def deserialize_simulator(simulator_gid, storage_path):
simulator_in_path = h5.path_for(storage_path, SimulatorH5,
simulator_gid)
simulator_in = SimulatorAdapterModel()
with SimulatorH5(simulator_in_path) as simulator_in_h5:
simulator_in_h5.load_into(simulator_in)
simulator_in.connectivity = simulator_in_h5.connectivity.load()
simulator_in.stimulus = simulator_in_h5.stimulus.load()
simulator_in.history_gid = simulator_in_h5.simulation_state.load()
for monitor in simulator_in.monitors:
if isinstance(monitor, Projection):
with SimulatorH5(simulator_in_path) as simulator_in_h5:
monitor_h5_path = simulator_in_h5.get_reference_path(
monitor.gid)
monitor_h5_class = h5_factory.monitor_h5_factory(type(monitor))
with monitor_h5_class(monitor_h5_path) as monitor_h5:
sensors_gid = monitor_h5.sensors.load()
projection_gid = monitor_h5.projection.load()
region_mapping_gid = monitor_h5.region_mapping.load()
sensors_index = ABCAdapter.load_entity_by_gid(sensors_gid.hex)
projection_index = ABCAdapter.load_entity_by_gid(
projection_gid.hex)
sensors_class = monitor.projection_class().sensors.field_type
sensors = h5.load_from_index(sensors_index,
dt_class=sensors_class)
projection_class = monitor.projection_class()
projection = h5.load_from_index(projection_index,
dt_class=projection_class)
region_mapping = ABCAdapter.load_traited_by_gid(
region_mapping_gid)
monitor.sensors = sensors
monitor.projection = projection
monitor.region_mapping = region_mapping
if simulator_in.surface:
cortex_path = h5.path_for(storage_path, CortexH5,
simulator_in.surface.gid)
with CortexH5(cortex_path) as cortex_h5:
simulator_in.surface.local_connectivity = cortex_h5.local_connectivity.load(
)
simulator_in.surface.region_mapping_data = cortex_h5.region_mapping_data.load(
)
rm_index = dao.get_datatype_by_gid(
simulator_in.surface.region_mapping_data.hex)
simulator_in.surface.surface_gid = uuid.UUID(
rm_index.fk_surface_gid)
return simulator_in
def deserialize_simulator(simulator_gid, storage_path):
simulator_in_path = h5.path_for(storage_path, SimulatorH5,
simulator_gid)
simulator_in = SimulatorAdapterModel()
with SimulatorH5(simulator_in_path) as simulator_in_h5:
simulator_in_h5.load_into(simulator_in)
simulator_in.connectivity = simulator_in_h5.connectivity.load()
simulator_in.stimulus = simulator_in_h5.stimulus.load()
simulator_in.history_gid = simulator_in_h5.simulation_state.load()
if isinstance(simulator_in.monitors[0], Projection):
# TODO: simplify this part
with SimulatorH5(simulator_in_path) as simulator_in_h5:
monitor_h5_path = simulator_in_h5.get_reference_path(
simulator_in.monitors[0].gid)
monitor_h5_class = h5_factory.monitor_h5_factory(
type(simulator_in.monitors[0]))
with monitor_h5_class(monitor_h5_path) as monitor_h5:
sensors_gid = monitor_h5.sensors.load()
region_mapping_gid = monitor_h5.region_mapping.load()
sensors = ABCAdapter.load_traited_by_gid(sensors_gid)
if isinstance(simulator_in.monitors[0], EEG):
sensors = SensorsEEG.build_sensors_subclass(sensors)
elif isinstance(simulator_in.monitors[0], MEG):
sensors = SensorsMEG.build_sensors_subclass(sensors)
elif isinstance(simulator_in.monitors[0], iEEG):
sensors = SensorsInternal.build_sensors_subclass(sensors)
simulator_in.monitors[0].sensors = sensors
region_mapping = ABCAdapter.load_traited_by_gid(region_mapping_gid)
simulator_in.monitors[0].region_mapping = region_mapping
if simulator_in.surface:
cortex_path = h5.path_for(storage_path, CortexH5,
simulator_in.surface.gid)
with CortexH5(cortex_path) as cortex_h5:
simulator_in.surface.local_connectivity = cortex_h5.local_connectivity.load(
)
simulator_in.surface.region_mapping_data = cortex_h5.region_mapping_data.load(
)
rm_index = dao.get_datatype_by_gid(
simulator_in.surface.region_mapping_data.hex)
simulator_in.surface.surface_gid = uuid.UUID(
rm_index.surface_gid)
return simulator_in
def test_export_simulator_configuration(self, operation_factory,
connectivity_factory):
"""
Test export of a simulator configuration
"""
operation = operation_factory()
simulator = SimulatorAdapterModel()
simulator.connectivity = connectivity_factory(4).gid
burst_configuration = BurstConfiguration(self.test_project.id)
burst_configuration.fk_simulation_id = operation.id
burst_configuration.simulator_gid = simulator.gid.hex
burst_configuration = dao.store_entity(burst_configuration)
storage_path = FilesHelper().get_project_folder(
self.test_project, str(operation.id))
h5_path = h5.path_for(storage_path, SimulatorH5, simulator.gid)
with SimulatorH5(h5_path) as h5_file:
h5_file.store(simulator)
export_file = self.export_manager.export_simulator_configuration(
burst_configuration.id)
assert export_file is not None, "Export process should return path to export file"
assert os.path.exists(
export_file
), "Could not find export file: %s on disk." % export_file
assert zipfile.is_zipfile(
export_file), "Generated file is not a valid ZIP file"
def test_export(self):
op = TestFactory.create_operation()
simulator_index = SimulatorIndex()
simulator_index.fill_from_has_traits(self.session_stored_simulator)
burst_config = BurstConfiguration(self.test_project.id,
simulator_index.id)
burst_config = dao.store_entity(burst_config)
simulator_index.fk_from_operation = op.id
simulator_index = dao.store_entity(simulator_index)
simulator_index.fk_parent_burst = burst_config.id
simulator_index = dao.store_entity(simulator_index)
simulator_h5 = h5.path_for_stored_index(simulator_index)
with SimulatorH5(simulator_h5) as h5_file:
h5_file.store(self.session_stored_simulator)
burst = dao.get_bursts_for_project(self.test_project.id)
self.sess_mock['burst_id'] = str(burst[0].id)
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_BURST_CONFIG,
self.session_stored_simulator)
common.add2session(common.KEY_BURST_CONFIG, burst_config)
result = self.simulator_controller.export(str(burst[0].id))
assert path.exists(result.input.name), "Simulation was not exported!"
def serialize_simulator(simulator, simulation_state_gid, storage_path):
simulator_path = h5.path_for(storage_path, SimulatorH5, simulator.gid)
with SimulatorH5(simulator_path) as simulator_h5:
simulator_h5.store(simulator)
if simulation_state_gid:
simulator_h5.simulation_state.store(
uuid.UUID(simulation_state_gid))
def test_export(self):
op = TestFactory.create_operation(test_user=self.test_user,
test_project=self.test_project)
burst_config = BurstConfiguration(self.test_project.id)
burst_config.fk_simulation = op.id
burst_config.simulator_gid = self.session_stored_simulator.gid.hex
burst_config = dao.store_entity(burst_config)
storage_path = FilesHelper().get_project_folder(
self.test_project, str(op.id))
h5_path = h5.path_for(storage_path, SimulatorH5,
self.session_stored_simulator.gid)
with SimulatorH5(h5_path) as h5_file:
h5_file.store(self.session_stored_simulator)
burst = dao.get_bursts_for_project(self.test_project.id)
self.sess_mock['burst_id'] = str(burst[0].id)
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_BURST_CONFIG,
self.session_stored_simulator)
common.add2session(common.KEY_BURST_CONFIG, burst_config)
result = self.simulator_controller.export(str(burst[0].id))
assert path.exists(result.input.name), "Simulation was not exported!"
