bug fix: resource allocation with process
This commit is contained in:
Steve Nyemba
parent
9c1adad347
commit
c3351900fa
|
|
@ -42,7 +42,7 @@ import sys
|
|||
import numpy as np
|
||||
from multiprocessing import Process
|
||||
import time
|
||||
|
||||
import x12
|
||||
|
||||
PATH = os.sep.join([os.environ['HOME'],'.healthcareio'])
|
||||
OUTPUT_FOLDER = os.sep.join([os.environ['HOME'],'healthcare-io'])
|
||||
|
|
@ -257,36 +257,29 @@ if __name__ == '__main__' :
|
|||
# @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']):
|
||||
# _map = {'claims':'837','remits':'835'}
|
||||
# key = _map[SYS_ARGS['parse']]
|
||||
# CONFIG = info['parser'][key]
|
||||
# if 'version' in SYS_ARGS and int(SYS_ARGS['version']) < len(CONFIG) :
|
||||
# CONFIG = CONFIG[ int(SYS_ARGS['version'])]
|
||||
if files : #and ('claims' in SYS_ARGS['parse'] or 'remits' in SYS_ARGS['parse']):
|
||||
# logger = factory.instance(type='disk.DiskWriter',args={'path':os.sep.join([info['out-folder'],SYS_ARGS['parse']+'.log'])})
|
||||
# if info['store']['type'] == 'disk.DiskWriter' :
|
||||
# info['store']['args']['path'] += (os.sep + 'healthcare-io.json')
|
||||
# elif info['store']['type'] == 'disk.SQLiteWriter' :
|
||||
# # info['store']['args']['path'] += (os.sep + 'healthcare-io.db3')
|
||||
# pass
|
||||
|
||||
|
||||
# if info['store']['type'] == 'disk.SQLiteWriter' :
|
||||
# info['store']['args']['table'] = SYS_ARGS['parse'].strip().lower()
|
||||
# _info = json.loads(json.dumps(info['store']))
|
||||
# _info['args']['table']='logs'
|
||||
# else:
|
||||
# CONFIG = CONFIG[-1]
|
||||
logger = factory.instance(type='disk.DiskWriter',args={'path':os.sep.join([info['out-folder'],SYS_ARGS['parse']+'.log'])})
|
||||
if info['store']['type'] == 'disk.DiskWriter' :
|
||||
info['store']['args']['path'] += (os.sep + 'healthcare-io.json')
|
||||
elif info['store']['type'] == 'disk.SQLiteWriter' :
|
||||
# info['store']['args']['path'] += (os.sep + 'healthcare-io.db3')
|
||||
pass
|
||||
# #
|
||||
# # if we are working with no-sql we will put the logs in it (performance )?
|
||||
|
||||
# info['store']['args']['doc'] = SYS_ARGS['parse'].strip().lower()
|
||||
# _info = json.loads(json.dumps(info['store']))
|
||||
# _info['args']['doc'] = 'logs'
|
||||
# logger = factory.instance(**_info)
|
||||
|
||||
if info['store']['type'] == 'disk.SQLiteWriter' :
|
||||
info['store']['args']['table'] = SYS_ARGS['parse'].strip().lower()
|
||||
_info = json.loads(json.dumps(info['store']))
|
||||
_info['args']['table']='logs'
|
||||
else:
