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er_triage_features.py
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er_triage_features.py
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# cx_Oracle ์ฐ๋ํ ์๊ธ์ค์ฆ๋ risk-factors 10๋
์น ์ถ์ถ @ 2021.02.01
import cx_Oracle
import csv, math
from datetime import datetime, timedelta
# oracle instant client ์ฐ๋ ๋ฐ path ์ง์
import os
LOCATION = r"C:\oracle\instantclient_11_2" # oracle db๋ฅผ ์ฐ๊ธฐ์ํ ์ ํธํ์ผ
os.environ["PATH"] = LOCATION + ";" + os.environ["PATH"] # ํ๊ฒฝ๋ณ์ ๋ฑ๋ก
import pandas as pd
# command-line-arguments ์ฐธ์กฐ : https://basketdeveloper.tistory.com/57
import argparse
# job-logging์ time์ ๋ณด ์ฐ๋ @ 2021.4.19.
import time
def main(db_list, duration_list):
# timestamp ์์์๊ฐ
jobStTime = datetime.now()
print('target DB : {}'.format(db_list))
print('searching duration : {}'.format(duration_list))
# ์ ์ํด์ผํ DB์๋ฒ์ IP์ฃผ์ (ํน์ ์๋ฒ์ด๋ฆ), ํฌํธ๋ฒํธ, SID ์ ๋ณด๋ฅผ ์
๋ ฅ
dsn = cx_Oracle.makedsn(db_list[0], db_list[1], "InputYourSID")
#print(dsn)
# ๋ฐ์ดํฐ ๋ฒ ์ด์ค์ ์ด๋ฆ, ๋น๋ฐ๋ฒํธ, dsn์ผ๋ก ๋ฐ์ดํฐ ๋ฒ ์ด์ค์ ์ฐ๊ฒฐ
db = cx_Oracle.connect("InputYourId", "InputYourPw", dsn)
#print(db)
# SQL๋ฌธ ์คํ ๋ฉ๋ชจ๋ฆฌ ์์ญ(cursor)๋ฅผ ์ด๊ณ ํ์ธ
cursor = db.cursor()
query4erlist = """
select
a.PATNO /* ํ์๋ฒํธ */
, substr(b.PATNAME, 1, 1) || '*' || substr(b.PATNAME, 3, 1) /* ํ์๋ช
*/
, b.SEX /* ์ฑ๋ณ */
, fn_calc_age(a.MEDDATE, b.BIRTDATE) /* ๋์ด(๋ง) */
, to_char(a.MEDDATE, 'yyyymmdd') /* ์ง๋ฃ์ผ์/์
์์ผ์ */
, to_char(a.MEDTIME, 'yyyymmddhh24mi') /* ์๊ธ์ค ๋์ฐฉ์๊ฐ */
, to_char(a.INDATE, 'yyyymmddhh24mi') /* ์๊ธ์ค๋์ฐฉ์ผ์ */
, '' /* [M180828-1] ํ์๋ชฉ๋ก ์กฐํ์๋ ๊ฐ์ ์ํด fn ์ฐ๋ ์ ์ธ */
, decode(a.ERRSLT, '1', a.RSLTRMK1, '3', '๊ท๊ฐ', '5', '์ฌ๋ง', '7', '๊ท๊ฐ', c.COMCDNM3) /* [M180829-1] ์ง๋ฃ(ํด์ค)๊ฒฐ๊ณผ */
, decode(a.PTMIKTS2, null, a.PTMIKTS1, a.PTMIKTS1 || '/' || a.PTMIKTS2) /* [M180829-1] KTAS ์ ์ */
from
์ง๋ฃ๊ณตํต์ฝ๋ c /* [M180829-1] */
, ํ์๋ง์คํฐ b
, ์๊ธ์ ๋ณด์กฐ์ฌ์ง a
where
a.MEDDATE between to_date(:erstdate, 'yyyy-mm-dd')
and to_date(:ereddate, 'yyyy-mm-dd')
and b.PATNO = a.PATNO
and nvl(a.ERRSLT, '*') <> '8' /* [M180829-1] ํด์ค๊ฒฐ๊ณผ <๊ธฐํ> ์ ์ธ */
and b.PATNO = a.PATNO
