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_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_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_no_nodes_h5():
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']
errors = test_module.validate(str(config_copy_path))
assert errors == {
Error(Error.FATAL, 'No "nodes" in {}.'.format(nodes_file)),
Error(Error.FATAL, 'No node population for "/edges/default/source_node_id"'),
Error(Error.FATAL, 'No node population for "/edges/default/target_node_id"'),
}
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')}
def test_invalid_config_nodes_file():
with copy_circuit() as (_, config_copy_path):
with edit_config(config_copy_path) as config:
del config["networks"]["nodes"][0]["nodes_file"]
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL, 'Invalid "nodes_file": None')}
with edit_config(config_copy_path) as config:
config["networks"]["nodes"][0]["nodes_file"] = "/"
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL, 'Invalid "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_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_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_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_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_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_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_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_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_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_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_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_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_required_edge_population_datasets_one_group():
required_datasets = sorted([
'edge_type_id', 'source_node_id', 'target_node_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:
for ds in required_datasets:
del h5f['edges/default/' + ds]
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL, 'Population default of {} misses datasets {}'.
format(edges_file, required_datasets))}
def test_no_required_node_multi_group_datasets():
required_datasets = ['node_group_id', 'node_group_index']
for ds in required_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:
del h5f['nodes/default/' + ds]
h5f.copy('nodes/default/0', 'nodes/default/1')
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL, 'Population default of {} misses datasets {}'.
format(nodes_file, [ds]))}
def test_no_required_bio_node_group_datasets():
required_datasets = sorted(['morphology', 'x', 'y', 'z'])
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 required_datasets:
del h5f['nodes/default/0/' + ds]
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL,
'Group default/0 of {} misses biophysical fields: {}'
.format(nodes_file, required_datasets))}
def test_no_required_node_group_datasets():
required_datasets = ['model_template', 'model_type']
for ds in required_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:
del h5f['nodes/default/0/' + ds]
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL,
'Group default/0 of {} misses "{}" field'
.format(nodes_file, ds))}
def test_edges_population_not_found_in_h5():
with copy_circuit() as (circuit_copy_path, config_copy_path):
edges_file = circuit_copy_path / "edges.h5"
with edit_config(config_copy_path) as config:
config["networks"]["edges"][0]["populations"]["fake_population"] = {}
errors = test_module.validate(str(config_copy_path), bbp_check=True)
assert errors == {
Error(
Error.FATAL,
"populations not found in {}:\n{}".format(edges_file, "\tfake_population\n"),
)
}
def test_no_config_edges_population():
with copy_circuit() as (_, config_copy_path):
expected = {Error(Error.FATAL, 'No "populations" defined in config "edges"')}
with edit_config(config_copy_path) as config:
del config["networks"]["edges"][0]["populations"]["default"]
errors = test_module.validate(str(config_copy_path), bbp_check=True)
assert errors == expected
with edit_config(config_copy_path) as config:
del config["networks"]["edges"][0]["populations"]
errors = test_module.validate(str(config_copy_path), bbp_check=True)
assert errors == expected
def test_edge_population_missing_edge_group_id_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_id"]
errors = test_module.validate(str(config_copy_path))
assert errors == {
Error(
Error.FATAL,
"Population default of {} misses dataset {}".format(edges_file, {"edge_group_id"}),
)
}
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_no_required_node_single_population_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:
del h5f['nodes/default2/']
del h5f['nodes/default/node_group_id']
del h5f['nodes/default/node_group_index']
errors = test_module.validate(str(config_copy_path))
assert errors == set()
with h5py.File(nodes_file, 'r+') as h5f:
del h5f['nodes/default/node_type_id']
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL, 'Population default of {} misses datasets {}'.
format(nodes_file, ['node_type_id']))}
