def load_data_api(path_credentials):
# Try loading objects from disk file; delete saveddata.pkl to force reload
try:
path_save = os.path.join(path_credentials, 'saveddata.pkl')
with open(path_save, 'rb') as f:
df_study, df_structure, df_report, df_report_structure, \
df_optiongroup_structure = pickle.load(f)
print('Loading data from file... Delete saveddata.pkl to force' +
'reload data from Castor')
except Exception:
print('Loading data from PC failed. Reloading from Castor server.')
df_study, df_structure, df_report, df_report_structure, \
df_optiongroup_structure = import_data_by_record(path_credentials)
path_credentials = os.path.join(path_credentials, 'saveddata.pkl')
with open(path_credentials, 'wb') as f:
pickle.dump([
df_study, df_structure, df_report, df_report_structure,
df_optiongroup_structure
], f)
df_study = df_study.reset_index(drop=True)
df_report = df_report.reset_index(drop=True)
df_study = df_study.rename({'Record ID': "Record Id"}, axis=1)
df_report = df_report.rename({'Record ID': "Record Id"}, axis=1)
# Remove test records
df_study = df_study.loc[df_study['Record Id'].astype(int) > 11000, :]
var_columns = [
'Form Type', 'Form Collection Name', 'Form Name',
'Field Variable Name', 'Field Label', 'Field Type', 'Option Name',
'Option Value'
]
data_struct = get_all_field_information(path_credentials)
data_struct = data_struct.loc[:, var_columns]
return df_study, df_report, data_struct
import configparser
config = configparser.ConfigParser()
config.read(os.path.join(os.path.dirname(__file__), '../user_settings.ini'))
# the excel file with all variables and answer options is stored here
target_excel = config['exportresults']['excel_file_variables']
# folder with all figures
figure_dir = config['exportresults']['figures_folder']
# # Get all data from Castor database (without any selection criterium)
# Note that you need export rights for every individual center.
if False:
study_data,study_struct,reports_data,reports_struct,optiongroups_struct = covid19_import.import_data_by_record(config['CastorCredentials']['local_private_path'])
with open(str(os.path.join(config['CastorCredentials']['local_private_path'],'objs.pkl')), 'wb') as f: # Python 3: open(..., 'wb')
pickle.dump([study_data,study_struct,reports_data,reports_struct,optiongroups_struct], f)
else:
# Getting back the objects:
with open(os.path.join(config['CastorCredentials']['local_private_path'],'objs.pkl'),'rb') as f: # Python 3: open(..., 'rb')
study_data,study_struct,reports_data,reports_struct,optiongroups_struct = pickle.load(f)
# %% Do a patient count on the data so far.
# # Patient counts
# ## Total number of patients
print('Total number of patients (with any data) is: '+str(len(study_data)))
# HOSPITAL ADMISSION ONSET & ADMISSION admission_dt Admission date at this facility: