def load_region_stimulus(self, region_stimulus_gid, from_step=None):
"""
Loads the interface for the selected region stimulus.
"""
selected_region_stimulus = ABCAdapter.load_entity_by_gid(region_stimulus_gid)
temporal_eq = selected_region_stimulus.temporal
spatial_eq = selected_region_stimulus.spatial
connectivity = selected_region_stimulus.connectivity
weights = selected_region_stimulus.weight
temporal_eq_type = temporal_eq.__class__.__name__
spatial_eq_type = spatial_eq.__class__.__name__
default_dict = {'temporal': temporal_eq_type, 'spatial': spatial_eq_type,
'connectivity': connectivity.gid, 'weight': json.dumps(weights)}
for param in temporal_eq.parameters:
prepared_name = 'temporal_parameters_option_' + str(temporal_eq_type)
prepared_name = prepared_name + '_parameters_parameters_' + str(param)
default_dict[prepared_name] = str(temporal_eq.parameters[param])
for param in spatial_eq.parameters:
prepared_name = 'spatial_parameters_option_' + str(spatial_eq_type) + '_parameters_parameters_' + str(param)
default_dict[prepared_name] = str(spatial_eq.parameters[param])
input_list = self.get_creator_and_interface(REGION_STIMULUS_CREATOR_MODULE,
REGION_STIMULUS_CREATOR_CLASS, StimuliRegion())[1]
input_list = ABCAdapter.fill_defaults(input_list, default_dict)
context = common.get_from_session(KEY_REGION_CONTEXT)
context.reset()
context.update_from_interface(input_list)
context.equation_kwargs[DataTypeMetaData.KEY_TAG_1] = selected_region_stimulus.user_tag_1
context.set_active_stimulus(region_stimulus_gid)
return self.do_step(from_step)
def update_default_values(portlet_interface, portlet_configuration):
"""
:param portlet_interface: a list of AdapterConfiguration entities.
:param portlet_configuration: a PortletConfiguration entity.
Update the defaults from each AdapterConfiguration entity with the
values stored in the corresponding workflow step held in the
PortletConfiguration entity.
"""
# Check for any defaults first in analyzer steps
if portlet_configuration.analyzers:
for adapter_idx in xrange(len(portlet_interface[:-1])):
saved_configuration = portlet_configuration.analyzers[adapter_idx]
replaced_defaults_dict = ABCAdapter.fill_defaults(
portlet_interface[adapter_idx].interface, saved_configuration.static_param
)
portlet_interface[adapter_idx].interface = replaced_defaults_dict
# Check for visualization defaults
if portlet_configuration.visualizer:
saved_configuration = portlet_configuration.visualizer
replaced_defaults_dict = ABCAdapter.fill_defaults(
portlet_interface[-1].interface, saved_configuration.static_param
)
portlet_interface[-1].interface = replaced_defaults_dict
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.
"""
self.logger.debug("Starting to read HDF5: " + entity_gid + "/" + dataset_name + "/" + str(kwargs))
entity = ABCAdapter.load_entity_by_gid(entity_gid)
datatype_kwargs = json.loads(datatype_kwargs)
if datatype_kwargs:
for key, value in datatype_kwargs.iteritems():
kwargs[key] = ABCAdapter.load_entity_by_gid(value)
dataset = getattr(entity, dataset_name)
if not kwargs:
# why the deep copy?
result = copy.deepcopy(dataset)
else:
result = dataset(**kwargs)
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
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 with a NumPy array
: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)
: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.
"""
try:
self.logger.debug("Starting to read HDF5: " + entity_gid + "/" + dataset_name + "/" + str(kwargs))
entity = ABCAdapter.load_entity_by_gid(entity_gid)
if kwargs is None:
kwargs = {}
datatype_kwargs = json.loads(datatype_kwargs)
if datatype_kwargs is not None:
for key in datatype_kwargs:
kwargs[key] = ABCAdapter.load_entity_by_gid(datatype_kwargs[key])
if len(kwargs) < 1:
numpy_array = copy.deepcopy(getattr(entity, dataset_name))
else:
numpy_array = eval("entity." + dataset_name + "(**kwargs)")
if (flatten is True) or (flatten == "True"):
numpy_array = numpy_array.flatten()
return numpy_array.tolist()
except Exception, excep:
self.logger.error("Could not retrieve complex entity field:" + str(entity_gid) + "/" + str(dataset_name))
self.logger.exception(excep)
def __init__(self, list_of_entities_to_store):
"""
Expacts a list of 'DataType' instances.
"""
ABCAdapter.__init__(self)
if (list_of_entities_to_store is None
or not isinstance(list_of_entities_to_store, list)
or len(list_of_entities_to_store) == 0):
raise Exception("The adapter expacts a list of entities")
self.list_of_entities_to_store = list_of_entities_to_store
def setUp(self):
"""
Set up any additionally needed parameters.
"""
super(GenshiTestGroup, self).setUp()
xml_group_path = os.path.join('tests', 'framework', 'interfaces', 'web', "test_group.xml")
algo_group = dao.find_group('tvb.tests.framework.adapters.testgroupadapter', 'TestGroupAdapter', xml_group_path)
self.xml_group_adapter = ABCAdapter.build_adapter(algo_group)
input_tree = self.xml_group_adapter.get_input_tree()
input_tree = ABCAdapter.prepare_param_names(input_tree)
self.template_specification['inputList'] = input_tree
self.template_specification[common.KEY_PARAMETERS_CONFIG] = False
resulted_html = _template2string(self.template_specification)
self.soup = BeautifulSoup(resulted_html)
def get_series_array_discrete(self, datatype_group_gid, backPage, color_metric=None, size_metric=None):
"""
Create new data for when the user chooses to refresh from the UI.
"""
if color_metric == 'None':
color_metric = None
if size_metric == 'None':
size_metric = None
algorithm = self.flow_service.get_algorithm_by_module_and_class(DISCRETE_PSE_ADAPTER_MODULE,
DISCRETE_PSE_ADAPTER_CLASS)
adapter = ABCAdapter.build_adapter(algorithm)
if self._is_compatible(algorithm, datatype_group_gid):
try:
pse_context = adapter.prepare_parameters(datatype_group_gid, backPage, color_metric, size_metric)
return dict(series_array=pse_context.series_array,
has_started_ops=pse_context.has_started_ops)
except LaunchException as ex:
error_msg = urllib.quote(ex.message)
else:
error_msg = urllib.quote(
"Discrete PSE is incompatible (most probably due to result size being too large).")
name = urllib.quote(adapter._ui_name)
raise cherrypy.HTTPRedirect(REDIRECT_MSG % (name, error_msg))
def step_2(self, **kwargs):
"""
Generate the html for the second step of the local connectivity page.
