config.read(os.path.join(os.path.dirname(__file__), '../user_settings.ini'))
c = Castor_api(config['CastorCredentials']['local_private_path'])
study_id = c.select_study_by_name(config['CastorCredentials']['study_name'])
varname = 'Outcome'
# select AMC + VUmc + MUMC
institutes = c.request_institutes()
inst_amc_vumc = [
inst['institute_id'] for inst in c.request_institutes()
if (inst['name'] == 'AUMC - AMC' or inst['name'] == 'AUMC - VUmc'
or inst['name'] == 'MUMC')
]
records = c.request_study_records(
institute=inst_amc_vumc[0]) + c.request_study_records(
institute=inst_amc_vumc[1])
options = c.request_fieldoptiongroup(
optiongroup_id=c.field_optiongroup_by_variable_name(varname))
values = c.field_values_by_variable_name(varname, records=records)
print('Total records: ' + str(len(values)))
print(' - records: \'' + varname + '\' data not present: ' +
str(sum([f == None for f in values])))
print(' - records: \'' + varname + '\' data present: ' +
str(sum([f != None for f in values])))
print(' - \'' + varname + '\' options (total n=' +
str(sum([f != None for f in values])) + '): ')
for o in options['options']:
print(' > ' + str(o['name']) + ': ' +
str(sum([o['value'] == f for f in values])))
# select AMC + VUmc
institutes = c.request_institutes()
inst_amc_vumc = [
inst['institute_id'] for inst in c.request_institutes()
if (inst['name'] == 'AUMC - AMC' or inst['name'] == 'AUMC - VUmc')
]
records = c.request_study_records(
institute=inst_amc_vumc[0]) + c.request_study_records(
institute=inst_amc_vumc[1])
ct_perf_values = c.field_values_by_variable_name('CT_thorax_performed',
records=records)
corad_values = c.field_values_by_variable_name('corads_admission',
records=records)
options_corad = c.request_fieldoptiongroup(
optiongroup_id=c.field_optiongroup_by_variable_name('corads_admission'))
# %%
print('Total COVID-19 records (AMC + VUmc): ' + str(len(ct_perf_values)))
print(' - records: CT data not present: ' +
str(sum([f == None for f in ct_perf_values])))
print(' - records: CT data present: ' +
str(sum([f != None for f in ct_perf_values])))
print(' - CORAD scores available (n=' +
str(sum([f != None for f in corad_values])) + '): ')
for o in options_corad['options']:
print(' ' + str(o['name']) + ': ' +
str(sum([f == o['value'] for f in corad_values])))