parser/healthcareio/x12/__init__.py

"""
    (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
# version 2.0
# import util
# from parser import X12Parser
#-- end

from itertools import islice
from multiprocessing import Process
import transport
from transport import providers
import jsonmerge
# import plugins

import copy

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_parser = self.sv2
        self.sv3_parser = self.sv3
        self.sv3_parse = self.sv3
        self.format_proc = self.procedure
        self.format_diag = self.diagnosis
        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 
        """
        
        value = []
        if row.startswith(prefix) is False:
                        
            for row_value in row.replace('~','').split(sep) :
                
                if '>' in row_value and not row_value.startswith('HC'):
                    # if row_value.startswith('HC') or row_value.startswith('AD'):
                    if row_value.startswith('AD'):
                    
                        value += row_value.split('>')[:2] 
                        pass
                    else:
                        
                        
                        value += [row_value]
                        # value += row_value.split('>')   if row.startswith('CLM') is False else [row_value]
                        
                else :
                    
                    value.append(row_value.replace('\n',''))
            value =  [xchar.replace('\r','') for xchar in value] #row.replace('~','').split(sep)
        else:
            
            value =  [ [prefix]+ self.split(item,'>') for item in row.replace('~','').split(sep)[1:] ]
        
        return value if type(value) == list and type(value[0]) != list else value[0]
    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 {}
        _rinfo = {}
        key = None
        if '@ref' in _info:
            keys = list(set(_row) & set(_info['@ref'].keys()))
            if keys :
                _rinfo = {}
                for key in keys :
                    _rinfo = jsonmerge.merge(_rinfo,_info['@ref'][key])
                return _rinfo
                # 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):
        value = value if type(value) != list else "-".join(value)
        if len(value) > 8 or '-' in value:
            #
            # This is the case of a thru date i.e the first part should be provided in a 435 entry
            #
            fdate = "-".join([value[:8][:4],value[:8][4:6],value[:8][6:8]])
            tdate = "-".join([value[9:][:4],value[9:][4:6],value[9:][6:8]])
            
            return {"from":fdate,"to":tdate}

        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:]
        elif value.isnumeric() and len(value) >= 10:
            #
            # Here I a will assume we have a numeric vale
            year = value[:4]
            month= value[4:6]
            day = value[6:8]
        else:
            
            #
            # We have a date formatting issue
            return value
        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()}
                
                if len(value.split(xchar)) >2 :
                    index = 1;
                    for modifier in value.split(xchar)[2:]  :
                        _value['modifier_'+str(index)] = modifier
                        index += 1
                break

            else:
                _value = str(value)
        return _value
    def diagnosis(self,value):
        return [ {"code":item[2], "type":item[1]} for item in value if len(item) > 1]
    def parse_loc(self,value):
        if ':' in value :
            return dict(zip(['place_of_service','claim_indicator','claim_frequency'],value.split(':')))
    def pos(self,value):
        """
            formatting place of service information within a segment (REF)
            @TODO: In order to accomodate the other elements they need to be specified in the configuration
                Otherwise it causes problems on export
        """
        
        xchar = '>' if '>' in value else ':'
        x = value.split(xchar)    
        x =  {"place_of_service":x[0],"indicator":x[1],"frequency":x[2]} if len(x) == 3 else {"place_of_service":x[0],"indicator":None,"frequency":None}
        return x
class Parser (Process):
    @staticmethod
    def setup (path):
        # self.config = _config['parser']
        config = json.loads(open(path).read())
        _config = config['parser']
        #
        # The parser may need some editing provided, this allows ease of developement and using alternate configurations
        #
        if type(_config['837']) == str or type(_config['835']) == str :
            for _id in ['837','835'] :
                if type(_config[_id]) == str and os.path.exists(_config[_id]):
                    _config[_id] = json.loads(open(_config[_id]).read())
                    if type(_config[_id]) == dict :
                        _config[_id] = [_config[_id]]     
        config['parser'] = _config
        return config   
    @staticmethod
    def init(**_args):
        """
        This function allows to initialize the database that will store the claims if need be 
        :path   configuration file
        """
        PATH = os.sep.join([os.environ['HOME'],'.healthcareio']) 
        filename = os.sep.join([PATH,'config.json']) 

        filename    = _args['path'] if 'path' in _args else filename
        info        = None
        if os.path.exists(filename):
            #
            # Loading the configuration file (JSON format)
            file = open(filename)
            info = json.loads(file.read())