:param kwargs: not actually used, but parameters are still submitted from UI since we just\
use the same js function for this. TODO: do this in a smarter way
"""
context = common.get_from_session(KEY_LCONN_CONTEXT)
left_side_interface = self.get_select_existent_entities('Load Local Connectivity:', LocalConnectivity,
context.selected_entity)
template_specification = dict(title="Surface - Local Connectivity")
template_specification['mainContent'] = 'spatial/local_connectivity_step2_main'
template_specification['existentEntitiesInputList'] = left_side_interface
template_specification['loadExistentEntityUrl'] = LOAD_EXISTING_URL
template_specification['resetToDefaultUrl'] = RELOAD_DEFAULT_PAGE_URL
template_specification['next_step_url'] = '/spatial/localconnectivity/step_1'
msg, _ = common.get_message_from_session()
template_specification['displayedMessage'] = msg
context = common.get_from_session(KEY_LCONN_CONTEXT)
if context.selected_entity is not None:
selected_local_conn = ABCAdapter.load_entity_by_gid(context.selected_entity)
template_specification.update(self.display_surface(selected_local_conn.surface.gid))
template_specification['no_local_connectivity'] = False
min_value, max_value = selected_local_conn.get_min_max_values()
template_specification['minValue'] = min_value
template_specification['maxValue'] = max_value
else:
template_specification['no_local_connectivity'] = True
template_specification[common.KEY_PARAMETERS_CONFIG] = False
return self.fill_default_attributes(template_specification)
def get_surface_model_parameters_data(self, default_selected_model_param=None):
"""
Returns a dictionary which contains all the data needed for drawing the
model parameters.
"""
context_model_parameters = base.get_from_session(KEY_CONTEXT_MPS)
if default_selected_model_param is None:
default_selected_model_param = context_model_parameters.prepared_model_parameter_names.values()[0]
equation_displayer = EquationDisplayer()
equation_displayer.trait.bound = interface.INTERFACE_ATTRIBUTES_ONLY
input_list = equation_displayer.interface[interface.INTERFACE_ATTRIBUTES]
input_list[0] = self._lock_midpoints(input_list[0])
options = []
for original_param, modified_param in context_model_parameters.prepared_model_parameter_names.items():
attributes = deepcopy(input_list)
self._fill_default_values(attributes, modified_param)
option = {'name': original_param, 'value': modified_param, 'attributes': attributes}
options.append(option)
input_list = [{'name': 'model_param', 'type': 'select', 'default': default_selected_model_param,
'label': 'Model param', 'required': True, 'options': options}]
input_list = ABCAdapter.prepare_param_names(input_list)
return {base.KEY_PARAMETERS_CONFIG: False, 'inputList': input_list,
'applied_equations': context_model_parameters.get_configure_info()}
def cdata2local_connectivity(local_connectivity_data, meta, storage_path, expected_length=0):
"""
From a CData entry in CFF, create LocalConnectivity entity.
"""
##### expected_length = cortex.region_mapping.shape[0]
tmpdir = os.path.join(gettempdir(), local_connectivity_data.parent_cfile.get_unique_cff_name())
LOG.debug("Using temporary folder for Local Connectivity import: " + tmpdir)
_zipfile = ZipFile(local_connectivity_data.parent_cfile.src, 'r', ZIP_DEFLATED)
local_connectivity_path = _zipfile.extract(local_connectivity_data.src, tmpdir)
gid = dao.get_last_data_with_uid(meta[constants.KEY_SURFACE_UID], surfaces.CorticalSurface)
surface_data = ABCAdapter.load_entity_by_gid(gid)
local_connectivity = surfaces.LocalConnectivity()
local_connectivity.storage_path = storage_path
local_connectivity_data = read_matlab_data(local_connectivity_path, constants.DATA_NAME_LOCAL_CONN)
if local_connectivity_data.shape[0] < expected_length:
padding = sparse.csc_matrix((local_connectivity_data.shape[0],
expected_length - local_connectivity_data.shape[0]))
local_connectivity_data = sparse.hstack([local_connectivity_data, padding])
padding = sparse.csc_matrix((expected_length - local_connectivity_data.shape[0],
local_connectivity_data.shape[1]))
local_connectivity_data = sparse.vstack([local_connectivity_data, padding])
local_connectivity.equation = None
local_connectivity.matrix = local_connectivity_data
local_connectivity.surface = surface_data
uid = meta[constants.KEY_UID] if constants.KEY_UID in meta else None
if os.path.isdir(tmpdir):
shutil.rmtree(tmpdir)
return local_connectivity, uid
def cdata2eeg_mapping(eeg_mapping_data, meta, storage_path, expected_shape=0):
"""
Currently not used
"""
tmpdir = os.path.join(gettempdir(), eeg_mapping_data.parent_cfile.get_unique_cff_name())
LOG.debug("Using temporary folder for EEG_Mapping import: " + tmpdir)
_zipfile = ZipFile(eeg_mapping_data.parent_cfile.src, 'r', ZIP_DEFLATED)
eeg_projection_path = _zipfile.extract(eeg_mapping_data.src, tmpdir)
eeg_projection_data = read_matlab_data(eeg_projection_path, constants.DATA_NAME_PROJECTION)
if eeg_projection_data.shape[1] < expected_shape:
padding = numpy.zeros((eeg_projection_data.shape[0], expected_shape - eeg_projection_data.shape[1]))
eeg_projection_data = numpy.hstack((eeg_projection_data, padding))
gid = dao.get_last_data_with_uid(meta[constants.KEY_SURFACE_UID], surfaces.CorticalSurface)
surface_data = ABCAdapter.load_entity_by_gid(gid)
projection_matrix = projections.ProjectionSurfaceEEG(storage_path = storage_path)
projection_matrix.projection_data = eeg_projection_data
projection_matrix.sources = surface_data
projection_matrix.sensors = None
### TODO if we decide to use this method, we will need to find a manner to fill the sensors.
return projection_matrix
def parse_event_node(self):
"""
Parse the stored event node to get required data and arguments.
"""
kw_parameters = {}
for one_arg in self.event_node.childNodes:
if one_arg.nodeType != Node.ELEMENT_NODE:
continue
if one_arg.nodeName == ELEM_ADAPTER:
#TODO: so far there is no need for it, but we should maybe
#handle cases where same module/class but different init parameter
group = dao.find_group(one_arg.getAttribute(ATT_MODULE), one_arg.getAttribute(ATT_CLASS))
adapter = ABCAdapter.build_adapter(group)
result_uid = one_arg.getAttribute(ATT_UID)
if result_uid:
kw_parameters[ATT_UID] = result_uid
LOGGER.debug("Adapter used is %s", str(adapter.__class__))
self.callable_object = adapter
continue
if one_arg.nodeName == ELEM_METHOD:
self.call_method = one_arg.getAttribute(ATT_NAME)
if one_arg.getAttribute(ATT_OPERATION_HIDDEN):
self.operation_visible = False
continue
if one_arg.nodeName == ELEM_ARGS:
kw_parameters.update(_parse_arguments(one_arg))
continue
LOGGER.info("Ignored undefined node %s", str(one_arg.nodeName))
self.arguments.update(kw_parameters)
def get_template_for_adapter(self, project_id, step_key, algo_group, submit_url, session_reset=True, is_burst=True):
""" Get Input HTML Interface template or a given adapter """
try:
if session_reset:
self.context.clean_from_session()
group = None
# Cache some values in session, for performance
previous_tree = self.context.get_current_input_tree()
previous_sub_step = self.context.get_current_substep()
if not session_reset and previous_tree is not None and previous_sub_step == algo_group.id:
adapter_interface = previous_tree
else:
group, adapter_interface = self.flow_service.prepare_adapter(project_id, algo_group)
self.context.add_adapter_to_session(algo_group, adapter_interface)
category = self.flow_service.get_category_by_id(step_key)
title = "Fill parameters for step " + category.displayname.lower()
if group:
title = title + " - " + group.displayname
current_defaults = self.context.get_current_default()
if current_defaults is not None:
#Change default values in tree, according to selected input
adapter_interface = ABCAdapter.fill_defaults(adapter_interface, current_defaults)
template_specification = dict(submitLink=submit_url, inputList=adapter_interface, title=title)
self._populate_section(algo_group, template_specification, is_burst)
return template_specification
except OperationException, oexc:
self.logger.error("Inconsistent Adapter")
self.logger.exception(oexc)
common.set_warning_message('Inconsistent Adapter! Please review the link (development problem)!')
