def get_creator_and_interface(self,
creator_module,
creator_class,
datatype_instance,
lock_midpoint_for_eq=None):
"""
Returns a Tuple: a creator instance and a dictionary for the creator interface.
The interface is prepared for rendering, it is populated with existent data, in case of a
parameter of type DataType. The name of the attributes are also prefixed to identify groups.
"""
algo_group = self.flow_service.get_algorithm_by_module_and_class(
creator_module, creator_class)[1]
group, _ = self.flow_service.prepare_adapter(
base.get_current_project().id, algo_group)
#I didn't use the interface(from the above line) returned by the method 'prepare_adapter' from flow service
# because the selects that display dataTypes will also have the 'All' entry.
datatype_instance.trait.bound = traited_interface.INTERFACE_ATTRIBUTES_ONLY
input_list = datatype_instance.interface[
traited_interface.INTERFACE_ATTRIBUTES]
if lock_midpoint_for_eq is not None:
for idx in lock_midpoint_for_eq:
input_list[idx] = self._lock_midpoints(input_list[idx])
category = self.flow_service.get_visualisers_category()
input_list = self.flow_service.prepare_parameters(
input_list,
base.get_current_project().id, category.id)
input_list = ABCAdapter.prepare_param_names(input_list)
return self.flow_service.build_adapter_instance(group), input_list
def index(self):
"""Get on burst main page"""
template_specification = dict(
mainContent="burst/main_burst",
title="Simulation Cockpit",
baseUrl=cfg.BASE_URL,
includedResources='project/included_resources')
portlets_list = self.burst_service.get_available_portlets()
session_stored_burst = base.get_from_session(base.KEY_BURST_CONFIG)
if session_stored_burst is None or session_stored_burst.id is None:
if session_stored_burst is None:
session_stored_burst = self.burst_service.new_burst_configuration(
base.get_current_project().id)
base.add2session(base.KEY_BURST_CONFIG, session_stored_burst)
adapter_interface = self.cached_simulator_input_tree
if session_stored_burst is not None:
current_data = session_stored_burst.get_all_simulator_values(
)[0]
adapter_interface = ABCAdapter.fill_defaults(
adapter_interface, current_data, True)
### Add simulator tree to session to be available in filters
self.context.add_adapter_to_session(
self.cached_simulator_algo_group, adapter_interface,
current_data)
template_specification['inputList'] = adapter_interface
selected_portlets = session_stored_burst.update_selected_portlets()
template_specification[
'burst_list'] = self.burst_service.get_available_bursts(
base.get_current_project().id)
template_specification['portletList'] = portlets_list
template_specification['selectedPortlets'] = json.dumps(
selected_portlets)
template_specification['draw_hidden_ranges'] = True
template_specification['burstConfig'] = session_stored_burst
### Prepare PSE available metrics
### We put here all available algorithms, because the metrics select area is a generic one,
### and not loaded with every Burst Group change in history.
algo_group = self.flow_service.get_algorithm_by_module_and_class(
MEASURE_METRICS_MODULE, MEASURE_METRICS_CLASS)[1]
adapter_instance = ABCAdapter.build_adapter(algo_group)
if adapter_instance is not None and hasattr(adapter_instance,
'available_algorithms'):
template_specification['available_metrics'] = [
metric_name for metric_name in
adapter_instance.available_algorithms.keys()
]
else:
template_specification['available_metrics'] = []
template_specification[base.KEY_PARAMETERS_CONFIG] = False
template_specification[base.KEY_SECTION] = 'burst'
return self.fill_default_attributes(template_specification)
def _compute_operation_details(self, entity_gid, is_group=False):
"""
Returns a dictionary which contains the details for the given operation.
