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parser
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steve 6 years ago
parent c428143ef1
commit 9d53b15e4d
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16
edi/__init__.py
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"""
(c) 2019 EDI Parser 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 xreader.py --parse claims|remits --config <path>
Embedded :
"""

100
edi/__main__.py
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"""
(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 --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 params import SYS_ARGS
from transport import factory
from parser import *
import os
import json
import sys
if __name__ == '__main__' :
"""
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:27217'}
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)
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(row= content)
if logs:
logger.write(row=logs)
pass
else:
print (__doc__)

18
edi/params.py
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import sys
SYS_ARGS = {'context':''}
if len(sys.argv) > 1:
N = len(sys.argv)
for i in range(1,N):
value = None
if sys.argv[i].startswith('--'):
key = sys.argv[i][2:] #.replace('-','')
SYS_ARGS[key] = 1
if i + 1 < N:
value = sys.argv[i + 1] = sys.argv[i+1].strip()
if key and value:
SYS_ARGS[key] = value
i += 2

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edi/parser.py
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"""
(c) 2019 EDI-Parser 1.0
Vanderbilt University Medical Center, Health Information Privacy Laboratory
https://hiplab.mc.vanderbilt.edu/tools
Authors:
Khanhly Nguyen,
Steve L. Nyemba<steve.l.nyemba@vanderbilt.edu>
License:
MIT, terms are available at https://opensource.org/licenses/MIT
This parser was originally written by Khanhly Nguyen for her internship and is intended to parse x12 835,837 and others provided the appropriate configuration
USAGE :
- COMMAND LINE
- EMBEDDED
"""
import os
import sys
def split(row,sep='*',prefix='HI'):
"""
This function is designed to split an x12 row and
"""
if row.startswith(prefix) is False:
value = []
for row_value in row.replace('~','').split(sep) :
if '>' in row_value :
if row_value.startswith('HC') or row_value.startswith('AD'):
value += row_value.split('>')[:2]
else:
value += row_value.split('>')
else :
value.append(row_value)
return [xchar.replace('\r','') for xchar in value] #row.replace('~','').split(sep)
else:
return [ [prefix]+ split(item,'>') for item in row.replace('~','').split(sep)[1:] ]
def get_config(config,row):
"""
This function will return the meaningfull parts of the configuration for a given item
"""
_row = list(row) if type(row[0]) == str else list(row[0])
_info = config[_row[0]] if _row[0] in config else {}
key = None
if '@ref' in _info:
key = list(set(_row) & set(_info['@ref'].keys()))
if key :
key = key[0]
return _info['@ref'][key]
else:
return {}
if not _info and 'SIMILAR' in config:
#
# Let's look for the nearest key using the edit distance
if _row[0] in config['SIMILAR'] :
key = config['SIMILAR'][_row[0]]
_info = config[key]
return _info
def format_date(value) :
year = value[:4]
month = value[4:6]
day = value[6:]
return "-".join([year,month,day])[:10] #{"year":year,"month":month,"day":day}
def format_time(value):
return ":".join([value[:2],value[2:] ])[:5]
def format_proc(value):
if ':' in value :
return {"procedure_type":value.split(':')[0].strip(),"procedure_code":value.split(':')[1].strip()}
else:
return value
def map(row,config,version):
label = config['label'] if 'label' in config else None
omap = config['map'] if version not in config else config[version]
anchors = config['anchors'] if 'anchors' in config else []
if type(row[0]) == str:
object_value = {}
for key in omap :
index = omap[key]
if anchors and set(anchors) & set(row):
_key = list(set(anchors) & set(row))[0]
aindex = row.index(_key)
index = aindex + index
if index < len(row) :
value = row[index]
if 'cast' in config and key in config['cast'] and value.strip() != '' :
value = eval(config['cast'][key])(value)
pass
if 'syn' in config and value in config['syn'] :
value = config['syn'][value]
if type(value) == dict :
object_value = dict(object_value, **value)
else:
object_value[key] = value
else:
#
# we are dealing with a complex object
object_value = []
for row_item in row :
object_value.append( list(map(row_item,config,version)))
# object_value = {label:object_value}
return object_value
def get_locations(x12_file,section='HL') :
locations = []
for line in x12_file :
if line.strip().startswith(section) :
i = x12_file.index(line)
locations.append(i)
return locations
#def get_claims(filename,config,section) :
def get_content(filename,config,section=None) :
"""
This function returns the of the EDI file parsed given the configuration specified
:section loop prefix (HL, CLP)
:config configuration with formatting rules, labels ...
:filename location of the file
"""
section = section if section else config['SECTION']
x12_file = open(filename).read().split('\n')
if len(x12_file) == 1 :
x12_file = x12_file[0].split('~')
locations = get_locations(x12_file,section)
claims = []
logs = []
# VERSION = x12_file[2].split('*')[3].replace('~','')
VERSION = x12_file[1].split('*')[-1].replace('~','')
row = split(x12_file[3])
_info = get_config(config,row)
_default_value = list(map(row,_info,VERSION)) if _info else None
N = len(locations)
for index in range(0,N-1):
beg = locations[index]
end = locations[index+1]
claim = {}
for row in x12_file[beg:end] :
row = split(row)
_info = get_config(config,row)
if _info :
try:
# tmp = map(row,_info,VERSION)
tmp = list(map(row,_info,VERSION))
except Exception as e:
if sys.verion_info[0] > 2 :
logs.append ({"version":VERSION,"filename":filename,"msg":e.args[0],"X12":x12_file[beg:end]})
else:
logs.append ({"version":VERSION,"filename":filename,"msg":e.message,"X12":x12_file[beg:end]})
claim = {}
break
if 'label' not in _info :
tmp['version'] = VERSION
claim = dict(claim, **tmp)
else:
label = _info['label']
if type(tmp) == list :
claim[label] = tmp if label not in claim else claim[label] + tmp
else:
if label not in claim:
claim[label] = [tmp]
elif len(list(tmp.keys())) == 1 :
# print "\t",len(claim[label]),tmp
index = len(claim[label]) -1
claim[label][index] = dict(claim[label][index],**tmp)
else:
claim[label].append(tmp)
if claim and 'claim_id' in claim:
claim = dict(claim,**_default_value)
claim['name'] = filename[:-5].split(os.sep)[-1] #.replace(ROOT,'')
claim['index'] = index
claims.append(claim)
return claims,logs
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