Update smart_fallback.py

smart_fallback.py

@@ -3,6 +3,7 @@ from Bio import Entrez, Medline
 import mtdna_classifier
 from NER.html import extractHTML
 import data_preprocess
+import pipeline
 # Setup
 def fetch_ncbi(accession_number):
   try:
@@ -168,7 +169,14 @@ def filter_links_by_metadata(search_results, saveLinkFolder, accession=None):
         keywords = [accession] + keywords
       title_snippet = link.lower()
       print("save link folder inside this filter function: ", saveLinkFolder)  
-      article_text = data_preprocess.extract_text(link,saveLinkFolder)
+      success_process, output_process = pipeline.run_with_timeout(data_preprocess.extract_text,args=(link,saveLinkFolder),timeout=60)
+      if success_process:
+          article_text = output_process
+          print("yes succeed for getting article text")
+      else: 
+          print("no suceed, fallback to no link")
+          article_text = ""  
+      #article_text = data_preprocess.extract_text(link,saveLinkFolder)
       print("article text")
       #print(article_text)  
       try: