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 validate_args(self, in_args, cmd_call):
valid_1, valid_2 = None, None
if len(in_args) > 0 and type(in_args) is not list:
args = in_args.split()
valid_1 = args[0]
elif type(in_args) is list and len(in_args) > 0:
args = in_args
valid_1 = args[0]
else:
args = []
if cmd_call in ['default']:
while True:
if len(args) == 2:
input_type = args[1].upper()
else:
input_type = input(
"What type of id is '{0}'? [LOCAL/RXCUI/NDC/SNOMED]".
format(args[0])).upper()
valid_type = self.validate_id_type(input_type)
if isinstance(valid_type, str) or valid_type is None:
return None
elif valid_type:
break
elif not valid_type:
print('Invalid Option, Please Try Again')
continue
valid_1 = input_type
elif cmd_call == 'rxn_ing':
valid_2, _ = self.validate_args(args, 'default')
valid_1 = args[0]
elif cmd_call == 'rxn_status':
valid_2, _ = self.validate_args(args, 'default')
valid_1 = args[0]
elif cmd_call == 'rxn_remap':
valid_2, _ = self.validate_args(args, 'default')
valid_1 = args[0]
elif cmd_call == 'rxn_lookup':
valid_2, _ = self.validate_args(
args, 'default') # Validated will provide the valid ID Type
valid_1 = args[0] if valid_2 and validate_id(args[0],
valid_2) else False
# Ensures the input id is a valid id of the specified type
elif cmd_call == 'errors':
_current_err = list(self.errors.keys())
if len(args) > 1:
smores_error('#Cx001.7', console_p=True)
return
elif len(args) == 1 and args[0].lower() in _current_err:
valid_1 = args[0]
elif len(args) == 1:
print('There are currently no errors logged for that command.')
return
else:
valid_1 = simple_input(
"Please choose a command from the list to see errors: ",
_current_err)
elif cmd_call in ['csv', 'remap', 'fhir', 'json']:
# Format: [File] [Output]
if not self.inputs['loaded']:
print(
"No Files Loaded!\nYou Must load a file containing local medications first"
)
else:
_file_opts = list(self.inputs['files'].keys()) + ['All']
_dict_opts = list(smores.get_dict_sources()) + ['All']
_file_or_dict = None
if cmd_call in ['csv', 'json']:
if len(args) == 0:
_file_or_dict = simple_input(
"Do you want results for a File or a constructed Dictionary?",
['File', 'Dictionary', 'exit'], True)
elif args[0] not in _file_opts and args[
0] not in _dict_opts:
print(
'That option was not recognized as a valid source.'
)
_file_or_dict = simple_input(
"Do you want results for a File or a constructed Dictionary?",
['File', 'Dictionary', 'exit'], True)
else:
valid_1 = args[0]
if _file_or_dict.upper() == 'FILE':
valid_1 = 'FILE|' + simple_input(
"Please choose a loaded file", _file_opts, True)
elif _file_or_dict.upper() == 'DICTIONARY':
valid_1 = 'DICT|' + simple_input(
"Please choose a code dictionary to output",
_dict_opts, True)
elif _file_or_dict.upper() == 'EXIT':
return None
else:
valid_1 = simple_input("Please choose a loaded file",
_file_opts, True)
if cmd_call in ['csv', 'json', 'fhir']:
if len(args) == 2 and len(args[1]) > 0:
valid_2 = args[1]
else:
valid_2 = input(
"Please provide an output file name:").strip()
if len(valid_2) > 0:
if "." in valid_2:
valid_2, ext = valid_2.split(".")
else:
valid_2 = ''
print('Empty file name provided, using default.')
else:
valid_2 = args[0]
elif cmd_call == 'file':
re_use = False
if self.inputs['loaded'] and len(in_args) == 0:
print("The following file(s) have already been loaded: \n" +
str(self.inputs['files']))
_load_more = simple_input(
"Would you like to load an additional file?",
['Y', 'N', 'exit'])
if _load_more == 'Y':
pass
elif _load_more == 'N':
_re_use = simple_input(
"Would you like to re-use a loaded file?",
['Y', 'N', 'exit'])
if _re_use == 'Y':
re_use = True
else:
return False, None
else:
return False, None
if in_args is not None and len(in_args) > 0:
valid_1 = in_args
else:
valid_1 = input("Please enter the name of the file to load: "
) if not re_use else simple_input(
'Select the file to be used: ',
list(self.inputs['files'].keys()),
index=True)
while True:
if valid_1 in self.inputs['files']:
if not re_use:
print(
"It looks like you've already loaded that file. Please try a different file."