def do_operation_launch(operation_id):
"""
Event attached to the local queue for executing an operation, when we will have resources available.
"""
LOGGER = get_logger('tvb.core.operation_async_launcher')
try:
LOGGER.debug("Loading operation with id=%s" % operation_id)
curent_operation = dao.get_operation_by_id(operation_id)
stored_adapter = curent_operation.algorithm
LOGGER.debug("Importing Algorithm: " + str(stored_adapter.classname) +
" for Operation:" + str(curent_operation.id))
PARAMS = parse_json_parameters(curent_operation.parameters)
adapter_instance = ABCAdapter.build_adapter(stored_adapter)
## Un-comment bellow for profiling an operation:
## import cherrypy.lib.profiler as profiler
## p = profiler.Profiler("/Users/lia.domide/TVB/profiler/")
## p.run(OperationService().initiate_prelaunch, curent_operation, adapter_instance, {}, **PARAMS)
OperationService().initiate_prelaunch(curent_operation, adapter_instance, {}, **PARAMS)
LOGGER.debug("Successfully finished operation " + str(operation_id))
except Exception as excep:
LOGGER.error("Could not execute operation " + str(sys.argv[1]))
LOGGER.exception(excep)
parent_burst = dao.get_burst_for_operation_id(operation_id)
if parent_burst is not None:
WorkflowService().mark_burst_finished(parent_burst, error_message=str(excep))
def test_build_adapter_instance(self):
"""
Test standard flow for building an adapter instance.
"""
algo_group = dao.find_group(TEST_ADAPTER_VALID_MODULE, TEST_ADAPTER_VALID_CLASS)
adapter = ABCAdapter.build_adapter(algo_group)
self.assertTrue(isinstance(adapter, ABCSynchronous), "Something went wrong with valid data!")
def create_adapter(module='tvb.tests.framework.adapters.ndimensionarrayadapter',
class_name='NDimensionArrayAdapter'):
"""
:returns: Adapter Class after initialization.
"""
algorithm = dao.get_algorithm_by_module(module, class_name )
return ABCAdapter.build_adapter(algorithm)
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 = ABCAdapter.load_entity_by_gid(entity_gid)
datatype_kwargs = json.loads(datatype_kwargs)
if datatype_kwargs:
for key, value in datatype_kwargs.iteritems():
kwargs[key] = ABCAdapter.load_entity_by_gid(value)
result = getattr(entity, dataset_name)
if callable(result):
if kwargs:
result = result(**kwargs)
else:
result = result()
return result
def import_sensors(user, project, zip_path, sensors_type):
### Retrieve Adapter instance
group = dao.find_group('tvb.adapters.uploaders.sensors_importer', 'Sensors_Importer')
importer = ABCAdapter.build_adapter(group)
args = {'sensors_file': zip_path, 'sensors_type': sensors_type}
### Launch Operation
FlowService().fire_operation(importer, user, project.id, **args)
def _create_value_wrapper(self):
"""Persist ValueWrapper"""
value_ = ValueWrapper(data_value=5.0, data_name="my_value")
self._store_entity(value_, "ValueWrapper", "tvb.datatypes.mapped_values")
valuew = self.get_all_entities(ValueWrapper)
self.assertEqual(1, len(valuew), "Should be one value wrapper")
return ABCAdapter.load_entity_by_gid(valuew[0].gid)
def fire_simulation(project_id=1, **kwargs):
project = dao.get_project_by_id(project_id)
flow_service = FlowService()
# below the holy procedure to launch with the correct parameters taken from the defaults
stored_adapter = flow_service.get_algorithm_by_module_and_class(SIMULATOR_MODULE, SIMULATOR_CLASS)
simulator_adapter = ABCAdapter.build_adapter(stored_adapter)
flatten_interface = simulator_adapter.flaten_input_interface()
itree_mngr = flow_service.input_tree_manager
prepared_flatten_interface = itree_mngr.fill_input_tree_with_options(flatten_interface, project.id,
stored_adapter.fk_category)
launch_args = {}
for entry in prepared_flatten_interface:
value = entry['default']
if isinstance(value, dict):
value = str(value)
if hasattr(value, 'tolist'):
value = value.tolist()
launch_args[entry['name']] = value
launch_args.update(**kwargs)
# end of magic
launched_operation = flow_service.fire_operation(simulator_adapter, project.administrator,
project.id, **launch_args)[0]
return launched_operation
def test_happy_flow_surface_import(self):
"""
Verifies the happy flow for importing a surface.