"""
selected_project = bc.get_current_project()
op_details = self.project_service.get_operation_details(
entity_gid, is_group)
operation_id = op_details.operation_id
display_reload_btn = True
operation = self.flow_service.load_operation(operation_id)
if (operation.fk_operation_group is not None) or (operation.burst
is not None):
display_reload_btn = False
else:
op_categ_id = operation.algorithm.algo_group.fk_category
raw_categories = self.flow_service.get_raw_categories()
for category in raw_categories:
if category.id == op_categ_id:
display_reload_btn = False
break
template_specification = dict()
template_specification["entity_gid"] = entity_gid
template_specification["nodeFields"] = op_details.get_ui_fields()
template_specification["operationId"] = operation_id
template_specification["displayReloadBtn"] = display_reload_btn
template_specification["project"] = selected_project
template_specification["isRelevant"] = operation.visible
return template_specification
def launch_burst(self, launch_mode, burst_name, **data):
"""
Do the actual burst launch, using the configuration saved in current session.
:param launch_mode: new/branch/continue
:param burst_name: user-given burst name. It can be empty (case in which we will fill with simulation_x)
:param data: kwargs for simulation input parameters.
"""
burst_config = base.get_from_session(base.KEY_BURST_CONFIG)
## Validate new burst-name
if burst_name != 'none_undefined':
self._validate_burst_name(burst_name)
burst_config.name = burst_name
## Fill all parameters
user_id = base.get_logged_user().id
data[base.KEY_ADAPTER] = self.cached_simulator_algorithm_id
burst_config.update_simulator_configuration(data)
burst_config.fk_project = base.get_current_project().id
## Do the asynchronous launch
burst_id, burst_name = self.burst_service.launch_burst(
burst_config, 0, self.cached_simulator_algorithm_id, user_id,
launch_mode)
return [burst_id, burst_name]
def get_available_selections(self, **data):
"""
Get all the saved selections for the current project and return
the ones that are compatible with the received connectivity labels.
"""
curent_project = base.get_current_project()
connectivity_gid = data['connectivity_gid']
selections = self.flow_service.get_selections_for_project(
curent_project.id, connectivity_gid)
default_selection = data['con_selection']
if not len(default_selection) > 0:
default_selection = data['con_labels']
nodes, ids, names = [], [], []
for selection in selections:
ids.append(selection.id)
labels = json.loads(selection.labels)
selected_labels = ''
for idx in json.loads(selection.selected_nodes):
selected_labels += labels[idx] + ','
nodes.append(selected_labels[:-1])
names.append(selection.ui_name)
result = dict(selection_nodes=nodes,
selection_names=names,
selection_ids=ids,
all_labels=default_selection,
new_selection_name=self.NEW_SELECTION_NAME)
return self.fill_default_attributes(result)
def get_portlet_configurable_interface(self, index_in_tab):
"""
From the position given by the tab index and the index from that tab,
get the portlet configuration and build the configurable interface
for that portlet.
"""
burst_config = base.get_from_session(base.KEY_BURST_CONFIG)
tab_index = burst_config.selected_tab
portlet_config = burst_config.tabs[tab_index].portlets[int(
index_in_tab)]
portlet_interface = self.burst_service.build_portlet_interface(
portlet_config,
base.get_current_project().id)
full_portlet_input_tree = []
for entry in portlet_interface:
full_portlet_input_tree.extend(entry.interface)
self.context.add_portlet_to_session(full_portlet_input_tree)
portlet_interface = {
"adapters_list": portlet_interface,
base.KEY_PARAMETERS_CONFIG: False,
base.KEY_SESSION_TREE: self.context.KEY_PORTLET_CONFIGURATION
}
return self.fill_default_attributes(portlet_interface)
def reset_burst(self):
"""
Called when click on "New Burst" entry happens from UI.
This will generate an empty new Burst Configuration.
"""
new_burst = self.burst_service.new_burst_configuration(base.get_current_project().id)
base.add2session(base.KEY_BURST_CONFIG, new_burst)
def invokeadaptermethod(self, adapter_id, method_name, **data):
"""
Public web method, to be used when invoking specific
methods from external Adapters/Algorithms.
