def test_overwrite():
tmp_dir = tempfile.mkdtemp() # tempfile.TemporaryDirectory()
output_dir = os.path.join(tmp_dir, 'output')
sim_config = {
'manifest': {
'$HOME_DIR': tmp_dir
},
'output': {
'output_dir': '${HOME_DIR}/output',
'log_file': 'simulation.log',
'log_to_console': False,
'overwrite_output_dir': False
}
}
cfg = SimulationConfig.from_dict(sim_config)
cfg.build_env()
assert(isinstance(cfg, SimulationConfig))
assert(os.path.exists(output_dir))
assert(os.path.exists(os.path.join(output_dir, 'simulation.log')))
assert(os.path.exists(os.path.join(output_dir, 'sonata_config.json')))
## Changed behavior so that even if overwrite_output_dir is false and dir exists, it will still run
# with pytest.raises(Exception):
# cfg = SimulationConfig.from_dict(sim_config)
# cfg.build_env()
sim_config['output']['overwrite_output_dir'] = True
cfg = SimulationConfig.from_dict(sim_config)
cfg.build_env()
assert(os.path.exists(output_dir))
assert(os.path.exists(os.path.join(output_dir, 'simulation.log')))
assert(os.path.exists(os.path.join(output_dir, 'sonata_config.json')))
def test_validate_components():
cfg = SimulationConfig.from_dict({
"components": {
"synaptic_models_dir": tempfile.mkdtemp(),
"morphologies_dir": tempfile.mkdtemp(),
"biophysical_neuron_models_dir": tempfile.mkdtemp()
}
})
assert (cfg.validate())
cfg = SimulationConfig.from_dict({
"components": {
"point_neuron_models_dir": tempfile.mkdtemp(),
"templates_dir": 'invaliddir',
}
})
with pytest.raises(Exception):
assert (cfg.validate())
def test_validate_network():
# Check that validate() passes when all the files exists
tmp_h5_file = tempfile.NamedTemporaryFile(suffix='.h5')
tmp_csv_types_file = tempfile.NamedTemporaryFile(suffix='.csv')
cfg = SimulationConfig.from_dict({
"networks": {
"nodes": [{
"nodes_file": tmp_h5_file.name,
"node_types_file": tmp_csv_types_file.name
}],
"edges": [{
"edges_file": tmp_h5_file.name,
"edge_types_file": tmp_csv_types_file.name
}]
}
})
assert (cfg.validate())
cfg = SimulationConfig.from_dict({
"networks": {
"nodes": [{
"nodes_file": tmp_h5_file.name,
"node_types_file": 'nameoffilethatdoesntexists.csv'
}]
}
})
with pytest.raises(Exception):
cfg.validate()
# edges_file does not exist should raise error
cfg = SimulationConfig.from_dict({
"networks": {
"edges": [{
"edges_file": 'blah',
"edge_types_file": tmp_csv_types_file.name
}]
}
})
with pytest.raises(Exception):
cfg.validate()
def test_validate_inputs():
spikes_file = tempfile.NamedTemporaryFile(suffix='.h5')
cfg = SimulationConfig.from_dict({
"inputs": {
"valid_input": {
"input_type": "spikes",
"input_file": spikes_file.name
}
}
})
assert (cfg.validate())
cfg = SimulationConfig.from_dict({
"inputs": {
"valid_input": {
"input_type": "spikes",
"input_file": 'notmyspikesfile.h5'
}
}
})
with pytest.raises(Exception):
assert (cfg.validate())
def from_config(cls, conf, **properties):
"""Generates a graph structure from a json config file or dictionary.
:param conf: name of json config file, or a dictionary with config parameters
:param properties: optional properties.
:return: A graph object of type cls
"""
graph = cls(**properties)
# The simulation run script should create a config-dict since it's likely to vary based on the simulator engine,
# however in the case the user doesn't we will try a generic conversion from dict/json to ConfigDict
if isinstance(conf, ConfigDict):
config = conf
else:
try:
config = ConfigDict.load(conf)
except Exception as e:
graph.io.log_exception('Could not convert {} (type "{}") to json.'.format(conf, type(conf)))
if not config.with_networks:
graph.io.log_exception('Could not find any network files. Unable to build network.')
# TODO: These are simulator specific
graph.spike_threshold = config.spike_threshold
graph.dL = config.dL
# load components
for name, value in config.components.items():
graph.add_component(name, value)
graph._validate_components()
# load nodes
gid_map = config.gid_mappings
for node_dict in config.nodes:
nodes_net = sonata.File(data_files=node_dict['nodes_file'], data_type_files=node_dict['node_types_file'],
gid_table=gid_map)
graph.add_nodes(nodes_net)
# load edges
for edge_dict in config.edges:
target_network = edge_dict['target'] if 'target' in edge_dict else None
source_network = edge_dict['source'] if 'source' in edge_dict else None
edge_net = sonata.File(data_files=edge_dict['edges_file'], data_type_files=edge_dict['edge_types_file'])
graph.add_edges(edge_net, source_pop=target_network, target_pop=source_network)
graph._node_sets['all'] = NodeSetAll(graph)
for ns_name, ns_filter in conf.node_sets.items():
graph._node_sets[ns_name] = NodeSet(ns_filter, graph)
return graph
def test_build_env():
tmp_dir = tempfile.mkdtemp() # tempfile.TemporaryDirectory()
output_dir = os.path.join(tmp_dir, 'output')
sim_config = {
'manifest': {
'$HOME_DIR': tmp_dir # .name
},
'output': {
'output_dir': '${HOME_DIR}/output',
'log_file': 'simulation.log',
'log_to_console': False
}
}
cfg = SimulationConfig.from_dict(sim_config)
cfg.build_env()
assert(isinstance(cfg, SimulationConfig))
assert(os.path.exists(output_dir))
assert(os.path.exists(os.path.join(output_dir, 'simulation.log')))
assert(os.path.exists(os.path.join(output_dir, 'sonata_config.json')))
def from_json(config_file, validate=False):
conf_dict = SimulationConfig.from_json(config_file)
conf_dict.io = io
return conf_dict