def test_bad_manifest():
# not abs path in
with copy_config() as config_path:
with edit_config(config_path) as config:
config["manifest"]["$BASE_DIR"] = "not_absolute"
with pytest.raises(BluepySnapError):
test_module.Config.parse(config_path)
with copy_config() as config_path:
with edit_config(config_path) as config:
config["manifest"]["$COMPONENT_DIR"] = "$BASE_DIR/$NETWORK_DIR"
with pytest.raises(BluepySnapError):
test_module.Config.parse(config_path)
with copy_config() as config_path:
with edit_config(config_path) as config:
config["components"]["other"] = "$COMPONENT_DIR/$BASE_DIR"
with pytest.raises(BluepySnapError):
test_module.Config.parse(config_path)
with copy_config() as config_path:
with edit_config(config_path) as config:
config["components"]["other"] = "something/$COMPONENT_DIR/"
with pytest.raises(BluepySnapError):
test_module.Config.parse(config_path)
with copy_config() as config_path:
with edit_config(config_path) as config:
config["components"]["other"] = "/something/$COMPONENT_DIR/"
with pytest.raises(BluepySnapError):
test_module.Config.parse(config_path)
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_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_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_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_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_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_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_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_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_bad_manifest():
# 2 anchors would result in the absolute path of the last one : misleading
with copy_config() as config_path:
with edit_config(config_path) as config:
config["manifest"]["$COMPONENT_DIR"] = "$BASE_DIR/$NETWORK_DIR"
with pytest.raises(BluepySnapError):
test_module.Config.parse(config_path)
# same but not in the manifest
with copy_config() as config_path:
with edit_config(config_path) as config:
config["components"]["other"] = "$COMPONENT_DIR/$BASE_DIR"
with pytest.raises(BluepySnapError):
test_module.Config.parse(config_path)
# relative path with an anchor in the middle is not allowed this breaks the purpose of the
# anchors (they are not just generic placeholders)
with copy_config() as config_path:
with edit_config(config_path) as config:
config["components"]["other"] = "something/$COMPONENT_DIR/"
with pytest.raises(BluepySnapError):
test_module.Config.parse(config_path)
# abs path with an anchor in the middle is not allowed
with copy_config() as config_path:
with edit_config(config_path) as config:
config["components"]["other"] = "/something/$COMPONENT_DIR/"
with pytest.raises(BluepySnapError):
test_module.Config.parse(config_path)
# unknown anchor
with copy_config() as config_path:
with edit_config(config_path) as config:
config["components"]["other"] = "$UNKNOWN/something/"
with pytest.raises(KeyError):
test_module.Config.parse(config_path)
def test_biophysical_in_library(self):
with copy_circuit() as (circuit_copy_path, config_copy_path):
with edit_config(config_copy_path) as config:
config["networks"]["nodes"][0]["nodes_file"] = "$NETWORK_DIR/nodes_quaternions.h5"
nodes_file = circuit_copy_path / 'nodes_quaternions.h5'
with h5py.File(nodes_file, 'r+') as h5f:
data = h5f['nodes/default/0/model_type'][:]
del h5f['nodes/default/0/model_type']
h5f.create_dataset('nodes/default/0/model_type',
data=np.zeros_like(data, dtype=int))
h5f.create_dataset('nodes/default/0/@library/model_type',
data=np.array(["biophysical", ], dtype=h5py.string_dtype()))
circuit = Circuit(str(config_copy_path))
assert isinstance(circuit.nodes['default'].morph, test_module.MorphHelper)
def test_no_alternate_morph_files():
with copy_circuit() as (circuit_copy_path, config_copy_path):
nodes_file = str(circuit_copy_path / "nodes.h5")
with edit_config(config_copy_path) as config:
config["networks"]["nodes"][0]["populations"]["default"]["alternate_morphologies"] = {
"neurolucida-asc": config["components"]["morphologies_dir"]
}
errors = test_module.validate(str(config_copy_path), bbp_check=True)
assert errors == {
Error(
Error.WARNING,
"missing 1 files in group morphology: default/0[{}]:\n\tmorph-A.asc\n".format(
nodes_file
),
)
}
def test_not_biophysical_population(self):
with copy_circuit() as (circuit_copy_path, config_copy_path):
with edit_config(config_copy_path) as config:
config["networks"]["nodes"][0]["nodes_file"] = "$NETWORK_DIR/nodes_quaternions.h5"
nodes_file = circuit_copy_path / 'nodes_quaternions.h5'
with h5py.File(nodes_file, 'r+') as h5f:
data = h5f['nodes/default/0/model_type'][:]
del h5f['nodes/default/0/model_type']
h5f.create_dataset('nodes/default/0/model_type',
data=np.zeros_like(data, dtype=int))
h5f.create_dataset('nodes/default/0/@library/model_type',
data=np.array(["virtual", ], dtype=h5py.string_dtype()))
with pytest.raises(BluepySnapError):
circuit = Circuit(str(config_copy_path))
circuit.nodes['default'].morph
def test_parse():
actual = test_module.Config.parse(
str(TEST_DATA_DIR / 'circuit_config.json'))