"""
dt_count_before = TestFactory.get_entity_count(self.test_project, ProjectionSurfaceEEG())
group = dao.find_group(
"tvb.adapters.uploaders.projection_matrix_importer", "ProjectionMatrixSurfaceEEGImporter"
)
importer = ABCAdapter.build_adapter(group)
file_path = os.path.join(
os.path.abspath(os.path.dirname(dataset.__file__)), "projection_eeg_65_surface_16k.npy"
)
args = {
"projection_file": file_path,
"dataset_name": "ProjectionMatrix",
"sensors": self.sensors.gid,
"surface": self.surface.gid,
DataTypeMetaData.KEY_SUBJECT: DataTypeMetaData.DEFAULT_SUBJECT,
}
FlowService().fire_operation(importer, self.test_user, self.test_project.id, **args)
dt_count_after = TestFactory.get_entity_count(self.test_project, ProjectionSurfaceEEG())
self.assertEqual(dt_count_before + 1, dt_count_after)
def launch_visualization(visualization, frame_width=None, frame_height=None,
method_name=ABCAdapter.LAUNCH_METHOD, is_preview=True):
"""
:param visualization: a visualization workflow step
"""
dynamic_params = visualization.dynamic_param
static_params = visualization.static_param
parameters_dict = static_params
current_project_id = 0
## Current operation id needed for export mechanism. So far just use ##
## the operation of the workflow_step from which the inputs are taken ####
for param in dynamic_params:
step_index = dynamic_params[param][WorkflowStepConfiguration.STEP_INDEX_KEY]
datatype_index = dynamic_params[param][WorkflowStepConfiguration.DATATYPE_INDEX_KEY]
referred_workflow_step = dao.get_workflow_step_by_step_index(visualization.fk_workflow, step_index)
referred_operation_id = referred_workflow_step.fk_operation
referred_operation = dao.get_operation_by_id(referred_operation_id)
current_project_id = referred_operation.fk_launched_in
if type(datatype_index) is IntType:
## Entry is the output of a previous step ##
datatypes = dao.get_results_for_operation(referred_operation_id)
parameters_dict[param] = datatypes[datatype_index].gid
else:
## Entry is the input of a previous step ###
parameters_dict[param] = json.loads(referred_operation.parameters)[datatype_index]
algorithm = dao.get_algorithm_by_id(visualization.fk_algorithm)
adapter_instance = ABCAdapter.build_adapter(algorithm.algo_group)
adapter_instance.current_project_id = current_project_id
prepared_inputs = adapter_instance.prepare_ui_inputs(parameters_dict)
if frame_width is not None:
prepared_inputs[ABCDisplayer.PARAM_FIGURE_SIZE] = (frame_width, frame_height)
if isinstance(adapter_instance, ABCMPLH5Displayer) and is_preview is True:
prepared_inputs[ABCMPLH5Displayer.SHOW_FULL_TOOLBAR] = False
result = eval("adapter_instance." + method_name + "(**prepared_inputs)")
return result, parameters_dict
def _import(self, import_file_path, surface_gid, connectivity_gid):
"""
This method is used for importing region mappings
:param import_file_path: absolute path of the file to be imported
"""
### Retrieve Adapter instance
group = dao.find_group("tvb.adapters.uploaders.region_mapping_importer", "RegionMapping_Importer")
importer = ABCAdapter.build_adapter(group)
args = {
"mapping_file": import_file_path,
"surface": surface_gid,
"connectivity": connectivity_gid,
DataTypeMetaData.KEY_SUBJECT: "test",
}
now = datetime.datetime.now()
### Launch import Operation
FlowService().fire_operation(importer, self.test_user, self.test_project.id, **args)
# During setup we import a CFF which creates an additional RegionMapping
# So, here we have to find our mapping (just imported)
data_filter = FilterChain(fields=[FilterChain.datatype + ".create_date"], operations=[">"], values=[now])
region_mapping = self._get_entity(RegionMapping(), data_filter)
return region_mapping
def _create_mapped_arrays(self, project_id):
"""
:param project_id: the project in which the arrays are created
:return: a list of dummy `MappedArray`
"""
count = self.flow_service.get_available_datatypes(project_id, "tvb.datatypes.arrays.MappedArray")[1]
self.assertEqual(count, 0)
group = dao.get_algorithm_by_module('tvb.tests.framework.adapters.ndimensionarrayadapter', 'NDimensionArrayAdapter')
adapter_instance = ABCAdapter.build_adapter(group)
data = {'param_1': 'some value'}
#create 3 data types
self.flow_service.fire_operation(adapter_instance, self.test_user, project_id, **data)
count = self.flow_service.get_available_datatypes(project_id, "tvb.datatypes.arrays.MappedArray")[1]
self.assertEqual(count, 1)
self.flow_service.fire_operation(adapter_instance, self.test_user, project_id, **data)
count = self.flow_service.get_available_datatypes(project_id, "tvb.datatypes.arrays.MappedArray")[1]
self.assertEqual(count, 2)
self.flow_service.fire_operation(adapter_instance, self.test_user, project_id, **data)
array_wrappers, count = self.flow_service.get_available_datatypes(project_id,
"tvb.datatypes.arrays.MappedArray")
self.assertEqual(count, 3)
return array_wrappers
def test_wrong_shape(self):
"""
Verifies that importing a different shape throws exception
"""
group = dao.find_group(
"tvb.adapters.uploaders.projection_matrix_importer", "ProjectionMatrixSurfaceEEGImporter"
)
importer = ABCAdapter.build_adapter(group)
file_path = os.path.join(
os.path.abspath(os.path.dirname(dataset.__file__)), "projection_eeg_62_surface_16k.mat"
)
args = {
"projection_file": file_path,
"dataset_name": "ProjectionMatrix",
"sensors": self.sensors.gid,
"surface": self.surface.gid,
DataTypeMetaData.KEY_SUBJECT: DataTypeMetaData.DEFAULT_SUBJECT,
}
try:
FlowService().fire_operation(importer, self.test_user, self.test_project.id, **args)
self.fail("This was expected not to run! 62 rows in proj matrix, but 65 sensors")
except OperationException:
pass
def get_configurable_interface(self):
"""
Given an algorithm identifier, go trough the adapter chain, and merge
their input tree with the declared overwrites
"""
chain_adapters = self.reader.get_adapters_chain(self.algo_identifier)
result = []
for adapter_declaration in chain_adapters:
adapter_instance, algorithm_group = self.build_adapter_from_declaration(adapter_declaration)
algorithm_field = adapter_declaration[KEY_FIELD]
if algorithm_field:
default_algorithm = adapter_declaration[ABCAdapter.KEY_DEFAULT]
else:
default_algorithm = ''
all_portlet_defined_params = self.reader.get_inputs(self.algo_identifier)
specific_adapter_overwrites = [entry for entry in all_portlet_defined_params
if ATT_OVERWRITE in entry and entry[ATT_OVERWRITE] ==
adapter_declaration[ABCAdapter.KEY_NAME]]
if default_algorithm:
alg_inputs = adapter_instance.xml_reader.get_inputs(default_algorithm)
prefix = ABCAdapter.form_prefix(algorithm_field, None, default_algorithm)
else:
alg_inputs = adapter_instance.get_input_tree()
prefix = ''
replace_values = self._prepare_input_tree(alg_inputs, specific_adapter_overwrites, prefix)
adapter_configuration = AdapterConfiguration(replace_values, algorithm_group, prefix=prefix,
subalgorithm_field=algorithm_field,
subalgorithm_value=default_algorithm)
result.append(adapter_configuration)
return result
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:
result = self.flow_service.fire_operation(adapter_instance, common.get_logged_user(), project_id, **data)
# Store input data in session, for informing user of it.
step = self.flow_service.get_category_by_id(step_key)
if not step.rawinput:
self.context.add_adapter_to_session(None, None, copy.deepcopy(data))
if isinstance(adapter_instance, ABCDisplayer):
if isinstance(result, dict):
result[common.KEY_OPERATION_ID] = adapter_instance.operation_id
return result
else:
common.set_error_message("Invalid result returned from Displayer! Dictionary is expected!")
else:
if isinstance(result, list):
result = "Launched %s operations." % len(result)
common.set_important_message(str(result))
except formencode.Invalid, excep:
errors = excep.unpack_errors()
def _create_value_wrapper(self):
"""Persist ValueWrapper"""
value_ = ValueWrapper(data_value=5.0, data_name="my_value")
self._store_entity(value_, "ValueWrapper", "tvb.datatypes.mapped_values")
valuew = self.flow_service.get_available_datatypes(self.test_project.id,
"tvb.datatypes.mapped_values.ValueWrapper")[0]
self.assertEqual(len(valuew), 1, "Should be only one value wrapper")
return ABCAdapter.load_entity_by_gid(valuew[0][2])
def _run_cff_importer(self, cff_path):
### Retrieve Adapter instance
group = dao.find_group('tvb.adapters.uploaders.cff_importer', 'CFF_Importer')
importer = ABCAdapter.build_adapter(group)
args = {'cff': cff_path, DataTypeMetaData.KEY_SUBJECT: DataTypeMetaData.DEFAULT_SUBJECT}
### Launch Operation
FlowService().fire_operation(importer, self.test_user, self.test_project.id, **args)
def _review_operation_inputs(operation_gid):
"""
:returns: A list of DataTypes that are used as input parameters for the specified operation.
