def __init__(self):
BaseController.__init__(self)
self.context = SelectedAdapterContext()
self.files_helper = FilesHelper()
self.operation_services = OperationService()
self.simulator_controller = SimulatorController()
analyze_category, groups = self.algorithm_service.get_analyze_groups()
adapters_list = []
for adapter_group in groups:
if len(adapter_group.children) > 1:
ids = [str(child.id) for child in adapter_group.children]
ids = ','.join(ids)
adapter_link = '/flow/show_group_of_algorithms/' + str(
analyze_category.id) + "/" + ids
else:
adapter_link = self.get_url_adapter(
analyze_category.id, adapter_group.children[0].id)
adapters_list.append({
common.KEY_TITLE:
adapter_group.name,
'link':
adapter_link,
'description':
adapter_group.description,
'subsection':
adapter_group.children[0].subsection_name
})
self.analyze_adapters = adapters_list
def setup_method(self):
"""
Sets up the environment for testing;
creates a `FlowController`
"""
self.init()
self.flow_c = FlowController()
self.burst_c = SimulatorController()
self.operation_service = OperationService()
def transactional_setup_method(self):
self.simulator_controller = SimulatorController()
self.test_user = TestFactory.create_user('SimulationController_User')
self.test_project = TestFactory.create_project(
self.test_user, "SimulationController_Project")
TvbProfile.current.web.RENDER_HTML = False
self.session_stored_simulator = SimulatorAdapterModel()
self.sess_mock = RamSession()
self.sess_mock[KEY_USER] = self.test_user
self.sess_mock[KEY_PROJECT] = self.test_project
cherrypy.request.method = "POST"
def transactional_setup_method(self):
self.simulator_controller = SimulatorController()
self.test_user = TestFactory.create_user('SimulationController_User')
self.test_project = TestFactory.create_project(self.test_user, "SimulationController_Project")
connectivity = TestFactory.import_zip_connectivity(self.test_user, self.test_project)
self.session_stored_simulator = SimulatorAdapterModel()
self.session_stored_simulator.connectivity = UUID(connectivity.gid)
self.sess_mock = RamSession()
self.sess_mock[KEY_USER] = self.test_user
self.sess_mock[KEY_PROJECT] = self.test_project
cherrypy.request.method = "POST"
def test_submit_noise_configuration_happy(self, connectivity_factory):
"""
Submit noise configuration writes the noise array on the required key in the burst configuration
"""
self.init()
noise_controller = NoiseConfigurationController()
SimulatorController().index()
simulator = cherrypy.session[common.KEY_SIMULATOR_CONFIG]
connectivity = connectivity_factory()
simulator.connectivity = connectivity.gid
simulator.integrator = HeunStochastic()
# a noise configuration in the format expected by submit. Assumes Generic2dOscillator model.
nodes_range = list(range(connectivity.number_of_regions))
noise_in = [{'V': 1.0, 'W': 2.0} for _ in nodes_range]
noise_in = json.dumps(noise_in)
self._expect_redirect('/burst/', noise_controller.submit, noise_in)
expected_noise_arr = [[1.0 for _ in nodes_range],
[2.0 for _ in nodes_range]]
actual_noise_arr = simulator.integrator.noise.nsig
assert (expected_noise_arr == actual_noise_arr).all()
self.cleanup()
def transactional_setup_method(self):
"""
Sets up the environment for testing;
creates a `RegionsModelParametersController` and a connectivity
"""
self.init()
self.region_m_p_c = RegionsModelParametersController()
SimulatorController().index()
self.simulator = cherrypy.session[common.KEY_SIMULATOR_CONFIG]
self._setup_dynamic()
def transactional_setup_fixture(self, region_mapping_index_factory):
self.init()
self.surface_m_p_c = SurfaceModelParametersController()
SimulatorController().index()
simulator = cherrypy.session[common.KEY_SIMULATOR_CONFIG]
region_mapping_index = region_mapping_index_factory()
simulator.connectivity = region_mapping_index.fk_connectivity_gid
simulator.surface = CortexViewModel()
simulator.surface.surface_gid = region_mapping_index.fk_surface_gid
simulator.surface.region_mapping_data = region_mapping_index.gid
def transactional_setup_fixture(self, connectivity_factory, surface_factory):
self.init()
self.surface_m_p_c = SurfaceModelParametersController()
SimulatorController().index()
stored_burst = cherrypy.session[common.KEY_BURST_CONFIG]
_, self.connectivity = connectivity_factory
_, self.surface = surface_factory
new_params = {}
for key, val in SIMULATOR_PARAMETERS.items():
new_params[key] = {'value': val}
new_params['connectivity'] = {'value': self.connectivity.gid}
new_params['surface'] = {'value': self.surface.gid}
stored_burst.simulator_configuration = new_params
def cancel_or_remove_operation(self,
operation_id,
is_group,
remove_after_stop=False):
"""
Stop the operation given by operation_id. If is_group is true stop all the
operations from that group.
"""
operation_id = int(operation_id)
is_group = int(is_group) != 0
if isinstance(remove_after_stop, str):
remove_after_stop = bool(remove_after_stop)
return SimulatorController.cancel_or_remove_operation(
operation_id, is_group, remove_after_stop)
def reload_burst_operation(self, operation_id, is_group, **_):
"""
Find out from which burst was this operation launched. Set that burst as the selected one and
redirect to the burst page.
"""
is_group = int(is_group)
if not is_group:
operation = OperationService.load_operation(int(operation_id))
else:
op_group = ProjectService.get_operation_group_by_id(operation_id)
first_op = ProjectService.get_operations_in_group(op_group)[0]
operation = OperationService.load_operation(int(first_op.id))
SimulatorController().copy_simulator_configuration(operation.burst.id)
raise cherrypy.HTTPRedirect("/burst/")
def init_cherrypy(arguments=None):
#### Mount static folders from modules marked for introspection
arguments = arguments or []
CONFIGUER = TvbProfile.current.web.CHERRYPY_CONFIGURATION
for module in arguments:
module_inst = importlib.import_module(str(module))
module_path = os.path.dirname(os.path.abspath(module_inst.__file__))
