def test_parse_name(get_oxidationstate_dict):
names, excepted = get_oxidationstate_dict
for name, expected_res in zip(names, excepted):
getoxstates = GetOxStatesCSD([])
result = getoxstates.parse_name(name)
print(result)
assert result == expected_res
def test_parser():
"""Test with some hand-selected MOFs"""
test_list = [
"ACIBOE",
"AZOHEC",
"BADJAU",
"ACOLIP",
"QAGWIG",
"GOCBAD",
"BUVYIB01",
"GIRNIH",
"FURVEU",
"GAHJUW",
]
expected = {
"ACIBOE": {
"Zn": [np.nan]
},
"AZOHEC": {
"Zn": [2]
},
"BADJAU": {
"Sc": [np.nan]
},
"ACOLIP": {
"Zn": [2]
},
"QAGWIG": {
"Fe": [2]
},
"GOCBAD": {
"Cu": [2]
},
"BUVYIB01": {
"Fe": [2]
},
"GIRNIH": {
"Cd": [2]
},
"FURVEU": {
"Fe": [2]
},
"GAHJUW": {
"Fe": [0]
},
}
getoxstates = GetOxStatesCSD(test_list)
result = getoxstates.run_parsing()
assert expected == result
def test_parser():
"""Test with some hand-selected MOFs"""
test_list = [
'ACIBOE',
'AZOHEC',
'BADJAU',
'ACOLIP',
'QAGWIG',
'GOCBAD',
'BUVYIB01',
'GIRNIH',
'FURVEU',
'GAHJUW',
]
expected = {
'ACIBOE': {
'Zn': [np.nan]
},
'AZOHEC': {
'Zn': [2]
},
'BADJAU': {
'Sc': [np.nan]
},
'ACOLIP': {
'Zn': [2]
},
'QAGWIG': {
'Fe': [2]
},
'GOCBAD': {
'Cu': [2]
},
'BUVYIB01': {
'Fe': [2]
},
'GIRNIH': {
'Cd': [2]
},
'FURVEU': {
'Fe': [2]
},
'GAHJUW': {
'Fe': [0]
},
}
getoxstates = GetOxStatesCSD(test_list)
result = getoxstates.run_parsing()
assert expected == result
def run_parsing(names_cleaned, output_name=None):
"""
Args:
names_cleaned (list): list of CSD identifiers
output_name (str): filestem for the output pickle file
Returns:
writes output as pickle file
"""
getoxstatesobject = GetOxStatesCSD(names_cleaned)
if output_name is None:
timestr = time.strftime('%Y%m%d-%H%M%S')
output_name = '-'.join([timestr, 'csd_ox_parse_output'])
outputdict = getoxstatesobject.run_parsing(njobs=4)
with open(output_name + '.pkl', 'wb') as filehandle:
pickle.dump(outputdict, filehandle)
def run_parsing(output_name=None):
"""
Args:
output_name (str): filestem for the output pickle file
Returns:
writes output as pickle file
"""
# all database entries
getoxstatesobject = GetOxStatesCSD(generate_id_list())
if output_name is None:
timestr = time.strftime('%Y%m%d-%H%M%S')
output_name = '-'.join([timestr, 'csd_ox_parse_output_reference'])
outputdict = getoxstatesobject.run_parsing(njobs=4)
with open(output_name + '.pkl', 'wb') as filehandle:
pickle.dump(outputdict, filehandle)