def test_msearch_init(self):
"""Basic initialization test for the MeasureSearch class.
"""
msearch = MeasureSearch()
self.assertIsInstance(msearch, MeasureSearch)
self.assertIsNone(msearch.log_fpath)
self.assertIsInstance(msearch.__str__(), str)
def test_error_optim_algo(self):
"""Measure search should error with invalid optimization algorithm.
"""
properties = np.random.normal(size=len(self.test_smiles))
text_fpath = self.smiles_seq_to_textfile(property_seq=properties)
msearch = MeasureSearch()
with self.assertRaises(InvalidConfigurationError):
msearch.get_best_measure(
molecule_set_configs={
'molecule_database_src': text_fpath,
'molecule_database_src_type': 'text',
},
subsample_subset_size=1.0,
optim_algo='fake algo',
)
remove(text_fpath)
def test_msearch_completion(self):
"""MeasureSearch should complete running, though output cannot be directly tested.
"""
properties = np.random.normal(size=len(self.test_smiles))
text_fpath = self.smiles_seq_to_textfile(property_seq=properties)
msearch = MeasureSearch()
try:
msearch.get_best_measure(
molecule_set_configs={
'molecule_database_src': text_fpath,
'molecule_database_src_type': 'text',
},
subsample_subset_size=1.0
)
except Exception as e:
self.fail("MeasureSearch failed basic no-args test.")
remove(text_fpath)
def test_fixed_fprint(self):
"""MeasureSearch should search for ideal metric when fingerprint is already chosen.
"""
properties = np.random.normal(size=len(self.test_smiles))
text_fpath = self.smiles_seq_to_textfile(property_seq=properties)
msearch = MeasureSearch()
try:
msearch.get_best_measure(
molecule_set_configs={
'molecule_database_src': text_fpath,
'molecule_database_src_type': 'text',
},
subsample_subset_size=1.0,
fingerprint_type='morgan_fingerprint',
)
except Exception as e:
self.fail("MeasureSearch failed fixed fingerprint test.")
remove(text_fpath)
def test_min_optim_algo(self):
"""Measure search using the "minimum" optimization algorithm.
"""
properties = np.random.normal(size=len(self.test_smiles))
text_fpath = self.smiles_seq_to_textfile(property_seq=properties)
msearch = MeasureSearch()
try:
msearch.get_best_measure(
molecule_set_configs={
'molecule_database_src': text_fpath,
'molecule_database_src_type': 'text',
},
subsample_subset_size=1.0,
optim_algo='min',
)
except Exception as e:
self.fail("MeasureSearch failed min optim_algo test.")
remove(text_fpath)
def test_only_metric_search(self):
"""Check that this configuration option is able to execute.
"""
properties = np.random.normal(size=len(self.test_smiles))
text_fpath = self.smiles_seq_to_textfile(property_seq=properties)
msearch = MeasureSearch()
try:
msearch.get_best_measure(
molecule_set_configs={
'molecule_database_src': text_fpath,
'molecule_database_src_type': 'text',
},
subsample_subset_size=1.0,
only_metric=True,
)
except Exception as e:
self.fail("MeasureSearch failed fixed metric test.")
remove(text_fpath)
def test_verbose_output(self):
"""Ensure execution does not raise an exception with verbose and show_top.
"""
properties = np.random.normal(size=len(self.test_smiles))
text_fpath = self.smiles_seq_to_textfile(property_seq=properties)
msearch = MeasureSearch()
try:
msearch.get_best_measure(
molecule_set_configs={
'molecule_database_src': text_fpath,
'molecule_database_src_type': 'text',
'is_verbose': True,
},
subsample_subset_size=1.0,
show_top=5,
)
except Exception as e:
self.fail("MeasureSearch failed verbose output test.")
remove(text_fpath)
pass
def test_logfile_generation(self):
"""When configured to do so, MeasureSearch should create a log file.
"""
properties = np.random.normal(size=len(self.test_smiles))
text_fpath = self.smiles_seq_to_textfile(property_seq=properties)
log_dir_name = 'molSim_msearch_logs'
log_dir_path = join(getcwd(), log_dir_name)
log_file_path = join(log_dir_path, 'logs.json')
msearch = MeasureSearch(log_file_path=log_file_path)
_ = msearch(molecule_set_configs={
'molecule_database_src': text_fpath,
'molecule_database_src_type': 'text'},
subsample_subset_size=1.0)
self.assertTrue(isfile(log_file_path))
self.assertTrue(isdir(log_dir_path))
rmtree(log_dir_path)
def test_msearch_init_error(self):
"""Erroneous confirgurations should raise a config error.
"""
with self.assertRaises(InvalidConfigurationError):
msearch = MeasureSearch(correlation_type='invalid name')