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