def test_server_fire_simulation(self, mocker, connectivity_factory):
input_folder = self.files_helper.get_project_folder(self.test_project)
sim_dir = os.path.join(input_folder, 'test_sim')
if not os.path.isdir(sim_dir):
os.makedirs(sim_dir)
simulator = Simulator()
simulator.connectivity = connectivity_factory()
sim_serializer = SimulatorSerializer()
sim_serializer.serialize_simulator(simulator, simulator.gid.hex, None,
sim_dir)
zip_filename = shutil.make_archive(sim_dir, 'zip', input_folder)
# Mock flask.request.files to return a dictionary
request_mock = mocker.patch.object(flask, 'request')
fp = open(zip_filename, 'rb')
request_mock.files = {
'file': FileStorage(fp, os.path.basename(zip_filename))
}
def launch_sim(self, user_id, project, algorithm, zip_folder_path,
simulator_file):
return Operation('', '', '', {})
# Mock simulation launch
mocker.patch.object(SimulatorService, 'prepare_simulation_on_server',
launch_sim)
operation_gid, status = self.simulation_resource.post(
self.test_project.gid)
fp.close()
assert type(operation_gid) is str
assert status == 201
def fire_simulation(self, project_gid, session_stored_simulator,
temp_folder):
simulator_index = SimulatorIndex()
temp_name = tempfile.mkdtemp(dir=TvbProfile.current.TVB_TEMP_FOLDER)
destination_folder = os.path.join(TvbProfile.current.TVB_TEMP_FOLDER,
temp_name)
simulation_state_gid = None
SimulatorSerializer().serialize_simulator(session_stored_simulator,
simulator_index.gid,
simulation_state_gid,
destination_folder)
zip_folder_path = os.path.join(
temp_folder, RequestFileKey.SIMULATION_FILE_NAME.value)
FilesHelper().zip_folder(zip_folder_path, destination_folder)
file_obj = open(zip_folder_path, 'rb')
return self.secured_request().post(
self.build_request_url(
RestLink.FIRE_SIMULATION.compute_url(
True, {LinkPlaceholder.PROJECT_GID.value: project_gid})),
files={
RequestFileKey.SIMULATION_FILE_KEY.value:
(RequestFileKey.SIMULATION_FILE_NAME.value, file_obj)
})
def async_launch_and_prepare_simulation(self, burst_config, user, project, simulator_algo,
session_stored_simulator, simulation_state_gid):
try:
metadata = {}
metadata.update({DataTypeMetaData.KEY_BURST: burst_config.id})
simulator_id = simulator_algo.id
algo_category = simulator_algo.algorithm_category
operation = self._prepare_operation(project.id, user.id, simulator_id, session_stored_simulator.gid,
algo_category, None, metadata)
storage_path = self.files_helper.get_project_folder(project, str(operation.id))
SimulatorSerializer().serialize_simulator(session_stored_simulator, simulation_state_gid, storage_path)
BurstService.update_simulation_fields(burst_config.id, operation.id, session_stored_simulator.gid)
wf_errs = 0
try:
OperationService().launch_operation(operation.id, True)
return operation
except Exception as excep:
self.logger.error(excep)
wf_errs += 1
if burst_config:
BurstService().mark_burst_finished(burst_config, error_message=str(excep))
self.logger.debug("Finished launching workflow. The operation was launched successfully, " +
str(wf_errs) + " had error on pre-launch steps")
except Exception as excep:
self.logger.error(excep)
if burst_config:
BurstService().mark_burst_finished(burst_config, error_message=str(excep))
def test_load_burst_only(self):
zip_path = path.join(path.dirname(tvb_data.__file__), 'connectivity', 'connectivity_66.zip')
connectivity = TestFactory.import_zip_connectivity(self.test_user, self.test_project, zip_path, "John")
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.name = 'Test_Burst'
burst_config = dao.store_entity(burst_config)
self.sess_mock['burst_id'] = str(burst_config.id)
self.sess_mock['connectivity'] = connectivity.gid
self.sess_mock['conduction_speed'] = "3.0"
self.sess_mock['coupling'] = "Sigmoidal"
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.set_connectivity(**self.sess_mock._data)
self.simulator_controller.set_stimulus(**self.sess_mock._data)
storage_path = FilesHelper().get_project_folder(self.test_project, str(op.id))
SimulatorSerializer().serialize_simulator(self.session_stored_simulator, None, storage_path)
with patch('cherrypy.session', self.sess_mock, create=True):
self.simulator_controller.load_burst_read_only(str(burst_config.id))
is_simulator_load = common.get_from_session(KEY_IS_SIMULATOR_LOAD)
is_simulator_copy = common.get_from_session(KEY_IS_SIMULATOR_COPY)
last_loaded_form_url = common.get_from_session(KEY_LAST_LOADED_FORM_URL)
assert is_simulator_load, "Simulator Load Flag should be True!"