)
valid_1, valid_2 = input(
"Please enter the name of the file to load: ")
else:
break
elif len(valid_1) == 0:
smores_error('#Cx001.7', logger=smoresLog)
valid_1, valid_2 = input(
"Please enter the name of the file to load: ")
else:
break
if not resolve_target_path(valid_1):
valid_1, valid_2 = self.validate_args('', 'file')
elif '.smr' in valid_1:
if len(self.inputs['files']) > 0:
print(
'It looks like you are trying to load a session, this will replace the current session and '
'all previous work.')
_save = simple_input(
'Do you want to save the current session first?',
['Y', 'N', 'EXIT'])
if _save == 'Y':
smores.save_session(self.__version__)
elif _save == 'EXIT':
return False, None
valid_2 = 'session'
else:
valid_2 = 'file'
smoresLog.debug('Args: {0}, Validated as: {1}'.format(
valid_1, valid_2))
return valid_1, valid_2
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
def validate_args(self, in_args, cmd_call):
valid_1, valid_2 = None, None
if len(in_args) > 0 and type(in_args) is not list:
args = in_args.split()
valid_1 = args[0]
elif type(in_args) is list and len(in_args) > 0:
args = in_args
valid_1 = args[0]
else:
args = []
if cmd_call in ['default']:
while True:
if len(args) == 2:
input_type = args[1].upper()
else:
input_type = input(
"What type of id is '{0}'? [LOCAL/RXCUI/NDC/SNOMED]".
format(args[0])).upper()
valid_type = self.validate_id_type(input_type)
if isinstance(valid_type, str) or valid_type is None:
return None
elif valid_type:
break
elif not valid_type:
print('Invalid Option, Please Try Again')
continue
valid_1 = input_type
elif cmd_call == 'rxn_ing':
valid_2, _ = self.validate_args(args, 'default')
valid_1 = args[0]
elif cmd_call == 'rxn_status':
valid_2, _ = self.validate_args(args, 'default')
valid_1 = args[0]
elif cmd_call == 'rxn_remap':
valid_2, _ = self.validate_args(args, 'default')
valid_1 = args[0]
elif cmd_call == 'rxn_lookup':
valid_2, _ = self.validate_args(
args, 'default') # Validated will provide the valid ID Type
valid_1 = args[0] if valid_2 and validate_id(
args[0], valid_2
) else False # Ensures the input id is a valid id of the specified type
elif cmd_call == 'errors':
_current_err = list(self.errors.keys())
if len(args) > 1:
smores_error('#Cx001.7', console_p=True)
return
elif len(args) == 1 and args[0].lower() in _current_err:
valid_1 = args[0]
elif len(args) == 1:
print('There are currently no errors logged for that command.')
return
else:
valid_1 = self.simple_input(
"Please choose a command from the list to see errors: ",
_current_err)
elif cmd_call in ['csv', 'remap', 'fhir', 'json']:
# Format: [File] [Output]
if not self.inputs['loaded']:
print(
"No Files Loaded!\nYou Must load a file containing local medications first"
)
return
else:
_file_opts = list(self.inputs['files'].keys()) + ['All']
_dict_opts = list(smores.get_dict_sources()) + ['All']
_file_or_dict = None
if cmd_call in ['csv', 'json']:
if len(args) == 0:
_file_or_dict = self.simple_input(
"Do you want results for a File or a constructed Dictionary?",
['File', 'Dictionary', 'exit'], True)
elif args[0] not in _file_opts and args[
0] not in _dict_opts:
print(
'That option was not recognized as a valid source.'
)
_file_or_dict = self.simple_input(
"Do you want results for a File or a constructed Dictionary?",
['File', 'Dictionary', 'exit'], True)
else:
valid_1 = args[0]
if _file_or_dict.upper() == 'FILE':
valid_1 = 'FILE|' + self.simple_input(
"Please choose a loaded file", _file_opts, True)
elif _file_or_dict.upper() == 'DICTIONARY':
valid_1 = 'DICT|' + self.simple_input(
"Please choose a code dictionary to output",
_dict_opts, True)
elif _file_or_dict.upper() == 'EXIT':
return
else:
valid_1 = self.simple_input("Please choose a loaded file",
_file_opts, True)
if cmd_call in ['csv', 'json', 'fhir']:
if len(args) == 2 and len(args[1]) > 0:
valid_2 = args[1]
else:
valid_2 = input(
"Please provide an output file name: ").strip()
if len(valid_2) > 0:
if "." in valid_2:
valid_2, ext = valid_2.split(".")
else:
valid_2 = ''
print('Empty file name provided, using default.')
else:
valid_2 = args[0]
smoresLog.debug('Args: {0}, Validated as: {1}'.format(
valid_1, valid_2))
return valid_1, valid_2