CONFIGUER["/static_" + str(module)] = {'tools.staticdir.on': True,
'tools.staticdir.dir': '.',
'tools.staticdir.root': module_path}
#### Mount controllers, and specify the root URL for them.
cherrypy.tree.mount(BaseController(), "/", config=CONFIGUER)
cherrypy.tree.mount(UserController(), "/user/", config=CONFIGUER)
cherrypy.tree.mount(ProjectController(), "/project/", config=CONFIGUER)
cherrypy.tree.mount(FigureController(), "/project/figure/", config=CONFIGUER)
cherrypy.tree.mount(FlowController(), "/flow/", config=CONFIGUER)
cherrypy.tree.mount(SettingsController(), "/settings/", config=CONFIGUER)
cherrypy.tree.mount(HelpController(), "/help/", config=CONFIGUER)
cherrypy.tree.mount(SimulatorController(), "/burst/", config=CONFIGUER)
cherrypy.tree.mount(ParameterExplorationController(), "/burst/explore/", config=CONFIGUER)
cherrypy.tree.mount(DynamicModelController(), "/burst/dynamic/", config=CONFIGUER)
cherrypy.tree.mount(SpatioTemporalController(), "/spatial/", config=CONFIGUER)
cherrypy.tree.mount(RegionsModelParametersController(), "/burst/modelparameters/regions/", config=CONFIGUER)
cherrypy.tree.mount(SurfaceModelParametersController(), "/spatial/modelparameters/surface/", config=CONFIGUER)
cherrypy.tree.mount(RegionStimulusController(), "/spatial/stimulus/region/", config=CONFIGUER)
cherrypy.tree.mount(SurfaceStimulusController(), "/spatial/stimulus/surface/", config=CONFIGUER)
cherrypy.tree.mount(LocalConnectivityController(), "/spatial/localconnectivity/", config=CONFIGUER)
cherrypy.tree.mount(NoiseConfigurationController(), "/burst/noise/", config=CONFIGUER)
cherrypy.tree.mount(HPCController(), "/hpc/", config=CONFIGUER)
cherrypy.config.update(CONFIGUER)
# ----------------- Register additional request handlers -----------------
# This tool checks for MAX upload size
cherrypy.tools.upload = Tool('on_start_resource', RequestHandler.check_upload_size)
# This tools clean up files on disk (mainly after export)
cherrypy.tools.cleanup = Tool('on_end_request', RequestHandler.clean_files_on_disk)
# ----------------- End register additional request handlers ----------------
# Register housekeeping job
if TvbProfile.current.hpc.IS_HPC_RUN and TvbProfile.current.hpc.CAN_RUN_HPC:
cherrypy.engine.housekeeper = cherrypy.process.plugins.BackgroundTask(
TvbProfile.current.hpc.BACKGROUND_JOB_INTERVAL, HPCOperationService.check_operations_job)
cherrypy.engine.housekeeper.start()
# HTTP Server is fired now ######
cherrypy.engine.start()
def transactional_setup_fixture(self, connectivity_factory):
"""
Sets up the environment for testing;
creates a `RegionsModelParametersController` and a connectivity
"""
self.init()
self.region_m_p_c = RegionsModelParametersController()
SimulatorController().index()
stored_burst = cherrypy.session[common.KEY_BURST_CONFIG]
self.connectivity = connectivity_factory()
new_params = {}
for key, val in SIMULATOR_PARAMETERS.items():
new_params[key] = {'value': val}
new_params['connectivity'] = {'value': self.connectivity.gid}
stored_burst.simulator_configuration = new_params
self._setup_dynamic()
def test_submit_noise_configuration_happy(self, connectivity_factory):
self.init()
self.noise_c = NoiseConfigurationController()
self.connectivity = connectivity_factory()
SimulatorController().index()
stored_burst = cherrypy.session[common.KEY_BURST_CONFIG]
new_params = {}
for key, val in SIMULATOR_PARAMETERS.items():
new_params[key] = {'value': val}
new_params['connectivity'] = {'value': self.connectivity.gid}
# Simulate selection of a specific integration from the ui
new_params[PARAM_INTEGRATOR] = {'value': EulerStochastic.__name__}
new_params[PARAM_MODEL] = {
'value': ModelsEnum.GENERIC_2D_OSCILLATOR.get_class().__name__
}
new_params[INTEGRATOR_PARAMETERS + '_option_EulerStochastic_noise'] = {
'value': Additive.__name__
}
stored_burst.simulator_configuration = new_params
"""
Submit noise configuration writes the noise array on the required key in the burst configuration
"""
# a noise configuration in the format expected by submit. Assumes Generic2dOscillator model.
nodes_range = list(range(self.connectivity.number_of_regions))
noise_in = [{'V': 1.0, 'W': 2.0} for _ in nodes_range]
noise_in = json.dumps(noise_in)
# expected noise array in burst config
expected_noise_arr = [[1.0 for _ in nodes_range],
[2.0 for _ in nodes_range]]
self._expect_redirect('/burst/', self.noise_c.submit, noise_in)
simulator_configuration = cherrypy.session[
common.KEY_BURST_CONFIG].simulator_configuration
nsig_key = 'integrator_parameters_option_EulerStochastic_noise_parameters_option_Additive_nsig'
actual_noise_arr = json.loads(
simulator_configuration[nsig_key]['value'])
assert expected_noise_arr == actual_noise_arr
def test_edit_model_parameters(self, region_mapping_index_factory):
self.init()
surface_m_p_c = SurfaceModelParametersController()
SimulatorController().index()
simulator = cherrypy.session[common.KEY_SIMULATOR_CONFIG]
region_mapping_index = region_mapping_index_factory()
simulator.connectivity = region_mapping_index.fk_connectivity_gid
simulator.surface = CortexViewModel()
simulator.surface.surface_gid = region_mapping_index.fk_surface_gid
simulator.surface.region_mapping_data = region_mapping_index.gid
result_dict = surface_m_p_c.edit_model_parameters()
expected_keys = [
'urlNormals', 'urlNormalsPick', 'urlTriangles', 'urlTrianglesPick',
'urlVertices', 'urlVerticesPick', 'mainContent',
'parametersEquationPlotForm', 'baseUrl', 'equationsPrefixes',
'brainCenter', 'applied_equations'
]
# map(lambda x: self.assertTrue(x in result_dict), expected_keys)
assert all(x in result_dict for x in expected_keys)
assert result_dict['baseUrl'] == '/spatial/modelparameters/surface'
assert result_dict['mainContent'] == 'spatial/model_param_surface_main'
class FlowController(BaseController):
"""
This class takes care of executing steps in projects.
"""
def __init__(self):
BaseController.__init__(self)
self.context = SelectedAdapterContext()
self.files_helper = FilesHelper()
self.operation_services = OperationService()
self.simulator_controller = SimulatorController()
analyze_category, groups = self.algorithm_service.get_analyze_groups()
adapters_list = []
for adapter_group in groups:
if len(adapter_group.children) > 1:
ids = [str(child.id) for child in adapter_group.children]
ids = ','.join(ids)
adapter_link = '/flow/show_group_of_algorithms/' + str(
analyze_category.id) + "/" + ids
else:
adapter_link = self.get_url_adapter(
analyze_category.id, adapter_group.children[0].id)
adapters_list.append({
common.KEY_TITLE:
adapter_group.name,
'link':
adapter_link,
'description':
adapter_group.description,
'subsection':
adapter_group.children[0].subsection_name
})
self.analyze_adapters = adapters_list
@expose_page
@settings
@context_selected
def step_analyzers(self):
"""
Choose exact action/adapter for current step.
"""
try:
analyze_category, groups = self.algorithm_service.get_analyze_groups(
)
step_name = analyze_category.displayname.lower()
template_specification = dict(mainContent="header_menu",
section_name=step_name,
controlPage=None,
title="Select an analyzer",
displayControl=False)
template_specification[
common.KEY_SUBMENU_LIST] = self.analyze_adapters
return self.fill_default_attributes(template_specification)
except ValueError:
message = 'Could not load analyzers!'
common.set_warning_message(message)
self.logger.warning(message)
raise cherrypy.HTTPRedirect('/tvb')
@expose_page
@settings
@context_selected
def step_connectivity(self):
"""
Display menu for Connectivity Footer tab.
"""
template_specification = dict(mainContent="header_menu",
section_name='connectivity',
controlPage=None,
title="Select an algorithm",
displayControl=False,
subsection_name='step',
submenu_list=self.connectivity_submenu)
return self.fill_default_attributes(template_specification)
@staticmethod
def _compute_back_link(back_indicator, project):
"""
Based on a simple indicator, compute URL for anchor BACK.
"""
if back_indicator is None:
# This applies to Connectivity and other visualizers when RELAUNCH button is used from Operation page.
back_page_link = None
elif back_indicator == 'burst':
back_page_link = "/burst"
elif back_indicator == 'operations':
back_page_link = '/project/viewoperations/' + str(project.id)
else:
back_page_link = '/project/editstructure/' + str(project.id)
return back_page_link
@expose_page
@settings
@context_selected
def show_group_of_algorithms(self, step_key, algorithm_ids):
project = common.get_current_project()
category = self.algorithm_service.get_category_by_id(step_key)
algorithms = []
for i in algorithm_ids.split(','):
algorithm_id = int(i)
algorithm = self.algorithm_service.get_algorithm_by_identifier(
algorithm_id)
algorithm.link = self.get_url_adapter(step_key, algorithm_id)
adapter_instance = self.algorithm_service.prepare_adapter(
algorithm)
adapter_form = self.algorithm_service.prepare_adapter_form(
adapter_instance, project.id)
algorithm.form = self.render_adapter_form(adapter_form)
algorithms.append(algorithm)
template_specification = dict(
mainContent="flow/algorithms_list",
algorithms=algorithms,
title="Select an algorithm",
section_name=category.displayname.lower())
self._populate_section(algorithms[0], template_specification)
self.fill_default_attributes(template_specification,
algorithms[0].group_name)
return template_specification
@expose_page
@settings
@context_selected
def prepare_group_launch(self, group_gid, step_key, algorithm_id, **data):
"""
Receives as input a group gid and an algorithm given by category and id, along
with data that gives the name of the required input parameter for the algorithm.
Having these generate a range of GID's for all the DataTypes in the group and
launch a new operation group.
"""
prj_service = ProjectService()
dt_group = prj_service.get_datatypegroup_by_gid(group_gid)
datatypes = prj_service.get_datatypes_from_datatype_group(dt_group.id)
range_param_name = data.pop('range_param_name')
data[RANGE_PARAMETER_1] = range_param_name
data[range_param_name] = ','.join(dt.gid for dt in datatypes)
self.operation_services.group_operation_launch(
common.get_logged_user().id, common.get_current_project(),
int(algorithm_id), int(step_key), **data)
redirect_url = self._compute_back_link('operations',
common.get_current_project())
raise cherrypy.HTTPRedirect(redirect_url)
@expose_page
@settings
@context_selected
def default(self,
step_key,
adapter_key,
cancel=False,
back_page=None,
**data):
"""
Render a specific adapter.
'data' are arguments for POST
"""
project = common.get_current_project()
algorithm = self.algorithm_service.get_algorithm_by_identifier(
adapter_key)
back_page_link = self._compute_back_link(back_page, project)
if algorithm is None:
raise cherrypy.HTTPRedirect("/tvb?error=True")
if cherrypy.request.method == 'POST' and cancel:
raise cherrypy.HTTPRedirect(back_page_link)
submit_link = self.get_url_adapter(step_key, adapter_key, back_page)
is_burst = back_page not in ['operations', 'data']
if cherrypy.request.method == 'POST':
data[common.KEY_ADAPTER] = adapter_key
template_specification = self.execute_post(project.id, submit_link,
step_key, algorithm,
**data)
self._populate_section(algorithm, template_specification, is_burst)
else:
template_specification = self.get_template_for_adapter(
project.id,
step_key,
algorithm,
submit_link,
is_burst=is_burst)
if template_specification is None:
raise cherrypy.HTTPRedirect('/tvb')
if KEY_CONTROLLS not in template_specification:
template_specification[KEY_CONTROLLS] = None
if common.KEY_SUBMIT_LINK not in template_specification:
template_specification[common.KEY_SUBMIT_LINK] = submit_link
if KEY_CONTENT not in template_specification:
template_specification[KEY_CONTENT] = "flow/full_adapter_interface"
template_specification[common.KEY_DISPLAY_MENU] = False
else:
template_specification[common.KEY_DISPLAY_MENU] = True
template_specification[common.KEY_BACK_PAGE] = back_page_link
template_specification[common.KEY_ADAPTER] = adapter_key
template_specification[ABCDisplayer.KEY_IS_ADAPTER] = True
self.fill_default_attributes(template_specification,
algorithm.displayname)
return template_specification
@expose_fragment('form_fields/options_field')
@settings
@context_selected
def get_filtered_datatypes(self, dt_module, dt_class, filters,
has_all_option, has_none_option):
"""
Given the name from the input tree, the dataType required and a number of
filters, return the available dataType that satisfy the conditions imposed.
"""
index_class = getattr(sys.modules[dt_module], dt_class)()
filters_dict = json.loads(filters)
fields = []
operations = []
values = []
for idx in range(len(filters_dict['fields'])):
fields.append(filters_dict['fields'][idx])
operations.append(filters_dict['operations'][idx])
values.append(filters_dict['values'][idx])
filter = FilterChain(fields=fields,
operations=operations,
values=values)
project = common.get_current_project()
form = Form(project_id=project.id)
data_type_gid_attr = DataTypeGidAttr(
linked_datatype=REGISTRY.get_datatype_for_index(index_class))
data_type_gid_attr.required = not string2bool(has_none_option)
select_field = TraitDataTypeSelectField(
data_type_gid_attr,
form.project_id,
conditions=filter,
has_all_option=string2bool(has_all_option))
return {'options': select_field.options()}
def execute_post(self, project_id, submit_url, step_key, algorithm,
**data):
""" Execute HTTP POST on a generic step."""
errors = None
adapter_instance = ABCAdapter.build_adapter(algorithm)
try:
form = adapter_instance.get_form()(project_id=project_id)
if 'fill_defaults' in data:
form.fill_from_post_plus_defaults(data)
else:
form.fill_from_post(data)
view_model = None
if form.validate():
try:
view_model = form.get_view_model()()
form.fill_trait(view_model)
self.context.add_view_model_to_session(view_model)
except NotImplementedError:
self.logger.exception(
"Form and/or ViewModel not fully implemented for " +
str(form))
raise InvalidFormValues(
"Invalid form inputs! Could not find a model for this form!",
error_dict=form.get_errors_dict())
else:
raise InvalidFormValues(
"Invalid form inputs! Could not fill algorithm from the given inputs!",
error_dict=form.get_errors_dict())
adapter_instance.submit_form(form)
if issubclass(type(adapter_instance), ABCDisplayer):
adapter_instance.current_project_id = project_id
adapter_instance.user_id = common.get_logged_user().id
result = adapter_instance.launch(view_model)
if isinstance(result, dict):
return result
else:
common.set_error_message(
"Invalid result returned from Displayer! Dictionary is expected!"
)
return {}
result = self.operation_services.fire_operation(
adapter_instance,
common.get_logged_user(),
project_id,
view_model=view_model)
if isinstance(result, list):
result = "Launched %s operations." % len(result)
common.set_important_message(str(result))
except formencode.Invalid as excep:
errors = excep.unpack_errors()
common.set_error_message("Invalid form inputs")
self.logger.warning("Invalid form inputs %s" % errors)
except (OperationException, LaunchException,
TraitValueError) as excep1:
self.logger.exception("Error while executing a Launch procedure:" +
excep1.message)
common.set_error_message(excep1.message)
except InvalidFormValues as excep2:
message, errors = excep2.display_full_errors()
common.set_error_message(message)
self.logger.warning("%s \n %s" % (message, errors))
template_specification = self.get_template_for_adapter(
project_id, step_key, algorithm, submit_url)
if (errors is not None) and (template_specification is not None):
template_specification[common.KEY_ERRORS] = errors
return template_specification
def get_template_for_adapter(self,
project_id,
step_key,
stored_adapter,
submit_url,
is_burst=True,
is_callout=False):
""" Get Input HTML Interface template or a given adapter """
try:
group = None
category = self.algorithm_service.get_category_by_id(step_key)
title = "Fill parameters for step " + category.displayname.lower()
if group:
title = title + " - " + group.displayname
adapter_instance = self.algorithm_service.prepare_adapter(
stored_adapter)
adapter_form = self.algorithm_service.prepare_adapter_form(
adapter_instance, project_id)
vm = self.context.get_view_model_from_session()
if vm and type(vm) == adapter_form.get_view_model():
adapter_form.fill_from_trait(vm)
else:
self.context.clean_from_session()
template_specification = dict(
submitLink=submit_url,
adapter_form=self.render_adapter_form(adapter_form,
is_callout=is_callout),
title=title)
self._populate_section(stored_adapter, template_specification,
is_burst)
return template_specification
except OperationException as oexc:
self.logger.error("Inconsistent Adapter")
self.logger.exception(oexc)
common.set_warning_message(
'Inconsistent Adapter! Please review the link (development problem)!'
)
return None
@cherrypy.expose
@handle_error(redirect=False)
@check_user
def readserverstaticfile(self, coded_path):
"""
Retrieve file from Local storage, having a File System Path.
"""
try:
with open(url2path(coded_path), "rb") as f:
return f.read()
except Exception as excep:
self.logger.error("Could not retrieve file from path:" +
str(coded_path))
self.logger.exception(excep)
def _read_datatype_attribute(self,
entity_gid,
dataset_name,
datatype_kwargs='null',
**kwargs):
self.logger.debug("Starting to read HDF5: " + entity_gid + "/" +
dataset_name + "/" + str(kwargs))
entity = load_entity_by_gid(entity_gid)
entity_dt = h5.load_from_index(entity)
datatype_kwargs = json.loads(datatype_kwargs)
if datatype_kwargs:
for key, value in six.iteritems(datatype_kwargs):
kwargs[key] = load_entity_by_gid(value)
result = getattr(entity_dt, dataset_name)
if callable(result):
if kwargs:
result = result(**kwargs)
else:
result = result()
return result
@expose_json
def invoke_adapter(self, algo_id, method_name, entity_gid, **kwargs):
algorithm = self.algorithm_service.get_algorithm_by_identifier(algo_id)
adapter_instance = ABCAdapter.build_adapter(algorithm)
entity = load_entity_by_gid(entity_gid)
storage_path = self.files_helper.get_project_folder(
entity.parent_operation.project, str(entity.fk_from_operation))
adapter_instance.storage_path = storage_path
method = getattr(adapter_instance, method_name)
if kwargs:
return method(entity_gid, **kwargs)
return method(entity_gid)
@expose_json
def read_from_h5_file(self,
entity_gid,
method_name,
flatten=False,
datatype_kwargs='null',
**kwargs):
self.logger.debug("Starting to read HDF5: " + entity_gid + "/" +
method_name + "/" + str(kwargs))
entity = load_entity_by_gid(entity_gid)
entity_h5 = h5.h5_file_for_index(entity)
datatype_kwargs = json.loads(datatype_kwargs)
if datatype_kwargs:
for key, value in six.iteritems(datatype_kwargs):
kwargs[key] = load_entity_by_gid(value)
result = getattr(entity_h5, method_name)
if kwargs:
result = result(**kwargs)
else:
result = result()
entity_h5.close()
return self._prepare_result(result, flatten)
@expose_json
def read_datatype_attribute(self,
entity_gid,
dataset_name,
flatten=False,
datatype_kwargs='null',
**kwargs):
"""
Retrieve from a given DataType a property or a method result.
:returns: JSON representation of the attribute.
:param entity_gid: GID for DataType entity
:param dataset_name: name of the dataType property /method
:param flatten: result should be flatten before return (use with WebGL data mainly e.g vertices/triangles)
Ignored if the attribute is not an ndarray
:param datatype_kwargs: if passed, will contain a dictionary of type {'name' : 'gid'}, and for each such
pair, a load_entity will be performed and kwargs will be updated to contain the result
:param kwargs: extra parameters to be passed when dataset_name is method.
"""
result = self._read_datatype_attribute(entity_gid, dataset_name,
datatype_kwargs, **kwargs)
return self._prepare_result(result, flatten)
def _prepare_result(self, result, flatten):
if isinstance(result, numpy.ndarray):
# for ndarrays honor the flatten kwarg and convert to lists as ndarrs are not json-able
if flatten is True or flatten == "True":
result = result.flatten()
return result.tolist()
else:
return result
@expose_numpy_array
def read_binary_datatype_attribute(self,
entity_gid,
dataset_name,
datatype_kwargs='null',
**kwargs):
return self._read_datatype_attribute(entity_gid, dataset_name,
datatype_kwargs, **kwargs)
@expose_fragment("flow/genericAdapterFormFields")
def get_simple_adapter_interface(self,
algorithm_id,
parent_div='',
is_uploader=False):
"""
AJAX exposed method. Will return only the interface for a adapter, to
be used when tabs are needed.
"""
curent_project = common.get_current_project()
is_uploader = string2bool(is_uploader)
template_specification = self.get_adapter_template(
curent_project.id, algorithm_id, is_uploader)
template_specification[common.KEY_PARENT_DIV] = parent_div
return self.fill_default_attributes(template_specification)
@expose_fragment("flow/full_adapter_interface")
def getadapterinterface(self, project_id, algorithm_id, back_page=None):
"""
AJAX exposed method. Will return only a piece of a page,
to be integrated as part in another page.
"""
template_specification = self.get_adapter_template(project_id,
algorithm_id,
False,
back_page,
is_callout=True)
template_specification["isCallout"] = True
return self.fill_default_attributes(template_specification)
def get_adapter_template(self,
project_id,
algorithm_id,
is_upload=False,
back_page=None,
is_callout=False):
"""
Get the template for an adapter based on the algo group id.
"""
if not (project_id and int(project_id) and
(algorithm_id is not None) and int(algorithm_id)):
return ""
algorithm = self.algorithm_service.get_algorithm_by_identifier(
algorithm_id)
if is_upload:
submit_link = "/project/launchloader/" + str(
project_id) + "/" + str(algorithm_id)
else:
submit_link = self.get_url_adapter(algorithm.fk_category,
algorithm.id, back_page)
template_specification = self.get_template_for_adapter(
project_id,
algorithm.fk_category,
algorithm,
submit_link,
is_callout=is_callout)
if template_specification is None:
return ""
template_specification[common.KEY_DISPLAY_MENU] = not is_upload
return template_specification
@cherrypy.expose
@handle_error(redirect=True)
@context_selected
def reloadoperation(self, operation_id, **_):
"""Redirect to Operation Input selection page, with input data already selected."""
operation = OperationService.load_operation(operation_id)
# Reload previous parameters in session
adapter_instance = ABCAdapter.build_adapter(operation.algorithm)
view_model = adapter_instance.load_view_model(operation)
self.context.add_view_model_to_session(view_model)
# Display the inputs tree for the current op
category_id = operation.algorithm.fk_category
algo_id = operation.fk_from_algo
raise cherrypy.HTTPRedirect("/flow/" + str(category_id) + "/" +
str(algo_id))
@cherrypy.expose
@handle_error(redirect=True)
@context_selected
def reload_burst_operation(self, operation_id, is_group, **_):
"""
Find out from which burst was this operation launched. Set that burst as the selected one and
redirect to the burst page.
"""
is_group = int(is_group)
if not is_group:
operation = OperationService.load_operation(int(operation_id))
else:
op_group = ProjectService.get_operation_group_by_id(operation_id)
first_op = ProjectService.get_operations_in_group(op_group)[0]
operation = OperationService.load_operation(int(first_op.id))
self.simulator_controller.copy_simulator_configuration(
operation.burst.id)
raise cherrypy.HTTPRedirect("/burst/")
@expose_json
def cancel_or_remove_operation(self,
operation_id,
is_group,
remove_after_stop=False):
"""
Stop the operation given by operation_id. If is_group is true stop all the
operations from that group.
"""
operation_id = int(operation_id)
is_group = int(is_group) != 0
if isinstance(remove_after_stop, str):
remove_after_stop = bool(remove_after_stop)
return self.simulator_controller.cancel_or_remove_operation(
operation_id, is_group, remove_after_stop)
def fill_default_attributes(self, template_dictionary, title='-'):
"""
Overwrite base controller to add required parameters for adapter templates.
"""
if common.KEY_TITLE not in template_dictionary:
template_dictionary[common.KEY_TITLE] = title
if common.KEY_PARENT_DIV not in template_dictionary:
template_dictionary[common.KEY_PARENT_DIV] = ''
if common.KEY_PARAMETERS_CONFIG not in template_dictionary:
template_dictionary[common.KEY_PARAMETERS_CONFIG] = False
template_dictionary[
common.KEY_INCLUDE_RESOURCES] = 'flow/included_resources'
BaseController.fill_default_attributes(self, template_dictionary)
return template_dictionary
NEW_SELECTION_NAME = 'New selection'
def _get_available_selections(self, datatype_gid):
"""
selection retrieval common to selection component and connectivity selection
"""
curent_project = common.get_current_project()
selections = self.algorithm_service.get_selections_for_project(
curent_project.id, datatype_gid)
names, sel_values = [], []
for selection in selections:
names.append(selection.ui_name)
sel_values.append(selection.selected_nodes)
return names, sel_values
@expose_fragment('visualizers/commons/channel_selector_opts')
def get_available_selections(self, **data):
sel_names, sel_values = self._get_available_selections(
data['datatype_gid'])
return dict(namedSelections=list(zip(sel_names, sel_values)))
@expose_json
def store_measure_points_selection(self, ui_name, **data):
"""
Save a MeasurePoints selection (new or update existing entity).
"""
if ui_name and ui_name != self.NEW_SELECTION_NAME:
sel_project_id = common.get_current_project().id
# client sends integers as strings:
selection = json.dumps(
[int(s) for s in json.loads(data['selection'])])
datatype_gid = data['datatype_gid']
self.algorithm_service.save_measure_points_selection(
ui_name, selection, datatype_gid, sel_project_id)
return [True, 'Selection saved successfully.']
else:
error_msg = self.NEW_SELECTION_NAME + " or empty name are not valid as selection names."
return [False, error_msg]
@expose_fragment(
"visualizers/pse_discrete/inserting_new_threshold_spec_bar")
def create_row_of_specs(self, count):
return dict(id_increment_count=count)
@expose_json
def store_pse_filter(self, config_name, **data):
# this will need to be updated in such a way that the expose_json actually gets used
## also this is going to be changed to be storing through the flow service and dao. Stay updated
try:
##this is to check whether there is already an entry in the
for i, (name, Val) in enumerate(self.PSE_names_list):
if name == config_name:
self.PSE_names_list[i] = (
config_name,
(data['threshold_value'] + "," +
data['threshold_type'] + "," + data['not_presence'])
) # replace the previous occurence of the config name, and carry on.
self.get_pse_filters()
return [
True, 'Selected Text stored, and selection updated'
]
self.PSE_names_list.append(
(config_name,
(data['threshold_value'] + "," + data['threshold_type'] +
"," + data['not_presence'])))
except AttributeError:
self.PSE_names_list = [
(config_name,
(data['threshold_value'] + "," + data['threshold_type'] +
"," + data['not_presence']))
]
self.get_pse_filters()
return [True, 'Selected Text stored, and selection updated']
@expose_fragment("visualizers/commons/channel_selector_opts")
def get_pse_filters(self):
try:
return dict(namedSelections=self.PSE_names_list)
except AttributeError:
return dict(
namedSelections=[]
) # this will give us back atleast the New Selection option in the select
except:
raise
@expose_json
def store_exploration_section(self, val_range, step, dt_group_guid):
"""
Launching method for further simulations.