"""
algo_group = self.flow_service.get_algo_group_by_identifier(adapter_id)
try:
adapter_instance = self.flow_service.build_adapter_instance(
algo_group)
result = self.flow_service.fire_operation(
adapter_instance, base.get_logged_user(),
base.get_current_project().id, method_name, **data)
base.set_info_message("Submit OK!")
if isinstance(adapter_instance, ABCDisplayer) and isinstance(
result, dict):
base.remove_from_session(base.KEY_MESSAGE)
result[ABCDisplayer.KEY_IS_ADAPTER] = True
result[base.KEY_DISPLAY_MENU] = True
result[base.KEY_OPERATION_ID] = adapter_instance.operation_id
result[base.KEY_ADAPTER] = adapter_id
if KEY_CONTROLLS not in result:
result[KEY_CONTROLLS] = None
return self.fill_default_attributes(result, algo_group)
except OperationException, excep:
base.set_warning_message('Problem when submitting data!')
self.logger.error(
"Invalid method, or wrong parameters when invoking external method on post!"
)
self.logger.exception(excep)
def load_burst_history(self):
"""
Load the available burst that are stored in the database at this time.
This is one alternative to 'chrome-back problem'.
"""
session_burst = base.get_from_session(base.KEY_BURST_CONFIG)
return {'burst_list': self.burst_service.get_available_bursts(base.get_current_project().id),
'selectedBurst': session_burst.id}
def storeresultfigure(self, img_type, operation_id, **data):
"""Create preview for current displayed canvas and
store image in current session, for future comparison."""
project = base.get_current_project()
user = base.get_logged_user()
self.figure_service.store_result_figure(project, user, img_type,
operation_id,
data['export_data'])
def index(self):
"""
Display project main-menu. Choose one project to work with.
"""
current_project = bc.get_current_project()
if current_project is None:
raise cherrypy.HTTPRedirect("/project/viewall")
template_specification = dict(mainContent="project_submenu",
title="TVB Project Menu")
return self.fill_default_attributes(template_specification)
def cached_simulator_input_tree(self):
"""
Cache Simulator's input tree, for performance issues.
Anyway, without restart, the introspected tree will not be different on multiple executions.
:return: Simulator's Input Tree (copy from cache or just loaded)
"""
if self._cached_simulator_input_tree is None:
self._cached_simulator_input_tree = self.flow_service.prepare_adapter(base.get_current_project().id,
self.cached_simulator_algo_group)[1]
return copy.deepcopy(self._cached_simulator_input_tree)
def prepare_group_launch(self, group_gid, step_key, adapter_key, **data):
"""
Recieves 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['range_param_name']
del data['range_param_name']
data[PARAM_RANGE_1] = range_param_name
data[range_param_name] = ','.join([dt.gid for dt in datatypes])
OperationService().group_operation_launch(
base.get_logged_user().id,
base.get_current_project().id, int(adapter_key), int(step_key),
**data)
redirect_url = self._compute_back_link('operations',
base.get_current_project())
raise cherrypy.HTTPRedirect(redirect_url)
def _persist_project(self, data, project_id, is_create, current_user):
"""Private method to persist"""
data = EditForm().to_python(data)
saved_project = self.project_service.store_project(
current_user, is_create, project_id, **data)
selected_project = bc.get_current_project()
if len(
self.project_service.retrieve_projects_for_user(
current_user.id, 1)) == 1:
selected_project = saved_project
if selected_project is None or (saved_project.id
== selected_project.id):
self._mark_selected(saved_project)
def get_simple_adapter_interface(self,
algo_group_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 = base.get_current_project()
is_uploader = string2bool(is_uploader)
template_specification = self.get_adapter_template(
curent_project.id, algo_group_id, is_uploader)
template_specification[base.KEY_PARENT_DIV] = parent_div
return self.fill_default_attributes(template_specification)
def start_dti_pipeline(self, cancel=False, start=False, **data):
"""
Prepare DTI Pipeline run.
