Update pipeline.py

pipeline.py

@@ -403,6 +403,7 @@ def pipeline_with_gemini(accessions,stop_flag=None, niche_cases=None, save_df=No
         print(f"🛑 Stop processing {accession}, aborting early...")
         return {}    
       # check doi first
+      print("acc sscore for file all output and chunk: ", acc_score["file_all_output"], acc_score["file_chunk"])  
       if len(acc_score["file_all_output"]) == 0 and len(acc_score["file_chunk"]) == 0:  
           if doi != "unknown":
             link = 'https://doi.org/' + doi
@@ -445,14 +446,15 @@ def pipeline_with_gemini(accessions,stop_flag=None, niche_cases=None, save_df=No
           links = unique_preserve_order(links)
           acc_score["source"] = links
       else:
+        print("no chunk or all output")  
         try:
             temp_source = False
             if save_df is not None and not save_df.empty:
                 print("save df not none")  
-                print(str(chunks_filename))
+                print(str(chunk_filename))
                 print(str(all_filename))
-                if str(chunks_filename) != "":
-                  link = save_df.loc[save_df["file_chunk"]==str(chunks_filename),"Sources"].iloc[0]
+                if str(chunk_filename) != "":
+                  link = save_df.loc[save_df["file_chunk"]==str(chunk_filename),"Sources"].iloc[0]
                   #link = row["Sources"].iloc[0]
                   if "http" in link:   
                     print("yeah http in save df source") 
@@ -558,9 +560,9 @@ def pipeline_with_gemini(accessions,stop_flag=None, niche_cases=None, save_df=No
       if not chunk and not all_output:
         print("not chunk and all output")  
         # else: check if we can reuse these chunk and all output of existed accession to find another
-        if str(chunks_filename) != "":
-          print("first time have chunk path: ", str(chunks_filename))
-          acc_score["file_chunk"] = str(chunks_filename)
+        if str(chunk_filename) != "":
+          print("first time have chunk path: ", str(chunk_filename))
+          acc_score["file_chunk"] = str(chunk_filename)
         if str(all_filename) != "":
           print("first time have all path: ", str(all_filename))
           acc_score["file_all_output"] = str(all_filename)