and c.COMCD1(+) = '204' /* [M180829-1] ํด์ค๊ฒฐ๊ณผ ํญ๋ชฉ */
and c.COMCD2(+) = '000'
and c.COMCD3(+) = a.ERRSLT
order by
7 desc
"""
cursor.execute(query4erlist, erstdate=duration_list[0], ereddate=duration_list[1])
er_list_tuple = cursor.fetchall()
#print(er_list_tuple)
#print("length of er_list = ", str(len(er_list_tuple)))
# job ์ฒ๋ฆฌ๊ฑด์ init
jobCount = 0
for i in range(len(er_list_tuple)):
print(str(er_list_tuple[i][0]).replace(',','').replace('(', '').replace(')', '').replace("'", ''))
#print(str(er_list_tuple[i][4]).replace(',','').replace('(', '').replace(')', '').replace("'", ''))
#print(str(er_list_tuple[i][5]).replace(',','').replace('(', '').replace(')', '').replace("'", ''))
query4riskfactors = """
select
a.PATNO /* ํ์๋ฒํธ */
, substr(b.PATNAME, 1, 1) || '*' || substr(b.PATNAME, 3, 1) /* ํ์๋ช
*/
--, b.SEX /* ์ฑ๋ณ */
--, fn_calc_age(a.MEDDATE, b.BIRTDATE) /* ๋์ด(๋ง) */
, to_char(a.MEDDATE, 'yyyymmdd') /* ์ง๋ฃ์ผ์/์
์์ผ์ */
, to_char(a.MEDTIME, 'yyyymmddhh24mi') /* ์๊ธ์ค ๋์ฐฉ์๊ฐ */
--, to_char(a.INDATE, 'yyyymmddhh24mi') /* ์๊ธ์ค๋์ฐฉ์ผ์ */
, fn_get_er_triage('ALL_TOKEN', a.PATNO, a.MEDDATE, a.MEDTIME, '') /* ์ค์ฆ๋๋ถ๋ฅ ๊ณ์ฐ์ํ ๊ธฐ๋ณธ์ ๋ณด Token */
from
ํ์๋ง์คํฐ b
, ์๊ธ์ ๋ณด์กฐ์ฌ์ง a
where
a.PATNO = :patid
and a.MEDDATE = to_date(:erdate, 'yyyy-mm-dd')
and a.MEDTIME = to_date(:ertime, 'yyyy-mm-dd hh24:mi')
and b.PATNO = a.PATNO
"""
# ์ฐธ์กฐ : https://stackoverflow.com/questions/7465889/cx-oracle-and-exception-handling-good-practices
try:
cursor.execute(query4riskfactors, patid=str(er_list_tuple[i][0]).replace(',','').replace('(', '').replace(')', '').replace("'", ''),
erdate=str(er_list_tuple[i][4]).replace(',','').replace('(', '').replace(')', '').replace("'", ''),
ertime=str(er_list_tuple[i][5]).replace(',','').replace('(', '').replace(')', '').replace("'", '')
)
except cx_Oracle.DatabaseError as e:
print('cx_Oracle.DatabseError !! --> ' + str(e))
joblog(duration_list[0], duration_list[1], str(er_list_tuple[i]), str(e))
pass
result4riskfactors = cursor.fetchone()
print("#######################")
#print(type(dept_cd_tuple[0]))
#print(type(str(dept_cd_tuple[0])))
#print(result4riskfactors)
if result4riskfactors != None:
# ERํด์ค๊ฒฐ๊ณผ(8), KTAS(9) ์ถ๊ฐ @ 2021.6.4.
riskfactors = result4riskfactors + er_list_tuple[i][8] + er_list_tuple[i][9] + tuple(result4riskfactors[4].split('|'))
#print(riskfactors)
df_main = pd.DataFrame(riskfactors, index = ['PAT_ID', 'PAT_NM', 'MEDDATE', 'MEDTIME', 'TOKENS', 'ERRSLT', 'KTAS', 'AST', 'AMYLASE', 'HR', 'DBP', 'BT', 'BS', 'AVPU',
'SEX', 'AGE', 'WBC', 'TROPONIN', 'NA', 'PT-P', 'ALT', 'PAO2', 'SPO2', 'SBP', 'RR', 'PH', 'PASTHIST', 'PAIN', 'LACTATE',
'PT-INR', 'POTASSIUM', 'HGB', 'HCT', 'CRP', 'CREATININE', 'CK-MB', 'T-BIL', 'C.C', ''])
df = df_main.transpose()
#print(df.head())
# ์ปฌ๋ผ ๋ถ์ฌ์ฃผ๊ธฐ
#df.columns = ['PAT_ID', 'PAT_NM', 'SEX_ORG', 'AGE_ORG', 'MEDDATE', 'MEDTIME', 'INDATE', 'TOKENS', 'AST', 'AMYLASE', 'HR', 'DBP', 'BT', 'BS', 'AVPU',
# 'SEX', 'AGE', 'WBC', 'TROPONIN', 'NA', 'PT-P', 'ALT', 'PAO2', 'SPO2', 'SBP', 'RR', 'PH', 'PASTHIST', 'PAIN', 'LACTATE',
# 'PT-INR', 'POTASSIUM', 'HGB', 'HCT', 'CRP', 'CREATININE', 'CK-MB', 'T-BIL', 'C.C', '']
#print(df)
# ์ฐธ์กฐ: https://hogni.tistory.com/10
try:
if not os.path.exists('./output_' + duration_list[0] + '_' + duration_list[1] + '.csv'):
df.to_csv('./output_' + duration_list[0] + '_' + duration_list[1] + '.csv', index=False, mode='w', encoding="utf-8-sig")
print('first write finished successfuly')
else:
df.to_csv('./output_' + duration_list[0] + '_' + duration_list[1] + '.csv', index=False, mode='a', encoding="utf-8-sig", header=False)
print('concatanation finished successfuly')
# job ์ฒ๋ฆฌ๊ฑด์ ++
jobCount = jobCount + 1
except Exception as e:
df.to_csv('./raised_error_' + duration_list[0] + '_' + duration_list[1] + '.csv', index=False, encoding="utf-8-sig")
print('DataFrame append error!!!! please check it out. : ', e)
break
else:
print(str(er_list_tuple[i]).replace(',','').replace('(', '').replace(')', '') + " skipped....")
continue
cursor.close()
db.close()
# timestamp ์ข
๋ฃ์๊ฐ
jobFnTime = datetime.now()
print('============================')
print('์์
์์์๊ฐ(A) : ', jobStTime)
print('์์
์ข
๋ฃ์๊ฐ(B) : ', jobFnTime)
if (jobFnTime-jobStTime).seconds / 3600 > 1 :
print('*์์์๊ฐ(B-A) : ', str(round(((jobFnTime-jobStTime).seconds / 3600), 1)) + '์๊ฐ')
elif (jobFnTime-jobStTime).seconds / 60 > 1 :
print('*์์์๊ฐ(B-A) : ', str(round(((jobFnTime-jobStTime).seconds / 60), 1)) + '๋ถ')
else:
print('*์์์๊ฐ(B-A) : ', str(round(((jobFnTime-jobStTime).seconds), 1)) + '์ด')
print('*์ด ์์
๊ฑด์ : ', str(jobCount) + '๊ฑด')
# command-line ๋ณ์ ๊ฐ์ ธ์ค๊ธฐ
# ์ฐธ์กฐ : https://basketdeveloper.tistory.com/57
def get_arguments():
parser = argparse.ArgumentParser()
parser.add_argument(nargs='+', help='e.g.) ipAddress portNo --> 152.x.x.xxx 9999', dest='db')
parser.add_argument('--duration', '-d', nargs='*', help='e.g.) startDate endDate --> 2020-01-01 2020-12-31', default=[], dest='duration')
db_list = parser.parse_args().db
duration_list = parser.parse_args().duration
return db_list, duration_list
# ์์
๋ก๊น
def joblog(startDate, endDate, erInfo, logMsg):
row = [time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(time.time())), erInfo, logMsg]
# ์ฐธ์กฐ : https://stackoverflow.com/questions/21980500/logging-data-to-csv-with-python
with open('./joblog_' + startDate + '_' + endDate + '.csv', 'a') as f:
w = csv.writer(f)
w.writerow(row)
if __name__ == '__main__':
db_list, duration_list = get_arguments()
main(db_list, duration_list)