And a dictionary will all operation parameters different then the default ones.
"""
operation = dao.get_operation_by_gid(operation_gid)
parameters = json.loads(operation.parameters)
adapter = ABCAdapter.build_adapter(operation.algorithm.algo_group)
return adapter.review_operation_inputs(parameters)
def get_template_from_context(self):
"""
Return the parameters for the local connectivity in case one is stored in context. Load the entity
and use it to populate the defaults from the interface accordingly.
"""
context = common.get_from_session(KEY_LCONN_CONTEXT)
selected_local_conn = ABCAdapter.load_entity_by_gid(
context.selected_entity)
cutoff = selected_local_conn.cutoff
equation = selected_local_conn.equation
surface = selected_local_conn.surface
default_dict = {'surface': surface.gid, 'cutoff': cutoff}
if equation is not None:
equation_type = equation.__class__.__name__
default_dict['equation'] = equation_type
for param in equation.parameters:
prepared_name = 'equation_parameters_option_' + str(
equation_type)
prepared_name = prepared_name + '_parameters_parameters_' + str(
param)
default_dict[prepared_name] = equation.parameters[param]
else:
msg = "There is no equation specified for this local connectivity. "
msg += "The default equation is displayed into the spatial field."
self.logger.warning(msg)
common.set_info_message(msg)
default_dict[
DataTypeMetaData.KEY_TAG_1] = selected_local_conn.user_tag_1
input_list = self.get_creator_and_interface(LOCAL_CONN_CREATOR_MODULE,
LOCAL_CONN_CREATOR_CLASS,
LocalConnectivity(),
lock_midpoint_for_eq=[1
])[1]
input_list = self._add_extra_fields_to_interface(input_list)
input_list = InputTreeManager.fill_defaults(input_list, default_dict)
template_specification = {
'inputList': input_list,
common.KEY_PARAMETERS_CONFIG: False,
'equationViewerUrl':
'/spatial/localconnectivity/get_equation_chart',
'equationsPrefixes': json.dumps(self.plotted_equations_prefixes)
}
return template_specification
def import_surface_zip(user, project, zip_path, surface_type, zero_based):
### Retrieve Adapter instance
group = dao.find_group('tvb.adapters.uploaders.zip_surface_importer',
'ZIPSurfaceImporter')
importer = ABCAdapter.build_adapter(group)
importer.meta_data = {
DataTypeMetaData.KEY_SUBJECT: DataTypeMetaData.DEFAULT_SUBJECT,
DataTypeMetaData.KEY_STATE: "RAW"
}
args = {
'uploaded': zip_path,
'surface_type': surface_type,
'zero_based_triangles': zero_based
}
### Launch Operation
FlowService().fire_operation(importer, user, project.id, **args)
def setUp(self):
"""
This method sets up the necessary paths for testing.
"""
self.folder_path = os.path.dirname(__file__)
#tvb_test path
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
self.old_path = cfg.CURRENT_DIR
cfg.CURRENT_DIR = os.path.dirname(core_path)
adapters_init.__xml_folders__ = [os.path.join('core', 'adapters')]
self.introspector = Introspector("tvb_test")
self.introspector.introspect(True)
xml_group_path = os.path.join('core', 'adapters', "test_group.xml")
algo_group = dao.find_group('tvb_test.adapters.testgroupadapter',
'TestGroupAdapter', xml_group_path)
self.xml_group_adapter = ABCAdapter.build_adapter(algo_group)
self.xml_group_reader = self.xml_group_adapter.xml_reader
def prepare_adapter(self, project_id, stored_adapter):
"""
Having a StoredAdapter, return the Tree Adapter Interface object, populated with datatypes from 'project_id'.
"""
adapter_module = stored_adapter.module
adapter_name = stored_adapter.classname
try:
# Prepare Adapter Interface, by populating with existent data,
# in case of a parameter of type DataType.
adapter_instance = ABCAdapter.build_adapter(stored_adapter)
interface = adapter_instance.get_input_tree()
interface = self.input_tree_manager.fill_input_tree_with_options(interface, project_id, stored_adapter.fk_category)
interface = self.input_tree_manager.prepare_param_names(interface)
return interface
except Exception:
self.logger.exception('Not found:' + adapter_name + ' in:' + adapter_module)
raise OperationException("Could not prepare " + adapter_name)
def get_node_matrix(self, datatype_group_gid):
algorithm = self.flow_service.get_algorithm_by_module_and_class(ISOCLINE_PSE_ADAPTER_MODULE,
ISOCLINE_PSE_ADAPTER_CLASS)
adapter = ABCAdapter.build_adapter(algorithm)
if self._is_compatible(algorithm, datatype_group_gid):
try:
datatype_group = dao.get_datatype_group_by_gid(datatype_group_gid)
return adapter.prepare_node_data(datatype_group)
except LaunchException as ex:
self.logger.error(ex.message)
error_msg = urllib.quote(ex.message)
else:
error_msg = urllib.quote("Isocline PSE requires a 2D range of floating point values.")
name = urllib.quote(adapter._ui_name)
raise cherrypy.HTTPRedirect(REDIRECT_MSG % (name, error_msg))
def _import(self,
import_file_path=None,
expected_result_class=StructuralMRIIndex,
connectivity_gid=None):
"""
This method is used for importing data in NIFIT format
:param import_file_path: absolute path of the file to be imported
"""
# Retrieve Adapter instance
importer = TestFactory.create_adapter(
'tvb.adapters.uploaders.nifti_importer', 'NIFTIImporter')
form = NIFTIImporterForm()
form.fill_from_post({
'data_file':
Part(import_file_path, HeaderMap({}), ''),
'apply_corrections':
'True',
'connectivity':
connectivity_gid,
'mappings_file':
Part(self.TXT_FILE, HeaderMap({}), ''),
'Data_Subject':
'bla bla'
})
form.data_file.data = import_file_path
form.mappings_file.data = self.TXT_FILE
view_model = form.get_view_model()()
view_model.data_subject = 'bla bla'
form.fill_trait(view_model)
importer.submit_form(form)
# Launch import Operation
FlowService().fire_operation(importer,
self.test_user,
self.test_project.id,
view_model=view_model)
dts, count = dao.get_values_of_datatype(self.test_project.id,
expected_result_class, None)
assert 1, count == "Project should contain only one data type."
result = ABCAdapter.load_entity_by_gid(dts[0][2])
assert result is not None, "Result should not be none"
return result
def submit_noise_configuration(self):
"""
Collects the model parameters values from all the models used for the connectivity nodes.
