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: