def import_data_by_record(path_to_api_creds=None):
config = configparser.ConfigParser()
config.read(os.path.join(os.path.dirname(__file__), 'user_settings.ini'))
if path_to_api_creds == None:
path_to_api_creds = config['CastorCredentials']['local_private_path']
# alternative for import_data if import_data fails due to server-side timeout errors (i.e. for large datasets)
# this alternative loops over de records and report instances to load the data
# input: private folder where client & secret files (no extension, 1 string only per file) from castor are saved by the user
# see also: https://helpdesk.castoredc.com/article/124-application-programming-interface-api
c = Castor_api(path_to_api_creds) # e.g. in user dir outside of GIT repo
# get study ID for COVID study
c.select_study_by_name(config['CastorCredentials']['study_name'])
df_study, df_structure_study, df_report, df_structure_report, df_optiongroups_structure = c.records_reports_all(report_names=['Daily'])
# remove test institute and archived (deleted) records
test_inst = [i for i in c.request_institutes() if 'test' in i['name'].lower()][0]
test_records = [r['record_id'] for r in c.request_study_records(institute=test_inst['institute_id'])]
test_records += [r['record_id'] for r in c.request_study_records() if r['archived']==1]
df_study.drop(index=df_study[df_study['Record Id'].isin(test_records)].index, inplace=True)
df_report.drop(index=df_report[df_report['Record Id'].isin(test_records)].index, inplace=True)
return df_study, df_structure_study, df_report, df_structure_report, df_optiongroups_structure
"""
import site
site.addsitedir(
'./../') # add directory to path to enable import of castor_api
from castor_api import Castor_api
import configparser
config = configparser.ConfigParser()
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: ' +