|
||||
#
|
||||
# if we are working with no-sql we will put the logs in it (performance )?
|
||||
|
||||
info['store']['args']['doc'] = SYS_ARGS['parse'].strip().lower()
|
||||
_info = json.loads(json.dumps(info['store']))
|
||||
_info['args']['doc'] = 'logs'
|
||||
logger = factory.instance(**_info)
|
||||
|
||||
writer = factory.instance(**info['store'])
|
||||
# writer = factory.instance(**info['store'])
|
||||
|
||||
#
|
||||
# we need to have batches ready for this in order to run some of these queries in parallel
|
||||
|
|
@ -295,23 +288,19 @@ if __name__ == '__main__' :
|
|||
#
|
||||
BATCH_COUNT = 1 if 'batch' not in SYS_ARGS else int (SYS_ARGS['batch'])
|
||||
|
||||
#logger = factory.instance(type='mongo.MongoWriter',args={'db':'healthcareio','doc':SYS_ARGS['parse']+'_logs'})
|
||||
# schema = info['schema']
|
||||
|
||||
# for key in schema :
|
||||
# sql = schema[key]['create']
|
||||
# writer.write(sql)
|
||||
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,))
|
||||
proc.start()
|
||||
procs.append(proc)
|
||||
index = index + 1
|
||||
# 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)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,446 @@
|
|||
"""
|
||||
(c) 2019 Healthcare/IO 1.0
|
||||
Vanderbilt University Medical Center, Health Information Privacy Laboratory
|
||||
https://hiplab.mc.vanderbilt.edu/healthcareio
|
||||
|
||||
|
||||
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 hashlib
|
||||
import json
|
||||
import os
|
||||
import sys
|
||||
from itertools import islice
|
||||
from multiprocessing import Process
|
||||
import transport
|
||||
class void :
|
||||
pass
|
||||
class Formatters :
|
||||
def __init__(self):
|
||||
# self.config = config
|
||||
self.get = void()
|
||||
self.get.config = self.get_config
|
||||
|
||||
self.parse = void()
|
||||
self.parse.sv3 = self.sv3
|
||||
self.parse.sv2 = self.sv2
|
||||
self.sv2_parse = self.sv2
|
||||
self.sv3_parse = self.sv3
|
||||
self.parse.procedure = self.procedure
|
||||
self.parse.diagnosis = self.diagnosis
|
||||
self.parse.date = self.date
|
||||
self.format_date = self.date
|
||||
self.format_pos = self.pos
|
||||
self.format_time = self.time
|
||||
def split(self,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('>') if row.startswith('CLM') is False else [row_value]
|
||||
|
||||
else :
|
||||
|
||||
value.append(row_value.replace('\n',''))
|
||||
return [xchar.replace('\r','') for xchar in value] #row.replace('~','').split(sep)
|
||||
else:
|
||||
|
||||
return [ [prefix]+ self.split(item,'>') for item in row.replace('~','').split(sep)[1:] ]
|
||||
def get_config(self,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 hash(self,value):
|
||||
salt = os.environ['HEALTHCAREIO_SALT'] if 'HEALTHCAREIO_SALT' in os.environ else ''
|
||||
_value = str(value)+ salt
|
||||
if sys.version_info[0] > 2 :
|
||||
return hashlib.md5(_value.encode('utf-8')).hexdigest()
|
||||
else:
|
||||
return hashlib.md5(_value).hexdigest()
|
||||
|
||||
def suppress (self,value):
|
||||
return 'N/A'
|
||||
def date(self,value):
|
||||
if len(value) > 8 or '-' in value:
|
||||
value = value.split('-')[0]
|
||||
|
||||
if len(value) == 8 :
|
||||
year = value[:4]
|
||||
month = value[4:6]
|
||||
day = value[6:]
|
||||
return "-".join([year,month,day])[:10] #{"year":year,"month":month,"day":day}