"""
range_list = [float(num) for num in val_range.split(",")]
step_list = [float(num) for num in step.split(",")]
datatype_group_ob = ProjectService().get_datatypegroup_by_gid(
dt_group_guid)
operation_grp = datatype_group_ob.parent_operation_group
operation_obj = OperationService.load_operation(
datatype_group_ob.fk_from_operation)
parameters = {}
range1name, range1_dict = json.loads(operation_grp.range1)
range2name, range2_dict = json.loads(operation_grp.range2)
parameters[RANGE_PARAMETER_1] = range1name
parameters[RANGE_PARAMETER_2] = range2name
# change the existing simulator parameters to be min max step types
range1_dict = {
constants.ATT_MINVALUE: range_list[0],
constants.ATT_MAXVALUE: range_list[1],
constants.ATT_STEP: step_list[0]
}
range2_dict = {
constants.ATT_MINVALUE: range_list[2],
constants.ATT_MAXVALUE: range_list[3],
constants.ATT_STEP: step_list[1]
}
parameters[range1name] = json.dumps(
range1_dict) # this is for the x axis parameter
parameters[range2name] = json.dumps(
range2_dict) # this is for the y axis parameter
OperationService().group_operation_launch(
common.get_logged_user().id, common.get_current_project(),
operation_obj.algorithm.id, operation_obj.algorithm.fk_category,
datatype_group_ob, **parameters)
return [True, 'Stored the exploration material successfully']
class TestSimulationController(BaseTransactionalControllerTest):
def transactional_setup_method(self):
self.simulator_controller = SimulatorController()
self.test_user = TestFactory.create_user('SimulationController_User')
self.test_project = TestFactory.create_project(self.test_user, "SimulationController_Project")
connectivity = TestFactory.import_zip_connectivity(self.test_user, self.test_project)
self.session_stored_simulator = SimulatorAdapterModel()
self.session_stored_simulator.connectivity = UUID(connectivity.gid)
self.sess_mock = RamSession()
self.sess_mock[KEY_USER] = self.test_user
self.sess_mock[KEY_PROJECT] = self.test_project
cherrypy.request.method = "POST"
def test_set_connectivity(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")
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)
assert self.session_stored_simulator.connectivity.hex == connectivity.gid, "Connectivity was not set correctly."
assert self.session_stored_simulator.conduction_speed == 3.0, "Conduction speed was not set correctly."
assert isinstance(self.session_stored_simulator.coupling, Sigmoidal), "Coupling was not set correctly."
def test_set_coupling_params(self):
self.sess_mock['a'] = '[0.00390625]'
self.sess_mock['b'] = '[0.0]'
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.set_coupling_params(**self.sess_mock._data)
assert self.session_stored_simulator.coupling.a[0] == [0.00390625], "a value was not set correctly."
assert self.session_stored_simulator.coupling.b[0] == [0.0], "b value was not set correctly."
def test_set_surface(self):
zip_path = path.join(path.dirname(tvb_data.surfaceData.__file__), 'cortex_16384.zip')
TestFactory.import_surface_zip(self.test_user, self.test_project, zip_path, CORTICAL, True)
surface = TestFactory.get_entity(self.test_project, SurfaceIndex)
self.sess_mock['surface'] = surface.gid
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.set_surface(**self.sess_mock._data)
assert self.session_stored_simulator.surface is not None, "Surface was not set."
def test_set_surface_none(self):
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.set_surface(**self.sess_mock._data)
assert self.session_stored_simulator.surface is None, "Surface should not be set."
def test_set_cortex_without_local_connectivity(self):
zip_path = path.join(path.dirname(tvb_data.__file__), 'connectivity', 'connectivity_76.zip')
connectivity = TestFactory.import_zip_connectivity(self.test_user, self.test_project, zip_path, "John")
zip_path = path.join(path.dirname(tvb_data.surfaceData.__file__), 'cortex_16384.zip')
surface = TestFactory.import_surface_zip(self.test_user, self.test_project, zip_path, CORTICAL, True)
text_file = path.join(path.dirname(tvb_data.regionMapping.__file__), 'regionMapping_16k_76.txt')
region_mapping = TestFactory.import_region_mapping(self.test_user, self.test_project, text_file, surface.gid,
connectivity.gid)
self.session_stored_simulator.surface = CortexViewModel()
self.sess_mock['region_mapping'] = region_mapping.gid
self.sess_mock['local_connectivity'] = 'explicit-None-value'
self.sess_mock['coupling_strength'] = '[1.0]'
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.set_cortex(**self.sess_mock._data)
assert self.session_stored_simulator.surface.region_mapping_data.hex == region_mapping.gid, \
'Region mapping was not set correctly'
assert self.session_stored_simulator.surface.local_connectivity is None, \
'Default value should have been set to local connectivity.'
assert self.session_stored_simulator.surface.coupling_strength == [1.0], \
"coupling_strength was not set correctly."
def test_set_stimulus_none(self):
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.set_stimulus(**self.sess_mock._data)
assert self.session_stored_simulator.stimulus is None, "Stimulus should not be set."
def test_set_stimulus(self):
zip_path = path.join(path.dirname(tvb_data.__file__), 'connectivity', 'connectivity_66.zip')
connectivity_index = TestFactory.import_zip_connectivity(self.test_user, self.test_project, zip_path)
weight_array = numpy.zeros(connectivity_index.number_of_regions)
region_stimulus_creator = RegionStimulusCreator()
view_model = region_stimulus_creator.get_view_model_class()()
view_model.connectivity = UUID(connectivity_index.gid)
view_model.weight = weight_array
view_model.temporal = TemporalApplicableEquation()
view_model.temporal.parameters['a'] = 1.0
view_model.temporal.parameters['b'] = 2.0
FlowService().fire_operation(region_stimulus_creator, self.test_user, self.test_project.id,
view_model=view_model)
region_stimulus_index = TestFactory.get_entity(self.test_project, StimuliRegionIndex)
self.sess_mock['region_stimuli'] = UUID(region_stimulus_index.gid)
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.set_stimulus(**self.sess_mock._data)
assert self.session_stored_simulator.stimulus.hex == region_stimulus_index.gid, \
"Stimuli was not set correctly."
def test_set_model(self):
self.sess_mock['model'] = 'Generic 2d Oscillator'
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.set_model(**self.sess_mock._data)
assert isinstance(self.session_stored_simulator.model,
ModelsEnum.GENERIC_2D_OSCILLATOR.get_class()), "Model class is incorrect."
def test_set_model_params(self):
self.sess_mock['tau'] = '[1.0]'
self.sess_mock['I'] = '[0.0]'
self.sess_mock['a'] = '[-2.0]'
self.sess_mock['b'] = '[-10.0]'
self.sess_mock['c'] = '[0.0]'
self.sess_mock['d'] = '[0.02]'
self.sess_mock['e'] = '[3.0]'
self.sess_mock['f'] = '[1.0]'
self.sess_mock['g'] = '[0.0]'
self.sess_mock['alpha'] = '[1.0]'
self.sess_mock['beta'] = '[1.0]'
self.sess_mock['gamma'] = '[1.0]'
self.sess_mock['variables_of_interest'] = 'V'
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.set_model_params(**self.sess_mock._data)
assert self.session_stored_simulator.model.tau == [1.0], "Tau has incorrect value."
assert self.session_stored_simulator.model.I == [0.0], "I has incorrect value."
assert self.session_stored_simulator.model.a == [-2.0], "a has incorrect value."
assert self.session_stored_simulator.model.b == [-10.0], "b has incorrect value."
assert self.session_stored_simulator.model.c == [0.0], "c has incorrect value."
assert self.session_stored_simulator.model.d == [0.02], "d has incorrect value."
assert self.session_stored_simulator.model.e == [3.0], "e has incorrect value."
