Update pipeline.py

pipeline.py

@@ -445,9 +445,9 @@ def pipeline_with_gemini(accessions,stop_flag=None, niche_cases=None, save_df=No
           links = unique_preserve_order(links)
           acc_score["source"] = links
       else:
-          try:
-              temp_source = False
-              if save_df is not None and not save_df.empty:
+        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(all_filename))
@@ -478,11 +478,11 @@ def pipeline_with_gemini(accessions,stop_flag=None, niche_cases=None, save_df=No
                   print("tempo source") 
                   #acc_score["source"] = [str(file_all_path), str(file_chunk_path)]  
                   temp_source = True
-              else:  # temporary  
-                  print("tempo source") 
+            else:  # temporary  
+                print("tempo source") 
                   #acc_score["source"] = [str(file_all_path), str(file_chunk_path)]  
-                  temp_source = True      
-              if temp_source:
+                temp_source = True      
+            if temp_source:
                 if doi != "unknown":
                     link = 'https://doi.org/' + doi
                     # get the file to create listOfFile for each id
@@ -524,8 +524,8 @@ def pipeline_with_gemini(accessions,stop_flag=None, niche_cases=None, save_df=No
                 links = unique_preserve_order(links)
                 acc_score["source"] = links
         except:
-              print("except for source")  
-              acc_score["source"] = []
+            print("except for source")  
+            acc_score["source"] = []
       # chunk_path = "/"+saveTitle+"_merged_document.docx"
       # all_path = "/"+saveTitle+"_all_merged_document.docx"
       # # if chunk and all output not exist yet