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)