housekeeping cleanup
This commit is contained in:
Steve Nyemba
parent
d80b00106b
commit
cae983fdde
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@ -1,3 +0,0 @@
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{
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"provider":"postgresql","database":"healthcareio","schema":"public","context":"write"
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}
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@ -1,397 +0,0 @@
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#!/usr/bin/env python3
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"""
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(c) 2019 Claims Toolkit,
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Health Information Privacy Lab, Vanderbilt University Medical Center
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Steve L. Nyemba <steve.l.nyemba@vanderbilt.edu>
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Khanhly Nguyen <khanhly.t.nguyen@gmail.com>
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This code is intended to process and parse healthcare x12 837 (claims) and x12 835 (remittances) into human readable JSON format.
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The claims/outpout can be forwarded to a NoSQL Data store like couchdb and mongodb
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Usage :
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Commandline :
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python edi-parser --scope --config <path> --folder <path> --store <[mongo|disk|couch]> --<db|path]> <id|path>
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with :
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--scope <claims|remits>
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--config path of the x12 to be parsed i.e it could be 835, or 837
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--folder location of the files (they must be decompressed)
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--store data store could be disk, mongodb, couchdb
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--db|path name of the folder to store the output or the database name
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Embedded in Code :
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import edi.parser
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import json
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file = '/data/claim_1.x12'
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conf = json.loads(open('config/837.json').read())
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edi.parser.get_content(filename,conf)
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"""
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from healthcareio.params import SYS_ARGS
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from transport import factory
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import requests
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from healthcareio import analytics
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from healthcareio import server
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from healthcareio.parser import get_content
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import os
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import json
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import sys
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import numpy as np
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from multiprocessing import Process
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import time
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from healthcareio import x12
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from healthcareio.export import export
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import smart
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import transport
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from healthcareio.server import proxy
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import pandas as pd
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PATH = os.sep.join([os.environ['HOME'],'.healthcareio'])
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OUTPUT_FOLDER = os.sep.join([os.environ['HOME'],'healthcare-io'])
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INFO = None
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URL = "https://healthcareio.the-phi.com"
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if not os.path.exists(PATH) :
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os.mkdir(PATH)
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import platform
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import sqlite3 as lite
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# PATH = os.sep.join([os.environ['HOME'],'.edi-parser'])
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CONFIG_FILE = os.sep.join([PATH,'config.json']) if 'config' not in SYS_ARGS else SYS_ARGS['config']
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HELP_MESSAGE = """
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cli:
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#
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# Signup, allows parsing configuration to be downloaded
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#
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# Support for SQLite3
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healthcare-io.py --signup steve@the-phi.com --store sqlite
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#or support for mongodb
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healthcare-io.py --signup steve@the-phi.com --store mongo
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healthcare-io.py --<[signup|init]> <email> --store <sqlite|mongo> [--batch <value>]
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healthcare-io.py --parse --folder <path> [--batch <value>] [--resume]
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healthcare-io.py --check-update
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healthcare-io.py --export <835|837> --config <config-path>
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action :
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--signup|init signup user and get configuration file
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--parse starts parsing
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--check-update checks for updates
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--export export data of a 835 or 837 into another database
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parameters :
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--<[signup|init]> signup or get a configuration file from a parsing server
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--folder location of the files (the program will recursively traverse it)
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--store data store mongo or sqlite or mongodb
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--resume will attempt to resume if there was an interruption
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"""
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def signup (**args) :
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"""
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:email user's email address
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:url url of the provider to signup
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"""
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email = args['email']
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url = args['url'] if 'url' in args else URL
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folders = [PATH,OUTPUT_FOLDER]
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for path in folders :
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if not os.path.exists(path) :
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os.mkdir(path)
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#
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#
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store = args['store'] if 'store' in args else 'sqlite'
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headers = {"email":email,"client":platform.node(),"store":store,"db":args['db']}
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http = requests.session()
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r = http.post(url,headers=headers)
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#
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# store = {"type":"disk.DiskWriter","args":{"path":OUTPUT_FOLDER}}
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# if 'store' in args :
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# store = args['store']
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# filename = (os.sep.join([PATH,'config.json']))
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filename = CONFIG_FILE
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info = r.json() #{"parser":r.json(),"store":store}
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info = dict({"owner":email},**info)
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info['store']['args']['path'] =os.sep.join([OUTPUT_FOLDER,'healthcare-io.db3']) #-- sql
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info['out-folder'] = OUTPUT_FOLDER
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file = open( filename,'w')
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file.write( json.dumps(info))
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file.close()
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_m = """
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Thank you for signingup!!
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Your configuration file is store in :path,
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- More information visit https://healthcareio.the-phi.com/parser
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- Access the source https://healthcareio.the-phi.com/git/code/parser
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""".replace(":path",CONFIG_FILE)
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print (_m)
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#
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# Create the sqlite3 database to
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def log(**args):
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"""
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This function will perform a log of anything provided to it
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"""
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pass
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def init():
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"""
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read all the configuration from disk.
