import pandas as pd from multiprocessing import Pool def get_encounter_dates(df_list, pif_key): encounter_dates = [] for df in df_list: df['encounter_date'].fillna('', inplace=True) df_date = df.loc[df['pif_key'].astype(str) == str(pif_key), 'encounter_date'].values if len(df_date) > 0: encounter_dates.extend(df_date) return encounter_dates def get_latest_date(encounter_dates): if encounter_dates: return max(encounter_dates) return '' def create_date_insert_dict(ingested_date): return { 'attribute_name': 'report_date', 'attribute_method': 'cv', 'attribute_normalized_prediction': '', 'attribute_prediction': str(ingested_date), 'attribute_version': 'v2_090523', 'attribute_vocab': '', 'attribute_code': '', 'date_of_service': '' } def add_logging_entry(logging_df, pif_key, json_report_date_exists, encounter_dates, ingested_date, multiple_date, old_date): logging_df = logging_df.append({ 'pif_key': pif_key, 'json_report_date_exists': json_report_date_exists, 'encounter_dates': encounter_dates, 'ingested_date': ingested_date, 'multiple_date': multiple_date, 'old_date': old_date }, ignore_index=True) return logging_df def date_dict(df_list, pif_key): encounter_dates = get_encounter_dates(df_list, pif_key) ingested_date = get_latest_date(encounter_dates) return create_date_insert_dict(ingested_date), encounter_dates, ingested_date def report_date_insertion(dict_list, df_list, logging_df): col_names = {col['attribute_name'] for col in dict_list} pif_key = next((col['attribute_prediction'] for col in dict_list if col['attribute_name'] == 'pif_key'), None) if 'report_date' not in col_names and pif_key is not None: date_insert_dict, encounter_dates, ingested_date = date_dict(df_list, pif_key) dict_list.insert(1, date_insert_dict) logging_df = add_logging_entry(logging_df, pif_key, False, encounter_dates, ingested_date, len(encounter_dates) > 1, 'missing' if not ingested_date else '') elif 'report_date' in col_names and pif_key is not None: date_insert_dict, encounter_dates, ingested_date = date_dict(df_list, pif_key) if ingested_date: for report_date_idx, tm in enumerate(dict_list): if tm['attribute_name'] == 'report_date': old_date = tm['attribute_prediction'] break dict_list.pop(report_date_idx) dict_list.insert(1, date_insert_dict) logging_df = add_logging_entry(logging_df, pif_key, True, encounter_dates, ingested_date, len(encounter_dates) > 1, old_date) else: for report_date_idx, tm in enumerate(dict_list): if tm['attribute_name'] == 'report_date': old_date = tm['attribute_prediction'] break logging_df = add_logging_entry(logging_df, pif_key, True, None, '', False, old_date) return dict_list, logging_df def process_biomarker_detail(args): biomarker_detail, df_list, logging_df = args attributes = biomarker_detail['attribute'] for attribute in attributes: attribute_details = attribute['attribute_details'] attribute['attribute_details'], logging_df = report_date_insertion(attribute_details, df_list, logging_df) return biomarker_detail, logging_df def json_report_date_insertion(json_data, df_list, logging_df): biomarker_details = json_data['patient_level']['biomarkers']['details'] with Pool() as pool: results = pool.map(process_biomarker_detail, [(biomarker_detail, df_list, logging_df) for biomarker_detail in biomarker_details]) updated_biomarker_details, updated_logging_df = zip(*results) json_data['patient_level']['biomarkers']['details'] = updated_biomarker_details return json_data, updated_logging_df