            
            OUTPUT_FOLDER = info['out-folder']
            if 'output-folder' not in info and not os.path.exists(OUTPUT_FOLDER) :
                os.mkdir(OUTPUT_FOLDER)
            elif 'output-folder' in info and not os.path.exists(info['out-folder']) :
                os.mkdir(info['out-folder'])
            # if 'type' in info['store'] :            
            lwriter = None
            IS_SQL = False 
            if'type' in info['store'] and info['store']['type'] == 'disk.SQLiteWriter'   :
                lwriter = transport.factory.instance(**info['store'])
                IS_SQL = True
            elif 'provider' in info['store'] and info['store']['provider'] == 'sqlite' :
                lwriter = transport.instance(**info['store']) ;
                IS_SQL = [providers.SQLITE,providers.POSTGRESQL,providers.NETEZZA,providers.MYSQL,providers.MARIADB]
            
            if lwriter and IS_SQL:
                for key in info['schema'] :
                    if key != 'logs' :
                        _id = 'claims' if key == '837' else 'remits'
                    else:
                        _id = key
                    
                    if not lwriter.has(table=_id) :                    
                        lwriter.apply(info['schema'][key]['create'])

                # [lwriter.apply( info['schema'][key]['create']) for key in info['schema'] if not lwriter.has(table=key)]
                lwriter.close()

        return info        

    def __init__(self,path):
        """
            :path       path of the configuration file (it can be absolute)
        """
        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._custom_config = self.get_custom(path)
        # self.config = _config['parser']
        # #
        # # The parser may need some editing provided, this allows ease of developement and using alternate configurations
        # #
        # if type(self.config['837']) == str or type(self.config['835']) == str :
        #     for _id in ['837','835'] :
        #         if type(self.config[_id]) == str:
        #             self.config[_id] = json.loads(open(self.config[_id]).read())
        #             if type(self.config[_id]) == dict :
        #                 self.config[_id] = [self.config[_id]]
        _config = Parser.setup(path)
        self.config = _config['parser']
        
        self.store  = _config['store']        
        self.cache  = {}
        self.files  = []
        self.set    = void()
        self.set.files = self.set_files
        self.emit = void()
        self.emit.pre =  None
        self.emit.post = None
    def get_custom(self,path) :
        """
        :path   path of the configuration file (it can be absolute)
        """
        #
        #
        _path = path.replace('config.json','')
        if _path.endswith(os.sep) :
            _path = _path[:-1]
        
        _config = {}
        _path = os.sep.join([_path,'custom'])
        if os.path.exists(_path) :
            
            files = os.listdir(_path)
            if files :
                fullname = os.sep.join([_path,files[0]])                
                _config = json.loads ( (open(fullname)).read() )
        return _config

    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
        #
        # Pull the goto configuration that skips  rows
        #
        omap = config['map'] if not version or version not in config else config[version]
        anchors = config['anchors'] if 'anchors' in config else []
        rewrite = config['rewrite'] if 'rewrite' in config else {}
        if len(row) == 2 and row[0] == 'HI' :
            row = ([row[0]] + row[1].split(':'))
        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']:
                            try:
                                value = eval(config['cast'][key])(value)
                            except Exception as e:
                                pass
                            #
                            # Sometimes shit hits the fan when the anchor is missing
                            # This is typical but using the hardened function helps circumvent this (SV2,SV3)
                            #
                        elif hasattr(handler,config['cast'][key]):
                            
                            pointer = getattr(handler,config['cast'][key])                            
                            value   = pointer(value)
                            
                            
                        else:
                            print ("Missing Pointer ",key,config['cast'])

                        
                        
                    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]]
                                pass
                            
                        if key in rewrite :
                            
                            _key = rewrite[key]
                            if _key in value :
                                value = value[_key]
                            else:
                                value = ""
                            value = {key:value} if key not  in value else value
                    else:
                        
                        if 'syn' in config and value in config['syn'] :
                            # value = config['syn'][value]
                            pass
                            
                    if type(value) == dict :                          
                        object_value = jsonmerge.merge(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)
        return object_value
    def set_cache(self,tmp,_info) :
        """
        insert into cache a value that the, these are in reference to a loop
        """
        if 'cache' in _info :
            key = _info['cache']['key']
            value=_info['cache']['value']
            field = _info['cache']['field']
            if value in tmp :

                self.cache [key] = {field:tmp[value]}
        pass 
    def get_cache(self,row) :
        """
        retrieve cache element for a current 
        """
        key = row[0]        
        return self.cache[key] if key in self.cache else {}
        
    def apply(self,content,_code) :
        """
        :content    content of a file i.e a segment with the envelope
        :_code  837 or 835 (helps get the appropriate configuration)
        """
        util   = Formatters()
        # header       = default_value.copy()
        value = {}
        
        for row in content[:] :
            row     = util.split(row.replace('\n','').replace('~',''))
            _info   = util.get.config(self.config[_code][0],row)
            if self._custom_config and _code in self._custom_config:
                _cinfo   = util.get.config(self._custom_config[_code],row)
            else:
                _cinfo = {}
            
            if _info or _cinfo:

                try:
                    