|
||||
elif len(value) == 6 :
|
||||
year = '20' + value[:2]
|
||||
month = value[2:4]
|
||||
day = value[4:]
|
||||
|
||||
#
|
||||
# We have a date formatting issue
|
||||
|
||||
return "-".join([year,month,day])
|
||||
def time(self,value):
|
||||
pass
|
||||
def sv3(self,value):
|
||||
if '>' in value [1]:
|
||||
terms = value[1].split('>')
|
||||
return {'type':terms[0],'code':terms[1],"amount":float(value[2])}
|
||||
else:
|
||||
|
||||
return {"code":value[2],"type":value[1],"amount":float(value[3])}
|
||||
def sv2(self,value):
|
||||
#
|
||||
# @TODO: Sometimes there's a suffix (need to inventory all the variations)
|
||||
#
|
||||
if '>' in value or ':' in value:
|
||||
xchar = '>' if '>' in value else ':'
|
||||
_values = value.split(xchar)
|
||||
modifier = {}
|
||||
|
||||
if len(_values) > 2 :
|
||||
|
||||
modifier= {"code":_values[2]}
|
||||
if len(_values) > 3 :
|
||||
modifier['type'] = _values[3]
|
||||
_value = {"code":_values[1],"type":_values[0]}
|
||||
if modifier :
|
||||
_value['modifier'] = modifier
|
||||
|
||||
return _value
|
||||
else:
|
||||
return value
|
||||
def procedure(self,value):
|
||||
for xchar in [':','<'] :
|
||||
if xchar in value and len(value.split(xchar)) > 1 :
|
||||
#_value = {"type":value.split(':')[0].strip(),"code":value.split(':')[1].strip()}
|
||||
_value = {"type":value.split(xchar)[0].strip(),"code":value.split(xchar)[1].strip()}
|
||||
break
|
||||
else:
|
||||
_value = str(value)
|
||||
return _value
|
||||
def diagnosis(self,alue):
|
||||
|
||||
return [ {"code":item[2], "type":item[1]} for item in value if len(item) > 1]
|
||||
def pos(self,value):
|
||||
"""
|
||||
formatting place of service information within a segment (REF)
|
||||
"""
|
||||
|
||||
xchar = '>' if '>' in value else ':'
|
||||
x = value.split(xchar)
|
||||
x = {"code":x[0],"indicator":x[1],"frequency":x[2]} if len(x) == 3 else {"code":x[0],"indicator":None,"frequency":None}
|
||||
return x
|
||||
class Parser (Process):
|
||||
def __init__(self,path):
|
||||
Process.__init__(self)
|
||||
self.utils = Formatters()
|
||||
self.get = void()
|
||||
self.get.value = self.get_map
|
||||
self.get.default_value = self.get_default_value
|
||||
_config = json.loads(open(path).read())
|
||||
|
||||
self.config = _config['parser']
|
||||
self.store = _config['store']
|
||||
|
||||
self.files = []
|
||||
self.set = void()
|
||||
self.set.files = self.set_files
|
||||
def set_files(self,files):
|
||||
self.files = files
|
||||
def get_map(self,row,config,version=None):
|
||||
|
||||
# label = config['label'] if 'label' in config else None
|
||||
handler = Formatters()
|
||||
if 'map' not in config and hasattr(handler,config['apply']):
|
||||
|
||||
pointer = getattr(handler,config['apply'])
|
||||
object_value = pointer(row)
|
||||
return object_value
|
||||
|
||||
omap = config['map'] if not version or 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() != '' :
|
||||
if config['cast'][key] in ['float','int'] :
|
||||
value = eval(config['cast'][key])(value)
|
||||
elif hasattr(handler,config['cast'][key]):
|
||||
pointer = getattr(handler,config['cast'][key])
|
||||
value = pointer(value)
|
||||
else:
|
||||
print ("Missing Pointer ",config['cast'][key])
|
||||
|
||||
# print (key,value)
|
||||
|
||||
if type(value) == dict :
|
||||
for objkey in value :
|
||||
|