assert not is_simulator_copy, "Simulator Copy Flag should be False!"
assert last_loaded_form_url == '/burst/setup_pse', "Incorrect last form URL!"
def async_launch_and_prepare_pse(self, burst_config, user, project, simulator_algo, range_param1, range_param2,
session_stored_simulator):
try:
simulator_id = simulator_algo.id
algo_category = simulator_algo.algorithm_category
operation_group = burst_config.operation_group
metric_operation_group = burst_config.metric_operation_group
operations = []
range_param2_values = []
if range_param2:
range_param2_values = range_param2.get_range_values()
first_simulator = None
for param1_value in range_param1.get_range_values():
for param2_value in range_param2_values:
# Copy, but generate a new GUID for every Simulator in PSE
simulator = copy.deepcopy(session_stored_simulator)
simulator.gid = uuid.uuid4()
self._set_simulator_range_parameter(simulator, range_param1.name, param1_value)
self._set_simulator_range_parameter(simulator, range_param2.name, param2_value)
ranges = json.dumps({range_param1.name: param1_value[0], range_param2.name: param2_value[0]})
operation = self._prepare_operation(project.id, user.id, simulator_id, simulator.gid,
algo_category, operation_group,
{DataTypeMetaData.KEY_BURST: burst_config.id}, ranges)
storage_path = self.files_helper.get_project_folder(project, str(operation.id))
SimulatorSerializer().serialize_simulator(simulator, None, storage_path)
operations.append(operation)
if first_simulator is None:
first_simulator = simulator
first_operation = operations[0]
BurstService.update_simulation_fields(burst_config.id, first_operation.id, first_simulator.gid)
datatype_group = DataTypeGroup(operation_group, operation_id=first_operation.id,
fk_parent_burst=burst_config.id,
state=json.loads(first_operation.meta_data)[DataTypeMetaData.KEY_STATE])
dao.store_entity(datatype_group)
metrics_datatype_group = DataTypeGroup(metric_operation_group, fk_parent_burst=burst_config.id)
dao.store_entity(metrics_datatype_group)
wf_errs = 0
for operation in operations:
try:
OperationService().launch_operation(operation.id, True)
except Exception as excep:
self.logger.error(excep)
wf_errs += 1
BurstService().mark_burst_finished(burst_config, error_message=str(excep))
self.logger.debug("Finished launching workflows. " + str(len(operations) - wf_errs) +
" were launched successfully, " + str(wf_errs) + " had error on pre-launch steps")
except Exception as excep:
self.logger.error(excep)
BurstService().mark_burst_finished(burst_config, error_message=str(excep))
def test_load_burst_only(self):
zip_path = path.join(path.dirname(tvb_data.__file__), 'connectivity',
'connectivity_66.zip')
TestFactory.import_zip_connectivity(self.test_user, self.test_project,
zip_path, "John")
connectivity = TestFactory.get_entity(self.test_project,
ConnectivityIndex)
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 = burst_config.id
simulator_index = dao.store_entity(simulator_index)
simulator_index.fk_parent_burst = burst_config.id
simulator_index = dao.store_entity(simulator_index)
burst = dao.get_bursts_for_project(self.test_project.id)
self.sess_mock['burst_id'] = str(burst[0].id)
self.sess_mock['_connectivity'] = connectivity.gid
self.sess_mock['_conduction_speed'] = "3.0"
self.sess_mock['_coupling'] = "Sigmoidal"
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG,
self.session_stored_simulator)
self.simulator_controller.set_connectivity(**self.sess_mock._data)
self.simulator_controller.set_stimulus(**self.sess_mock._data)
storage_path = FilesHelper().get_project_folder(
self.test_project, str(simulator_index.fk_from_operation))
simulator_service = SimulatorService()
SimulatorSerializer().serialize_simulator(
self.session_stored_simulator, simulator_index.gid, None,
storage_path)
with patch('cherrypy.session', self.sess_mock, create=True):
self.simulator_controller.load_burst_read_only(str(burst[0].id))
is_simulator_load = common.get_from_session(KEY_IS_SIMULATOR_LOAD)
is_simulator_copy = common.get_from_session(KEY_IS_SIMULATOR_COPY)
last_loaded_form_url = common.get_from_session(
KEY_LAST_LOADED_FORM_URL)
database_simulator = dao.get_generic_entity(SimulatorIndex,
burst_config.id,
'fk_parent_burst')[0]
assert simulator_index.gid == database_simulator.gid, "Simulator was not added correctly!"