"""
project_id = basecontroller.get_current_project().id
if cherrypy.request.method == 'POST' and cancel:
raise cherrypy.HTTPRedirect("/project/editstructure/" +
str(project_id))
template_specification = dict(
title="Import Connectivity",
data=data,
section_name='project',
subsection_name='pipeline',
mainContent="pipeline/get_connectivity",
includedResources='project/included_resources')
if cherrypy.request.method == 'POST' and start:
form = ImportForm()
try:
data = form.to_python(data)
service = DTIPipelineService(data['server_ip'],
data['username'])
current_project = basecontroller.get_current_project()
current_user = basecontroller.get_logged_user()
service.fire_pipeline(data['dti_scans'], current_project,
current_user, data['threads_number'])
okmessage = "Import Started! You will see results after few hours on Data Structure Page!"
basecontroller.set_info_message(okmessage)
raise cherrypy.HTTPRedirect("/project/editstructure/" +
str(project_id))
except formencode.Invalid, excep:
basecontroller.set_error_message(
"Some parameters are invalid!")
template_specification[
basecontroller.KEY_ERRORS] = excep.unpack_errors()
def cached_simulator_input_tree(self):
"""
Cache Simulator's input tree, for performance issues.
Anyway, without restart, the introspected tree will not be different on multiple executions.
:returns: Simulator's Input Tree (copy from cache or just loaded)
"""
cached_simulator_tree = base.get_from_session(
base.KEY_CACHED_SIMULATOR_TREE)
if cached_simulator_tree is None:
cached_simulator_tree = self.flow_service.prepare_adapter(
base.get_current_project().id,
self.cached_simulator_algo_group)[1]
base.add2session(base.KEY_CACHED_SIMULATOR_TREE,
cached_simulator_tree)
return copy.deepcopy(cached_simulator_tree)
def get_select_existent_entities(self, label, entity_type, entity_gid=None):
"""
Returns the dictionary needed for drawing the select which display all
the created entities of the specified type.
"""
project_id = base.get_current_project().id
category = self.flow_service.get_visualisers_category()
interface = [{'name': 'existentEntitiesSelect', 'label': label, 'type': entity_type}]
if entity_gid is not None:
interface[0]['default'] = entity_gid
interface = self.flow_service.prepare_parameters(interface, project_id, category.id)
interface = ABCAdapter.prepare_param_names(interface)
return interface
def downloaddata(self, data_gid, export_module):
""" Export the data to a default path of TVB_STORAGE/PROJECTS/project_name """
current_prj = bc.get_current_project()
# Load data by GID
entity = ABCAdapter.load_entity_by_gid(data_gid)
# Do real export
export_mng = ExportManager()
file_name, file_path, delete_file = export_mng.export_data(
entity, export_module, current_prj)
if delete_file:
# We force parent folder deletion because export process generated it.
self.mark_file_for_delete(file_path, True)
self.logger.debug("Data exported in file: " + str(file_path))
return serve_file(file_path, "application/x-download", "attachment",
file_name)
def create_stimulus(self):
"""
Creates a stimulus from the given data.
"""
try:
context = base.get_from_session(KEY_SURFACE_CONTEXT)
surface_stimulus_creator = self.get_creator_and_interface(SURFACE_STIMULUS_CREATOR_MODULE,
SURFACE_STIMULUS_CREATOR_CLASS, StimuliSurface())[0]
self.flow_service.fire_operation(surface_stimulus_creator, base.get_logged_user(),
base.get_current_project().id, **context.equation_kwargs)
base.set_info_message("The operation for creating the stimulus was successfully launched.")
context.selected_stimulus = None
except (NameError, ValueError, SyntaxError), _:
base.set_error_message("The operation failed due to invalid parameter input.")
return False
def create_local_connectivity(self, **kwargs):
"""
Used for creating and storing a local connectivity.
"""
context = base.get_from_session(KEY_LCONN_CONTEXT)
local_connectivity_creator = self.get_creator_and_interface(
LOCAL_CONN_CREATOR_MODULE, LOCAL_CONN_CREATOR_CLASS,
LocalConnectivity())[0]
self.flow_service.fire_operation(local_connectivity_creator,
base.get_logged_user(),
base.get_current_project().id,
**kwargs)
base.set_info_message(
"The operation for creating the local connectivity was successfully launched."
