def test_empty_group_size():
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:
grp = h5f["nodes/default/"].create_group("3")
with pytest.raises(BluepySnapError):
test_module._get_group_size(grp)
def test_invalid_edge_node_ids():
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["edges/default/source_node_id"][0] = 99999
h5f["edges/default/target_node_id"][0] = 99999
errors = test_module.validate(str(config_copy_path))
assert errors == {
Error(
Error.FATAL,
"/edges/default/source_node_id misses node ids in its node population: [99999]",
),
Error(
Error.FATAL,
"/edges/default/target_node_id misses node ids in its node population: [99999]",
),
Error(
Error.FATAL,
"Population {} edges [99999] have node ids [0 1] instead of "
"single id 2".format(edges_file),
),
Error(
Error.FATAL,
"Population {} edges [99999] have node ids [0 1] instead of "
"single id 0".format(edges_file),
),
}
def test_no_edge_group():
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']
errors = test_module.validate(str(config_copy_path))
assert errors == set()
def test_empty_group_size():
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:
grp = h5f['nodes/default/'].create_group('3')
with pytest.raises(BluepySnapError):
test_module._get_group_size(grp)
def test_ok_nonbio_node_group_datasets():
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:
h5f['nodes/default/0/model_type'][:] = ''
errors = test_module.validate(str(config_copy_path))
assert errors == set()
def test_ok_node_ids_dataset():
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:
h5f['nodes/default/node_id'] = list(range(len(h5f['nodes/default/node_type_id'])))
errors = test_module.validate(str(config_copy_path))
assert errors == set()
def test_invalid_edge_node_ids():
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['edges/default/source_node_id'][0] = 99999
h5f['edges/default/target_node_id'][0] = 99999
errors = test_module.validate(str(config_copy_path))
assert errors == {
Error(
Error.FATAL,
'/edges/default/source_node_id misses node ids in its node population: [99999]'
),
Error(
Error.FATAL,
'/edges/default/target_node_id misses node ids in its node population: [99999]'
),
Error(
Error.FATAL,
'Population {} edges [99999] have node ids [0 1] instead of '
'single id 2'.format(edges_file)),
Error(
Error.FATAL,
'Population {} edges [99999] have node ids [0 1] instead of '
'single id 0'.format(edges_file)),
}
def test_no_morph_files():
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:
h5f["nodes/default/0/morphology"][0] = "noname"
errors = test_module.validate(str(config_copy_path))
assert errors == {
Error(
Error.WARNING,
"missing 1 files in group morphology: default/0[{}]:\n\tnoname.swc\n".format(
nodes_file
),
)
}
with h5py.File(nodes_file, "r+") as h5f:
morph = h5f["nodes/default/0/morphology"]
morph[:] = ["noname" + str(i) for i in range(len(morph))]
errors = test_module.validate(str(config_copy_path))
assert errors == {
Error(
Error.WARNING,
"missing 3 files in group morphology: default/0[{}]:\n\tnoname0.swc\n\t...\n".format(
nodes_file
),
)
}
def test_no_edges_h5():
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']
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL, 'No "edges" in {}.'.format(edges_file))}
def test_invalid_edge_population_type():
with copy_circuit() as (_, config_copy_path):
fake_type = "fake_type"
with edit_config(config_copy_path) as config:
config["networks"]["edges"][0]["populations"]["default"]["type"] = fake_type
errors = test_module.validate(str(config_copy_path), bbp_check=True)
assert errors == {Error(Error.WARNING, "Invalid edge type: {}".format(fake_type))}
def test_edge_population_missing_edge_group_index_one_group():
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/edge_group_index']
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL, 'Population default of {} misses dataset {}'.
format(edges_file, {"edge_group_index"}))}
def test_edge_population_missing_edge_group_id_index_one_group():
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/edge_group_index']
del h5f['edges/default/edge_group_id']
errors = test_module.validate(str(config_copy_path))
assert errors == set()
def test_no_config_edges():
with copy_circuit() as (_, config_copy_path):
with edit_config(config_copy_path) as config:
del config['networks']['edges']
errors = test_module.validate(str(config_copy_path))
assert errors == {
Error(Error.FATAL, 'No "edges" in config "networks"')
}
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_ok_virtual_node_group_datasets():
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:
h5f["nodes/default/0/model_type"][:] = "virtual"
del h5f["nodes/default/0/model_template"]
errors = test_module.validate(str(config_copy_path))
assert errors == set()
def test_nodes_multi_group_wrong_group_id():
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:
h5f.copy('nodes/default/0', 'nodes/default/1')
h5f['nodes/default/node_group_id'][-1] = 2
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL, 'Population /nodes/default of {} misses group(s): {}'.
