Merge branch 'dev' of lab/parse-edi into master
This commit is contained in:
steve
Gogs
commit
ddda9528e3
19
README.md
19
README.md
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@ -27,11 +27,21 @@ We wrote this frame to be used in both command line or as a library within in yo
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1. signup to get parsing configuration
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The parser is driven by a configuration, file you need by signing up.
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healthcare-io.py --signup <email> [--store <mongo|sqlite>]
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2. parsing claims in a folder
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2. check version
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healthcare-io.py --parse <claims|remits> --folder <path> [--batch <n>] [--resume]
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Occasionally the attributes in the configuration file may change, This function will determine if there is a new version available.
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healthcare-io.py --check-update
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3. parsing data in a folder
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The parser will recursively traverse a directory with claims and or remittances
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healthcare-io.py --parse --folder <path> [--batch <n>] [--resume]
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with :
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--parse tells the engine what to parse claims or remits
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@ -39,11 +49,6 @@ We wrote this frame to be used in both command line or as a library within in yo
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--batch number of processes to spawn to parse the files
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--resume tells the parser to resume parsing
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if all files weren't processed or new files were added into the folder
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3. dashboard
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There is a built-in dashboard that has displays descriptive analytics in a web browser
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healthcare-io.py --server <port> [--context <name>]
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**Embedded in Code :**
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@ -17,4 +17,6 @@ Usage :
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from healthcareio import analytics
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import healthcareio.x12 as x12
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import healthcareio.params as params
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# from healthcareio import server
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@ -32,9 +32,10 @@ Usage :
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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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@ -56,10 +57,10 @@ if not os.path.exists(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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def register (**args) :
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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 register
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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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@ -203,12 +204,27 @@ def upgrade(**args):
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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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@ -217,10 +233,10 @@ if __name__ == '__main__' :
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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 'https://healthcareio.the-phi.com'
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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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register(email=email,url=url,store=store,db=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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@ -244,11 +260,17 @@ if __name__ == '__main__' :
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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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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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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 erro
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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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@ -256,40 +278,13 @@ if __name__ == '__main__' :
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if 'resume' in SYS_ARGS :
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store_config = json.loads( (open(os.sep.join([PATH,'config.json']))).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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# 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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# logger = factory.instance(type='disk.DiskWriter',args={'path':os.sep.join([info['out-folder'],SYS_ARGS['parse']+'.log'])})
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# if info['store']['type'] == 'disk.DiskWriter' :
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# info['store']['args']['path'] += (os.sep + 'healthcare-io.json')
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# elif info['store']['type'] == 'disk.SQLiteWriter' :
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# # info['store']['args']['path'] += (os.sep + 'healthcare-io.db3')
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# pass
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# if info['store']['type'] == 'disk.SQLiteWriter' :
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# info['store']['args']['table'] = SYS_ARGS['parse'].strip().lower()
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# _info = json.loads(json.dumps(info['store']))
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# _info['args']['table']='logs'
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# else:
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# #
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# # if we are working with no-sql we will put the logs in it (performance )?
