#!/usr/bin/env python3 """ (c) 2019 Claims Toolkit, Health Information Privacy Lab, Vanderbilt University Medical Center Steve L. Nyemba Khanhly Nguyen 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 --folder --store <[mongo|disk|couch]> -- with : --scope --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 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']) 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 ] # """ # 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 # format = SYS_ARGS['format'] if 'format' in SYS_ARGS else 'csv' format = format.lower() if set([format]) not in ['xls','csv'] : format = 'csv' else: msg = """ cli: healthcare-io.py --<[signup|init]> --store [--batch ] healthcare-io.py --parse --folder [--batch ] [--resume] healthcare-io.py --check-update action : --signup|init signup user and get configuration file --parse starts parsing --check checks for updates 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 """ print(msg) pass # """ # The program was called from the command line thus we are expecting # parse in [claims,remits] # config os.sep.path.exists(path) # folder os.sep.path.exists(path) # store store () # """ # p = len( set(['store','config','folder']) & set(SYS_ARGS.keys())) == 3 and ('db' in SYS_ARGS or 'path' in SYS_ARGS) # TYPE = { # 'mongo':'mongo.MongoWriter', # 'couch':'couch.CouchWriter', # 'disk':'disk.DiskWriter' # } # INFO = { # '837':{'scope':'claims','section':'HL'}, # '835':{'scope':'remits','section':'CLP'} # } # if p : # args = {} # scope = SYS_ARGS['config'][:-5].split(os.sep)[-1] # CONTEXT = INFO[scope]['scope'] # # # # @NOTE: # # improve how database and data stores are handled. # if SYS_ARGS['store'] == 'couch' : # args = {'url': SYS_ARGS['url'] if 'url' in SYS_ARGS else 'http://localhost:5984'} # args['dbname'] = SYS_ARGS['db'] # elif SYS_ARGS ['store'] == 'mongo': # args = {'host':SYS_ARGS['host']if 'host' in SYS_ARGS else 'localhost:27017'} # if SYS_ARGS['store'] in ['mongo','couch']: # args['dbname'] = SYS_ARGS['db'] if 'db' in SYS_ARGS else 'claims_outcomes' # args['doc'] = CONTEXT # TYPE = TYPE[SYS_ARGS['store']] # writer = factory.instance(type=TYPE,args=args) # if SYS_ARGS['store'] == 'disk': # writer.init(path = 'output-claims.json') # logger = factory.instance(type=TYPE,args= dict(args,**{"doc":"logs"})) # files = os.listdir(SYS_ARGS['folder']) # CONFIG = json.loads(open(SYS_ARGS['config']).read()) # SECTION = INFO[scope]['section'] # for file in files : # if 'limit' in SYS_ARGS and files.index(file) == int(SYS_ARGS['limit']) : # break # else: # filename = os.sep.join([SYS_ARGS['folder'],file]) # try: # content,logs = get_content(filename,CONFIG,SECTION) # except Exception as e: # if sys.version_info[0] > 2 : # logs = [{"filename":filename,"msg":e.args[0]}] # else: # logs = [{"filename":filename,"msg":e.message}] # content = None # if content : # writer.write(content) # if logs: # logger.write(logs) # pass # else: # print (__doc__)