usage_text = ""