413 lines
16 KiB
Python
413 lines
16 KiB
Python
#!/usr/bin/env python3
|
|
"""
|
|
(c) 2019 Claims Toolkit,
|
|
Health Information Privacy Lab, Vanderbilt University Medical Center
|
|
|
|
Steve L. Nyemba <steve.l.nyemba@vanderbilt.edu>
|
|
Khanhly Nguyen <khanhly.t.nguyen@gmail.com>
|
|
|
|
|
|
This code is intended to process and parse healthcare x12 837 (claims) and x12 835 (remittances) into human readable JSON format.
|
|
The claims/outpout can be forwarded to a NoSQL Data store like couchdb and mongodb
|
|
Usage :
|
|
Commandline :
|
|
python edi-parser --scope --config <path> --folder <path> --store <[mongo|disk|couch]> --<db|path]> <id|path>
|
|
|
|
with :
|
|
--scope <claims|remits>
|
|
--config path of the x12 to be parsed i.e it could be 835, or 837
|
|
--folder location of the files (they must be decompressed)
|
|
--store data store could be disk, mongodb, couchdb
|
|
--db|path name of the folder to store the output or the database name
|
|
|
|
Embedded in Code :
|
|
|
|
import edi.parser
|
|
import json
|
|
|
|
file = '/data/claim_1.x12'
|
|
conf = json.loads(open('config/837.json').read())
|
|
edi.parser.get_content(filename,conf)
|
|
"""
|
|
from healthcareio.params import SYS_ARGS
|
|
from transport import factory
|
|
import requests
|
|
from healthcareio import analytics
|
|
from healthcareio import server
|
|
|
|
|
|
from healthcareio.parser import get_content
|
|
import os
|
|
import json
|
|
import sys
|
|
import numpy as np
|
|
from multiprocessing import Process
|
|
import time
|
|
from healthcareio import x12
|
|
from healthcareio.export import export
|
|
import smart
|
|
from healthcareio.server import proxy
|
|
import pandas as pd
|
|
|
|
PATH = os.sep.join([os.environ['HOME'],'.healthcareio'])
|
|
OUTPUT_FOLDER = os.sep.join([os.environ['HOME'],'healthcare-io'])
|
|
INFO = None
|
|
URL = "https://healthcareio.the-phi.com"
|
|
if not os.path.exists(PATH) :
|
|
os.mkdir(PATH)
|
|
import platform
|
|
import sqlite3 as lite
|
|
# PATH = os.sep.join([os.environ['HOME'],'.edi-parser'])
|
|
HELP_MESSAGE = """
|
|
cli:
|
|
|
|
healthcare-io.py --<[signup|init]> <email> --store <sqlite|mongo> [--batch <value>]
|
|
healthcare-io.py --parse --folder <path> [--batch <value>] [--resume]
|
|
healthcare-io.py --check-update
|
|
healthcare-io.py --export <835|837> --config <config-path>
|
|
action :
|
|
--signup|init signup user and get configuration file
|
|
--parse starts parsing
|
|
--check checks for updates
|
|
--export export data of a 835 or 837 into another database
|
|
parameters :
|
|
--<[signup|init]> signup or get a configuration file from a parsing server
|
|
--folder location of the files (the program will recursively traverse it)
|
|
--store data store mongo or sqlite or mongodb
|
|
--resume will attempt to resume if there was an interruption
|
|
"""
|
|
def signup (**args) :
|
|
"""
|
|
:email user's email address
|
|
:url url of the provider to signup
|
|
"""
|
|
|
|
email = args['email']
|
|
url = args['url'] if 'url' in args else URL
|
|
folders = [PATH,OUTPUT_FOLDER]
|
|
for path in folders :
|
|
if not os.path.exists(path) :
|
|
os.mkdir(path)
|
|
|
|
#
|
|
#
|
|
store = args['store'] if 'store' in args else 'sqlite'
|
|
headers = {"email":email,"client":platform.node(),"store":store,"db":args['db']}
|
|
http = requests.session()
|
|
r = http.post(url,headers=headers)
|
|
|
|
#
|
|
# store = {"type":"disk.DiskWriter","args":{"path":OUTPUT_FOLDER}}
|
|
# if 'store' in args :
|
|
# store = args['store']
|
|
filename = (os.sep.join([PATH,'config.json']))
|
|