)
context.reset()
return self.step_1()
def create_stimulus(self):
"""
Creates a stimulus from the given data.
"""
context = base.get_from_session(KEY_REGION_CONTEXT)
local_connectivity_creator = self.get_creator_and_interface(
REGION_STIMULUS_CREATOR_MODULE, REGION_STIMULUS_CREATOR_CLASS,
StimuliRegion())[0]
context.equation_kwargs.update(
{'weight': json.dumps(context.get_weights())})
self.flow_service.fire_operation(local_connectivity_creator,
base.get_logged_user(),
base.get_current_project().id,
**context.equation_kwargs)
base.set_info_message(
"The operation for creating the stimulus was successfully launched."
)
def displayresultfigures(self, selected_session='all_sessions'):
""" Collect and display saved previews, grouped by session."""
project = base.get_current_project()
user = base.get_logged_user()
data, all_sessions_info = self.figure_service.retrieve_result_figures(
project, user, selected_session)
manage_figure_title = "Figures for " + str(
selected_session) + " category"
if selected_session == 'all_sessions':
manage_figure_title = "Figures for all categories"
template_specification = dict(mainContent="project/figures_display",
title="Stored Visualizer Previews",
controlPage=None,
displayControl=False,
selected_sessions_data=data,
all_sessions_info=all_sessions_info,
selected_session=selected_session,
manageFigureTitle=manage_figure_title)
template_specification = self.fill_default_attributes(
template_specification, subsection='figures')
return template_specification
def readprojectsforlink(self, data_id, return_both=False):
""" For a given user return a dictionary in form {project_ID: project_Name}. """
for_link, linked = self.project_service.get_linkable_projects_for_user(
bc.get_logged_user().id, data_id)
to_link_result, linked_result = None, None
current_project = bc.get_current_project()
if for_link:
to_link_result = {}
for project in for_link:
if project.id != current_project.id:
to_link_result[project.id] = project.name
to_link_result = json.dumps(to_link_result)
if return_both:
if linked:
linked_result = {}
for project in linked:
linked_result[project.id] = project.name
return to_link_result, linked_result
return to_link_result
def store_connectivity_selection(self, ui_name, **data):
"""
Save the passed connectivity selection. Since cherryPy/Ajax seems to
have problems when passing arrays, the data is passed as a string
that needs to be split.
"""
if ui_name and ui_name != self.NEW_SELECTION_NAME:
sel_project_id = base.get_current_project().id
selection = data['selection']
labels = data['labels']
#We need to split as cherryPy/AJAX doesn't support lists
used_names = data['select_names'].split(',')
selection = json.dumps([int(idx) for idx in selection.split(',')])
labels = json.dumps(labels.split(','))
self.flow_service.save_connectivity_selection(
ui_name, sel_project_id, selection, labels, used_names)
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]
def default(self,
step_key,
adapter_key,
cancel=False,
back_page=None,
not_reset=False,
**data):
"""
Render a specific adapter.
'data' are arguments for POST
"""
project = base.get_current_project()
algo_group = self.flow_service.get_algo_group_by_identifier(
adapter_key)
back_page_link = self._compute_back_link(back_page, project)
if algo_group 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)
if cherrypy.request.method == 'POST':
back_indicator = back_page if back_page == 'burst' else 'operations'
success_url = self._compute_back_link(back_indicator, project)
data[base.KEY_ADAPTER] = adapter_key
template_specification = self.execute_post(project.id, submit_link,
success_url, step_key,
algo_group, **data)
else:
if (('Referer' not in cherrypy.request.headers or
('Referer' in cherrypy.request.headers
and 'step' not in cherrypy.request.headers['Referer']))
and 'View' in algo_group.group_category.displayname):
