parser/edi/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
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 get_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(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']
    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 = get_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 = get_map(row,_info,VERSION)
                    tmp = get_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