Update pipeline.py

pipeline.py

@@ -200,6 +200,7 @@ def pipeline_with_gemini(accessions):
       # first way: ncbi method
       if country.lower() != "unknown":
         stand_country = standardize_location.smart_country_lookup(country.lower())
+        print("stand_country: ", stand_country)  
         if stand_country.lower() != "not found":
           acc_score["country"][stand_country.lower()] = ["ncbi"]
         else: acc_score["country"][country.lower()] = ["ncbi"]   
@@ -211,6 +212,7 @@ def pipeline_with_gemini(accessions):
         acc_score["sample_type"][sample_type.lower()] = ["ncbi"]
       # second way: LLM model
       # Preprocess the input token
+      print(acc_score)  
       accession, isolate = None, None
       if acc != "unknown":  accession = acc
       if iso != "unknown":  isolate = iso
@@ -218,6 +220,7 @@ def pipeline_with_gemini(accessions):
       if doi != "unknown":
         link = 'https://doi.org/' + doi
         # get the file to create listOfFile for each id
+        print("link of doi: ", link)  
         html = extractHTML.HTML("",link)
         jsonSM = html.getSupMaterial()
         article_text = html.getListSection()