Update pipeline.py

pipeline.py

@@ -327,7 +327,7 @@ def pipeline_with_gemini(accessions,stop_flag=None, niche_cases=None, save_df=No
           saveName = saveTitle.replace(" ", "_")
           chunk_filename = f"{saveName}_merged_document.docx"
           all_filename = f"{saveName}_all_merged_document.docx"
-      print(chunk_filename, all_filename)  
+      print("chunk file name and all filename: ", chunk_filename, all_filename)  
       # Define local temp paths for reading/writing
       # import tempfile
       # tmp_dir = tempfile.mkdtemp()
@@ -340,7 +340,7 @@ def pipeline_with_gemini(accessions,stop_flag=None, niche_cases=None, save_df=No
       if stop_flag is not None and stop_flag.value:
         print(f"🛑 Stop processing {accession}, aborting early...")
         return {}
-      print(file_chunk_path)
+      print("this is file chunk path: ", file_chunk_path)
       chunk_id = find_drive_file(chunk_filename, sample_folder_id)
       all_id = find_drive_file(all_filename, sample_folder_id)
     
@@ -447,6 +447,8 @@ def pipeline_with_gemini(accessions,stop_flag=None, niche_cases=None, save_df=No
           acc_score["source"] = links
       else:
         print("no chunk or all output")  
+        print("chunk filename: ", str(chunks_filename))  
+          
         try:
             temp_source = False
             if save_df is not None and not save_df.empty: