def run_med_to_csv(file:str=None,out_file:str=None, params:dict=None):
'''
Only supports outputing bundles, not individual meds
:param file: the target input file to be output to CSV, or ALL
:param out_file: basename to be used for file outputs, can be None: default name will be used
:param params: Customization parameters for the CSV output
:param incr: Number of medications to be saved per file (not rows)
:return:
'''
smoresLog.debug('Preparing to generate CSV')
incr = int(util.read_config_value('OUTPUT_CONF')['file_size_max'])
csv_files = {}
csv_outputs = params.keys() if params is not None else ''
if 'detail' in csv_outputs:
for _d in params['detail'].values():
base_filename, ext = process_filename(_d['type'])
csv_files[_d] = {'file': base_filename, 'ext': ext, 'detail': _d}
if file is not None:
kits = MedKit.get_medkit(file)
if type(kits) is dict:
i=1
for file, kit in kits.items():
_file, ext = process_filename(out_file=out_file, info_type=kit.file_name.split('.')[0])
save_csv_bundle(kit.m_dict, _file, incr=incr, ext=ext)
i += 1
else:
_file, ext = process_filename(out_file=out_file, info_type=kits.file_name.split('.')[0])
save_csv_bundle(kits.m_dict, _file, incr=incr, ext=ext)
else:
smores_error('#Kx001.2')
return
def get_bundle_json(in_dict: md.MedicationDictionary, json_file: str):
incr = int(util.read_config_value('OUTPUT_CONF')['file_size_max'])
_total = in_dict.get_med_count()
_iters = int(math.ceil(_total / incr)) if incr is not None else 1
_med_list = list(in_dict.med_list.values())
fhir_construct = {
'resourceType': 'Bundle',
'date': datetime.today().strftime('%Y-%m-%d %H:%M:%S%z'),
'total': 0,
'entry': []
}
if _iters > 1:
_count = 0
print('Medications will be saved across {0} files.'.format(_iters))
for i in trange(_iters, desc='File Number', position=0):
bundle = fhir_construct.copy()
list_end = _count + incr if (_count +
incr) < _total else _total
_b = [med.get_fhir() for med in _med_list[_count:list_end]]
bundle['entry'] = _b
bundle['total'] = list_end - _count
write_file(output_file=json_file,
iter=i + 1,
data=bundle,
ext='json')
_count += incr
else:
bundle = fhir_construct
for med in _med_list:
bundle['entry'].append(med.get_fhir())
bundle['total'] += 1
write_file(output_file=json_file, data=fhir_construct, ext='json')
return
def line_read(medkit, input, last_id=None, skip1=True):
_n, line = input
if _n == 0 and skip1:
return False, False, None, None
else:
try:
config_i_keys = util.read_config_value('INFILE_KEYS')
i_local_key = config_i_keys['local_id_col_id']
i_code_key = config_i_keys['code_col_id']
i_code_type_key = config_i_keys['code_type_col_id']
i_name_key = config_i_keys['local_name_col_id']
i_code_name = config_i_keys['code_name_col_id']
except KeyError as e:
print(e)
return None, "#Cx001.6", None, None
is_dup = False
has_err = {}
cui_type = None
local_id = line[i_local_key]
if local_id == last_id or m.med_exists(local_id, medkit.file_name):
temp_med = m.get_med_by_id(local_id, medkit.file_name)
is_dup = True
else:
temp_med = m.LocalMed(input_key=local_id, source=medkit.file_name)
if len(line[i_code_key]) != 0:
cui_type = line[i_code_type_key].upper()
cui_type = 'RXNORM' if cui_type == 'RXCUI' else cui_type # Prevent automatic fail incase RXCUI instead of RXNORM
if util.validate_id(line[i_code_key], cui_type):
# Support for inclusion of local name for local code id's
if cui_type == 'LOCAL' and not temp_med.isNameSet():
temp_med.set_name(line[i_code_name])
elif cui_type in util.OPTIONS_CUI_TYPES:
if i_code_name in line.keys() and len(
line[i_code_name]) > 0:
_e = temp_med.add_cui(line[i_code_key], cui_type,
line[i_code_name])
else:
_e = temp_med.add_cui(line[i_code_key], cui_type)
if _e > 0:
smores_error('#Ax000.1', line[i_local_key])
has_err[line[i_code_key]] = "#Ax000.1"
else:
smores_error('#Ax000.3', line[i_local_key])
has_err[line[i_code_key]] = "#Ax000.3"
if i_name_key in line.keys() and len(line[i_name_key]) > 0:
clean_rx = r'\\["n]'
temp_med.set_name(re.sub(clean_rx, '', line[i_name_key]))
return local_id, is_dup, has_err, cui_type
def run_dict_to_csv(src_dict: str, out_file: str = None, params=None):