                    
                    _info = jsonmerge.merge(_info,_cinfo)         
                    tmp = self.get.value(row,_info)
                    
                   
                   
                    if not tmp :
                        continue 
                    #
                    # At this point we have the configuration and the row parsed into values
                    # We should check to see if we don't have anything in the cache to be added to it
                    #
                    if row[0] in self.cache :
                       tmp = jsonmerge.merge(tmp,self.get_cache(row))
                    
                    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 'DTM' in row :
                            #     print ([label,tmp,label in value])
                            if label not in value :                                
                                value[label] = []
                            value[label].append(tmp)
                            # if label not in value:   
                                
                            #     value[label] = [tmp]
                            # else:
                            #     value[label].append(tmp)    
                                        
                        if '_index' not in tmp :
                            #
                            # In case we asked it to be overriden, then this will not apply
                            # X12  occasionally requires references to other elements in a loop (alas)
                            #
                            tmp['_index'] = len(value[label]) -1 
                        
                    elif 'field' in _info :
                                           
                        name = _info['field']
                        # value[name] = tmp
                        # value = jsonmerge.merge(value,{name:tmp})
                        if name not in value :
                            value = dict(value,**{name:tmp})
                        else:
                            value[name] = dict(value[name],**tmp)
                      
                    else:
                        value = dict(value,**tmp)
                    
                    pass
                except Exception as e :
                    print (e.args[0])
                    # print ('__',(dir(e.args)))
                    pass
                #
                # At this point the object is completely built, 
                # if there ar any attributes to be cached it will be done here
                #
                
                if 'cache' in _info :   
                                     
                    self.set_cache(tmp,_info)
        
        return value if value else {}

    def get_default_value(self,content,_code):
        
        
        util = Formatters()
        TOP_ROW = content[1].split('*')        
        
        SUBMITTED_DATE  = util.parse.date(TOP_ROW[4])
        
        CATEGORY= content[2].split('*')[1].strip()
        
        VERSION         = content[1].split('*')[-1].replace('~','').replace('\n','')           
        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": _code,"version":'X'+VERSION.split('X')[1],"id":VERSION.split('X')[0].strip()} 
        value["submitted"] = SUBMITTED_DATE
        value['sender_id'] = SENDER_ID
          
        # value = dict(value,**self.apply(content,_code))
        value = jsonmerge.merge(value,self.apply(content,_code))
        # Let's parse this for default values            
        return value #jsonmerge.merge(value,self.apply(content,_code))

    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  = []
        _code = 'UNKNOWN'
        try:
            self.cache = {}
            file = open(filename.strip())
            file = file.read().split('CLP')
            _code = '835'
            section = 'CLP'
            
            if len(file) == 1 :
                
                file = file[0].split('CLM') #.split('HL')
                _code = '837'
                section = 'CLM' #'HL'
            
            INITIAL_ROWS = file[0].split(section)[0].split('\n')
            
            if len(INITIAL_ROWS) == 1 :
                
                INITIAL_ROWS = INITIAL_ROWS[0].split('~')
                
                # for item in file[1:] :
                #     item = item.replace('~','\n')
            # print (INITIAL_ROWS)
            
            DEFAULT_VALUE =  self.get.default_value(INITIAL_ROWS,_code)            
            DEFAULT_VALUE['name'] = filename.strip()
            
            
            file = section.join(file).split('\n')
            if len(file) ==  1:
                
                file = file[0].split('~')
            #
            # 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;
            _toprows = []
            _default = None
            
            for row in file :
                
                row = row.replace('\r','')
                # if not segment and not row.startswith(section):
                #     _toprows += [row]
                
                if row.startswith(section) and not segment:
                    
                    segment = [row]

                    continue
                    
                elif segment and not row.startswith(section):
                   
                    segment.append(row)
                
                    
                if len(segment) > 1 and row.startswith(section):
                    #
                    # process the segment somewhere (create a thread maybe?)
                    # 
                    