assert is_simulator_load, "Simulator Load Flag should be True!"
assert not is_simulator_copy, "Simulator Copy Flag should be False!"
assert last_loaded_form_url == '/burst/setup_pse', "Incorrect last form URL!"
def test_server_fire_simulation(self, mocker, connectivity_factory):
self._mock_user(mocker)
input_folder = self.files_helper.get_project_folder(self.test_project)
sim_dir = os.path.join(input_folder, 'test_sim')
if not os.path.isdir(sim_dir):
os.makedirs(sim_dir)
simulator = Simulator()
simulator.connectivity = connectivity_factory()
sim_serializer = SimulatorSerializer()
sim_serializer.serialize_simulator(simulator, None, sim_dir)
zip_filename = os.path.join(input_folder,
RequestFileKey.SIMULATION_FILE_NAME.value)
FilesHelper().zip_folder(zip_filename, sim_dir)
# Mock flask.request.files to return a dictionary
request_mock = mocker.patch.object(flask, 'request')
fp = open(zip_filename, 'rb')
request_mock.files = {
RequestFileKey.SIMULATION_FILE_KEY.value:
FileStorage(fp, os.path.basename(zip_filename))
}
def launch_sim(self, user_id, project, algorithm, zip_folder_path,
simulator_file):
return Operation('', '', '', {})
# Mock simulation launch and current user
mocker.patch.object(SimulatorService, 'prepare_simulation_on_server',
launch_sim)
operation_gid, status = self.simulation_resource.post(
project_gid=self.test_project.gid)
fp.close()
assert type(operation_gid) is str
assert status == 201
def load_view_model(self, adapter_instance, operation):
storage_path = self.file_helper.get_project_folder(
operation.project, str(operation.id))
input_gid = json.loads(operation.parameters)['gid']
# TODO: review location, storage_path, op params deserialization
if isinstance(adapter_instance, SimulatorAdapter):
view_model = SimulatorSerializer().deserialize_simulator(
input_gid, storage_path)
else:
view_model_class = adapter_instance.get_view_model_class()
view_model = view_model_class()
h5_path = h5.path_for(storage_path, ViewModelH5, input_gid)
h5_file = ViewModelH5(h5_path, view_model)
h5_file.load_into(view_model)
return view_model
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
def fire_simulation(self, project_gid, session_stored_simulator,
temp_folder):
temporary_folder = FilesHelper.create_temp_folder()
simulation_state_gid = None
SimulatorSerializer().serialize_simulator(session_stored_simulator,
simulation_state_gid,
temporary_folder)
zip_folder_path = os.path.join(
temp_folder, RequestFileKey.SIMULATION_FILE_NAME.value)
FilesHelper().zip_folder(zip_folder_path, temporary_folder)
shutil.rmtree(temporary_folder)
file_obj = open(zip_folder_path, 'rb')
return self.secured_request().post(
self.build_request_url(
RestLink.FIRE_SIMULATION.compute_url(
True, {LinkPlaceholder.PROJECT_GID.value: project_gid})),
files={
RequestFileKey.SIMULATION_FILE_KEY.value:
(RequestFileKey.SIMULATION_FILE_NAME.value, file_obj)
})