def test_no_required_bbp_edge_group_datasets():
with copy_circuit() as (circuit_copy_path, config_copy_path):
edges_file = circuit_copy_path / 'edges.h5'
with h5py.File(edges_file, 'r+') as h5f:
del h5f['edges/default/0/syn_weight']
errors = test_module.validate(str(config_copy_path), True)
assert errors == {BbpError(Error.WARNING, 'Group default/0 of {} misses fields: {}'.
format(edges_file, ['syn_weight']))}
def test_edge_population_multiple_groups():
with copy_circuit() as (circuit_copy_path, config_copy_path):
edges_file = circuit_copy_path / 'edges.h5'
with h5py.File(edges_file, 'r+') as h5f:
h5f.create_group('edges/default/1')
errors = test_module.validate(str(config_copy_path), bbp_check=True)
assert BbpError(Error.WARNING, 'Population default of {} have multiple groups. '
'Cannot be read via bluepysnap or libsonata'.
format(edges_file)) in errors
def test_no_bio_component_dirs():
dirs = ['morphologies_dir', 'biophysical_neuron_models_dir']
for dir_ in dirs:
with copy_circuit() as (_, config_copy_path):
with edit_config(config_copy_path) as config:
del config['components'][dir_]
errors = test_module.validate(str(config_copy_path), True)
# multiplication by 2 because we have 2 populations, each produces the same error.
assert errors == {BbpError(Error.FATAL,
'Invalid components "{}": {}'.format(dir_, None))}
def test_no_required_bbp_edge_group_datasets():
with copy_circuit() as (circuit_copy_path, config_copy_path):
edges_file = circuit_copy_path / "edges.h5"
with h5py.File(edges_file, "r+") as h5f:
del h5f["edges/default/0/syn_weight"]
errors = test_module.validate(str(config_copy_path), True)
assert errors == {
BbpError(
Error.WARNING,
"Group default/0 of {} misses fields: {}".format(edges_file, ["syn_weight"]),
)
}
def test_invalid_bio_alternate_morphology_dir():
with copy_circuit() as (circuit_copy_path, config_copy_path):
component = "neurolucida-asc"
fake_path = str(circuit_copy_path / "fake/path")
with edit_config(config_copy_path) as config:
config["networks"]["nodes"][0]["populations"]["default"]["alternate_morphologies"] = {
component: fake_path
}
errors = test_module.validate(str(config_copy_path), True)
assert errors == {
BbpError(Error.FATAL, 'Invalid components "{}": {}'.format(component, fake_path))
}
def test_edge_population_multiple_groups():
with copy_circuit() as (circuit_copy_path, config_copy_path):
edges_file = circuit_copy_path / "edges.h5"
with h5py.File(edges_file, "r+") as h5f:
h5f.create_group("edges/default/1")
errors = test_module.validate(str(config_copy_path), bbp_check=True)
assert (
BbpError(
Error.WARNING,
"Population default of {} have multiple groups. "
"Cannot be read via bluepysnap or libsonata".format(edges_file),
)
in errors
)
def test_no_rotation_bbp_node_group_datasets():
angle_datasets = ['rotation_angle_xaxis', 'rotation_angle_yaxis', 'rotation_angle_zaxis']
with copy_circuit() as (circuit_copy_path, config_copy_path):
nodes_file = circuit_copy_path / 'nodes.h5'
with h5py.File(nodes_file, 'r+') as h5f:
for ds in angle_datasets:
shape = h5f['nodes/default/0/' + ds].shape
del h5f['nodes/default/0/' + ds]
h5f['nodes/default/0/'].create_dataset('orientation_w', shape, fillvalue=0)
errors = test_module.validate(str(config_copy_path), bbp_check=True)
assert errors == {
Error(Error.WARNING, 'Group default/0 of {} has no rotation fields'.format(nodes_file)),
BbpError(Error.WARNING,
'Group default/0 of {} has no rotation fields'.format(nodes_file))
}
def test_no_rotation_bbp_node_group_datasets():
angle_datasets = ["rotation_angle_xaxis", "rotation_angle_yaxis", "rotation_angle_zaxis"]
with copy_circuit() as (circuit_copy_path, config_copy_path):
nodes_file = circuit_copy_path / "nodes.h5"
with h5py.File(nodes_file, "r+") as h5f:
for ds in angle_datasets:
shape = h5f["nodes/default/0/" + ds].shape
del h5f["nodes/default/0/" + ds]
h5f["nodes/default/0/"].create_dataset("orientation_w", shape, fillvalue=0)
errors = test_module.validate(str(config_copy_path), bbp_check=True)
assert errors == {
Error(Error.WARNING, "Group default/0 of {} has no rotation fields".format(nodes_file)),
BbpError(
Error.WARNING, "Group default/0 of {} has no rotation fields".format(nodes_file)
),
}