                    _claim = self.apply(segment,_code)
                    
                    if _claim :
                        _claim['index'] = index #len(claims)
                        # claims.append(dict(DEFAULT_VALUE,**_claim))  
                        #                       
                        # schema = [ {key:{"mergeStrategy":"append" if list( type(_claim[key])) else "overwrite"}} for key in _claim.keys()] # if type(_claim[key]) == list]
                        # _schema = set(DEFAULT_VALUE.keys()) - schema
                        # if schema :
                            # schema  = {"properties":dict.fromkeys(schema,{"mergeStrategy":"append"})}
                            
                        # else:
                            
                        #     schema = {"properties":{}}
                        
                        # schema = jsonmerge.merge(schema['properties'],dict.fromkeys(_schema,{"mergeStrategy":"overwrite"}))
                        schema = {"properties":{}}
                        for attr in _claim.keys() :
                            schema['properties'][attr]  = {"mergeStrategy": "append" if type(_claim[attr]) == list else "overwrite" }
                        
                        
                        merger = jsonmerge.Merger(schema)         
                        _baseclaim = None
                        _baseclaim = merger.merge(_baseclaim,copy.deepcopy(DEFAULT_VALUE))
                        _claim = merger.merge(_baseclaim,_claim)

                        # _claim = merger.merge(DEFAULT_VALUE.copy(),_claim)
                        
                        claims.append( _claim)
                    segment = [row]
                    
                    index += 1
                    
                    
                pass
            #
            # Handling the last claim found 
            
            if segment and segment[0].startswith(section) :
                # default_claim = dict({"name":index},**DEFAULT_VALUE)

                claim = self.apply(segment,_code)
                if claim :
                    claim['index'] = len(claims)
                    # schema = [key for key in claim.keys() if type(claim[key]) == list]
                    # if schema :
                    #     schema  = {"properties":dict.fromkeys(schema,{"mergeStrategy":"append"})}
                        
                    # else:
                    #     print (claim.keys())
                    #     schema = {}
                    #
                    # @TODO: Fix merger related to schema (drops certain fields ... NOT cool)
                    
                    # merger = jsonmerge.Merger(schema)
                    # top_row_claim = self.apply(_toprows,_code)
                    
                    # claim = merger.merge(claim,self.apply(_toprows,_code))
                    # claims.append(dict(DEFAULT_VALUE,**claim))
                    schema = {"properties":{}}
                    for attr in claim.keys() :
                        schema['properties'][attr]  = {"mergeStrategy": "append" if type(claim[attr]) == list else "overwrite" }                    
                    merger = jsonmerge.Merger(schema)    
                    _baseclaim = None
                    _baseclaim = merger.merge(_baseclaim,copy.deepcopy(DEFAULT_VALUE))
                    claim = merger.merge(_baseclaim,claim)
                    claims.append(claim)

                    # claims.append(merger.merge(DEFAULT_VALUE.copy(),claim))
            if type(file) != list :
                file.close()

            # x12_file = open(filename.strip(),errors='ignore').read().split('\n')
        except Exception as e:
           
            logs.append ({"parse":_code,"completed":False,"name":filename,"msg":e.args[0]})
            return [],logs,None
        
        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):
        if self.emit.pre :
            self.emit.pre()

        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))
        ISNEW_MONGO = 'provider' in args and args['provider'] in ['mongo', 'mongodb']
        ISLEG_MONGO = ('type' in args and args['type'] == 'mongo.MongoWriter') 
        if ISLEG_MONGO or ISNEW_MONGO:
            if ISLEG_MONGO:
                # Legacy specification ...
                args['args']['doc'] = 'claims' if _code == '837' else 'remits'
                _args['args']['doc'] = 'logs'
            else:
                args['doc'] = 'claims' if _code == '837' else 'remits'
                _args['doc'] = 'logs'
            
        else:
            if 'type' in args :
                # Legacy specification ...
                args['args']['table'] = 'claims' if _code == '837' else 'remits'
                _args['args']['table'] = 'logs'
                table = args['args']['table']
            else:
                args['table']= 'claims' if _code == '837' else 'remits'
                _args['table'] = 'logs'
                table = args['table']
                
        
        writer = transport.factory.instance(**args)
        IS_SQLITE = type(writer) == transport.disk.SQLiteWriter 
        if content:       
            if IS_SQLITE :
                for row in content :
                    writer.apply("""insert into :table(data) values (':values')""".replace(":values",json.dumps(row)).replace(":table",table) )
            else:     
                writer.write(content)
            writer.close()
        if logs :            
            logger = transport.factory.instance(**_args)
            if IS_SQLITE:
                for row in logs:
                    logger.apply("""insert into logs values (':values')""".replace(":values",json.dumps(row)))
            else:
                logger.write(logs)
            
            logger.close()
        if self.emit.post :
            self.emit.post(content,logs)