"""
Retrieves the corresponding MedicationDictionary for an input src and saves to CSV
:param src_dict: Name of the src to be saved. Will identify the medication "bundle" to be saved
:param out_file: output filename specified by the user. Def None results in default name generated
:param params: Additional output parameters to be applied in building the csv
:return: Function call to save the bundle of medications
"""
incr = int(util.read_config_value('OUTPUT_CONF')['file_size_max'])
dict_to_save = md.get_med_dict_by_src(src_dict)
_file, ext = process_filename(out_file=out_file, info_type=src_dict)
return save_csv_bundle(dict_to_save, _file, incr, params, ext=ext)
def __init__(self, in_file, file_delim=','):
self.path = in_file
self.file_name = util.get_filename(in_file)
self.delim = file_delim
self.file_lines = self.get_file_lines()
self.c_records = 0
self.records = {}
self.headers = util.read_config_value('INFILE_KEYS')
self.trackers = {}
self.cui_types = []
self.m_dict = md.MedicationDictionary(self.file_name, link=self)
MedKit.med_kits[self.file_name] = self
m.Medication.med_id_list[self.file_name] = {}
self.med_list = m.Medication.med_id_list[self.file_name]
def get_headers(self, delim=','):
try:
data = open(self.path, "r+").readline()
keys = list(util.read_config_value('INFILE_KEYS').values())
map = {}
_d = data.split(delim)
for key in keys:
for i in range(len(_d)):
if _d[i].replace('\n', '') == key:
map[key] = i
return map
except FileNotFoundError:
smores_error('#Cx001.1')
return None
except PermissionError:
smores_error('#Cx001.2')
return None
def run_dict_to_csv(dict:str, out_file:str=None, params=None):
csv_details = {'cui': {'src': dict}}
incr = int(util.read_config_value('OUTPUT_CONF')['file_size_max'])
dict_to_save = md.get_med_dict_by_src(dict)
_file, ext = process_filename(out_file=out_file, info_type=dict)
return save_csv_bundle(dict_to_save, _file, incr, csv_details, ext=ext)
def line_read (medkit, input, last_id=None, skip1=True):
_n, line = input
if _n == 0 and skip1:
return False, False, None, None
else:
try:
config_i_keys = util.read_config_value('INFILE_KEYS')
i_local_key = config_i_keys['local_id_col_id']
i_code_key = config_i_keys['code_col_id']
i_code_type_key = config_i_keys['code_type_col_id']
i_name_key = config_i_keys['local_name_col_id']
i_code_name = config_i_keys['code_name_col_id']
except KeyError as e:
print(e)
return None, "#Cx001.6", None, None
is_dup = False
has_err = {}
cui_type = None
local_id = line[i_local_key]
if local_id == last_id or m.med_exists(local_id, medkit.file_name):
temp_med = m.get_med_by_id(local_id, medkit.file_name)
is_dup = True
else:
temp_med = m.LocalMed(input_key=local_id, source=medkit.file_name)
if len(line[i_code_key]) != 0:
if util.validate_id(line[i_code_key], line[i_code_type_key].upper()):
cui_type = line[i_code_type_key].upper()
# Support for inclusion of local name for local code id's
if cui_type == 'LOCAL' and not temp_med.isNameSet():
temp_med.set_name(line[i_code_name])
elif cui_type in ['RXCUI', 'RXNORM']:
rxcui = m.get_rxcui(line[i_code_key])
_e = temp_med.add_cui(rxcui, 'RXNORM')
if _e > 0:
smores_error('#Ax000.1', line[i_local_key])
has_err[line[i_code_key]] = "#Ax000.1"
elif cui_type == 'NDC':
if i_code_name in line.keys() and len(line[i_code_name]) > 0:
_e = temp_med.add_cui(line[i_code_key], cui_type, line[i_code_name])
else:
_e = temp_med.add_cui(line[i_code_key], cui_type)
if _e > 0:
smores_error('#Ax000.1', line[i_local_key])
has_err[line[i_code_key]] = "#Ax000.1"
elif cui_type == 'UMLS':
smoresLog.debug('Code Type Check: UMLS')
# TODO To Be Supported in Later Version
pass
elif cui_type == 'CPT':
smoresLog.debug('Code Type Check: CPT')
# TODO To Be Supported in Later Version
pass
elif cui_type == 'SNOMED':
smoresLog.debug('Code Type Check: SNOMED')
# TODO To Be Supported in Later Version
pass
else:
smores_error('#Ax000.3', line[i_local_key])
has_err[line[i_code_key]] = "#Ax000.3"
if i_name_key in line.keys() and len(line[i_name_key]) > 0:
clean_rx = r'\\["n]'
temp_med.set_name(re.sub(clean_rx, '', line[i_name_key]))
return local_id, is_dup, has_err, cui_type