info = r.json() #{"parser":r.json(),"store":store}
|
|
info = dict({"owner":email},**info)
|
|
info['store']['args']['path'] =os.sep.join([OUTPUT_FOLDER,'healthcare-io.db3']) #-- sql
|
|
info['out-folder'] = OUTPUT_FOLDER
|
|
|
|
file = open( filename,'w')
|
|
file.write( json.dumps(info))
|
|
file.close()
|
|
|
|
#
|
|
# Create the sqlite3 database to
|
|
|
|
|
|
def log(**args):
|
|
"""
|
|
This function will perform a log of anything provided to it
|
|
"""
|
|
pass
|
|
def init():
|
|
"""
|
|
read all the configuration from the
|
|
"""
|
|
filename = os.sep.join([PATH,'config.json'])
|
|
info = None
|
|
if os.path.exists(filename):
|
|
file = open(filename)
|
|
info = json.loads(file.read())
|
|
if not os.path.exists(info['out-folder']) :
|
|
os.mkdir(info['out-folder'])
|
|
|
|
if info['store']['type'] == 'disk.SQLiteWriter' and not os.path.exists(info['store']['args']['path']) :
|
|
conn = lite.connect(info['store']['args']['path'],isolation_level=None)
|
|
for key in info['schema'] :
|
|
_sql = info['schema'][key]['create']
|
|
# r = conn.execute("select * from sqlite_master where name in ('claims','remits')")
|
|
conn.execute(_sql)
|
|
conn.commit()
|
|
conn.close()
|
|
|
|
return info
|
|
#
|
|
# Global variables that load the configuration files
|
|
|
|
# def parse(**args):
|
|
# """
|
|
# This function will parse the content of a claim or remittance (x12 format) give the following parameters
|
|
# :filename absolute path of the file to be parsed
|
|
# :type claims|remits in x12 format
|
|
# """
|
|
# global INFO
|
|
# if not INFO :
|
|
# INFO = init()
|
|
# if args['type'] == 'claims' :
|
|
# CONFIG = INFO['parser']['837']
|
|
# elif args['type'] == 'remits' :
|
|
# CONFIG = INFO['parser']['835']
|
|
# else:
|
|
# CONFIG = None
|
|
# if CONFIG :
|
|
# # CONFIG = CONFIG[-1] if 'version' not in args and (args['version'] < len(CONFIG)) else CONFIG[0]
|
|
# CONFIG = CONFIG[int(args['version'])-1] if 'version' in SYS_ARGS and int(SYS_ARGS['version']) < len(CONFIG) else CONFIG[-1]
|
|
# SECTION = CONFIG['SECTION']
|
|
# os.environ['HEALTHCAREIO_SALT'] = INFO['owner']
|
|
|
|
|
|
# return get_content(args['filename'],CONFIG,SECTION)
|
|
# def resume (files,id,config):
|
|
# _args = config['store'].copy()
|
|
# if 'mongo' in config['store']['type'] :
|
|
# _args['type'] = 'mongo.MongoReader'
|
|
# reader = factory.instance(**_args)
|
|
# _files = []
|
|
# if 'resume' in config['analytics'] :
|
|
# _args = config['analytics']['resume'][id]
|
|
# _files = reader.read(**_args)
|
|
# _files = [item['name'] for item in _files if item['name'] != None]
|
|
# return list(set(files) - set(_files))
|
|
|
|
# return files
|
|
# pass
|
|
# def apply(files,store_info,logger_info=None):
|
|
# """
|
|
# :files list of files to be processed in this given thread/process
|
|
# :store_info information about data-store, for now disk isn't thread safe
|
|
# :logger_info information about where to store the logs
|
|
# """
|
|
|
|
# if not logger_info :
|
|
# logger = factory.instance(type='disk.DiskWriter',args={'path':os.sep.join([info['out-folder'],SYS_ARGS['parse']+'.log'])})
|
|
# else:
|
|
# logger = factory.instance(**logger_info)
|
|
|
|
# writer = factory.instance(**store_info)
|
|
# for filename in files :
|
|
|
|
# if filename.strip() == '':
|
|
# continue
|
|
# # content,logs = get_content(filename,CONFIG,CONFIG['SECTION'])
|
|
# #
|
|
# try:
|
|
# content,logs = parse(filename = filename,type=SYS_ARGS['parse'])
|
|
|
|
# if content :
|
|
# writer.write(content)
|
|
# if logs :
|
|
# [logger.write(dict(_row,**{"parse":SYS_ARGS['parse']})) for _row in logs]
|