assert self.session_stored_simulator.model.f == [1.0], "f has incorrect value."
assert self.session_stored_simulator.model.g == [0.0], "g has incorrect value."
assert self.session_stored_simulator.model.alpha == [1.0], "alpha has incorrect value."
assert self.session_stored_simulator.model.beta == [1.0], "beta has incorrect value."
assert self.session_stored_simulator.model.gamma == [1.0], "gamma has incorrect value."
assert self.session_stored_simulator.model.variables_of_interest == ['V'], \
"variables_of_interest has incorrect value."
def test_set_integrator(self):
self.sess_mock['integrator'] = 'Heun'
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.set_integrator(**self.sess_mock._data)
assert isinstance(self.session_stored_simulator.integrator,
HeunDeterministic), "Integrator was not set correctly."
def test_set_integrator_params(self):
self.sess_mock['dt'] = '0.01220703125'
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.set_integrator_params(**self.sess_mock._data)
assert self.session_stored_simulator.integrator.dt == 0.01220703125, 'dt value was not set correctly.'
def test_set_integrator_params_stochastic(self):
self.sess_mock['dt'] = '0.01220703125'
self.sess_mock['noise'] = 'Multiplicative'
self.session_stored_simulator.integrator = Dopri5Stochastic()
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.set_integrator_params(**self.sess_mock._data)
assert isinstance(self.session_stored_simulator.integrator, IntegratorStochastic), \
"Coupling should be Stochastic Dormand-Prince."
assert self.session_stored_simulator.integrator.dt == 0.01220703125, 'dt value was not set correctly.'
assert isinstance(self.session_stored_simulator.integrator.noise, Multiplicative), 'Noise class is incorrect.'
def test_set_noise_params(self):
self.sess_mock['ntau'] = '0.0'
self.sess_mock['noise_seed'] = '42'
self.sess_mock['nsig'] = '[1.0]'
self.session_stored_simulator.integrator = EulerStochastic()
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.set_noise_params(**self.sess_mock._data)
assert self.session_stored_simulator.integrator.noise.ntau == 0.0, "ntau value was not set correctly."
assert self.session_stored_simulator.integrator.noise.noise_seed == 42, \
"noise_seed value was not set correctly."
assert self.session_stored_simulator.integrator.noise.nsig == [1.0], "nsig value was not set correctly."
def test_set_noise_equation_params(self):
self.sess_mock['low'] = '0.1'
self.sess_mock['high'] = '1.0'
self.sess_mock['midpoint'] = '1.0'
self.sess_mock['sigma'] = '0.3'
self.session_stored_simulator.integrator = Dopri5Stochastic()
self.session_stored_simulator.integrator.noise = Multiplicative()
self.session_stored_simulator.integrator.noise.b = GeneralizedSigmoid()
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.set_noise_equation_params(**self.sess_mock._data)
assert self.session_stored_simulator.integrator.noise.b.parameters['low'] == 0.1, \
"low value was not set correctly"
assert self.session_stored_simulator.integrator.noise.b.parameters['high'] == 1.0, \
"high value was not set correctly"
assert self.session_stored_simulator.integrator.noise.b.parameters['midpoint'] == 1.0, \
"midpoint value was not set correctly"
assert self.session_stored_simulator.integrator.noise.b.parameters['sigma'] == 0.3, \
"sigma value was not set correctly"
def test_set_monitors(self):
self.sess_mock['monitors'] = ['Temporal average']
self.session_stored_simulator.monitors[0].variables_of_interest = numpy.array([0])
self.session_stored_simulator.model.variables_of_interest = ['V', 'W']
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
common.add2session(common.KEY_BURST_CONFIG, BurstConfiguration(self.test_project.id))
self.simulator_controller.set_monitors(**self.sess_mock._data)
assert isinstance(self.session_stored_simulator.monitors[0], TemporalAverage), 'Monitor class is incorrect.'
def test_set_monitor_params(self):
self.session_stored_simulator.model.variables_of_interest = ('V', 'W', 'V - W')
variable_of_interest_indexes = {'W': 1, 'V - W': 2}
self.sess_mock['variables_of_interest'] = list(variable_of_interest_indexes.keys())
self.sess_mock['period'] = '0.8'
self.session_stored_simulator.monitors = [SubSample()]
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
common.add2session(common.KEY_BURST_CONFIG, BurstConfiguration(self.test_project.id))
self.simulator_controller.set_monitor_params('SubSample', **self.sess_mock._data)
assert self.session_stored_simulator.monitors[0].period == 0.8, "Period was not set correctly."
assert list(self.session_stored_simulator.monitors[0].variables_of_interest) == \
list(variable_of_interest_indexes.values()), "Variables of interest were not set correctly."
def set_region_mapping(self):
zip_path = path.join(path.dirname(tvb_data.__file__), 'connectivity', 'connectivity_76.zip')
connectivity = TestFactory.import_zip_connectivity(self.test_user, self.test_project, zip_path, "John")
zip_path = path.join(path.dirname(tvb_data.surfaceData.__file__), 'cortex_16384.zip')
surface = TestFactory.import_surface_zip(self.test_user, self.test_project, zip_path, CORTICAL, True)
text_file = path.join(path.dirname(tvb_data.regionMapping.__file__), 'regionMapping_16k_76.txt')
region_mapping = TestFactory.import_region_mapping(self.test_user, self.test_project, text_file, surface.gid,
connectivity.gid)
return region_mapping
def test_set_eeg_monitor_params(self):
region_mapping = self.set_region_mapping()
eeg_sensors_file = path.join(path.dirname(tvb_data.sensors.__file__), 'eeg_unitvector_62.txt')
eeg_sensors = TestFactory.import_sensors(self.test_user, self.test_project, eeg_sensors_file,
SensorsImporterModel.OPTIONS['EEG Sensors'])
surface_file = path.join(path.dirname(tvb_data.surfaceData.__file__), 'cortex_16384.zip')
surface = TestFactory.import_surface_zip(self.test_user, self.test_project, surface_file, CORTICAL, True)
eeg_projection_file = path.join(path.dirname(tvb_data.projectionMatrix.__file__),
'projection_eeg_62_surface_16k.mat')
eeg_projections = TestFactory.import_projection_matrix(self.test_user, self.test_project, eeg_projection_file,
eeg_sensors.gid, surface.gid)
self.session_stored_simulator.model.variables_of_interest = ('V', 'W', 'V - W')
variable_of_interest_indexes = {'W': 1, 'V - W': 2}
self.sess_mock['variables_of_interest'] = list(variable_of_interest_indexes.keys())
self.sess_mock['period'] = '0.75'
self.sess_mock['region_mapping'] = region_mapping.gid
self.sess_mock['projection'] = eeg_projections.gid
self.sess_mock['sigma'] = "1.0"
self.sess_mock['sensors'] = eeg_sensors.gid
self.session_stored_simulator.monitors = [EEG()]
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
common.add2session(common.KEY_BURST_CONFIG, BurstConfiguration(self.test_project.id))
self.simulator_controller.set_monitor_params('EEG', **self.sess_mock._data)
assert self.session_stored_simulator.monitors[0].period == 0.75, "Period was not set correctly."
assert list(self.session_stored_simulator.monitors[0].variables_of_interest) == \
list(variable_of_interest_indexes.values()), "Variables of interest were not set correctly."
assert self.session_stored_simulator.monitors[0].region_mapping.gid.hex == region_mapping.gid, \
"Region Mapping wasn't set and stored correctly."
assert self.session_stored_simulator.monitors[0].sensors.gid.hex == eeg_sensors.gid, \
"Region Mapping wasn't set and stored correctly."
assert self.session_stored_simulator.monitors[0].projection.gid is not None, \
"Projection wasn't stored correctly."