||||
if type(value[objkey]) == dict :
|
||||
continue
|
||||
if 'syn' in config and value[objkey] in config['syn'] :
|
||||
value[objkey] = config['syn'][ value[objkey]]
|
||||
|
||||
value = {key:value} if key not in value else value
|
||||
|
||||
else:
|
||||
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 :
|
||||
|
||||
value = self.get.value(row_item,config,version)
|
||||
object_value.append(value)
|
||||
#
|
||||
# We need to add the index of the object it matters in determining the claim types
|
||||
#
|
||||
|
||||
# object_value.append( list(get_map(row_item,config,version)))
|
||||
# object_value = {label:object_value}
|
||||
return object_value
|
||||
def apply(self,content,_code,default_value) :
|
||||
"""
|
||||
:file content i.e a segment with the envelope
|
||||
:_code 837 or 835 (helps get the appropriate configuration)
|
||||
"""
|
||||
util = Formatters()
|
||||
claim = default_value.copy()
|
||||
value = {}
|
||||
for row in content[:] :
|
||||
|
||||
row = util.split(row)
|
||||
_info = util.get.config(self.config[_code][0],row)
|
||||
|
||||
if _info :
|
||||
try:
|
||||
|
||||
tmp = self.get.value(row,_info)
|
||||
|
||||
if not tmp :
|
||||
continue
|
||||
if 'label' in _info :
|
||||
label = _info['label']
|
||||
|
||||
if type(tmp) == list :
|
||||
|
||||
value[label] = tmp if label not in value else value[label] + tmp
|
||||
|
||||
else:
|
||||
if label not in value:
|
||||
value[label] = [tmp]
|
||||
elif len(list(tmp.keys())) == 1 :
|
||||
# print "\t",len(claim[label]),tmp
|
||||
index = len(value[label]) -1
|
||||
value[label][index] = dict(value[label][index],**tmp)
|
||||
else:
|
||||
value[label].append(tmp)
|
||||
if len(value[label]) > 0 :
|
||||
labels = []
|
||||
for item in value[label] :
|
||||
item['_index'] = len(labels)
|
||||
if item not in labels :
|
||||
|
||||
labels.append(item)
|
||||
value[label] = labels
|
||||
elif 'field' in _info :
|
||||
name = _info['field']
|
||||
value[name] = tmp
|
||||
else:
|
||||
|
||||
|
||||
value = dict(value,**tmp)
|
||||
|
||||
pass
|
||||
except Exception as e :
|
||||
print ('__',e)
|
||||
pass
|
||||
|
||||
return dict(claim,**value) if value else {}
|
||||
|
||||
def get_default_value(self,content,_code):
|
||||
util = Formatters()
|
||||
TOP_ROW = content[1].split('*')
|
||||
CATEGORY= content[2].split('*')[1].strip()
|
||||
VERSION = content[1].split('*')[-1].replace('~','').replace('\n','')
|
||||
SUBMITTED_DATE = util.parse.date(TOP_ROW[4])
|
||||
SENDER_ID = TOP_ROW[2]
|
||||
row = util.split(content[3])
|
||||
|
||||
_info = util.get_config(self.config[_code][0],row)
|
||||
|
||||
value = self.get.value(row,_info,VERSION) if _info else {}
|
||||
value['category'] = {"setid": CATEGORY,"version":'X'+VERSION.split('X')[1],"id":VERSION.split('X')[0].strip()}
|
||||
value["submitted"] = SUBMITTED_DATE
|
||||
# value['version'] = VERSION
|
||||
if _code== '835' :
|
||||
value['payer_id'] = SENDER_ID
|
||||
else:
|
||||
value['provider_id'] = SENDER_ID
|
||||
return value
|
||||
|
||||
def read(self,filename) :
|
||||
"""
|
||||
:formerly get_content
|
||||
This function returns the of the EDI file parsed given the configuration specified. it is capable of identifying a file given the content
|
||||
:section loop prefix (HL, CLP)
|
||||
:config configuration with formatting rules, labels ...
