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 = 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_simulator_configuration(self, operation_factory,
connectivity_index_factory):
"""
Test export of a simulator configuration
"""
conn_gid = uuid.UUID(connectivity_index_factory().gid)
operation = operation_factory(is_simulation=True,
store_vm=True,
test_project=self.test_project,
conn_gid=conn_gid)
burst_configuration = BurstConfiguration(self.test_project.id)
burst_configuration.fk_simulation = operation.id
burst_configuration.simulator_gid = operation.view_model_gid
burst_configuration.name = "Test_burst"
burst_configuration = dao.store_entity(burst_configuration)
op_folder = StorageInterface().get_project_folder(
self.test_project.name, str(operation.id))
BurstService().store_burst_configuration(burst_configuration,
op_folder)
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_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 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 store_burst(project_id, operation=None):
"""
Build and persist BurstConfiguration entity.
"""
burst = BurstConfiguration(project_id)
if operation is not None:
burst.name = 'dummy_burst'
burst.status = BurstConfiguration.BURST_FINISHED
burst.start_time = datetime.now()
burst.range1 = '["conduction_speed", {"lo": 50, "step": 1.0, "hi": 100.0}]'
burst.range2 = '["connectivity", null]'
burst.fk_simulation = operation.id
burst.simulator_gid = uuid.uuid4().hex
BurstService().store_burst_configuration(burst)
return dao.store_entity(burst)
def get_burst_for_migration(burst_id, burst_match_dict, date_format, selected_db):
"""
This method is supposed to only be used when migrating from version 4 to version 5.
It finds a BurstConfig in the old format (when it did not inherit from HasTraitsIndex), deletes it
and returns its parameters.
"""
session = SA_SESSIONMAKER()
burst_params = session.execute("""SELECT * FROM "BURST_CONFIGURATION" WHERE id = """ + burst_id).fetchone()
session.close()
if burst_params is None:
return None, False
burst_params_dict = {'datatypes_number': burst_params['datatypes_number'],
'dynamic_ids': burst_params['dynamic_ids'], 'range_1': burst_params['range1'],
'range_2': burst_params['range2'], 'fk_project': burst_params['fk_project'],
'name': burst_params['name'], 'status': burst_params['status'],
'error_message': burst_params['error_message'], 'start_time': burst_params['start_time'],
'finish_time': burst_params['finish_time'], 'fk_simulation': burst_params['fk_simulation'],
'fk_operation_group': burst_params['fk_operation_group'],
'fk_metric_operation_group': burst_params['fk_metric_operation_group']}
if selected_db == 'sqlite':
burst_params_dict['start_time'] = string2date(burst_params_dict['start_time'], date_format=date_format)
burst_params_dict['finish_time'] = string2date(burst_params_dict['finish_time'], date_format=date_format)
if burst_id not in burst_match_dict:
burst_config = BurstConfiguration(burst_params_dict['fk_project'])
burst_config.datatypes_number = burst_params_dict['datatypes_number']
burst_config.dynamic_ids = burst_params_dict['dynamic_ids']
burst_config.error_message = burst_params_dict['error_message']
burst_config.finish_time = burst_params_dict['finish_time']
burst_config.fk_metric_operation_group = burst_params_dict['fk_metric_operation_group']
burst_config.fk_operation_group = burst_params_dict['fk_operation_group']
burst_config.fk_project = burst_params_dict['fk_project']
burst_config.fk_simulation = burst_params_dict['fk_simulation']
burst_config.name = burst_params_dict['name']
burst_config.range1 = burst_params_dict['range_1']
burst_config.range2 = burst_params_dict['range_2']
burst_config.start_time = burst_params_dict['start_time']
burst_config.status = burst_params_dict['status']
new_burst = True
else:
burst_config = dao.get_burst_by_id(burst_match_dict[burst_id])
new_burst = False
return burst_config, new_burst
def load_datatype_from_file(self,
current_file,
op_id,
datatype_group=None,
current_project_id=None):
