healthcareio
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parser
mirror of https://hiplab.mc.vanderbilt.edu/git/hiplab/parser.git
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bug fix: poor config handling

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master
Steve L. Nyemba 4 years ago
parent 760eba62e1
commit 7b04b05154
1 changed files with 29 additions and 16 deletions
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45
healthcareio/x12/__init__.py
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@ -25,6 +25,9 @@ from itertools import islice
from multiprocessing import Process from multiprocessing import Process
import transport import transport
import jsonmerge import jsonmerge
import copy
class void : class void :
pass pass
class Formatters : class Formatters :
@ -86,12 +89,17 @@ class Formatters :
_row = list(row) if type(row[0]) == str else list(row[0]) _row = list(row) if type(row[0]) == str else list(row[0])
_info = config[_row[0]] if _row[0] in config else {} _info = config[_row[0]] if _row[0] in config else {}
_rinfo = {}
key = None key = None
if '@ref' in _info: if '@ref' in _info:
key = list(set(_row) & set(_info['@ref'].keys())) keys = list(set(_row) & set(_info['@ref'].keys()))
if key : if keys :
key = key[0] _rinfo = {}
return _info['@ref'][key] for key in keys :
_rinfo = jsonmerge.merge(_rinfo,_info['@ref'][key])
return _rinfo
# key = key[0]
# return _info['@ref'][key]
else: else:
return {} return {}
@ -315,11 +323,11 @@ class Parser (Process):
if type(value) == dict : if type(value) == dict :
object_value = dict(object_value, **value) # object_value = dict(object_value, **value)
object_value = jsonmerge.merge(object_value, value)
else: else:
object_value[key] = value object_value[key] = value
@ -360,9 +368,6 @@ class Parser (Process):
_cinfo = util.get.config(self._custom_config[_code],row) _cinfo = util.get.config(self._custom_config[_code],row)
else: else:
_cinfo = {} _cinfo = {}
if 'SV3' in row :
print (row)
print (_info)
if _info or _cinfo: if _info or _cinfo:
try: try:
@ -370,10 +375,13 @@ class Parser (Process):
_info = jsonmerge.merge(_info,_cinfo) _info = jsonmerge.merge(_info,_cinfo)
tmp = self.get.value(row,_info) tmp = self.get.value(row,_info)
#
# let's prune the objects not found
if not tmp : if not tmp :
continue continue
if 'label' in _info : if 'label' in _info :
label = _info['label'] label = _info['label']
@ -398,10 +406,10 @@ class Parser (Process):
name = _info['field'] name = _info['field']
# value[name] = tmp # value[name] = tmp
value = jsonmerge.merge(value,{name:tmp}) # value = jsonmerge.merge(value,{name:tmp})
value = dict(value,**{name:tmp})
else: else:
value = dict(value,**tmp) value = dict(value,**tmp)
pass pass
@ -433,9 +441,10 @@ class Parser (Process):
value['category'] = {"setid": _code,"version":'X'+VERSION.split('X')[1],"id":VERSION.split('X')[0].strip()} value['category'] = {"setid": _code,"version":'X'+VERSION.split('X')[1],"id":VERSION.split('X')[0].strip()}
value["submitted"] = SUBMITTED_DATE value["submitted"] = SUBMITTED_DATE
value['sender_id'] = SENDER_ID value['sender_id'] = SENDER_ID
value = dict(value,**self.apply(content,_code))
# Let's parse this for default values # Let's parse this for default values
return jsonmerge.merge(value,self.apply(content,_code)) return value #jsonmerge.merge(value,self.apply(content,_code))
def read(self,filename) : def read(self,filename) :
""" """
@ -449,7 +458,7 @@ class Parser (Process):
logs = [] logs = []
claims = [] claims = []
try: try:
file = open(filename.strip(),errors='ignore') file = open(filename.strip())
file = file.read().split('CLP') file = file.read().split('CLP')
_code = '835' _code = '835'
section = 'CLP' section = 'CLP'
@ -473,6 +482,7 @@ class Parser (Process):
DEFAULT_VALUE = self.get.default_value(INITIAL_ROWS,_code) DEFAULT_VALUE = self.get.default_value(INITIAL_ROWS,_code)
DEFAULT_VALUE['name'] = filename.strip() DEFAULT_VALUE['name'] = filename.strip()
file = section.join(file).split('\n') file = section.join(file).split('\n')
if len(file) == 1: if len(file) == 1:
@ -525,9 +535,11 @@ class Parser (Process):
schema = {"properties":{}} schema = {"properties":{}}
for attr in _claim.keys() : for attr in _claim.keys() :
schema['properties'][attr] = {"mergeStrategy": "append" if type(_claim[attr]) == list else "overwrite" } schema['properties'][attr] = {"mergeStrategy": "append" if type(_claim[attr]) == list else "overwrite" }
merger = jsonmerge.Merger(schema) merger = jsonmerge.Merger(schema)
_baseclaim = None _baseclaim = None
_baseclaim = merger.merge(_baseclaim,DEFAULT_VALUE.copy()) _baseclaim = merger.merge(_baseclaim,copy.deepcopy(DEFAULT_VALUE))
_claim = merger.merge(_baseclaim,_claim) _claim = merger.merge(_baseclaim,_claim)
# _claim = merger.merge(DEFAULT_VALUE.copy(),_claim) # _claim = merger.merge(DEFAULT_VALUE.copy(),_claim)
@ -566,8 +578,9 @@ class Parser (Process):
schema = {"properties":{}} schema = {"properties":{}}
for attr in _claim.keys() : for attr in _claim.keys() :
schema['properties'][attr] = {"mergeStrategy": "append" if type(_claim[attr]) == list else "overwrite" } schema['properties'][attr] = {"mergeStrategy": "append" if type(_claim[attr]) == list else "overwrite" }
_baseclaim = None _baseclaim = None
_baseclaim = merger.merge(_baseclaim,DEFAULT_VALUE.copy()) _baseclaim = merger.merge(_baseclaim,copy.deepcopy(DEFAULT_VALUE))
claim = merger.merge(_baseclaim,claim) claim = merger.merge(_baseclaim,claim)
claims.append(claim) claims.append(claim)

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