Update pipeline.py

pipeline.py

@@ -83,6 +83,15 @@ def download_file_from_drive(remote_name, folder_id, local_path):
     while not done:
         _, done = downloader.next_chunk()
     return True
+def download_drive_file_content(file_id):
+    request = drive_service.files().get_media(fileId=file_id)
+    fh = io.BytesIO()
+    downloader = MediaIoBaseDownload(fh, request)
+    done = False
+    while not done:
+        _, done = downloader.next_chunk()
+    fh.seek(0)
+    return fh.read().decode("utf-8")
 
 def run_with_timeout(func, args=(), kwargs={}, timeout=20):
     """
@@ -198,6 +207,7 @@ def pipeline_with_gemini(accessions):
       all_exists = download_file_from_drive(all_filename, sample_folder_id, file_all_path)
       print("chunk exist: ", chunk_exists)  
       # first way: ncbi method
+      print("country.lower: ",country.lower())  
       if country.lower() != "unknown":
         stand_country = standardize_location.smart_country_lookup(country.lower())
         print("stand_country: ", stand_country)