|
|
@@ -0,0 +1,397 @@
|
|
|
+#!/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
|
|
|
+import transport
|
|
|
+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'])
|
|
|
+CONFIG_FILE = os.sep.join([PATH,'config.json']) if 'config' not in SYS_ARGS else SYS_ARGS['config']
|
|
|
+HELP_MESSAGE = """
|
|
|
+ cli:
|
|
|
+ #
|
|
|
+ # Signup, allows parsing configuration to be downloaded
|
|
|
+ #
|
|
|
+
|
|
|
+ # Support for SQLite3
|
|
|
+ healthcare-io.py --signup steve@the-phi.com --store sqlite
|
|
|
+
|
|
|
+ #or support for mongodb
|
|
|
+ healthcare-io.py --signup steve@the-phi.com --store mongo
|
|
|
+
|
|
|
+
|
|
|
+ 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-update 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']))
|
|
|
+ filename = CONFIG_FILE
|
|
|
+ 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()
|
|
|
+ _m = """
|
|
|
+ Thank you for signingup!!
|
|
|
+ Your configuration file is store in :path,
|
|
|
+ - More information visit https://healthcareio.the-phi.com/parser
|
|
|
+ - Access the source https://healthcareio.the-phi.com/git/code/parser
|
|
|
+
|
|
|
+ """.replace(":path",CONFIG_FILE)
|
|
|
+ print (_m)
|
|
|
+ #
|
|
|
+ # 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 disk.
|
|
|
+ Requirements for configuration file :
|
|
|
+ {out-folder,store,837,835 }
|
|
|
+ """
|
|
|
+ # filename = os.sep.join([PATH,'config.json'])
|
|
|
+ filename = CONFIG_FILE
|
|
|
+ info = None
|
|
|
+ if os.path.exists(filename):
|
|
|
+ #
|
|
|
+ # Loading the configuration file (JSON format)
|
|
|
+ file = open(filename)
|
|
|
+ info = json.loads(file.read())
|
|
|
+
|
|
|
+
|
|
|
+ if 'output-folder' not in info and not os.path.exists(OUTPUT_FOLDER) :
|
|
|
+ os.mkdir(OUTPUT_FOLDER)
|
|
|
+ elif 'output-folder' in info and not os.path.exists(info['out-folder']) :
|
|
|
+ os.mkdir(info['out-folder'])
|
|
|
+ # if 'type' in info['store'] :
|
|
|
+ lwriter = None
|
|
|
+ is_sqlite = False
|
|
|
+ if'type' in info['store'] and info['store']['type'] == 'disk.SQLiteWriter' and not os.path.exists(info['store']['args']['path']) :
|
|
|
+ lwriter = transport.factory.instance(**info['store'])
|
|
|
+ is_sqlite = True
|
|
|
+ elif 'provider' in info['store'] and info['store']['provider'] == 'sqlite' :
|
|
|
+ lwriter = transport.instance(**info['store']) ;
|
|
|
+ is_sqlite = True
|
|
|
+ if lwriter and is_sqlite:
|
|
|
+ for key in info['schema'] :
|
|
|
+ if key != 'logs' :
|
|
|
+ _id = 'claims' if key == '837' else 'remits'
|
|
|
+ else:
|
|
|
+ _id = key
|
|
|
+
|
|
|
+ if not lwriter.has(table=_id) :
|
|
|
+ lwriter.apply(info['schema'][key]['create'])
|
|
|
+
|
|
|
+ # [lwriter.apply( info['schema'][key]['create']) for key in info['schema'] if not lwriter.has(table=key)]
|
|
|
+ lwriter.close()
|
|
|
+
|
|
|
+ return info
|
|
|
+
|
|
|
+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(CONFIG_FILE)).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 = x12.Parser(CONFIG_FILE)
|
|
|
+ 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)
|
|
|
+ uri = OUTPUT_FOLDER
|
|
|
+ store_config = json.loads( (open(CONFIG_FILE)).read() )['store']
|
|
|
+ if 'type' in store_config :
|
|
|
+ uri = store_config['args']['host'] if 'host' in store_config['args'] else ( store_config['args']['path'] if 'path' in store_config['args'] else store_config['args']['database'])
|
|
|
+ if 'SQLite' in store_config['type']:
|
|
|
+ provider = 'sqlite'
|
|
|
+ elif 'sql' in store_config['type'] :
|
|
|
+ provider = 'SQL'
|
|
|
+ else:
|
|
|
+ provider = 'mongo'
|
|
|
+
|
|
|
+ else:
|
|
|
+ provider = store_config['provider']
|
|
|
+ _msg = """
|
|
|
+ Completed Parsing, The data is available in :provider database at :uri
|
|
|
+ Logs are equally available for errors and summary statistics to be compiled
|
|
|
+ """.replace(":provider",provider).replace(":uri",uri)
|
|
|
+ print (_msg)
|
|
|
+
|
|
|
+ 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(CONFIG_FILE) :
|
|
|
+ e = analytics.engine(CONFIG_FILE) #--@TODO: make the configuration file globally accessible
|
|
|
+ e.apply(type='claims',serialize=True)
|
|
|
+ SYS_ARGS['engine'] = e
|
|
|
+ SYS_ARGS['config'] = json.loads(open(CONFIG_FILE ).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 is mandatory
|
|
|
+ # SYS_ARGS['config']['args']['folder'] = SYS_ARGS['folder']
|
|
|
+
|
|
|
+ # 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(CONFIG_FILE) :
|
|
|
+ SYS_ARGS['config'] = json.loads(open(CONFIG_FILE ).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['export-config']
|
|
|
+
|
|
|
+ X12_TYPE = SYS_ARGS['export'] if 'export' in SYS_ARGS else '835'
|
|
|
+ if not os.path.exists(path) or X12_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())}
|
|
|
+ _store = json.loads( (open(path) ).read())
|
|
|
+
|
|
|
+ pipes = export.Factory.instance(type=X12_TYPE,write_store=_store,config = CONFIG_FILE) #"inspect":0,"cast":0}})
|
|
|
+ # pipes[0].run()
|
|
|
+ # print (pipes)
|
|
|
+
|
|
|
+
|
|
|
+ for thread in pipes:
|
|
|
+
|
|
|
+ if 'table' in SYS_ARGS and SYS_ARGS['table'] != thread.table :
|
|
|
+ continue
|
|
|
+ thread.start()
|
|
|
+ time.sleep(1)
|
|
|
+ thread.join()
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+ else:
|
|
|
+
|
|
|
+ print(HELP_MESSAGE)
|
Steve Nyemba