format(nodes_file, {2}))}
def test_ok_circuit():
errors = test_module.validate(str(TEST_DATA_DIR / 'circuit_config.json'))
assert errors == set()
with copy_circuit() as (_, config_copy_path):
with edit_config(config_copy_path) as config:
config['networks']['nodes'][0]['node_types_file'] = None
errors = test_module.validate(str(config_copy_path))
assert errors == set()
def test_explicit_edges_no_node_population_attr():
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/source_node_id'].attrs['node_population']
errors = test_module.validate(str(config_copy_path))
assert errors == {
Error(Error.FATAL,
'Missing "node_population" attribute for "/edges/default/source_node_id"')}
def test_no_edge_source_to_target():
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/indices/source_to_target']
del h5f['edges/default/indices/target_to_source']
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL, 'No "source_to_target" in {}'.format(edges_file)),
Error(Error.FATAL, 'No "target_to_source" in {}'.format(edges_file))}
def test_edge_population_wrong_group_index():
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/edge_group_index']
h5f.create_dataset('edges/default/edge_group_index', data=[0, 1, 2, 12])
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL, 'Group default/0 in file {} should have ids up to {}'.
format(edges_file, 12))}
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_edge_population_wrong_group_id():
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/edge_group_id']
h5f.create_dataset('edges/default/edge_group_id', data=[0, 1, 0, 0])
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL, 'Population /edges/default of {} misses group(s): {}'.
format(edges_file, {1}))}
def test_missing_optional_edge_population_datasets_one_group():
optional_datasets = sorted(['edge_group_id', 'edge_group_index'])
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:
for ds in optional_datasets:
del h5f['edges/default/' + ds]
errors = test_module.validate(str(config_copy_path))
assert errors == set()
def test_no_edge_group_no_optional_datasets():
with copy_circuit() as (circuit_copy_path, config_copy_path):
optional_datasets = sorted(["edge_group_id", "edge_group_index"])
edges_file = circuit_copy_path / "edges.h5"
with h5py.File(edges_file, "r+") as h5f:
del h5f["edges/default/0"]
for ds in optional_datasets:
del h5f["edges/default/" + ds]
errors = test_module.validate(str(config_copy_path))
assert errors == set()
def test_edge_population_edge_group_different_length():
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/edge_group_index']
h5f.create_dataset('edges/default/edge_group_index', data=[0, 1, 2, 3, 4])
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL,
'Population {} of {} has different sizes of "group_id" and "group_index"'.
format('/edges/default', edges_file))}
def test_no_rotation_bio_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:
del h5f['nodes/default/0/' + ds]
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.WARNING,
'Group default/0 of {} has no rotation fields'.format(nodes_file))}
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_template_files():
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:
h5f['nodes/default/0/model_template'][0] = 'hoc:noname'
errors = test_module.validate(str(config_copy_path))
assert errors == {
Error(Error.WARNING,
'missing 1 files in group model_template: default/0[{}]:\n\tnoname.hoc\n'
.format(nodes_file))}
def test_invalid_config_edges_file():
with copy_circuit() as (_, config_copy_path):
with edit_config(config_copy_path) as config:
del config['networks']['edges'][0]['edges_file']
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL, 'Invalid "edges_file": None')}
with edit_config(config_copy_path) as config:
config['networks']['edges'][0]['edges_file'] = '/'
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL, 'Invalid "edges_file": /')}
def test_no_edge_all_node_ids():
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:
del h5f['nodes/default/0']
errors = test_module.validate(str(config_copy_path))
assert errors == {
Error(Error.FATAL,
'/edges/default/source_node_id does not have node ids in its node population'),
Error(Error.FATAL,
'/edges/default/target_node_id does not have node ids in its node population')}
