parser/healthcareio/parser.py

"""
    (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
import hashlib
import json
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('>')   if row.startswith('CLM') is False else [row_value]
                    
            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 hash(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(value):
    return 'N/A'
    
def format_date(value) :
    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:]
        return "-".join([year,month,day])
def format_time(value):
    return ":".join([value[:2],value[2:] ])[:5]
def sv3_parse(value):
    if '>' in value :
        terms = value.split('>')
        return {'type':terms[0],'code':terms[1]}
        
    pass
def sv2_parse(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 format_proc(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 format_diag(value):

    return [ {"code":item[2], "type":item[1]} for item in value if len(item) > 1]
def format_pos(value):
    
    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
    
def get_map(row,config,version=None):
    
    label = config['label'] if 'label' in config else None    
    
    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() != '' :
                    
                    value = eval(config['cast'][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 = get_map(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 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']
    logs = []
    try:

        x12_file = open(filename.strip(),errors='ignore').read().split('\n')
    except Exception as e:
        #
        # We have an error here that should be logged 
        if sys.version_info[0] > 2 :
            # logs.append ({"version":VERSION,"filename":filename,"msg":e.args[0],"X12":x12_file[beg:end]})
            logs.append ({"version":"unknown","filename":filename,"msg":e.args[0]})
        else:
            # logs.append ({"version":VERSION,"filename":filename,"msg":e.message,"X12":x12_file[beg:end]})
            logs.append ({"version":"unknown","filename":filename,"msg":e.message})
        return [],logs

        pass
    
    if len(x12_file) == 1 :
        
        x12_file = x12_file[0].split('~')
        
    #partitions = '\n'.join(x12_file).split(section+'*')
    locations = get_locations(x12_file,section)
    claims = []
    #
    # given locations it is possible to build up the partitions (made of segments)
    
    beg = locations [0]
    partitions = []
    for end in locations[1:] :
        partitions.append ("\n".join(x12_file[beg:end]))
        beg = end
    
    # VERSION = x12_file[2].split('*')[3].replace('~','')    
    TOP_ROW = x12_file[1].split('*')
    CATEGORY= x12_file[2].split('*')[1].strip()
    VERSION         = x12_file[1].split('*')[-1].replace('~','')   
    SUBMITTED_DATE  = format_date(TOP_ROW[4])
    SENDER_ID       = TOP_ROW[2]
    row = split(x12_file[3])
    _info = get_config(config,row)    
    
    _default_value = get_map(row,_info,VERSION) if _info else {}    
    
    N = len(locations)

    # for index in range(0,N-1):
    #     beg = locations[index]
    #     end = locations[index+1]
    #     claim = {}
    for segment in partitions :
        
        claim = {}   
        # for row in x12_file[beg:end] :
        segment = segment.replace('\n','').split('~')
        for row in segment :
            row = split(row)
            
            _info = get_config(config,row)
            if _info :
                try:                    
                    # tmp = get_map(row,_info,VERSION)
                    # if 'parser' in _info :
                    #     pointer = eval(_info['parser'])
                    #     print (pointer(row))
                    tmp = get_map(row,_info,VERSION)
                    
                except Exception as e:                    
                    if sys.version_info[0] > 2 :
                        # logs.append ({"version":VERSION,"filename":filename,"msg":e.args[0],"X12":x12_file[beg:end]})
                        logs.append ({"version":VERSION,"filename":filename,"msg":e.args[0],"X12":row,"completed":False,"rows":len(row)})
                    else:
                        # logs.append ({"version":VERSION,"filename":filename,"msg":e.message,"X12":x12_file[beg:end]})
                        logs.append ({"version":VERSION,"filename":filename,"msg":e.message,"X12":row,"rows":len(row),"completed":False})
                    claim = {}
                    break
                
                if 'label' not in _info :
                    tmp['version']      = VERSION   
                    tmp['submitted']    = SUBMITTED_DATE
                    if TOP_ROW[1] == 'HP' :
                        tmp['payer_id'] = SENDER_ID
                        
                    elif TOP_ROW[1] == 'HC':
                        tmp['provider_id'] = SENDER_ID
                        
                    tmp['category'] = {"setid": CATEGORY,"version":'X'+VERSION.split('X')[1],"id":VERSION.split('X')[0].strip()}
                    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 len(claim[label]) > 0 :                    
                        labels = []
                        for item in claim[label] :
                            item['_index'] = len(labels)
                            if item not in labels :
                                
                                labels.append(item)
                        claim[label] = labels
                        # claim[label] = list( set(claim[label])) #-- removing redundancies
        if claim and 'claim_id' in claim:
            
            claim = dict(claim,**_default_value)
            claim['name'] = filename.split(os.sep)[-1] #.replace(ROOT,'')
            claim['index'] = len(claims) if len(claims) > 0 else 0
            claims.append(claim)
        else:
            #
            # Could not find claim identifier associated with data 
            #
            pass
            
            
    return claims,logs