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Requirements for configuration file :
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{out-folder,store,837,835 }
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"""
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# filename = os.sep.join([PATH,'config.json'])
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filename = CONFIG_FILE
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info = None
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if os.path.exists(filename):
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#
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# Loading the configuration file (JSON format)
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file = open(filename)
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info = json.loads(file.read())
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if 'output-folder' not in info and not os.path.exists(OUTPUT_FOLDER) :
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os.mkdir(OUTPUT_FOLDER)
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elif 'output-folder' in info and not os.path.exists(info['out-folder']) :
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os.mkdir(info['out-folder'])
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# if 'type' in info['store'] :
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lwriter = None
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is_sqlite = False
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if'type' in info['store'] and info['store']['type'] == 'disk.SQLiteWriter' and not os.path.exists(info['store']['args']['path']) :
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lwriter = transport.factory.instance(**info['store'])
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is_sqlite = True
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elif 'provider' in info['store'] and info['store']['provider'] == 'sqlite' :
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lwriter = transport.instance(**info['store']) ;
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is_sqlite = True
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if lwriter and is_sqlite:
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for key in info['schema'] :
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if key != 'logs' :
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_id = 'claims' if key == '837' else 'remits'
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else:
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_id = key
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if not lwriter.has(table=_id) :
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lwriter.apply(info['schema'][key]['create'])
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# [lwriter.apply( info['schema'][key]['create']) for key in info['schema'] if not lwriter.has(table=key)]
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lwriter.close()
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return info
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def upgrade(**args):
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"""
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:email provide us with who you are
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:key upgrade key provided by the server for a given email
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"""
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url = args['url'] if 'url' in args else URL+"/upgrade"
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headers = {"key":args['key'],"email":args["email"],"url":url}
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def check(**_args):
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"""
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This function will check if there is an update available (versions are in the configuration file)
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:param url
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"""
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url = _args['url'][:-1] if _args['url'].endswith('/') else _args['url']
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url = url + "/version"
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if 'version' not in _args :
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version = {"_id":"version","current":0.0}
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else:
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version = _args['version']
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http = requests.session()
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r = http.get(url)
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return r.json()
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if __name__ == '__main__' :
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info = init()
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if 'out-folder' in SYS_ARGS :
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OUTPUT_FOLDER = SYS_ARGS['out-folder']
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SYS_ARGS['url'] = SYS_ARGS['url'] if 'url' in SYS_ARGS else URL
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if set(list(SYS_ARGS.keys())) & set(['signup','init']):
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#
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# This command will essentially get a new copy of the configurations
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# @TODO: Tie the request to a version ?
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#
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email = SYS_ARGS['signup'].strip() if 'signup' in SYS_ARGS else SYS_ARGS['init']
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url = SYS_ARGS['url'] if 'url' in SYS_ARGS else URL
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store = SYS_ARGS['store'] if 'store' in SYS_ARGS else 'sqlite'
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db='healthcareio' if 'db' not in SYS_ARGS else SYS_ARGS['db']
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signup(email=email,url=url,store=store,db=db)
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# else:
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# m = """
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# usage:
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# healthcareio --signup --email myemail@provider.com [--url <host>]
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# """
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# print (m)
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elif 'upgrade' in SYS_ARGS :
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#
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# perform an upgrade i.e some code or new parsers information will be provided
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#
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pass
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elif 'parse' in SYS_ARGS and info:
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"""
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In this section of the code we are expecting the user to provide :
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:folder location of the files to process or file to process
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:
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"""
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files = []
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if 'file' in SYS_ARGS :
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files = [SYS_ARGS['file']] if not os.path.isdir(SYS_ARGS['file']) else []
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if 'folder' in SYS_ARGS and os.path.exists(SYS_ARGS['folder']):
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for root,_dir,f in os.walk(SYS_ARGS['folder']) :
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if f :
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files += [os.sep.join([root,name]) for name in f]
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# names = os.listdir(SYS_ARGS['folder'])
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# files += [os.sep.join([SYS_ARGS['folder'],name]) for name in names if not os.path.isdir(os.sep.join([SYS_ARGS['folder'],name]))]
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else:
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#
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# raise an error
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pass
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#
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# if the user has specified to resume, we should look into the logs and pull the files processed and those that haven't
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#
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if 'resume' in SYS_ARGS :
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store_config = json.loads( (open(CONFIG_FILE)).read() )
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files = proxy.get.resume(files,store_config )
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# print (["Found ",len(files)," files unprocessed"])
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#