def test_set_meg_monitor_params(self):
region_mapping = self.set_region_mapping()
meg_sensors_file = path.join(path.dirname(tvb_data.sensors.__file__), 'meg_brainstorm_276.txt')
meg_sensors = TestFactory.import_sensors(self.test_user, self.test_project, meg_sensors_file,
SensorsImporterModel.OPTIONS['MEG Sensors'])
surface_file = path.join(path.dirname(tvb_data.surfaceData.__file__), 'cortex_16384.zip')
surface = TestFactory.import_surface_zip(self.test_user, self.test_project, surface_file, CORTICAL, True)
meg_projection_file = path.join(path.dirname(tvb_data.projectionMatrix.__file__),
'projection_meg_276_surface_16k.npy')
meg_projections = TestFactory.import_projection_matrix(self.test_user, self.test_project, meg_projection_file,
meg_sensors.gid, surface.gid)
self.session_stored_simulator.model.variables_of_interest = ('V', 'W', 'V - W')
variable_of_interest_indexes = {'W': 1, 'V - W': 2}
self.sess_mock['variables_of_interest'] = list(variable_of_interest_indexes.keys())
self.sess_mock['period'] = '0.75'
self.sess_mock['region_mapping'] = region_mapping.gid
self.sess_mock['projection'] = meg_projections.gid
self.sess_mock['sigma'] = 1.0
self.sess_mock['sensors'] = meg_sensors.gid
self.session_stored_simulator.monitors = [MEG()]
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
common.add2session(common.KEY_BURST_CONFIG, BurstConfiguration(self.test_project.id))
self.simulator_controller.set_monitor_params('MEG', **self.sess_mock._data)
assert self.session_stored_simulator.monitors[0].period == 0.75, "Period was not set correctly."
assert list(self.session_stored_simulator.monitors[0].variables_of_interest) == \
list(variable_of_interest_indexes.values()), "Variables of interest were not set correctly."
assert self.session_stored_simulator.monitors[0].region_mapping.gid.hex == region_mapping.gid, \
"Region Mapping wasn't set and stored correctly."
assert self.session_stored_simulator.monitors[0].sensors.gid.hex == meg_sensors.gid, \
"Region Mapping wasn't set and stored correctly."
assert self.session_stored_simulator.monitors[0].projection.gid is not None, \
"Projection wasn't stored correctly."
def test_set_seeg_monitor_params(self):
region_mapping = self.set_region_mapping()
seeg_sensors_file = path.join(path.dirname(tvb_data.sensors.__file__), 'seeg_588.txt')
seeg_sensors = TestFactory.import_sensors(self.test_user, self.test_project, seeg_sensors_file,
SensorsImporterModel.OPTIONS['Internal Sensors'])
surface_file = path.join(path.dirname(tvb_data.surfaceData.__file__), 'cortex_16384.zip')
surface = TestFactory.import_surface_zip(self.test_user, self.test_project, surface_file, CORTICAL, True)
seeg_projection_file = path.join(path.dirname(tvb_data.projectionMatrix.__file__),
'projection_seeg_588_surface_16k.npy')
seeg_projections = TestFactory.import_projection_matrix(self.test_user, self.test_project, seeg_projection_file,
seeg_sensors.gid, surface.gid)
self.session_stored_simulator.model.variables_of_interest = ('V', 'W', 'V - W')
variable_of_interest_indexes = {'W': 1, 'V - W': 2}
self.sess_mock['variables_of_interest'] = list(variable_of_interest_indexes.keys())
self.sess_mock['period'] = '0.75'
self.sess_mock['region_mapping'] = region_mapping.gid
self.sess_mock['projection'] = seeg_projections.gid
self.sess_mock['sigma'] = "1.0"
self.sess_mock['sensors'] = seeg_sensors.gid
self.session_stored_simulator.monitors = [iEEG()]
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
common.add2session(common.KEY_BURST_CONFIG, BurstConfiguration(self.test_project.id))
self.simulator_controller.set_monitor_params('iEEG', **self.sess_mock._data)
assert self.session_stored_simulator.monitors[0].period == 0.75, "Period was not set correctly."
assert list(self.session_stored_simulator.monitors[0].variables_of_interest) == \
list(variable_of_interest_indexes.values()), "Variables of interest were not set correctly."
assert self.session_stored_simulator.monitors[0].region_mapping.gid.hex == region_mapping.gid, \
"Region Mapping wasn't set and stored correctly."
assert self.session_stored_simulator.monitors[0].sensors.gid.hex == seeg_sensors.gid, \
"Region Mapping wasn't set and stored correctly."
assert self.session_stored_simulator.monitors[0].projection.gid is not None, \
"Projection wasn't stored correctly."
def test_set_bold_monitor_params(self):
self.session_stored_simulator.model.variables_of_interest = ('V', 'W', 'V - W')
variable_of_interest_indexes = {'W': 1, 'V - W': 2}
self.sess_mock['variables_of_interest'] = list(variable_of_interest_indexes.keys())
self.sess_mock['period'] = '2000.0'
self.sess_mock['hrf_kernel'] = 'HRF kernel: Volterra Kernel'
self.session_stored_simulator.monitors = [Bold()]
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.set_monitor_params('Bold', **self.sess_mock._data)
assert self.session_stored_simulator.monitors[0].period == 2000.0, "Period was not set correctly."
assert list(self.session_stored_simulator.monitors[0].variables_of_interest) == \
list(variable_of_interest_indexes.values()), "Variables of interest were not set correctly."
def test_set_monitor_equation(self):
self.sess_mock['tau_s'] = '0.8'
self.sess_mock['tau_f'] = '0.4'
self.sess_mock['k_1'] = '5.6'
self.sess_mock['V_0'] = '0.02'
self.session_stored_simulator.monitors = [Bold()]
self.session_stored_simulator.monitors[0].equation = FirstOrderVolterra()
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
common.add2session(common.KEY_BURST_CONFIG, BurstConfiguration(self.test_project.id))
self.simulator_controller.set_monitor_equation('Bold', **self.sess_mock._data)
assert self.session_stored_simulator.monitors[0].equation.parameters[
'tau_s'] == 0.8, "tau_s value was not set correctly."
assert self.session_stored_simulator.monitors[0].equation.parameters[
'tau_f'] == 0.4, "tau_f value was not set correctly."
assert self.session_stored_simulator.monitors[0].equation.parameters[
'k_1'] == 5.6, "k_1 value was not set correctly."
assert self.session_stored_simulator.monitors[0].equation.parameters[
'V_0'] == 0.02, "V_0 value was not set correctly."
def test_load_burst_history(self):
burst_config1 = BurstConfiguration(self.test_project.id)
burst_config2 = BurstConfiguration(self.test_project.id)
burst_config3 = BurstConfiguration(self.test_project.id)
dao.store_entity(burst_config1)
dao.store_entity(burst_config2)
dao.store_entity(burst_config3)
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_BURST_CONFIG, burst_config1)
burst_parameters = self.simulator_controller.load_burst_history()
assert len(burst_parameters['burst_list']) == 3, "The burst configurations where not stored."
def test_reset_simulator_configuration(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")
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)
rendering_rules = self.simulator_controller.set_connectivity(**self.sess_mock._data)
assert rendering_rules['renderer'].is_first_fragment is False, \
"Page should have advanced past the first fragment."
with patch('cherrypy.session', self.sess_mock, create=True):
rendering_rules = self.simulator_controller.reset_simulator_configuration()
assert rendering_rules['renderer'].is_first_fragment is True, \
"Page should be set to the first fragment."
def test_get_history_status(self):
burst_config = BurstConfiguration(self.test_project.id)
burst_config.start_time = datetime.now()
dao.store_entity(burst_config)
burst = dao.get_bursts_for_project(self.test_project.id)
self.sess_mock['burst_ids'] = '["' + 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.get_history_status(**self.sess_mock._data).split(',')
assert int(result[0][2:]) == burst[0].id, "Incorrect burst was used."
assert result[1] == ' "running"', "Status should be set to running."
assert result[2] == ' false', "Burst shouldn't be group."
assert result[3] == ' ""', "Message should be empty, which means that there shouldn't be any errors."
assert int(result[4][2:-4]) >= 0, "Running time should be greater than or equal to 0."
def test_rename_burst(self):
new_name = "Test Burst Configuration 2"
operation = TestFactory.create_operation()
burst_config = TestFactory.store_burst(self.test_project.id, operation)
burst = dao.get_bursts_for_project(self.test_project.id)
self.sess_mock['burst_id'] = str(burst[0].id)
self.sess_mock['burst_name'] = new_name
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.rename_burst(burst[0].id, new_name)
assert result == '{"success": "Simulation successfully renamed!"}', \
"Some error happened at renaming, probably because of invalid new name."
assert dao.get_bursts_for_project(self.test_project.id)[0].name == new_name, "Name wasn't actually changed."
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_copy_simulator_configuration(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.name = 'test_burst'
burst_config.simulator_gid = self.session_stored_simulator.gid.hex
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.copy_simulator_configuration(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)
assert not is_simulator_load, "Simulator Load Flag should be True!"
assert is_simulator_copy, "Simulator Copy Flag should be False!"