# type: (str, int, DataTypeGroup, int) -> HasTraitsIndex
"""
Creates an instance of datatype from storage / H5 file
:returns: DatatypeIndex
"""
self.logger.debug("Loading DataType from file: %s" % current_file)
h5_class = H5File.h5_class_from_file(current_file)
if h5_class is BurstConfigurationH5:
if current_project_id is None:
op_entity = dao.get_operationgroup_by_id(op_id)
current_project_id = op_entity.fk_launched_in
h5_file = BurstConfigurationH5(current_file)
burst = BurstConfiguration(current_project_id)
burst.fk_simulation = op_id
h5_file.load_into(burst)
result = burst
else:
datatype, generic_attributes = h5.load_with_links(current_file)
index_class = h5.REGISTRY.get_index_for_datatype(
datatype.__class__)
datatype_index = index_class()
datatype_index.fill_from_has_traits(datatype)
datatype_index.fill_from_generic_attributes(generic_attributes)
# Add all the required attributes
if datatype_group:
datatype_index.fk_datatype_group = datatype_group.id
if len(datatype_group.subject) == 0:
datatype_group.subject = datatype_index.subject
dao.store_entity(datatype_group)
datatype_index.fk_from_operation = op_id
associated_file = h5.path_for_stored_index(datatype_index)
if os.path.exists(associated_file):
datatype_index.disk_size = FilesHelper.compute_size_on_disk(
associated_file)
result = datatype_index
return result
def test_export_simulator_configuration(self, operation_factory):
"""
Test export of a simulator configuration
"""
operation = operation_factory(is_simulation=True, store_vm=True)
burst_configuration = BurstConfiguration(self.test_project.id)
burst_configuration.fk_simulation = operation.id
burst_configuration.simulator_gid = operation.view_model_gid
burst_configuration = dao.store_entity(burst_configuration)
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 load_datatype_from_file(self,
current_file,
op_id,
datatype_group=None,
current_project_id=None):
# type: (str, int, DataTypeGroup, int) -> HasTraitsIndex
"""
Creates an instance of datatype from storage / H5 file
:returns: DatatypeIndex
"""
self.logger.debug("Loading DataType from file: %s" % current_file)
h5_class = H5File.h5_class_from_file(current_file)
if h5_class is BurstConfigurationH5:
if current_project_id is None:
op_entity = dao.get_operationgroup_by_id(op_id)
current_project_id = op_entity.fk_launched_in
h5_file = BurstConfigurationH5(current_file)
burst = BurstConfiguration(current_project_id)
burst.fk_simulation = op_id
h5_file.load_into(burst)
result = burst
else:
datatype, generic_attributes = h5.load_with_links(current_file)
already_existing_datatype = h5.load_entity_by_gid(datatype.gid)
if datatype_group is not None and already_existing_datatype is not None:
raise DatatypeGroupImportException(
"The datatype group that you are trying to import"
" already exists!")
index_class = h5.REGISTRY.get_index_for_datatype(
datatype.__class__)
datatype_index = index_class()
datatype_index.fill_from_has_traits(datatype)
datatype_index.fill_from_generic_attributes(generic_attributes)
if datatype_group is not None and hasattr(datatype_index, 'fk_source_gid') and \
datatype_index.fk_source_gid is not None:
ts = h5.load_entity_by_gid(datatype_index.fk_source_gid)
if ts is None:
op = dao.get_operations_in_group(
datatype_group.fk_operation_group,
only_first_operation=True)
op.fk_operation_group = None
dao.store_entity(op)
dao.remove_entity(OperationGroup,
datatype_group.fk_operation_group)
dao.remove_entity(DataTypeGroup, datatype_group.id)
raise DatatypeGroupImportException(
"Please import the time series group before importing the"
" datatype measure group!")
# Add all the required attributes
if datatype_group:
datatype_index.fk_datatype_group = datatype_group.id
if len(datatype_group.subject) == 0:
datatype_group.subject = datatype_index.subject
dao.store_entity(datatype_group)
datatype_index.fk_from_operation = op_id
associated_file = h5.path_for_stored_index(datatype_index)
if os.path.exists(associated_file):
datatype_index.disk_size = StorageInterface.compute_size_on_disk(
associated_file)
result = datatype_index
return result
