def test_to_from_json(self, structure_klifs_id):
"""
Test if saving/loading a fingerprint to/from a json file.
"""
fingerprint = Fingerprint.from_structure_klifs_id(
structure_klifs_id, LOCAL)
json_filepath = Path("fingerprint.json")
with enter_temp_directory():
# Save json file
fingerprint.to_json(json_filepath)
assert json_filepath.exists()
# Load json file
fingerprint_reloaded = Fingerprint.from_json(json_filepath)
# Test if class attributes from ID and from json are the same
assert fingerprint.structure_klifs_id == fingerprint_reloaded.structure_klifs_id
assert np.allclose(
fingerprint.values_array(True, True, True),
fingerprint_reloaded.values_array(True, True, True),
rtol=0,
atol=0,
equal_nan=True,
)
assert fingerprint.residue_ids == fingerprint_reloaded.residue_ids
assert fingerprint.residue_ixs == fingerprint_reloaded.residue_ixs
def test_from_file(
distance_matrix_path,
tree_path,
annotation_path,
clustering_method,
similarity,
node_means,
tree_string,
):
with enter_temp_directory():
tree_nodes_calculated, node_means_calculated = tree.from_file(
distance_matrix_path, tree_path, annotation_path,
clustering_method, similarity)
assert isinstance(tree_nodes_calculated, hierarchy.ClusterNode)
assert node_means == pytest.approx(node_means_calculated, abs=1e-6)
if tree_path:
tree_path = Path(tree_path)
# Tree file there?
assert tree_path.exists()
# Tree file correct?
with open(tree_path, "r") as f:
assert f.read() == tree_string
tree_path.unlink()
if annotation_path:
annotation_path = Path(annotation_path)
# Annotation file there?
assert annotation_path.exists()
annotation_path.unlink()
def test_encode_from_cli(args):
with enter_temp_directory():
encode_from_cli(args)
# Fingerprints JSON there?
assert Path("fingerprints.json").exists()
# Fingerprints LOG there?
if platform.system() != "Windows":
assert Path("fingerprints.log").exists()
def test_encode(
structure_klifs_ids, fingerprints_json_filepath, local_klifs_download_path, n_cores
):
with enter_temp_directory():
fingerprint_generator = encode(
structure_klifs_ids, fingerprints_json_filepath, local_klifs_download_path, n_cores
)
assert isinstance(fingerprint_generator, FingerprintGenerator)
if fingerprints_json_filepath is not None:
assert Path(fingerprints_json_filepath).exists()
def test_weights(feature_distances_path, feature_weights,
fingerprint_distances_path):
with enter_temp_directory():
fingerprint_distances = weights(feature_distances_path,
feature_weights,
fingerprint_distances_path)
assert isinstance(fingerprint_distances, FingerprintDistanceGenerator)
if fingerprint_distances_path is not None:
fingerprint_distances_path = Path(fingerprint_distances_path)
assert fingerprint_distances_path.exists()
assert fingerprint_distances_path.parent / f"{fingerprint_distances_path.stem}.log"
def test_to_from_csv(self, feature_distances_generator):
with enter_temp_directory():
filepath = Path("test.csv")
feature_distances_generator.to_csv(filepath)
assert filepath.exists()
feature_distances_generator_from_csv = FeatureDistancesGenerator.from_csv(
filepath)
assert isinstance(feature_distances_generator_from_csv,
FeatureDistancesGenerator)
def test_compare_from_cli(args):
with enter_temp_directory():
compare_from_cli(args)
# Feature distances CSV there?
assert Path("feature_distances.csv").exists()
# Fingerprint distance CSV there?
assert Path("fingerprint_distances.csv").exists()
# Distances LOG there?
if platform.system() != "Windows":
assert Path("distances.log").exists()
def test_main_outliers(args):
"""
Test CLI for outliers using subprocesses.
"""
output = Path("fingerprints_clean_test.json")
args = args.split()
with enter_temp_directory():
subprocess.run(args, check=True)
# Json file there?
assert output.exists()
# Log file there?
assert Path(f"{output.stem}.log").exists()
def test_main_weights(args):
"""
Test CLI for outliers using subprocesses.
"""
output = Path("fingerprint_distances_test.csv") # See -o in CLI command
args = args.split()
with enter_temp_directory():
subprocess.run(args, check=True)
# Json file there?
assert output.exists()
# Log file there?
assert Path(f"{output.stem}.log").exists()
def test_outliers(
fingerprints_path, distance_cutoff, fingerprints_wo_outliers_path, n_fingerprints_wo_outliers
):
with enter_temp_directory():
fingerprints = outliers(fingerprints_path, distance_cutoff, fingerprints_wo_outliers_path)
assert isinstance(fingerprints, FingerprintGenerator)
assert len(fingerprints.data) == n_fingerprints_wo_outliers
if fingerprints_wo_outliers_path is not None:
fingerprints_wo_outliers_path = Path(fingerprints_wo_outliers_path)
assert fingerprints_wo_outliers_path.exists()
assert (
fingerprints_wo_outliers_path.parent / f"{fingerprints_wo_outliers_path.stem}.log"
)
def test_encode(args):
"""
Test CLI for encoding using subprocesses.
"""
tree_path = Path("kissim.tree")
annotation_path = Path("kinase_annotation.csv")
args = args.split()
with enter_temp_directory():
subprocess.run(args, check=True)
# Tree file there?
assert tree_path.exists()
print(args)
print("-a" in args)
if "-a" in args:
# Annotation file there?
assert annotation_path.exists()
def test_main_encode(args):
"""
Test CLI for encoding using subprocesses.
"""
output = Path("fingerprints.json")
args = args.split()
with enter_temp_directory():
subprocess.run(args, check=True)
# Json file there?
assert output.exists()
# Log file there?
assert Path(f"{output.stem}.log").exists()
# Json file can be loaded as FingerprintGenerator object?
fingerprint_generator = FingerprintGenerator.from_json(output)
assert isinstance(fingerprint_generator, FingerprintGenerator)
assert isinstance(list(fingerprint_generator.data.values())[0], Fingerprint)
def test_to_from_json(self, structure_klifs_ids, normalize,
values_array_sum):
"""
Test if saving/loading a fingerprint to/from a json file.
"""
fingerprints = FingerprintGenerator.from_structure_klifs_ids(
structure_klifs_ids, LOCAL, 1)
json_filepath = Path("fingerprints.json")
with enter_temp_directory():
# Save json file
fingerprints.to_json(json_filepath)
assert json_filepath.exists()
# Load json file
fingerprints_reloaded = FingerprintGenerator.from_json(
json_filepath, normalize)
assert isinstance(fingerprints_reloaded, FingerprintGenerator)
# Attribute data
assert list(fingerprints.data.keys()) == list(
fingerprints_reloaded.data.keys())
if normalize:
assert list(fingerprints.data_normalized.keys()) == list(
fingerprints_reloaded.data_normalized.keys())
else:
assert fingerprints_reloaded.data_normalized is None
values_array_sum_calculated = sum([
np.nansum(fingerprint.values_array(True, True, True))
for structure_klifs_id, fingerprint in
fingerprints_reloaded.data.items()
])
assert pytest.approx(values_array_sum_calculated,
abs=1e-4) == values_array_sum
def test_encode_from_cli(args):
with enter_temp_directory():
encode_from_cli(args)
assert Path("fingerprints.json").exists()
assert Path("fingerprints.log").exists()
