def test_get_filepath_biophysical():
nodes = create_node_population(str(TEST_DATA_DIR / "nodes.h5"), "default")
config = Config(TEST_DATA_DIR / "circuit_config.json").resolve()
test_obj = test_module.NeuronModelsHelper(config["components"], nodes)
node_id = 0
assert nodes.get(node_id,
properties=Node.MODEL_TEMPLATE) == "hoc:small_bio-A"
actual = test_obj.get_filepath(node_id)
expected = Path(config["components"]["biophysical_neuron_models_dir"],
"small_bio-A.hoc")
assert actual == expected
actual = test_obj.get_filepath(np.int64(node_id))
assert actual == expected
actual = test_obj.get_filepath(np.uint64(node_id))
assert actual == expected
actual = test_obj.get_filepath(np.int32(node_id))
assert actual == expected
actual = test_obj.get_filepath(np.uint32(node_id))
assert actual == expected
node_id = CircuitNodeId("default", 0)
assert nodes.get(node_id,
properties=Node.MODEL_TEMPLATE) == "hoc:small_bio-A"
actual = test_obj.get_filepath(node_id)
assert actual == expected
node_id = CircuitNodeId("default", 2)
assert nodes.get(node_id,
properties=Node.MODEL_TEMPLATE) == "hoc:small_bio-C"
actual = test_obj.get_filepath(node_id)
expected = Path(config["components"]["biophysical_neuron_models_dir"],
"small_bio-C.hoc")
assert actual == expected
def test_get_filepath_point():
with copy_config() as config_copy_path:
with edit_config(config_copy_path) as config:
config["components"][
"point_neuron_models_dir"] = "$COMPONENT_DIR/point_neuron_models"
circuit = Circuit(config_copy_path)
nodes = create_node_population(str(TEST_DATA_DIR / "nodes_points.h5"),
"default", circuit)
test_obj = test_module.NeuronModelsHelper(circuit.config["components"],
nodes)
node_id = 0
assert nodes.get(node_id,
properties=Node.MODEL_TEMPLATE) == "nml:empty_bio"
actual = test_obj.get_filepath(node_id)
expected = Path(
circuit.config["components"]["point_neuron_models_dir"],
"empty_bio.nml")
assert actual == expected
node_id = 1
assert nodes.get(
node_id,
properties=Node.MODEL_TEMPLATE) == "nml:/abs/path/empty_bio"
actual = test_obj.get_filepath(node_id)
expected = Path("/abs/path/empty_bio.nml")
assert actual == expected
def test_get_filepath_biophysical():
nodes = create_node_population(str(TEST_DATA_DIR / 'nodes.h5'), "default")
config = Config(TEST_DATA_DIR / 'circuit_config.json').resolve()
test_obj = test_module.NeuronModelsHelper(config['components'], nodes)
node_id = 0
assert nodes.get(node_id,
properties=Node.MODEL_TEMPLATE) == "hoc:small_bio-A"
actual = test_obj.get_filepath(node_id)
expected = Path(config['components']['biophysical_neuron_models_dir'],
'small_bio-A.hoc')
assert actual == expected
node_id = CircuitNodeId('default', 0)
assert nodes.get(node_id,
properties=Node.MODEL_TEMPLATE) == "hoc:small_bio-A"
actual = test_obj.get_filepath(node_id)
assert actual == expected
node_id = CircuitNodeId('default', 2)
assert nodes.get(node_id,
properties=Node.MODEL_TEMPLATE) == "hoc:small_bio-C"
actual = test_obj.get_filepath(node_id)
expected = Path(config['components']['biophysical_neuron_models_dir'],
'small_bio-C.hoc')
assert actual == expected
def test_get_invalid_node_id():
nodes = create_node_population(str(TEST_DATA_DIR / "nodes.h5"), "default")
config = Config(TEST_DATA_DIR / "circuit_config.json").resolve()
test_obj = test_module.NeuronModelsHelper(config["components"], nodes)
with pytest.raises(BluepySnapError) as e:
test_obj.get_filepath("1")
assert "node_id must be a int or a CircuitNodeId" in e.value.args[0]
def test_no_biophysical_dir():
nodes = create_node_population(str(TEST_DATA_DIR / "nodes.h5"), "default")
config = Config(TEST_DATA_DIR / "circuit_config.json").resolve()
del config["components"]["biophysical_neuron_models_dir"]
test_obj = test_module.NeuronModelsHelper(config["components"], nodes)
with pytest.raises(BluepySnapError) as e:
test_obj.get_filepath(0)
assert "Missing 'biophysical_neuron_models_dir'" in e.value.args[0]
def test_no_point_dir():
nodes = create_node_population(str(TEST_DATA_DIR / 'nodes_points.h5'),
"default")
config = Config(TEST_DATA_DIR / 'circuit_config.json').resolve()
test_obj = test_module.NeuronModelsHelper(config['components'], nodes)
with pytest.raises(BluepySnapError) as e:
test_obj.get_filepath(0)
assert "Missing 'point_neuron_models_dir'" in e.value.args[0]
def test_invalid_model_type():
"""test that model type, other than 'biophysical' or 'point_neuron', throws an error"""
with copy_circuit() as (circuit_copy_path, config_copy_path):
config = Config(config_copy_path).resolve()
nodes_file = config["networks"]["nodes"][0]["nodes_file"]
with h5py.File(nodes_file, "r+") as h5f:
grp_name = "nodes/default/0/model_type"
data = h5f[grp_name][:]
del h5f[grp_name]
h5f.create_dataset(grp_name,
data=["virtual"] * data.shape[0],
dtype=h5py.string_dtype())
nodes = create_node_population(nodes_file, "default")
with pytest.raises(BluepySnapError) as e:
test_module.NeuronModelsHelper({}, nodes)
assert "biophysical or point node population" in e.value.args[0]