Update pipeline.py

pipeline.py

@@ -355,17 +355,17 @@ 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")
-        try:  
-            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
-        except:
-            links = tem_links
-        #links = smart_fallback.filter_links_by_metadata(tem_links, saveLinkFolder=sample_folder_id, accession=acc)
+        # try:  
+        #     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
+        # except:
+        #     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