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# info['store']['args']['doc'] = SYS_ARGS['parse'].strip().lower()
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# _info = json.loads(json.dumps(info['store']))
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# _info['args']['doc'] = 'logs'
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# logger = factory.instance(**_info)
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# writer = factory.instance(**info['store'])
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#
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# we need to have batches ready for this in order to run some of these queries in parallel
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# @TODO: Make sure it is with a persistence storage (not disk .. not thread/process safe yet)
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# - Make sure we can leverage this on n-cores later on, for now the assumption is a single core
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#
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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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@ -308,26 +303,6 @@ if __name__ == '__main__' :
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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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# for filename in files :
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# if filename.strip() == '':
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# continue
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# # content,logs = get_content(filename,CONFIG,CONFIG['SECTION'])
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# #
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# try:
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# content,logs = parse(filename = filename,type=SYS_ARGS['parse'])
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# if content :
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# writer.write(content)
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# if logs :
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# [logger.write(dict(_row,**{"parse":SYS_ARGS['parse']})) for _row in logs]
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# else:
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# logger.write({"parse":SYS_ARGS['parse'],"name":filename,"completed":True,"rows":len(content)})
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# except Exception as e:
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# logger.write({"parse":SYS_ARGS['parse'],"filename":filename,"completed":False,"rows":-1,"msg":e.args[0]})
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# # print ([filename,len(content)])
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# #
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# # @TODO: forward this data to the writer and log engine
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# #
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@ -358,6 +333,28 @@ if __name__ == '__main__' :
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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(os.sep.join([PATH,'config.json'])) :
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SYS_ARGS['config'] = json.loads((open(os.sep.join([PATH,'config.json']))).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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@ -373,11 +370,15 @@ if __name__ == '__main__' :
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cli:
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healthcare-io.py --<[signup|init]> <email> --store <sqlite|mongo> [--batch <value>]
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healthcare-io.py --parse claims --folder <path> [--batch <value>]
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healthcare-io.py --parse remits --folder <path> [--batch <value>] [--resume]
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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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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 checks for updates
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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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@ -11,11 +11,11 @@ import numpy as np
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from healthcareio import x12
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from multiprocessing import Process
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from flask_socketio import SocketIO, emit, disconnect,send
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# from flask_socketio import SocketIO, emit, disconnect,send
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from healthcareio.server import proxy
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PATH = os.sep.join([os.environ['HOME'],'.healthcareio','config.json'])
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app = Flask(__name__)
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socket_ = SocketIO(app)
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# socket_ = SocketIO(app)
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def resume (files):
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_args = SYS_ARGS['config']['store'].copy()
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@ -30,7 +30,7 @@ def resume (files):
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_files = [item['name'] for item in _files]
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except Exception as e :
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pass
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print (["found ",len(files),"\tProcessed ",len(_files)])
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return list(set(files) - set(_files))
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@ -66,14 +66,14 @@ def push() :
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_args = {"aggregate":"logs","cursor":{},"allowDiskUse":True,"pipeline":pipeline}
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r = pd.DataFrame(reader.read(mongo=_args))
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r = healthcareio.analytics.Apex.apply({"chart":{"type":"donut","axis":{"x":"count","y":"type"}},"data":r})
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emit("update",r,json=True)
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# emit("update",r,json=True)