"""
context_noise_config = base.get_from_session(KEY_CONTEXT_NC)
burst_configuration = base.get_from_session(base.KEY_BURST_CONFIG)
_, simulator_group = FlowService().get_algorithm_by_module_and_class(
SIMULATOR_MODULE, SIMULATOR_CLASS)
simulator_adapter = ABCAdapter.build_adapter(simulator_group)
for param_name in simulator_adapter.noise_configurable_parameters():
burst_configuration.update_simulation_parameter(
param_name, str(context_noise_config.noise_values))
### Clean from session drawing context
base.remove_from_session(KEY_CONTEXT_NC)
### Update in session BURST configuration for burst-page.
base.add2session(base.KEY_BURST_CONFIG, burst_configuration.clone())
raise cherrypy.HTTPRedirect("/burst/")
def step_2(self):
"""
Generate the required template dictionary for the second step.
"""
current_region_stimulus = common.get_from_session(KEY_REGION_STIMULUS)
region_stim_selector_form = StimulusRegionSelectorForm(
common.get_current_project().id)
region_stim_selector_form.region_stimulus.data = current_region_stimulus.gid.hex
region_stim_selector_form.display_name.data = common.get_from_session(
KEY_REGION_STIMULUS_NAME)
template_specification = dict(
title="Spatio temporal - Region stimulus")
template_specification[
'mainContent'] = 'spatial/stimulus_region_step2_main'
template_specification[
'next_step_url'] = '/spatial/stimulus/region/step_2_submit'
template_specification[
'regionStimSelectorForm'] = self.render_adapter_form(
region_stim_selector_form)
default_weights = current_region_stimulus.weight
if len(default_weights) == 0:
selected_connectivity = ABCAdapter.load_entity_by_gid(
current_region_stimulus.connectivity.hex)
if selected_connectivity is None:
common.set_error_message(self.MSG_MISSING_CONNECTIVITY)
default_weights = numpy.array([])
else:
default_weights = StimuliRegion.get_default_weights(
selected_connectivity.number_of_regions)
template_specification['baseUrl'] = self.base_url
self.plotted_equation_prefixes = {
self.DISPLAY_NAME_FIELD:
region_stim_selector_form.display_name.name
}
template_specification['fieldsWithEvents'] = json.dumps(
self.plotted_equation_prefixes)
template_specification['node_weights'] = json.dumps(
default_weights.tolist())
template_specification[common.KEY_PARAMETERS_CONFIG] = False
template_specification.update(
self.display_connectivity(
current_region_stimulus.connectivity.hex))
return self.fill_default_attributes(template_specification)
def test_h5_import(self):
"""
This method tests import of TVB data in h5 format. Single data type / import
"""
self._import(self.h5_file_path)
data_types = FlowService().get_available_datatypes(
self.test_project.id,
self.datatype.module + "." + self.datatype.type)[0]
self.assertEqual(1, len(data_types),
"Project should contain only one data type.")
data_type_entity = ABCAdapter.load_entity_by_gid(data_types[0][2])
self.assertTrue(data_type_entity is not None,
"Datatype should not be none")
self.assertEqual(self.datatype.gid, data_type_entity.gid,
"Imported datatype should have the same gid")
def launch_operation(self, operation_id, send_to_cluster=False, adapter_instance=None):
"""
Method exposed for Burst-Workflow related calls.
It is used for cascading operation in the same workflow.
"""
if operation_id is not None:
operation = dao.get_operation_by_id(operation_id)
if adapter_instance is None:
algorithm = operation.algorithm
group = dao.get_algo_group_by_id(algorithm.fk_algo_group)
adapter_instance = ABCAdapter.build_adapter(group)
PARAMS = parse_json_parameters(operation.parameters)
if send_to_cluster:
self._send_to_cluster([operation], adapter_instance)
else:
self.initiate_prelaunch(operation, adapter_instance, {}, **PARAMS)
def _importSurface(self, import_file_path=None):
### Retrieve Adapter instance
importer = TestFactory.create_adapter('tvb.adapters.uploaders.obj_importer', 'ObjSurfaceImporter')
args = {'data_file': import_file_path,
"surface_type": FACE,
DataTypeMetaData.KEY_SUBJECT: "John"}
### Launch import Operation
FlowService().fire_operation(importer, self.test_user, self.test_project.id, **args)
data_types = FlowService().get_available_datatypes(self.test_project.id, FaceSurface)[0]
self.assertEqual(1, len(data_types), "Project should contain only one data type.")
surface = ABCAdapter.load_entity_by_gid(data_types[0][2])
self.assertTrue(surface is not None, "Surface should not be None")
return surface
def fill_from_trait(self, trait):
super(SpatialAverageMonitorForm, self).fill_from_trait(trait)
connectivity_index = ABCAdapter.load_entity_by_gid(
self.session_stored_simulator.connectivity)
if self.session_stored_simulator.is_surface_simulation is False:
self.default_mask.choices.pop(SpatialAverage.REGION_MAPPING)
if connectivity_index.has_cortical_mask is False:
self.default_mask.choices.pop(SpatialAverage.CORTICAL)
if connectivity_index.has_hemispheres_mask is False:
self.default_mask.choices.pop(SpatialAverage.HEMISPHERES)
else:
self.default_mask.data = SpatialAverage.REGION_MAPPING
self.default_mask.disabled = True
def launch_visualization(visualization,
frame_width=None,
frame_height=None,
method_name=ABCAdapter.LAUNCH_METHOD,
is_preview=True):
"""
:param visualization: a visualization workflow step
"""
dynamic_params = visualization.dynamic_param
static_params = visualization.static_param
parameters_dict = static_params
current_project_id = 0
## Current operation id needed for export mechanism. So far just use ##
## the operation of the workflow_step from which the inputs are taken ####
for param in dynamic_params:
step_index = dynamic_params[param][
WorkflowStepConfiguration.STEP_INDEX_KEY]
datatype_index = dynamic_params[param][
WorkflowStepConfiguration.DATATYPE_INDEX_KEY]
referred_workflow_step = dao.get_workflow_step_by_step_index(
visualization.fk_workflow, step_index)
referred_operation_id = referred_workflow_step.fk_operation
referred_operation = dao.get_operation_by_id(referred_operation_id)
current_project_id = referred_operation.fk_launched_in
if type(datatype_index) is IntType:
## Entry is the output of a previous step ##
datatypes = dao.get_results_for_operation(
referred_operation_id)
parameters_dict[param] = datatypes[datatype_index].gid
else:
## Entry is the input of a previous step ###
parameters_dict[param] = json.loads(
referred_operation.parameters)[datatype_index]
algorithm = dao.get_algorithm_by_id(visualization.fk_algorithm)
adapter_instance = ABCAdapter.build_adapter(algorithm.algo_group)
adapter_instance.current_project_id = current_project_id
prepared_inputs = adapter_instance.prepare_ui_inputs(parameters_dict)
if frame_width is not None:
prepared_inputs[ABCDisplayer.PARAM_FIGURE_SIZE] = (frame_width,
frame_height)
if isinstance(adapter_instance,
ABCMPLH5Displayer) and is_preview is True:
prepared_inputs[ABCMPLH5Displayer.SHOW_FULL_TOOLBAR] = False
result = eval("adapter_instance." + method_name +
"(**prepared_inputs)")
return result, parameters_dict
def _get_new_form_view_model(operation, xml_parameters):
# type (Operation) -> ViewModel
ad = ABCAdapter.build_adapter(operation.algorithm)
view_model = ad.get_view_model_class()()
if xml_parameters:
params = json.loads(xml_parameters)
declarative_attrs = type(view_model).declarative_attrs
for param in params:
new_param_name = param
if param[0] == "_":
new_param_name = param[1:]
new_param_name = new_param_name.lower()
if new_param_name in declarative_attrs:
setattr(view_model, new_param_name, params[param])
return view_model
def build(test_user, test_project):
view_model = BaseBCTModel()
view_model.connectivity = get_filtered_datatypes(test_project.id, ConnectivityIndex, page_size=1)[0][0][2]
adapter = ABCAdapter.build_adapter_from_class(TransitivityBinaryDirected)
op = OperationService().fire_operation(adapter, test_user, test_project.id, view_model=view_model)
# wait for the operation to finish
tries = 5
while not op.has_finished and tries > 0:
sleep(5)
tries = tries - 1
op = dao.get_operation_by_id(op.id)
value_wrapper = try_get_last_datatype(test_project.id, ValueWrapperIndex)
count = dao.count_datatypes(test_project.id, ValueWrapperIndex)
assert 1 == count
return value_wrapper
def _review_operation_inputs(self, operation_gid):
"""
:returns: A list of DataTypes that are used as input parameters for the specified operation.
