543 lines
20 KiB
Python
543 lines
20 KiB
Python
"""
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(c) 2019 Healthcare/IO 1.0
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Vanderbilt University Medical Center, Health Information Privacy Laboratory
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https://hiplab.mc.vanderbilt.edu/healthcareio
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Authors:
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Khanhly Nguyen,
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Steve L. Nyemba<steve.l.nyemba@vanderbilt.edu>
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License:
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MIT, terms are available at https://opensource.org/licenses/MIT
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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
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USAGE :
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- COMMAND LINE
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- EMBEDDED
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"""
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import hashlib
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import json
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import os
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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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def __init__(self):
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# self.config = config
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self.get = void()
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self.get.config = self.get_config
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self.parse = void()
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self.parse.sv3 = self.sv3
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self.parse.sv2 = self.sv2
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self.sv2_parse = self.sv2
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self.sv3_parse = self.sv3
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self.format_proc = self.procedure
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self.format_diag = self.diagnosis
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self.parse.procedure = self.procedure
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self.parse.diagnosis = self.diagnosis
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self.parse.date = self.date
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self.format_date = self.date
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self.format_pos = self.pos
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self.format_time = self.time
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def split(self,row,sep='*',prefix='HI') :
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"""
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This function is designed to split an x12 row and
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"""
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value = []
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if row.startswith(prefix) is False:
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for row_value in row.replace('~','').split(sep) :
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if '>' in row_value :
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if row_value.startswith('HC') or row_value.startswith('AD'):
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value += row_value.split('>')[:2]
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else:
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value += row_value.split('>') if row.startswith('CLM') is False else [row_value]
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else :
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value.append(row_value.replace('\n',''))
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value = [xchar.replace('\r','') for xchar in value] #row.replace('~','').split(sep)
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else:
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value = [ [prefix]+ self.split(item,'>') for item in row.replace('~','').split(sep)[1:] ]
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return value if type(value) == list and type(value[0]) != list else value[0]
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def get_config(self,config,row):
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"""
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This function will return the meaningfull parts of the configuration for a given item
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"""
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_row = list(row) if type(row[0]) == str else list(row[0])
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_info = config[_row[0]] if _row[0] in config else {}
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key = None
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if '@ref' in _info:
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key = list(set(_row) & set(_info['@ref'].keys()))
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if key :
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key = key[0]
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return _info['@ref'][key]
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else:
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return {}
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if not _info and 'SIMILAR' in config:
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#
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# Let's look for the nearest key using the edit distance
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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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salt = os.environ['HEALTHCAREIO_SALT'] if 'HEALTHCAREIO_SALT' in os.environ else ''
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_value = str(value)+ salt
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if sys.version_info[0] > 2 :
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return hashlib.md5(_value.encode('utf-8')).hexdigest()
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else:
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return hashlib.md5(_value).hexdigest()
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def suppress (self,value):
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return 'N/A'
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def date(self,value):
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if len(value) > 8 or '-' in value:
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value = value.split('-')[0]
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if len(value) == 8 :
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year = value[:4]
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month = value[4:6]
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day = value[6:]
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return "-".join([year,month,day])[:10] #{"year":year,"month":month,"day":day}
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elif len(value) == 6 :
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year = '20' + value[:2]
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month = value[2:4]
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day = value[4:]
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#
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# We have a date formatting issue
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return "-".join([year,month,day])
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def time(self,value):
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pass
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def sv3(self,value):
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if '>' in value [1]:
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terms = value[1].split('>')
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return {'type':terms[0],'code':terms[1],"amount":float(value[2])}
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else:
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return {"code":value[2],"type":value[1],"amount":float(value[3])}
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def sv2(self,value):
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#
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# @TODO: Sometimes there's a suffix (need to inventory all the variations)
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#
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if '>' in value or ':' in value:
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xchar = '>' if '>' in value else ':'
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_values = value.split(xchar)
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modifier = {}
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if len(_values) > 2 :
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modifier= {"code":_values[2]}
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if len(_values) > 3 :
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modifier['type'] = _values[3]
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_value = {"code":_values[1],"type":_values[0]}
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if modifier :
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_value['modifier'] = modifier
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return _value
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else:
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return value
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def procedure(self,value):
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for xchar in [':','<'] :
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if xchar in value and len(value.split(xchar)) > 1 :
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#_value = {"type":value.split(':')[0].strip(),"code":value.split(':')[1].strip()}
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_value = {"type":value.split(xchar)[0].strip(),"code":value.split(xchar)[1].strip()}
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break
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else:
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_value = str(value)
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return _value
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def diagnosis(self,alue):
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return [ {"code":item[2], "type":item[1]} for item in value if len(item) > 1]
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def pos(self,value):
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"""
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formatting place of service information within a segment (REF)
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@TODO: In order to accomodate the other elements they need to be specified in the configuration
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Otherwise it causes problems on export
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"""
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xchar = '>' if '>' in value else ':'
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x = value.split(xchar)
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x = {"code":x[0],"indicator":x[1],"frequency":x[2]} if len(x) == 3 else {"code":x[0],"indicator":None,"frequency":None}
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return x['code']
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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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self.files = []