|
||||
:filename location of the file
|
||||
"""
|
||||
# section = section if section else config['SECTION']
|
||||
logs = []
|
||||
claims = []
|
||||
try:
|
||||
file = open(filename.strip(),errors='ignore')
|
||||
INITIAL_ROWS = list(islice(file,4)) #.readlines(4)
|
||||
|
||||
if len(INITIAL_ROWS) == 1 :
|
||||
file = INITIAL_ROWS[0].split('~')
|
||||
INITIAL_ROWS = file[:4]
|
||||
section = 'CLM' if INITIAL_ROWS[1].split('*')[1] == 'HC' else 'CLP'
|
||||
_code = '837' if section == 'CLM' else '835'
|
||||
DEFAULT_VALUE = self.get.default_value(INITIAL_ROWS,_code)
|
||||
DEFAULT_VALUE['name'] = filename.strip()
|
||||
#
|
||||
# In the initial rows, there's redundant information (so much for x12 standard)
|
||||
# index 1 identifies file type i.e CLM for claim and CLP for remittance
|
||||
segment = []
|
||||
index = 0;
|
||||
for row in file :
|
||||
if row.startswith(section) and not segment:
|
||||
|
||||
segment = [row]
|
||||
continue
|
||||
|
||||
elif segment:
|
||||
|
||||
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)
|
||||
claim = self.apply(segment,_code,default_claim)
|
||||
|
||||
claims.append(claim)
|
||||
segment = [row]
|
||||
index += 1
|
||||
|
||||
|
||||
pass
|
||||
#
|
||||
# Handling the last claim found
|
||||
if segment[0].startswith(section) :
|
||||
default_claim = dict({"name":index},**DEFAULT_VALUE)
|
||||
|
||||
claim = self.apply(segment,_code,DEFAULT_VALUE)
|
||||
claims.append(claim)
|
||||
if type(file) != list :
|
||||
file.close()
|
||||
|
||||
# x12_file = open(filename.strip(),errors='ignore').read().split('\n')
|
||||
except Exception as e:
|
||||
logs.append ({"parse":"claims" if _code == '837' else 'remits',"completed":False,"name":filename,"msg":e.args[0]})
|
||||
return [],logs
|
||||
|
||||
rate = 0 if len(claims) == 0 else (1 + index)/len(claims)
|
||||
logs.append ({"parse":"claims" if _code == '837' else 'remits',"completed":True,"name":filename,"rate":rate})
|
||||
# self.finish(claims,logs,_code)
|
||||
return claims,logs,_code
|
||||
def run(self):
|
||||
for filename in self.files :
|
||||
content,logs,_code = self.read(filename)
|
||||
self.finish(content,logs,_code)
|
||||
def finish(self,content,logs,_code) :
|
||||
args = self.store
|
||||
_args = json.loads(json.dumps(self.store))
|
||||
if args['type'] == 'mongo.MongoWriter' :
|
||||
args['args']['doc'] = 'claims' if _code == '837' else 'remits'
|
||||
_args['args']['doc'] = 'logs'
|
||||
if content :
|
||||
writer = transport.factory.instance(**args)
|
||||
writer.write(content)
|
||||
writer.close()
|
||||
if logs :
|
||||
logger = transport.factory.instance(**_args)
|
||||
logger.write(logs)
|
||||
logger.close()
|
||||
|
||||
|
||||
|
||||
# p = Parser('/home/steve/.healthcareio/config.json')
|
||||
# p.set.files(['../../data/small/claims/ssiUB1122042711220427127438.clm_191122T043504'])
|
||||
# path = '../../data/small/claims/ssiUB1122042711220427127438.clm_191122T043504'
|
||||
# path = '../../data/small/claims/problems-with-procs'
|
||||
# path = '../../data/small/remits/1SG03927258.dat_181018T074559'
|
||||
|
||||
# _path = "../../data/small/remits/1TR21426701.dat_180703T074559"
|
||||
# p.start()
|
||||
# p.join()
|
||||
# claims,logs = p.read(path)
|
||||
# print (json.dumps(claims[3]))
|
||||
# print (logs)
|
||||
Loading…
Reference in New Issue