if not password:
password = getpass('Input your password (blank for admin): ')
if not password:
password = '******'
bot = PhenoTipsBot(base_url, username, password)
if study == None:
studies = bot.list_studies()
if len(studies):
print('Available study forms:')
print('* ' + '\n* '.join(studies))
study = input('Input the study form to use (blank for default): ')
elif study == 'None':
study = None
#begin import
if yes or input('You are about to import ' + str(len(patients)) + ' patients. Type y to continue: ')[0] == 'y':
count = 0
start_time = time.time()
for patient, clinvar_variants in patients:
patient_id = bot.create(patient, study)
for clinvar_variant in clinvar_variants:
bot.create_object(patient_id, 'Main.ClinVarVariant', clinvar_variant)
count += 1
stdout.write(str(count) + '\r')
print()
print('All done! Elapsed time ' + str(timedelta(seconds=time.time() - start_time)))