# check double resolution and '.' works: $COMPONENT_DIR -> $BASE_DIR -> '.'
assert actual['components']['morphologies_dir'] == str(TEST_DATA_DIR /
'morphologies')
# check resolution and './' works: $NETWORK_DIR -> './'
assert actual['networks']['nodes'][0]['nodes_file'] == str(TEST_DATA_DIR /
'nodes.h5')
# check resolution of '../' works: $PARENT --> '../'
with copy_config() as config_path:
with edit_config(config_path) as config:
config["manifest"]["$PARENT"] = "../"
config["components"]["other"] = "$PARENT/other"
actual = test_module.Config.parse(config_path)
assert (actual['components']['other'] == str(
Path(config_path.parent / "../other").resolve()))
# check resolution of '../' works in a path outside manifest
with copy_config() as config_path:
with edit_config(config_path) as config:
config["components"]["other"] = "../other"
actual = test_module.Config.parse(config_path)
assert (actual['components']['other'] == str(
Path(config_path.parent / "../other").resolve()))
# check resolution without manifest of '../' works in a path outside
# i.e. : self.manifest contains the configdir even if manifest is not here
with copy_config() as config_path:
with edit_config(config_path) as config:
for k in list(config):
config.pop(k)
config["something"] = "../other"
actual = test_module.Config.parse(config_path)
assert actual["something"] == str(
Path(config_path.parent / "../other").resolve())
# check resolution with multiple slashes
with copy_config() as config_path:
with edit_config(config_path) as config:
config["something"] = "$COMPONENT_DIR/something////else"
actual = test_module.Config.parse(config_path)
assert actual["something"] == str(
Path(config_path.parent) / 'something' / 'else')
# check resolution with $ in a middle of the words
with copy_config() as config_path:
with edit_config(config_path) as config:
config["something"] = "$COMPONENT_DIR/somet$hing/else"
actual = test_module.Config.parse(config_path)
assert actual["something"] == str(
Path(config_path.parent) / 'somet$hing' / 'else')
# check resolution with relative path without "." in the manifest
with copy_config() as config_path:
with edit_config(config_path) as config:
config["manifest"]["$NOPOINT"] = "nopoint"
config["components"]["other"] = "$NOPOINT/other"
actual = test_module.Config.parse(config_path)
assert actual["components"]["other"] == str(
Path(config_path.parent) / 'nopoint' / 'other')
# check resolution for non path objects
with copy_config() as config_path:
with edit_config(config_path) as config:
for k in list(config):
config.pop(k)
config["string"] = "string"
config["int"] = 1
config["double"] = 0.2
# just to check because we use starting with '.' as a special case
config["tricky_double"] = .2
config["path"] = "./path"
actual = test_module.Config.parse(config_path)
# string
assert actual["string"] == "string"
# int
assert actual["int"] == 1
# double
assert actual["double"] == 0.2
assert actual["tricky_double"] == 0.2
# path
assert actual["path"] == str(
Path(config_path.parent / "./path").resolve())
def test_ok_edge_population_type():
with copy_circuit() as (_, config_copy_path):
with edit_config(config_copy_path) as config:
config["networks"]["edges"][0]["populations"]["default"]["type"] = "chemical"
errors = test_module.validate(str(config_copy_path), bbp_check=True)
assert errors == set()
def test_invalid_config_nodes_type_file():
with copy_circuit() as (_, config_copy_path):
with edit_config(config_copy_path) as config:
config['networks']['nodes'][0]['node_types_file'] = '/'
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL, 'Invalid "node_types_file": /')}
def test_no_config_components():
with copy_circuit() as (_, config_copy_path):
with edit_config(config_copy_path) as config:
del config['components']
errors = test_module.validate(str(config_copy_path))
assert errors == {Error(Error.FATAL, 'No "components" in config')}