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self.set = void()
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self.set.files = self.set_files
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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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_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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# label = config['label'] if 'label' in config else None
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handler = Formatters()
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if 'map' not in config and hasattr(handler,config['apply']):
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pointer = getattr(handler,config['apply'])
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object_value = pointer(row)
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return object_value
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omap = config['map'] if not version or version not in config else config[version]
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anchors = config['anchors'] if 'anchors' in config else []
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if type(row[0]) == str:
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object_value = {}
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for key in omap :
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index = omap[key]
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if anchors and set(anchors) & set(row):
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_key = list(set(anchors) & set(row))[0]
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aindex = row.index(_key)
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index = aindex + index
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if index < len(row) :
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value = row[index]
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if 'cast' in config and key in config['cast'] and value.strip() != '' :
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if config['cast'][key] in ['float','int'] :
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value = eval(config['cast'][key])(value)
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elif hasattr(handler,config['cast'][key]):
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pointer = getattr(handler,config['cast'][key])
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value = pointer(value)
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else:
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print ("Missing Pointer ",config['cast'][key])
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# print (key,value)
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if type(value) == dict :
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for objkey in value :
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if type(value[objkey]) == dict :
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continue
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if 'syn' in config and value[objkey] in config['syn'] :
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value[objkey] = config['syn'][ value[objkey]]
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value = {key:value} if key not in value else value
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else:
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if 'syn' in config and value in config['syn'] :
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value = config['syn'][value]
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if type(value) == dict :
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object_value = dict(object_value, **value)
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else:
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object_value[key] = value
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else:
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#
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# we are dealing with a complex object
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object_value = []
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for row_item in row :
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value = self.get.value(row_item,config,version)
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object_value.append(value)
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#
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# We need to add the index of the object it matters in determining the claim types
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#
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# object_value.append( list(get_map(row_item,config,version)))
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# object_value = {label:object_value}
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return object_value
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def apply(self,content,_code) :
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"""
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:content content of a file i.e a segment with the envelope
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:_code 837 or 835 (helps get the appropriate configuration)
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"""
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util = Formatters()
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# header = default_value.copy()
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value = {}
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for row in content[:] :
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row = util.split(row.replace('\n','').replace('~',''))
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_info = util.get.config(self.config[_code][0],row)
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if self._custom_config and _code in self._custom_config:
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_cinfo = util.get.config(self._custom_config[_code],row)
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else:
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_cinfo = {}
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# _info = self.consolidate(row=row,type=_code,config=_info,util=util)
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# print ([row[0],_info])
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# print ()
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# continue
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# _cinfo = util.get.config(self._custom_config[_code],row)
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if _info :
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try:
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_info = jsonmerge.merge(_info,_cinfo)
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tmp = self.get.value(row,_info)
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if not tmp :
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continue
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if 'label' in _info :
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label = _info['label']
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if type(tmp) == list :
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value[label] = tmp if label not in value else value[label] + tmp
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else:
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if label not in value:
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value[label] = [tmp]
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# elif len(list(tmp.keys())) == 1 :
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# # print "\t",len(claim[label]),tmp
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# index = len(value[label]) -1
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# value[label][index] = dict(value[label][index],**tmp)
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else:
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value[label].append(tmp)
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tmp['_index'] = len(value[label]) -1
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# if len(value[label]) > 0 :
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# labels = []
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# for item in value[label] :
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# item['_index'] = len(labels)
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# if item not in labels :
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# labels.append(item)
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# value[label] = labels
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elif 'field' in _info :
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name = _info['field']
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# value[name] = tmp
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value = jsonmerge.merge(value,{name:tmp})
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else:
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value = dict(value,**tmp)
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pass
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except Exception as e :
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print ('__',e.args)
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pass
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return value if value else {}
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def get_default_value(self,content,_code):
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util = Formatters()
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TOP_ROW = content[1].split('*')
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CATEGORY= content[2].split('*')[1].strip()
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VERSION = content[1].split('*')[-1].replace('~','').replace('\n','')
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SUBMITTED_DATE = util.parse.date(TOP_ROW[4])
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SENDER_ID = TOP_ROW[2]
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row = util.split(content[3])
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_info = util.get_config(self.config[_code][0],row)
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value = self.get.value(row,_info,VERSION) if _info else {}
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value['category'] = {"setid": CATEGORY,"version":'X'+VERSION.split('X')[1],"id":VERSION.split('X')[0].strip()}
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value["submitted"] = SUBMITTED_DATE
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# value['version'] = VERSION
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if _code== '835' :
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value['payer_id'] = SENDER_ID
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else:
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value['provider_id'] = SENDER_ID
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#
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# Let's parse this for default values
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return value
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def read(self,filename) :
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"""
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:formerly get_content
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This function returns the of the EDI file parsed given the configuration specified. it is capable of identifying a file given the content
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:section loop prefix (HL, CLP)
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:config configuration with formatting rules, labels ...