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# @TODO: Log this here so we know what is being processed or not
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SCOPE = None
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if files : #and ('claims' in SYS_ARGS['parse'] or 'remits' in SYS_ARGS['parse']):
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BATCH_COUNT = 1 if 'batch' not in SYS_ARGS else int (SYS_ARGS['batch'])
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files = np.array_split(files,BATCH_COUNT)
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procs = []
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index = 0
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for row in files :
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row = row.tolist()
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# logger.write({"process":index,"parse":SYS_ARGS['parse'],"file_count":len(row)})
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# proc = Process(target=apply,args=(row,info['store'],_info,))
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# parser = x12.Parser(os.sep.join([PATH,'config.json']))
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parser = x12.Parser(CONFIG_FILE)
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parser.set.files(row)
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parser.start()
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procs.append(parser)
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# index = index + 1
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while len(procs) > 0 :
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procs = [proc for proc in procs if proc.is_alive()]
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time.sleep(2)
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uri = OUTPUT_FOLDER
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store_config = json.loads( (open(CONFIG_FILE)).read() )['store']
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if 'type' in store_config :
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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'])
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if 'SQLite' in store_config['type']:
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provider = 'sqlite'
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elif 'sql' in store_config['type'] :
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provider = 'SQL'
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else:
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provider = 'mongo'
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else:
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provider = store_config['provider']
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_msg = """
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Completed Parsing, The data is available in :provider database at :uri
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Logs are equally available for errors and summary statistics to be compiled
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""".replace(":provider",provider).replace(":uri",uri)
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print (_msg)
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pass
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elif 'analytics' in SYS_ARGS :
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PORT = int(SYS_ARGS['port']) if 'port' in SYS_ARGS else 5500
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DEBUG= int(SYS_ARGS['debug']) if 'debug' in SYS_ARGS else 0
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SYS_ARGS['context'] = SYS_ARGS['context'] if 'context' in SYS_ARGS else ''
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#
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#
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# PATH= SYS_ARGS['config'] if 'config' in SYS_ARGS else os.sep.join([os.environ['HOME'],'.healthcareio','config.json'])
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if os.path.exists(CONFIG_FILE) :
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e = analytics.engine(CONFIG_FILE) #--@TODO: make the configuration file globally accessible
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e.apply(type='claims',serialize=True)
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SYS_ARGS['engine'] = e
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SYS_ARGS['config'] = json.loads(open(CONFIG_FILE ).read())
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else:
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SYS_ARGS['config'] = {"owner":None,"store":None}
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if 'args' not in SYS_ARGS['config'] :
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SYS_ARGS['config']["args"] = {"batch":1,"resume":True}
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#
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# folder is mandatory
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# SYS_ARGS['config']['args']['folder'] = SYS_ARGS['folder']
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# pointer = lambda : server.app.run(host='0.0.0.0',port=PORT,debug=DEBUG,threaded=False)
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# pthread = Process(target=pointer,args=())
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# pthread.start()
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elif 'check-update' in SYS_ARGS :
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_args = {"url":SYS_ARGS['url']}
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try:
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if os.path.exists(CONFIG_FILE) :
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SYS_ARGS['config'] = json.loads(open(CONFIG_FILE ).read())
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else:
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SYS_ARGS['config'] = {}
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if 'version' in SYS_ARGS['config'] :
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_args['version'] = SYS_ARGS['config']['version']
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version = check(**_args)
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_version = {"current":0.0}if 'version' not in SYS_ARGS['config'] else SYS_ARGS['config']['version']
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if _version['current'] != version['current'] :
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print ()
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print ("You need to upgrade your system to version to ",version['current'])
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print ("\t- signup (for new configuration)")
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print ("\t- use pip to upgrade the codebase")
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else:
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print ()
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print ("You are running the current configuraiton version ",_version['current'])
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except Exception as e:
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print (e)
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pass
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elif 'export' in SYS_ARGS:
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#
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# this function is designed to export the data to csv
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#
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path = SYS_ARGS['export-config']
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X12_TYPE = SYS_ARGS['export'] if 'export' in SYS_ARGS else '835'
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if not os.path.exists(path) or X12_TYPE not in ['835','837']:
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print (HELP_MESSAGE)
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else:
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#
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# Let's run the export function ..., This will push files into a data-store of choice Redshift, PostgreSQL, MySQL ...
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#
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# _store = {"type":"sql.SQLWriter","args":json.loads( (open(path) ).read())}
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_store = json.loads( (open(path) ).read())
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pipes = export.Factory.instance(type=X12_TYPE,write_store=_store,config = CONFIG_FILE) #"inspect":0,"cast":0}})
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# pipes[0].run()
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# print (pipes)
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for thread in pipes:
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if 'table' in SYS_ARGS and SYS_ARGS['table'] != thread.table :
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continue
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thread.start()
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time.sleep(1)
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thread.join()
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else:
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print(HELP_MESSAGE)
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