|
# else:
|
|
# logger.write({"parse":SYS_ARGS['parse'],"name":filename,"completed":True,"rows":len(content)})
|
|
# except Exception as e:
|
|
|
|
# logger.write({"parse":SYS_ARGS['parse'],"filename":filename,"completed":False,"rows":-1,"msg":e.args[0]})
|
|
# # print ([filename,len(content)])
|
|
# #
|
|
# # @TODO: forward this data to the writer and log engine
|
|
#
|
|
def upgrade(**args):
|
|
"""
|
|
:email provide us with who you are
|
|
:key upgrade key provided by the server for a given email
|
|
"""
|
|
url = args['url'] if 'url' in args else URL+"/upgrade"
|
|
headers = {"key":args['key'],"email":args["email"],"url":url}
|
|
def check(**_args):
|
|
"""
|
|
This function will check if there is an update available (versions are in the configuration file)
|
|
:param url
|
|
"""
|
|
url = _args['url'][:-1] if _args['url'].endswith('/') else _args['url']
|
|
url = url + "/version"
|
|
if 'version' not in _args :
|
|
version = {"_id":"version","current":0.0}
|
|
else:
|
|
version = _args['version']
|
|
http = requests.session()
|
|
r = http.get(url)
|
|
return r.json()
|
|
|
|
if __name__ == '__main__' :
|
|
info = init()
|
|
|
|
if 'out-folder' in SYS_ARGS :
|
|
OUTPUT_FOLDER = SYS_ARGS['out-folder']
|
|
SYS_ARGS['url'] = SYS_ARGS['url'] if 'url' in SYS_ARGS else URL
|
|
|
|
if set(list(SYS_ARGS.keys())) & set(['signup','init']):
|
|
#
|
|
# This command will essentially get a new copy of the configurations
|
|
# @TODO: Tie the request to a version ?
|
|
#
|
|
|
|
email = SYS_ARGS['signup'].strip() if 'signup' in SYS_ARGS else SYS_ARGS['init']
|
|
url = SYS_ARGS['url'] if 'url' in SYS_ARGS else URL
|
|
store = SYS_ARGS['store'] if 'store' in SYS_ARGS else 'sqlite'
|
|
db='healthcareio' if 'db' not in SYS_ARGS else SYS_ARGS['db']
|
|
signup(email=email,url=url,store=store,db=db)
|
|
# else:
|
|
# m = """
|
|
# usage:
|
|
# healthcareio --signup --email myemail@provider.com [--url <host>]
|
|
|
|
# """
|
|
# print (m)
|
|
elif 'upgrade' in SYS_ARGS :
|
|
#
|
|
# perform an upgrade i.e some code or new parsers information will be provided
|
|
#
|
|
|
|
pass
|
|
elif 'parse' in SYS_ARGS and info:
|
|
"""
|
|
In this section of the code we are expecting the user to provide :
|
|
:folder location of the files to process or file to process
|
|
:
|
|
"""
|
|
files = []
|
|
if 'file' in SYS_ARGS :
|
|
files = [SYS_ARGS['file']] if not os.path.isdir(SYS_ARGS['file']) else []
|
|
if 'folder' in SYS_ARGS and os.path.exists(SYS_ARGS['folder']):
|
|
for root,_dir,f in os.walk(SYS_ARGS['folder']) :
|
|
|
|
if f :
|
|
files += [os.sep.join([root,name]) for name in f]
|
|
|
|
# names = os.listdir(SYS_ARGS['folder'])
|
|
# files += [os.sep.join([SYS_ARGS['folder'],name]) for name in names if not os.path.isdir(os.sep.join([SYS_ARGS['folder'],name]))]
|
|
else:
|
|
#
|
|
# raise an error
|
|
|
|
pass
|
|
#
|
|
# if the user has specified to resume, we should look into the logs and pull the files processed and those that haven't
|
|
#
|
|
if 'resume' in SYS_ARGS :
|
|
store_config = json.loads( (open(os.sep.join([PATH,'config.json']))).read() )
|
|
files = proxy.get.resume(files,store_config )
|
|
# print (["Found ",len(files)," files unprocessed"])
|
|
#
|
|
# @TODO: Log this here so we know what is being processed or not
|
|
SCOPE = None
|
|
|
|
if files : #and ('claims' in SYS_ARGS['parse'] or 'remits' in SYS_ARGS['parse']):
|
|
|
|
BATCH_COUNT = 1 if 'batch' not in SYS_ARGS else int (SYS_ARGS['batch'])
|
|
|
|
files = np.array_split(files,BATCH_COUNT)
|
|
procs = []
|
|
index = 0
|
|