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return r
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@socket_.on('connect')
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def client_connect(**r):
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print ('Connection received')
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print (r)
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push()
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pass
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# @socket_.on('connect')
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# def client_connect(**r):
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# print ('Connection received')
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# print (r)
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# push()
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# pass
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@app.route("/favicon.ico")
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def _icon():
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@ -32,7 +32,7 @@ class get :
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_files = [item['name'] for item in _files]
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except Exception as e :
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pass
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print (["found ",len(files),"\tProcessed ",len(_files)])
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print ( [len(list(set(files) - set(_files))),' files to be processed'])
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return list(set(files) - set(_files))
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@staticmethod
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|
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@ -24,6 +24,7 @@ import sys
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from itertools import islice
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from multiprocessing import Process
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import transport
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import jsonmerge
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class void :
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pass
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class Formatters :
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@ -95,7 +96,6 @@ class Formatters :
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if _row[0] in config['SIMILAR'] :
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key = config['SIMILAR'][_row[0]]
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_info = config[key]
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return _info
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def hash(self,value):
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@ -181,13 +181,16 @@ class Formatters :
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return x
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class Parser (Process):
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def __init__(self,path):
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"""
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:path path of the configuration file (it can be absolute)
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"""
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Process.__init__(self)
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self.utils = Formatters()
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self.get = void()
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self.get.value = self.get_map
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self.get.default_value = self.get_default_value
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_config = json.loads(open(path).read())
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self._custom_config = self.get_custom(path)
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self.config = _config['parser']
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self.store = _config['store']
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@ -197,6 +200,27 @@ class Parser (Process):
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self.emit = void()
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self.emit.pre = None
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self.emit.post = None
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def get_custom(self,path) :
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"""
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:path path of the configuration file (it can be absolute)
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"""
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#
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#
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_path = path.replace('config.json','')
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if _path.endswith(os.sep) :
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_path = _path[:-1]
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_config = {}
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_path = os.sep.join([_path,'custom'])
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if os.path.exists(_path) :
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files = os.listdir(_path)
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if files :
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fullname = os.sep.join([_path,files[0]])
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||||
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_config = json.loads ( (open(fullname)).read() )
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return _config
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def set_files(self,files):
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self.files = files
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def get_map(self,row,config,version=None):
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|
@ -247,15 +271,18 @@ class Parser (Process):
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|||
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value = {key:value} if key not in value else value
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||||
|
||||
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||||
else:
|
||||
if 'syn' in config and value in config['syn'] :
