Update pipeline.py

pipeline.py

@@ -386,14 +386,14 @@ def pipeline_with_gemini(accessions,niche_cases=None):
         # filter the quality link  
         print("saveLinkFolder as sample folder id: ", sample_folder_id)  
         print("start the smart filter link") 
-        success_process, output_process = run_with_timeout(smart_fallback.filter_links_by_metadata,args=(tem_links,sample_folder_id),kwargs={"accession":acc})
-        if success_process:
-          links = output_process
-          print("yes succeed for smart filter link")
-        else: 
-          print("no suceed, fallback to all tem links")
-          links = tem_links
-        #links = smart_fallback.filter_links_by_metadata(tem_links, saveLinkFolder=sample_folder_id, accession=acc)
+        # success_process, output_process = run_with_timeout(smart_fallback.filter_links_by_metadata,args=(tem_links,sample_folder_id),kwargs={"accession":acc})
+        # if success_process:
+        #   links = output_process
+        #   print("yes succeed for smart filter link")
+        # else: 
+        #   print("no suceed, fallback to all tem links")
+        #   links = tem_links
+        links = smart_fallback.filter_links_by_metadata(tem_links, saveLinkFolder=sample_folder_id, accession=acc)
       print("this is links: ",links)    
       links = unique_preserve_order(links)
       acc_score["source"] = links