for row in files :
|
|
|
|
row = row.tolist()
|
|
# logger.write({"process":index,"parse":SYS_ARGS['parse'],"file_count":len(row)})
|
|
# proc = Process(target=apply,args=(row,info['store'],_info,))
|
|
parser = x12.Parser(os.sep.join([PATH,'config.json']))
|
|
parser.set.files(row)
|
|
parser.start()
|
|
procs.append(parser)
|
|
# index = index + 1
|
|
while len(procs) > 0 :
|
|
procs = [proc for proc in procs if proc.is_alive()]
|
|
time.sleep(2)
|
|
|
|
|
|
|
|
pass
|
|
elif 'analytics' in SYS_ARGS :
|
|
PORT = int(SYS_ARGS['port']) if 'port' in SYS_ARGS else 5500
|
|
DEBUG= int(SYS_ARGS['debug']) if 'debug' in SYS_ARGS else 0
|
|
SYS_ARGS['context'] = SYS_ARGS['context'] if 'context' in SYS_ARGS else ''
|
|
#
|
|
#
|
|
|
|
# PATH= SYS_ARGS['config'] if 'config' in SYS_ARGS else os.sep.join([os.environ['HOME'],'.healthcareio','config.json'])
|
|
|
|
if os.path.exists(os.sep.join([PATH,'config.json'])) :
|
|
e = analytics.engine(os.sep.join([PATH,'config.json'])) #--@TODO: make the configuration file globally accessible
|
|
e.apply(type='claims',serialize=True)
|
|
SYS_ARGS['engine'] = e
|
|
SYS_ARGS['config'] = json.loads(open(os.sep.join([PATH,'config.json'])).read())
|
|
else:
|
|
SYS_ARGS['config'] = {"owner":None,"store":None}
|
|
|
|
if 'args' not in SYS_ARGS['config'] :
|
|
SYS_ARGS['config']["args"] = {"batch":1,"resume":True,"folder":"/data"}
|
|
|
|
me = pd.DataFrame(smart.top.read(name='healthcare-io.py')).args.unique().tolist()
|
|
SYS_ARGS['me'] = me[0] #-- This key will identify the current process
|
|
|
|
pointer = lambda : server.app.run(host='0.0.0.0',port=PORT,debug=DEBUG,threaded=False)
|
|
pthread = Process(target=pointer,args=())
|
|
pthread.start()
|
|
elif 'check-update' in SYS_ARGS :
|
|
_args = {"url":SYS_ARGS['url']}
|
|
try:
|
|
if os.path.exists(os.sep.join([PATH,'config.json'])) :
|
|
SYS_ARGS['config'] = json.loads((open(os.sep.join([PATH,'config.json']))).read())
|
|
else:
|
|
SYS_ARGS['config'] = {}
|
|
if 'version' in SYS_ARGS['config'] :
|
|
_args['version'] = SYS_ARGS['config']['version']
|
|
version = check(**_args)
|
|
_version = {"current":0.0}if 'version' not in SYS_ARGS['config'] else SYS_ARGS['config']['version']
|
|
if _version['current'] != version['current'] :
|
|
print ()
|
|
print ("You need to upgrade your system to version to ",version['current'])
|
|
print ("\t- signup (for new configuration)")
|
|
print ("\t- use pip to upgrade the codebase")
|
|
else:
|
|
print ()
|
|
print ("You are running the current configuraiton version ",_version['current'])
|
|
except Exception as e:
|
|
print (e)
|
|
pass
|
|
|
|
elif 'export' in SYS_ARGS:
|
|
#
|
|
# this function is designed to export the data to csv
|
|
#
|
|
path = SYS_ARGS['config']
|
|
TYPE = SYS_ARGS['export'] if 'export' in SYS_ARGS else '835'
|
|
if not os.path.exists(path) or TYPE not in ['835','837']:
|
|
print (HELP_MESSAGE)
|
|
else:
|
|
#
|
|
# Let's run the export function ..., This will push files into a data-store of choice Redshift, PostgreSQL, MySQL ...
|
|
#
|
|
_store = {"type":"sql.SQLWriter","args":json.loads( (open(path) ).read())}
|
|
|
|
pipes = export.Factory.instance(type=TYPE,write_store=_store) #"inspect":0,"cast":0}})
|
|
# pipes[0].run()
|
|
|
|
for thread in pipes:
|
|
|
|
if 'table' in SYS_ARGS and SYS_ARGS['table'] != thread.table :
|
|
continue
|
|
thread.start()
|
|
time.sleep(1)
|
|
thread.join()
|
|
|
|
# print (Subject.cache)
|
|
# while pipes :
|
|
# pipes = [thread for thread in pipes if thread.is_alive()]
|
|
# time.sleep(1)
|
|
|
|
|
|
|
|
else:
|
|
|
|
print(HELP_MESSAGE)
|