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_launch_simulation_with_default_parameters(self):
self.sess_mock['input_simulation_name_id'] = 'HappySimulation'
self.sess_mock['simulation_length'] = '10'
launch_mode = 'new'
burst_config = BurstConfiguration(self.test_project.id)
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_BURST_CONFIG, burst_config)
common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator)
self.simulator_controller.launch_simulation(launch_mode, **self.sess_mock._data)
class TestFlowController(BaseControllersTest):
""" Unit tests for FlowController """
def setup_method(self):
"""
Sets up the environment for testing;
creates a `FlowController`
"""
self.init()
self.flow_c = FlowController()
self.burst_c = SimulatorController()
self.operation_service = OperationService()
def teardown_method(self):
""" Cleans up the testing environment """
self.cleanup()
self.clean_database()
@pytest.fixture()
def long_burst_launch(self, connectivity_factory):
def build(is_range=False):
self.burst_c.index()
connectivity = connectivity_factory()
launch_params = copy.deepcopy(SIMULATOR_PARAMETERS)
launch_params['connectivity'] = dao.get_datatype_by_id(
connectivity.id).gid
launch_params['simulation_length'] = '10000'
if is_range:
launch_params['conduction_speed'] = '[10,15,20]'
launch_params[RANGE_PARAMETER_1] = 'conduction_speed'
launch_params = {"simulator_parameters": json.dumps(launch_params)}
burst_id = json.loads(
self.burst_c.launch_burst("new", "test_burst",
**launch_params))['id']
return dao.get_burst_by_id(burst_id)
return build
def test_context_selected(self):
"""
Remove the project from CherryPy session and check that you are redirected to projects page.
"""
del cherrypy.session[common.KEY_PROJECT]
self._expect_redirect('/project/viewall', self.flow_c.step_analyzers)
def test_valid_step(self):
"""
For all algorithm categories check that a submenu is generated and the result
page has it's title given by category name.
"""
result_dict = self.flow_c.step_analyzers()
assert common.KEY_SUBMENU_LIST in result_dict,\
"Expect to have a submenu with available algorithms for category."
assert result_dict["section_name"] == 'analyze'
def test_step_connectivity(self):
"""
Check that the correct section name and connectivity sub-menu are returned for the connectivity step.
"""
result_dict = self.flow_c.step_connectivity()
assert result_dict['section_name'] == 'connectivity'
assert result_dict['submenu_list'] == self.flow_c.connectivity_submenu
def test_default(self):
"""
Test default method from step controllers. Check that the submit link is ok, that a mainContent
is present in result dict and that the isAdapter flag is set to true.
"""
cherrypy.request.method = "GET"
categories = dao.get_algorithm_categories()
for categ in categories:
algo_groups = dao.get_adapters_from_categories([categ.id])
for algo in algo_groups:
result_dict = self.flow_c.default(categ.id, algo.id)
assert result_dict[common.KEY_SUBMIT_LINK] == '/flow/%i/%i' % (
categ.id, algo.id)
assert 'mainContent' in result_dict
assert result_dict['isAdapter']
def test_default_cancel(self):
"""
On cancel we should get a redirect to the back page link.
"""
cherrypy.request.method = "POST"
categories = dao.get_algorithm_categories()
algo_groups = dao.get_adapters_from_categories([categories[0].id])
self._expect_redirect('/project/viewoperations/%i' %
self.test_project.id,
self.flow_c.default,
categories[0].id,
algo_groups[0].id,
cancel=True,
back_page='operations')
def test_default_invalid_key(self):
"""
Pass invalid keys for adapter and step and check you get redirect to tvb entry
page with error set.
"""
self._expect_redirect('/tvb?error=True', self.flow_c.default,
'invalid', 'invalid')
def test_read_datatype_attribute(self, dummy_datatype_index_factory):
"""
Read an attribute from a datatype.
"""
dt = dummy_datatype_index_factory(row1='This is stored data')
dt.subject = "test_subject"
dt.state = "RAW_STATE"
returned_data = self.flow_c.read_datatype_attribute(dt.gid, "row1")
assert returned_data == '"This is stored data"'
def test_read_datatype_attribute_method_call(self,
dummy_datatype_index_factory):
"""
Call method on given datatype.
"""
dt = dummy_datatype_index_factory(row1='This is stored data')
args = {'length': 101}
returned_data = self.flow_c.read_datatype_attribute(
dt.gid, 'return_test_data', **args)
assert returned_data.replace('"', '') == " ".join(
str(x) for x in range(101))
def test_get_simple_adapter_interface(self, test_adapter_factory):
test_adapter_factory()
form = TestAdapter1Form()
adapter = TestFactory.create_adapter(
'tvb.tests.framework.adapters.testadapter1', 'TestAdapter1')
algo = adapter.stored_adapter
adapter.submit_form(form)
result = self.flow_c.get_simple_adapter_interface(algo.id)
expected_interface = adapter.get_form()
assert type(result['form']) == type(expected_interface)
assert result[
'form'].test1_val1.value == expected_interface.test1_val1.value
assert result[
'form'].test1_val2.value == expected_interface.test1_val2.value
def _wait_for_burst_ops(self, burst_config):
""" sleeps until some operation of the burst is created"""
waited = 1
timeout = 50
operations = dao.get_operations_in_burst(burst_config.id)
while not len(operations) and waited <= timeout:
sleep(1)
waited += 1
operations = dao.get_operations_in_burst(burst_config.id)
operations = dao.get_operations_in_burst(burst_config.id)
return operations
def test_stop_burst_operation(self, long_burst_launch):
burst_config = long_burst_launch()
operation = self._wait_for_burst_ops(burst_config)[0]
assert not operation.has_finished
self.flow_c.stop_burst_operation(operation.id, 0, False)
operation = dao.get_operation_by_id(operation.id)
assert operation.status == STATUS_CANCELED
def test_stop_burst_operation_group(self, long_burst_launch):
burst_config = long_burst_launch(True)
operations = self._wait_for_burst_ops(burst_config)
operations_group_id = 0
for operation in operations:
assert not operation.has_finished
operations_group_id = operation.fk_operation_group
self.flow_c.stop_burst_operation(operations_group_id, 1, False)
for operation in operations:
operation = dao.get_operation_by_id(operation.id)
assert operation.status == STATUS_CANCELED
def test_remove_burst_operation(self, long_burst_launch):
burst_config = long_burst_launch()
operation = self._wait_for_burst_ops(burst_config)[0]
assert not operation.has_finished
self.flow_c.stop_burst_operation(operation.id, 0, True)
operation = dao.try_get_operation_by_id(operation.id)
assert operation is None
def test_remove_burst_operation_group(self, long_burst_launch):
burst_config = long_burst_launch(True)
operations = self._wait_for_burst_ops(burst_config)
operations_group_id = 0
for operation in operations:
assert not operation.has_finished
operations_group_id = operation.fk_operation_group
self.flow_c.stop_burst_operation(operations_group_id, 1, True)
for operation in operations:
operation = dao.try_get_operation_by_id(operation.id)
assert operation is None
def _launch_test_algo_on_cluster(self, **data):
adapter = TestFactory.create_adapter(
'tvb.tests.framework.adapters.testadapter1', 'TestAdapter1')
algo = adapter.stored_adapter
algo_category = dao.get_category_by_id(algo.fk_category)
operations, _ = self.operation_service.prepare_operations(
self.test_user.id, self.test_project, algo, algo_category, {},
**data)
self.operation_service._send_to_cluster(operations, adapter)
return operations
def test_stop_operations(self):
data = {"test1_val1": 5, 'test1_val2': 5}
operations = self._launch_test_algo_on_cluster(**data)
operation = dao.get_operation_by_id(operations[0].id)
assert not operation.has_finished
self.flow_c.stop_operation(operation.id, 0, False)
operation = dao.get_operation_by_id(operation.id)
assert operation.status == STATUS_CANCELED
def test_stop_operations_group(self):
data = {
RANGE_PARAMETER_1: "test1_val1",
"test1_val1": '5,6,7',
'test1_val2': 5
}
operations = self._launch_test_algo_on_cluster(**data)
operation_group_id = 0
for operation in operations:
operation = dao.get_operation_by_id(operation.id)
assert not operation.has_finished
operation_group_id = operation.fk_operation_group
self.flow_c.stop_operation(operation_group_id, 1, False)
for operation in operations:
operation = dao.get_operation_by_id(operation.id)
assert operation.status == STATUS_CANCELED