|
||||
value = config['syn'][value]
|
||||
if type(value) == dict :
|
||||
|
||||
object_value = dict(object_value, **value)
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||||
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||||
else:
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||||
|
||||
object_value[key] = value
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||||
|
||||
else:
|
||||
#
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||||
# we are dealing with a complex object
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||||
|
|
@ -275,26 +302,35 @@ class Parser (Process):
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|||
return object_value
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||||
def apply(self,content,_code) :
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"""
|
||||
:file content i.e a segment with the envelope
|
||||
:content content of a file i.e a segment with the envelope
|
||||
:_code 837 or 835 (helps get the appropriate configuration)
|
||||
"""
|
||||
util = Formatters()
|
||||
# header = default_value.copy()
|
||||
value = {}
|
||||
|
||||
for row in content[:] :
|
||||
|
||||
|
||||
row = util.split(row.replace('\n','').replace('~',''))
|
||||
_info = util.get.config(self.config[_code][0],row)
|
||||
if self._custom_config and _code in self._custom_config:
|
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_cinfo = util.get.config(self._custom_config[_code],row)
|
||||
else:
|
||||
_cinfo = {}
|
||||
# _info = self.consolidate(row=row,type=_code,config=_info,util=util)
|
||||
# print ([row[0],_info])
|
||||
# print ()
|
||||
# continue
|
||||
# _cinfo = util.get.config(self._custom_config[_code],row)
|
||||
|
||||
|
||||
if _info :
|
||||
try:
|
||||
|
||||
try:
|
||||
_info = jsonmerge.merge(_info,_cinfo)
|
||||
tmp = self.get.value(row,_info)
|
||||
|
||||
# if 'P1080351470' in content[0] and 'PLB' in row:
|
||||
# print (_info)
|
||||
# print (row)
|
||||
# print (tmp)
|
||||
if not tmp :
|
||||
continue
|
||||
if 'label' in _info :
|
||||
|
|
@ -326,7 +362,9 @@ class Parser (Process):
|
|||
elif 'field' in _info :
|
||||
|
||||
name = _info['field']
|
||||
value[name] = tmp
|
||||
# value[name] = tmp
|
||||
value = jsonmerge.merge(value,{name:tmp})
|
||||
|
||||
else:
|
||||
|
||||
|
||||
|
|
@ -341,6 +379,7 @@ class Parser (Process):
|
|||
return value if value else {}
|
||||
|
||||
def get_default_value(self,content,_code):
|
||||
|
||||
util = Formatters()
|
||||
TOP_ROW = content[1].split('*')
|
||||
CATEGORY= content[2].split('*')[1].strip()
|
||||
|
|
@ -359,6 +398,8 @@ class Parser (Process):
|
|||
value['payer_id'] = SENDER_ID
|
||||
else:
|
||||
value['provider_id'] = SENDER_ID
|
||||
#
|
||||
# Let's parse this for default values
|
||||
return value
|
||||
|
||||
def read(self,filename) :
|
||||
|
|
@ -381,8 +422,14 @@ class Parser (Process):
|
|||
INITIAL_ROWS = file[:4]
|
||||
if len(INITIAL_ROWS) < 3 :
|
||||
return None,[{"name":filename,"completed":False}],None
|
||||
section = 'HL' if INITIAL_ROWS[1].split('*')[1] == 'HC' else 'CLP'
|
||||
_code = '837' if section == 'HL' else '835'
|
||||
# section = 'HL' if INITIAL_ROWS[1].split('*')[1] == 'HC' else 'CLP'
|
||||
# _code = '837' if section == 'HL' else '835'
|
||||
# print ([_code,section])
|
||||
_code = INITIAL_ROWS[2].split('*')[1].strip()
|
||||
# section = 'CLP' if _code == '835' else 'HL'
|
||||
section = self.config[_code][0]['SECTION'].strip()
|
||||
#
|
||||
# adjusting the
|
||||
DEFAULT_VALUE = self.get.default_value(INITIAL_ROWS,_code)
|
||||
DEFAULT_VALUE['name'] = filename.strip()
|
||||
#
|
||||
|
|
@ -390,22 +437,30 @@ class Parser (Process):
|
|||
# index 1 identifies file type i.e CLM for claim and CLP for remittance
|
||||
segment = []
|
||||
index = 0;
|
||||
_toprows = []
|
||||
for row in file :
|
||||
row = row.replace('\r','')
|
||||
if not segment and not row.startswith(section):
|
||||
_toprows += [row]
|
||||
if row.startswith(section) and not segment:
|
||||
|
||||
segment = [row]
|
||||
|
||||
continue
|
||||
|
||||
elif segment and not row.startswith(section):
|
||||
|
||||
segment.append(row)
|
||||
|
||||
|
||||
if len(segment) > 1 and row.startswith(section):
|
||||
#
|
||||
# process the segment somewhere (create a thread maybe?)
|
||||
#
|
||||
# default_claim = dict({"index":index},**DEFAULT_VALUE)
|
||||
# print (_toprows)
|
||||
_claim = self.apply(segment,_code)
|
||||
|
||||
# if _claim['claim_id'] == 'P1080351470' :
|
||||
# print (_claim)
|
||||
# _claim = dict(DEFAULT_VALUE,**_claim)
|
||||
|
|
@ -425,12 +480,14 @@ class Parser (Process):
|
|||
claim = self.apply(segment,_code)
|
||||
if claim :
|
||||
claim['index'] = len(claims)
|
||||
claim = jsonmerge.merge(claim,self.apply(_toprows,_code))
|
||||
claims.append(dict(DEFAULT_VALUE,**claim))
|
||||
if type(file) != list :
|
||||
file.close()
|
||||
|
||||
# x12_file = open(filename.strip(),errors='ignore').read().split('\n')
|
||||
except Exception as e:
|
||||
|
||||
logs.append ({"parse":_code,"completed":False,"name":filename,"msg":e.args[0]})
|
||||
return [],logs,None
|
||||
|
||||
|
|
|
|||
5
setup.py
5
setup.py
|
|
@ -8,14 +8,15 @@ import sys
|
|||
def read(fname):
|
||||
return open(os.path.join(os.path.dirname(__file__), fname)).read()
|
||||
args = {
|
||||
"name":"healthcareio","version":"1.4.4",
|
||||
"name":"healthcareio","version":"1.4.6",
|
||||
"author":"Vanderbilt University Medical Center",
|
||||
"author_email":"steve.l.nyemba@vumc.org",
|
||||
"include_package_data":True,
|
||||
"license":"MIT",
|
||||
"packages":find_packages(),
|
||||
"keywords":["healthcare","edi","x12","analytics","835","837","data","transport","protocol"]
|
||||
}
|
||||
args["install_requires"] = ['flask-socketio','seaborn','jinja2', 'weasyprint','data-transport@git+https://dev.the-phi.com/git/steve/data-transport.git','pymongo','numpy','cloudant','pika','boto','flask-session','smart_open','smart-top@git+https://dev.the-phi.com/git/steve/monitor.git@data-collector']
|
||||
args["install_requires"] = ['flask-socketio','seaborn','jinja2','jsonmerge', 'weasyprint','data-transport@git+https://healthcareio.the-phi.com/git/code/transport.git','pymongo','numpy','cloudant','pika','boto','botocore','flask-session','smart_open','smart-top@git+https://healthcareio.the-phi.com/git/code/smart-top.git@data-collector']
|
||||
args['url'] = 'https://hiplab.mc.vanderbilt.edu'
|
||||
args['scripts']= ['healthcareio/healthcare-io.py']
|
||||
# args['entry_points'] = {
|
||||
|
|
|
|||
Loading…
Reference in New Issue