And a dictionary will all operation parameters different then the default ones.
"""
operation = dao.get_operation_by_gid(operation_gid)
try:
adapter = ABCAdapter.build_adapter(operation.algorithm)
return review_operation_inputs_from_adapter(adapter, operation)
except Exception:
self.logger.exception("Could not load details for operation %s" % operation_gid)
if operation.view_model_gid:
changed_parameters = dict(Warning="Algorithm changed dramatically. We can not offer more details")
else:
changed_parameters = dict(Warning="GID parameter is missing. Old implementation of the operation.")
return [], changed_parameters
def get_template_for_adapter(self,
project_id,
step_key,
algo_group,
submit_url,
session_reset=True):
""" Get Input HTML Interface template or a given adapter """
try:
if session_reset:
self.context.clean_from_session()
group = None
# Cache some values in session, for performance
previous_tree = self.context.get_current_input_tree()
previous_sub_step = self.context.get_current_substep()
if not session_reset and previous_tree is not None and previous_sub_step == algo_group.id:
adapter_interface = previous_tree
else:
group, adapter_interface = self.flow_service.prepare_adapter(
project_id, algo_group)
self.context.add_adapter_to_session(algo_group,
adapter_interface)
category = self.flow_service.get_category_by_id(step_key)
title = "Fill parameters for step " + category.displayname.lower()
if group:
title = title + " - " + group.displayname
current_defaults = self.context.get_current_default()
if current_defaults is not None:
#Change default values in tree, according to selected input
adapter_interface = ABCAdapter.fill_defaults(
adapter_interface, current_defaults)
template_specification = dict(submitLink=submit_url,
inputList=adapter_interface,
title=title)
self._populate_section(algo_group, template_specification)
return template_specification
except OperationException, oexc:
self.logger.error("Inconsistent Adapter")
self.logger.exception(oexc)
base.set_warning_message(
'Inconsistent Adapter! Please review the link (development problem)!'
)
def build_portlet_interface(self, portlet_configuration, project_id):
"""
From a portlet_id and a project_id, first build the portlet
entity then get it's configurable interface.
:param portlet_configuration: a portlet configuration entity. It holds at the
least the portlet_id, and in case any default parameters were saved
they can be rebuilt from the analyzers // visualizer parameters
:param project_id: the id of the current project
:returns: the portlet interface will be of the following form::
[{'interface': adapter_interface,
'prefix': prefix_for_parameter_names,
'subalg': {algorithm_field_name: default_algorithm_value},
'algo_group': algorithm_group,
'alg_ui_name': displayname},
......]
A list of dictionaries for each adapter that makes up the portlet.
"""
portlet_entity = dao.get_portlet_by_id(
portlet_configuration.portlet_id)
if portlet_entity is None:
raise InvalidPortletConfiguration(
"No portlet entity located in database with id=%s. "
"Portlet configuration %s is not valid." %
(portlet_configuration.portlet_id, portlet_configuration))
portlet_configurer = PortletConfigurer(portlet_entity)
portlet_interface = portlet_configurer.get_configurable_interface()
self.logger.debug("Created interface for portlet " +
str([portlet_entity]))
for adapter_conf in portlet_interface:
interface = adapter_conf.interface
interface = FlowService().prepare_parameters(
interface, project_id, adapter_conf.group.fk_category)
interface = ABCAdapter.prepare_param_names(interface,
adapter_conf.prefix)
adapter_conf.interface = interface
portlet_configurer.update_default_values(portlet_interface,
portlet_configuration)
portlet_configurer.prefix_adapters_parameters(portlet_interface)
return portlet_interface
def get_configurable_interface(self):
"""
Given an algorithm identifier, go trough the adapter chain, and merge
their input tree with the declared overwrites
"""
chain_adapters = self.reader.get_adapters_chain(self.algo_identifier)
result = []
for adapter_declaration in chain_adapters:
adapter_instance, algorithm_group = self.build_adapter_from_declaration(
adapter_declaration)
algorithm_field = adapter_declaration[KEY_FIELD]
if algorithm_field:
default_algorithm = adapter_declaration[ABCAdapter.KEY_DEFAULT]
else:
default_algorithm = ''
all_portlet_defined_params = self.reader.get_inputs(
self.algo_identifier)
specific_adapter_overwrites = [
entry for entry in all_portlet_defined_params
if ATT_OVERWRITE in entry and entry[ATT_OVERWRITE] ==
adapter_declaration[ABCAdapter.KEY_NAME]
]
if default_algorithm:
alg_inputs = adapter_instance.xml_reader.get_inputs(
default_algorithm)
prefix = ABCAdapter.form_prefix(algorithm_field, None,
default_algorithm)
else:
alg_inputs = adapter_instance.get_input_tree()
prefix = ''
replace_values = self._prepare_input_tree(
alg_inputs, specific_adapter_overwrites, prefix)
adapter_configuration = AdapterConfiguration(
replace_values,
algorithm_group,
prefix=prefix,
subalgorithm_field=algorithm_field,
subalgorithm_value=default_algorithm)
result.append(adapter_configuration)
return result
def load_surface_stimulus(self, surface_stimulus_gid, from_step):
"""
Loads the interface for the selected surface stimulus.