def test_export_simulator_configuration(self, operation_factory):
"""
Test export of a simulator configuration
"""
operation = operation_factory()
simulator = Simulator()
simulator_index = SimulatorIndex()
simulator_index.fill_from_has_traits(simulator)
simulator_index.fk_from_operation = operation.id
simulator_index = dao.store_entity(simulator_index)
burst_configuration = BurstConfiguration(self.test_project.id,
simulator_index.id)
burst_configuration = dao.store_entity(burst_configuration)
simulator_index.fk_parent_burst = burst_configuration.id
simulator_index = dao.store_entity(simulator_index)
simulator_h5 = h5.path_for_stored_index(simulator_index)
with SimulatorH5(simulator_h5) as h5_file:
h5_file.store(simulator)
export_file = self.export_manager.export_simulator_configuration(
burst_configuration.id)
assert export_file is not None, "Export process should return path to export file"
assert os.path.exists(
export_file
), "Could not find export file: %s on disk." % export_file
assert zipfile.is_zipfile(
export_file), "Generated file is not a valid ZIP file"
def deserialize_simulator(simulator_gid, storage_path):
simulator_in_path = h5.path_for(storage_path, SimulatorH5,
simulator_gid)
simulator_in = Simulator()
with SimulatorH5(simulator_in_path) as simulator_in_h5:
simulator_in_h5.load_into(simulator_in)
connectivity_gid = simulator_in_h5.connectivity.load()
stimulus_gid = simulator_in_h5.stimulus.load()
simulation_state_gid = simulator_in_h5.simulation_state.load()
conn_index = dao.get_datatype_by_gid(connectivity_gid.hex)
conn = h5.load_from_index(conn_index)
simulator_in.connectivity = conn
if simulator_in.surface:
cortex_path = h5.path_for(storage_path, CortexH5,
simulator_in.surface.gid)
with CortexH5(cortex_path) as cortex_h5:
local_conn_gid = cortex_h5.local_connectivity.load()
region_mapping_gid = cortex_h5.region_mapping_data.load()
region_mapping_index = dao.get_datatype_by_gid(
region_mapping_gid.hex)
region_mapping_path = h5.path_for_stored_index(
region_mapping_index)
region_mapping = RegionMapping()
with RegionMappingH5(region_mapping_path) as region_mapping_h5:
region_mapping_h5.load_into(region_mapping)
region_mapping.gid = region_mapping_h5.gid.load()
surf_gid = region_mapping_h5.surface.load()
surf_index = dao.get_datatype_by_gid(surf_gid.hex)
surf_h5 = h5.h5_file_for_index(surf_index)
surf = CorticalSurface()
surf_h5.load_into(surf)
surf_h5.close()
region_mapping.surface = surf
simulator_in.surface.region_mapping_data = region_mapping
if local_conn_gid:
local_conn_index = dao.get_datatype_by_gid(local_conn_gid.hex)
local_conn = h5.load_from_index(local_conn_index)
simulator_in.surface.local_connectivity = local_conn
if stimulus_gid:
stimulus_index = dao.get_datatype_by_gid(stimulus_gid.hex)
stimulus = h5.load_from_index(stimulus_index)
simulator_in.stimulus = stimulus
return simulator_in, simulation_state_gid
def serialize_simulator(simulator, simulator_gid, simulation_state_gid, storage_path):
simulator_path = h5.path_for(storage_path, SimulatorH5, simulator_gid)
with SimulatorH5(simulator_path) as simulator_h5:
simulator_h5.gid.store(uuid.UUID(simulator_gid))
simulator_h5.store(simulator)
simulator_h5.connectivity.store(simulator.connectivity.gid)
if simulator.stimulus:
simulator_h5.stimulus.store(uuid.UUID(simulator.stimulus.gid))
if simulation_state_gid:
simulator_h5.simulation_state.store(uuid.UUID(simulation_state_gid))
return simulator_gid
def prepare_simulation_on_server(self, user_id, project, algorithm, zip_folder_path, simulator_file):
with SimulatorH5(simulator_file) as simulator_h5:
simulator_gid = simulator_h5.gid.load()
metadata = {}
simulator_id = algorithm.id
algo_category = algorithm.algorithm_category
operation = self._prepare_operation(project.id, user_id, simulator_id, simulator_gid,
algo_category, None, metadata)
storage_operation_path = self.files_helper.get_project_folder(project, str(operation.id))
self.async_launch_simulation_on_server(operation, zip_folder_path, storage_operation_path)
return operation
def load_from_zip(self, zip_file, project):
import_service = ImportService()
simulator_folder = import_service.import_simulator_configuration_zip(
zip_file)
simulator_h5_filename = DirLoader(
simulator_folder, None).find_file_for_has_traits_type(Simulator)
with SimulatorH5(os.path.join(simulator_folder,
simulator_h5_filename)) as sim_h5:
simulator_gid = sim_h5.gid.load()
simulator = SimulatorSerializer.deserialize_simulator(
simulator_gid, simulator_folder)
burst_config = self.burst_service.load_burst_configuration_from_folder(
simulator_folder, project)
return simulator, burst_config