Update pipeline.py

pipeline.py

@@ -266,7 +266,7 @@ def pipeline_with_gemini(accessions):
               if iso != "unknown": query_kw = iso
               else: query_kw = acc
               #text_link, tables_link, final_input_link = data_preprocess.preprocess_document(link,saveLinkFolder, isolate=query_kw)
-              success_process, output_process = run_with_timeout(data_preprocess.preprocess_document,args=(link,saveLinkFolder),kwargs={"isolate":query_kw},timeout=180)
+              success_process, output_process = run_with_timeout(data_preprocess.preprocess_document,args=(link,sample_folder_id),kwargs={"isolate":query_kw},timeout=180)
               if success_process:
                 text_link, tables_link, final_input_link = output_process[0], output_process[1], output_process[2]
                 print("yes succeed for process document")