"""
surface_stim_index = ABCAdapter.load_entity_by_gid(
surface_stimulus_gid)
surface_stim_h5_path = h5.path_for_stored_index(surface_stim_index)
existent_surface_stim = SurfaceStimulusCreatorModel()
with StimuliSurfaceH5(surface_stim_h5_path) as surface_stim_h5:
surface_stim_h5.load_into(existent_surface_stim)
existent_surface_stim.surface = uuid.UUID(
surface_stim_index.fk_surface_gid)
common.add2session(KEY_SURFACE_STIMULI, existent_surface_stim)
common.add2session(KEY_SURFACE_STIMULI_NAME,
surface_stim_index.user_tag_1)
return self.do_step(from_step)
def draw_isocline_exploration(self, datatype_group_gid):
algorithm = self.flow_service.get_algorithm_by_module_and_class(
IntrospectionRegistry.ISOCLINE_PSE_ADAPTER_MODULE,
IntrospectionRegistry.ISOCLINE_PSE_ADAPTER_CLASS)
adapter = ABCAdapter.build_adapter(algorithm)
if self._is_compatible(algorithm, datatype_group_gid):
try:
return adapter.burst_preview(datatype_group_gid)
except LaunchException as ex:
self.logger.error(ex.message)
error_msg = urllib.parse.quote(ex.message)
else:
error_msg = urllib.parse.quote(
"Isocline PSE requires a 2D range of floating point values.")
name = urllib.parse.quote(adapter._ui_name)
raise cherrypy.HTTPRedirect(REDIRECT_MSG % (name, error_msg))
def _import(self, import_file_name):
### Retrieve Adapter instance
group = dao.find_group(
'tvb.adapters.uploaders.connectivity_measure_importer',
'ConnectivityMeasureImporter')
importer = ABCAdapter.build_adapter(group)
path = os.path.join(os.path.dirname(test_data.__file__),
import_file_name)
args = {
'data_file': path,
'connectivity': self.connectivity.gid,
DataTypeMetaData.KEY_SUBJECT: "John"
}
### Launch import Operation
FlowService().fire_operation(importer, self.test_user,
self.test_project.id, **args)
def display_connectivity(connectivity_gid):
"""
Generates the html for displaying the connectivity matrix.
"""
connectivity = ABCAdapter.load_entity_by_gid(connectivity_gid)
if connectivity is None:
raise MissingDataException(
RegionStimulusController.MSG_MISSING_CONNECTIVITY + "!!")
current_project = common.get_current_project()
conn_path = FilesHelper().get_project_folder(
current_project, str(connectivity.fk_from_operation))
connectivity_viewer_params = ConnectivityViewer.get_connectivity_parameters(
connectivity, conn_path)
template_specification = dict()
template_specification['isSingleMode'] = True
template_specification.update(connectivity_viewer_params)
return template_specification
def create_stimulus(self):
"""
Creates a stimulus from the given data.
"""
try:
current_surface_stim = common.get_from_session(KEY_SURFACE_STIMULI)
surface_stimulus_creator = ABCAdapter.build_adapter_from_class(SurfaceStimulusCreator)
self.flow_service.fire_operation(surface_stimulus_creator, common.get_logged_user(),
common.get_current_project().id, view_model=current_surface_stim)
common.set_important_message("The operation for creating the stimulus was successfully launched.")
except (NameError, ValueError, SyntaxError):
common.set_error_message("The operation failed due to invalid parameter input.")
return False
except Exception as ex:
common.set_error_message(ex)
return False
return True
def _get_entity(self, expected_data, filters=None):
"""
Checks there is exactly one datatype with required specifications and returns it
:param expected_data: a class whose entity is to be returned
:param filters: optional, the returned entity will also have the required filters
:return: an object of class `expected_data`
"""
dt_full_name = expected_data.__module__ + "." + expected_data.__name__
data_types = FlowService().get_available_datatypes(
self.test_project.id, dt_full_name, filters)[0]
self.assertEqual(
1, len(data_types), "Project should contain only one data type:" +
str(expected_data.type))
entity = ABCAdapter.load_entity_by_gid(data_types[0][2])
self.assertTrue(entity is not None, "Instance should not be none")
return entity
def import_h5(file_path, project_id):
service = OperationService()
# This ID of a project needs to exists in Db, and it can be taken from the WebInterface:
project = dao.get_project_by_id(project_id)
adapter_instance = ABCAdapter.build_adapter_from_class(TVBImporter)
# Prepare the input algorithms as if they were coming from web UI submit:
launch_args = {"data_file": file_path}
print("We will try to import file at path " + file_path)
# launch an operation and have the results stored both in DB and on disk
launched_operations = service.fire_operation(adapter_instance,
project.administrator,
project.id, **launch_args)
print("Operation launched. Check the web UI")
def _prelaunch(self,
operation,
view_model,
uid=None,
available_disk_space=0):
"""
Before going with the usual prelaunch, get from input parameters the 'subject'.
"""
self.generic_attributes.subject = view_model.data_subject
trait_upload_field_names = list(
self.get_form_class().get_upload_information().keys())
if view_model.encrypted_aes_key is not None:
for upload_field_name in trait_upload_field_names:
self._decrypt_content(view_model, upload_field_name)
return ABCAdapter._prelaunch(self, operation, view_model, uid,
available_disk_space)
def display_connectivity(connectivity_gid):
"""
Generates the html for displaying the connectivity matrix.
"""
connectivity = ABCAdapter.load_entity_by_gid(connectivity_gid)
current_project = common.get_current_project()
file_handler = FilesHelper()
conn_path = file_handler.get_project_folder(
current_project, str(connectivity.fk_from_operation))
connectivity_viewer_params = ConnectivityViewer.get_connectivity_parameters(
connectivity, conn_path)
template_specification = dict()
template_specification['isSingleMode'] = True
template_specification.update(connectivity_viewer_params)
return template_specification
def start_operation(operation_id):
LOGGER.info("Start processing operation id:{}".format(operation_id))
operation = dao.get_operation_by_id(operation_id)
operation.queue_full = False
dao.store_entity(operation)
thread = OperationExecutor(operation_id)
CURRENT_ACTIVE_THREADS.append(thread)
adapter_instance = ABCAdapter.build_adapter(operation.algorithm)
if adapter_instance.launch_mode is AdapterLaunchModeEnum.SYNC_DIFF_MEM:
thread.run()
operation = dao.get_operation_by_id(operation_id)
if operation.additional_info and operation.status == STATUS_ERROR:
raise TVBException(operation.additional_info)
else:
thread.start()
def apply_equation(self, **kwargs):
"""
Applies an equations for computing a model parameter.
"""
submitted_data = ABCAdapter.collapse_arrays(kwargs, ['model_param'])
model_param, equation = self._compute_equation(submitted_data)
context_model_parameters = common.get_from_session(KEY_CONTEXT_MPS)
context_model_parameters.apply_equation(model_param, equation)
common.add2session(KEY_CONTEXT_MPS, context_model_parameters)
template_specification = self.get_surface_model_parameters_data(
model_param)
template_specification = self._add_entra_equation_entries(
template_specification, kwargs['min_x'], kwargs['max_x'])
template_specification[
'equationViewerUrl'] = '/spatial/modelparameters/surface/get_equation_chart'
template_specification['equationsPrefixes'] = json.dumps(
self.plotted_equations_prefixes)
return self.fill_default_attributes(template_specification)