def _getNonNullLabs(self): query = SQLQuery() # SELECT query.addSelect('proc_code') # FROM query.addFrom('stride_order_proc') # WHERE query.addWhereLike('proc_code', 'LAB%') query.addWhere('abnormal_yn is not null') query.addGroupBy('proc_code') query.addOrderBy('proc_code') results = DBUtil.execute(query) df = pd.DataFrame(results, columns=query.select).to_csv( DATA_FOLDER + 'proc_codes.csv', index=False)
def _getLabs(self): query = SQLQuery() # SELECT query.addSelect(CLINICAL_ITEM_ID) query.addSelect('name') query.addSelect('description') # FROM query.addFrom('clinical_item') # WHERE query.addWhereLike('name','LAB%') # OTHER query.addOrderBy(CLINICAL_ITEM_ID, dir='asc') print(query) print(query.getParams()) DBUtil.runDBScript(self.SCRIPT_FILE, False) results = DBUtil.execute(str(query), query.getParams()) pd.DataFrame(results, columns=query.select).to_csv('data_summary_stats/labs.csv', index=False)