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:filename location of the file
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"""
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# section = section if section else config['SECTION']
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logs = []
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claims = []
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try:
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file = open(filename.strip(),errors='ignore')
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INITIAL_ROWS = list(islice(file,4)) #.readlines(4)
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_code = "unknown"
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if len(INITIAL_ROWS) == 1 :
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file = INITIAL_ROWS[0].split('~')
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INITIAL_ROWS = file[:4]
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if len(INITIAL_ROWS) < 3 :
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return None,[{"name":filename,"completed":False}],None
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# section = 'HL' if INITIAL_ROWS[1].split('*')[1] == 'HC' else 'CLP'
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# _code = '837' if section == 'HL' else '835'
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# print ([_code,section])
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_code = INITIAL_ROWS[2].split('*')[1].strip()
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# section = 'CLP' if _code == '835' else 'HL'
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section = self.config[_code][0]['SECTION'].strip()
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#
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# adjusting the
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DEFAULT_VALUE = self.get.default_value(INITIAL_ROWS,_code)
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DEFAULT_VALUE['name'] = filename.strip()
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#
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# In the initial rows, there's redundant information (so much for x12 standard)
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# index 1 identifies file type i.e CLM for claim and CLP for remittance
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segment = []
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index = 0;
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_toprows = []
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for row in file :
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row = row.replace('\r','')
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if not segment and not row.startswith(section):
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_toprows += [row]
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if row.startswith(section) and not segment:
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segment = [row]
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continue
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elif segment and not row.startswith(section):
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segment.append(row)
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if len(segment) > 1 and row.startswith(section):
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#
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# process the segment somewhere (create a thread maybe?)
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#
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# default_claim = dict({"index":index},**DEFAULT_VALUE)
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# print (_toprows)
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_claim = self.apply(segment,_code)
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# if _claim['claim_id'] == 'P1080351470' :
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# print (_claim)
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# _claim = dict(DEFAULT_VALUE,**_claim)
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if _claim :
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_claim['index'] = index #len(claims)
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claims.append(dict(DEFAULT_VALUE,**_claim))
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segment = [row]
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index += 1
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pass
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#
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# Handling the last claim found
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if segment[0].startswith(section) :
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default_claim = dict({"name":index},**DEFAULT_VALUE)
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claim = self.apply(segment,_code)
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if claim :
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claim['index'] = len(claims)
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claim = jsonmerge.merge(claim,self.apply(_toprows,_code))
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claims.append(dict(DEFAULT_VALUE,**claim))
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if type(file) != list :
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file.close()
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# x12_file = open(filename.strip(),errors='ignore').read().split('\n')
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except Exception as e:
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logs.append ({"parse":_code,"completed":False,"name":filename,"msg":e.args[0]})
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return [],logs,None
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rate = 0 if len(claims) == 0 else (1 + index)/len(claims)
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logs.append ({"parse":"claims" if _code == '837' else 'remits',"completed":True,"name":filename,"rate":rate})
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# self.finish(claims,logs,_code)
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return claims,logs,_code
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def run(self):
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if self.emit.pre :
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self.emit.pre()
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for filename in self.files :
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content,logs,_code = self.read(filename)
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self.finish(content,logs,_code)
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def finish(self,content,logs,_code) :
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args = self.store
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_args = json.loads(json.dumps(self.store))
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if args['type'] == 'mongo.MongoWriter' :
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args['args']['doc'] = 'claims' if _code == '837' else 'remits'
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_args['args']['doc'] = 'logs'
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else:
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args['args']['table'] = 'claims' if _code == '837' else 'remits'
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_args['args']['table'] = 'logs'
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if content :
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writer = transport.factory.instance(**args)
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writer.write(content)
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writer.close()
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if logs :
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logger = transport.factory.instance(**_args)
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logger.write(logs)
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logger.close()
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if self.emit.post :
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self.emit.post(content,logs)
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|
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# p = Parser('/home/steve/.healthcareio/config.json')
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# p.set.files(['../../data/small/claims/ssiUB1122042711220427127438.clm_191122T043504'])
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# path = '../../data/small/claims/ssiUB1122042711220427127438.clm_191122T043504'
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# path = '../../data/small/claims/problems-with-procs'
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# path = '../../data/small/remits/1SG03927258.dat_181018T074559'
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|
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# _path = "../../data/small/remits/1TR21426701.dat_180703T074559"
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# p.start()
|
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# p.join()
|
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# claims,logs = p.read(path)
|
|
# print (json.dumps(claims[3]))
|
|
# print (logs) |