152 lines
3.8 KiB
Python
152 lines
3.8 KiB
Python
|
#!/usr/bin/env python3
|
|||
|
|
# -*- coding: UTF-8 -*-
|
|||
|
|
|
|||
|
|
"""
|
|||
|
|
Created on: 2021-09-07
|
|||
|
|
@author: cjs
|
|||
|
|
# 用途：对接lims系统，post出样本信息
|
|||
|
|
# 版本：0.0.1
|
|||
|
|
# 最后编辑日期: 2021-09-07
|
|||
|
|
"""
|
|||
|
|
|
|||
|
|
from cjs_test.cjs_logger import Logger
|
|||
|
|
import datetime
|
|||
|
|
#import traceback
|
|||
|
|
import os
|
|||
|
|
import sys
|
|||
|
|
import json
|
|||
|
|
import requests
|
|||
|
|
|
|||
|
|
|
|||
|
|
# 运行模式
|
|||
|
|
RUN_MODE = 'formal'
|
|||
|
|
|
|||
|
|
# 运行参数
|
|||
|
|
URL_DD = {'login': {'test': 'https://gene.jmdna.wiki361.com/user/login/auth',
|
|||
|
|
'formal': 'https://dna.jmdna.com/user/login/auth'},
|
|||
|
|
'sample':
|
|||
|
|
{'test':
|
|||
|
|
'https://gene.jmdna.wiki361.com/sample/sample/search?report=true',
|
|||
|
|
'formal':
|
|||
|
|
'https://dna.jmdna.com/sample/sample/search?report=true'}}
|
|||
|
|
|
|||
|
|
USER_DD = {'test': {'USER_NAME': 'zlseq', 'USER_PASS': 'seq345'},
|
|||
|
|
'formal': {'USER_NAME': 'zlseq', 'USER_PASS': 'seq345@JM'}}
|
|||
|
|
|
|||
|
|
# 固定参数
|
|||
|
|
USER_NAME = USER_DD[RUN_MODE]['USER_NAME']
|
|||
|
|
USER_PASS = USER_DD[RUN_MODE]['USER_PASS']
|
|||
|
|
|
|||
|
|
# 全局参数
|
|||
|
|
GLog = None
|
|||
|
|
StartTime = None
|
|||
|
|
|
|||
|
|
SampleID = ''
|
|||
|
|
Output_dir = ''
|
|||
|
|
|
|||
|
|
|
|||
|
|
def usage(df_exe):
|
|||
|
|
print("Usage:")
|
|||
|
|
print("%s -s sample_id -o outdir" % df_exe)
|
|||
|
|
sys.exit(0)
|
|||
|
|
|
|||
|
|
|
|||
|
|
def Get_Argvs():
|
|||
|
|
|
|||
|
|
global GLog
|
|||
|
|
global StartTime
|
|||
|
|
global SampleID
|
|||
|
|
global Output_dir
|
|||
|
|
|
|||
|
|
argvs = sys.argv
|
|||
|
|
file_real = os.path.realpath(argvs[0])
|
|||
|
|
bin_name = os.path.basename(file_real)
|
|||
|
|
|
|||
|
|
# StartTime = datetime.datetime.now()
|
|||
|
|
# ymd = StartTime.__format__('%Y%m%d_%H%M%S')
|
|||
|
|
|
|||
|
|
# print(argvs)
|
|||
|
|
|
|||
|
|
if len(argvs) < 5:
|
|||
|
|
print('参数列表数量不对, %s' % argvs)
|
|||
|
|
usage(bin_name)
|
|||
|
|
|
|||
|
|
else:
|
|||
|
|
# 参数解析
|
|||
|
|
argv_index = 1
|
|||
|
|
for argv in argvs[1:]:
|
|||
|
|
argv_index += 1
|
|||
|
|
argv = argv.upper()
|
|||
|
|
|
|||
|
|
# 必选参数获取
|
|||
|
|
if argv == '-S':
|
|||
|
|
SampleID = argvs[argv_index]
|
|||
|
|
elif argv == '-O':
|
|||
|
|
Output_dir = os.path.realpath(argvs[argv_index])
|
|||
|
|
# 新建日志
|
|||
|
|
if not os.path.exists(Output_dir):
|
|||
|
|
os.makedirs(Output_dir)
|
|||
|
|
|
|||
|
|
# log_base = '%s_%s.log' % (bin_name, ymd)
|
|||
|
|
# log_full = os.path.join(Output_dir, log_base)
|
|||
|
|
# GLog = Logger(log_full, mode='w')
|
|||
|
|
# GLog.info('argvs, %s' % argvs)
|
|||
|
|
# GLog.info('start')
|
|||
|
|
|
|||
|
|
# 核对参数解析结果
|
|||
|
|
if SampleID == '':
|
|||
|
|
print('参数中未能解析出样本ID')
|
|||
|
|
usage(bin_name)
|
|||
|
|
|
|||
|
|
|
|||
|
|
def Get_Token():
|
|||
|
|
res_token = ''
|
|||
|
|
post_dict = {"userName": USER_NAME, "password": USER_PASS}
|
|||
|
|
url = URL_DD['login'][RUN_MODE]
|
|||
|
|
response = requests.post(url, data=json.dumps(post_dict))
|
|||
|
|
req_dd = json.loads(response.text)
|
|||
|
|
# print(req_dd)
|
|||
|
|
req_code = req_dd.get('code')
|
|||
|
|
if req_code != -1:
|
|||
|
|
print(req_dd)
|
|||
|
|
else:
|
|||
|
|
res_token = req_dd.get('data').get('accessToken')
|
|||
|
|
if res_token == '':
|
|||
|
|
print(req_dd)
|
|||
|
|
|
|||
|
|
# 写文件
|
|||
|
|
# json_out = 'accessToken.json'
|
|||
|
|
# with open(json_out, 'w', encoding='utf8') as ff:
|
|||
|
|
# json.dump(req_dd, ff, ensure_ascii=False, indent=4)
|
|||
|
|
return res_token
|
|||
|
|
|
|||
|
|
|
|||
|
|
def Post_SampleID(df_token):
|
|||
|
|
post_dict = {"search": {"barcode": SampleID}, "accessToken": df_token}
|
|||
|
|
url = URL_DD['sample'][RUN_MODE]
|
|||
|
|
response = requests.post(url, data=json.dumps(post_dict))
|
|||
|
|
req_dd = json.loads(response.text)
|
|||
|
|
req_nums = req_dd.get('total')
|
|||
|
|
# if req_nums == '1':
|
|||
|
|
# print(req_dd)
|
|||
|
|
|
|||
|
|
# 写文件
|
|||
|
|
json_out = ''.join([Output_dir,'/qc/',SampleID,'_post.json'])
|
|||
|
|
with open(json_out, 'w', encoding='utf8') as ff:
|
|||
|
|
json.dump(req_dd, ff, ensure_ascii=False, indent=4)
|
|||
|
|
|
|||
|
|
|
|||
|
|
if __name__ == '__main__':
|
|||
|
|
|
|||
|
|
Get_Argvs()
|
|||
|
|
token = Get_Token()
|
|||
|
|
Post_SampleID(token)
|
|||
|
|
# print(token)
|
|||
|
|
|
|||
|
|
# try:
|
|||
|
|
# pass
|
|||
|
|
# except BaseException:
|
|||
|
|
|
|||
|
|
# print(traceback.format_exc())
|
|||
|
|
# endtime = datetime.datetime.now()
|