# Avoid reset in case of Visualizers, as a supplementary GET
# might be enforced by MPLH5 on FF.
not_reset = True
template_specification = self.get_template_for_adapter(
project.id, step_key, algo_group, submit_link, not not_reset)
if template_specification is None:
raise cherrypy.HTTPRedirect('/tvb')
if KEY_CONTROLLS not in template_specification:
template_specification[KEY_CONTROLLS] = None
if base.KEY_SUBMIT_LINK not in template_specification:
template_specification[base.KEY_SUBMIT_LINK] = submit_link
if KEY_CONTENT not in template_specification:
template_specification[KEY_CONTENT] = "flow/full_adapter_interface"
template_specification[base.KEY_DISPLAY_MENU] = False
else:
template_specification[base.KEY_DISPLAY_MENU] = True
template_specification[base.KEY_BACK_PAGE] = back_page_link
template_specification[base.KEY_ADAPTER] = adapter_key
template_specification[ABCDisplayer.KEY_IS_ADAPTER] = True
self.fill_default_attributes(template_specification, algo_group)
if (back_page is not None and back_page in ['operations', 'data']
and not (base.KEY_SECTION in template_specification
and template_specification[base.KEY_SECTION]
== 'connectivity')):
template_specification[base.KEY_SECTION] = 'project'
return template_specification
def create_json(self, item_gid, item_type, visibility_filter):
"""
Method used for creating a JSON representation of a graph.
"""
selected_filter = StaticFiltersFactory.build_datatype_filters(
single_filter=visibility_filter)
graph_branches = []
project = bc.get_current_project()
is_upload_operation = (item_type == graph_structures.NODE_OPERATION_TYPE) and \
(self.project_service.is_upload_operation(item_gid) or item_gid == "firstOperation")
if is_upload_operation:
uploader_operations = self.project_service.get_all_operations_for_uploaders(
project.id)
for operation in uploader_operations:
dt_outputs = self.project_service.get_results_for_operation(
operation.id, selected_filter)
dt_outputs = self._create_datatype_nodes(dt_outputs)
parent_op = self._create_operation_nodes([operation], item_gid)
branch = graph_structures.GraphBranch([], parent_op,
dt_outputs, [])
graph_branches.append(branch)
graph = graph_structures.GraphStructure(graph_branches)
return graph.to_json()
dt_inputs, parent_op, dt_outputs, op_inputs = [], [], [], []
if item_type == graph_structures.NODE_OPERATION_TYPE:
dt_inputs = ProjectService.get_datatype_and_datatypegroup_inputs_for_operation(
item_gid, selected_filter)
parent_op = self.project_service.load_operation_by_gid(item_gid)
dt_outputs = self.project_service.get_results_for_operation(
parent_op.id, selected_filter)
#create graph nodes
dt_inputs, parent_op, dt_outputs, op_inputs = self._create_nodes(
dt_inputs, [parent_op], dt_outputs, [], item_gid)
elif item_type == graph_structures.NODE_OPERATION_GROUP_TYPE:
parent_op_group = self.project_service.get_operation_group_by_gid(
item_gid)
dt_inputs = self.project_service.get_datatypes_inputs_for_operation_group(
parent_op_group.id, selected_filter)
datatype_group = self.project_service.get_datatypegroup_by_op_group_id(
parent_op_group.id)
datatype = self.project_service.get_datatype_by_id(
datatype_group.id)
dt_inputs = self._create_datatype_nodes(dt_inputs)
parent_op = graph_structures.OperationGroupNodeStructure(
parent_op_group.gid)
parent_op.selected = True
parent_op = [parent_op]
if selected_filter.display_name == StaticFiltersFactory.RELEVANT_VIEW and datatype.visible is False:
dt_outputs = []
else:
dt_outputs = self._create_datatype_nodes([datatype])
elif item_type == graph_structures.NODE_DATATYPE_TYPE:
selected_dt = ABCAdapter.load_entity_by_gid(item_gid)
if self.project_service.is_datatype_group(item_gid):
datatype_group = self.project_service.get_datatypegroup_by_gid(
selected_dt.gid)
parent_op_group = self.project_service.get_operation_group_by_id(
datatype_group.fk_operation_group)
dt_inputs = self.project_service.get_datatypes_inputs_for_operation_group(
parent_op_group.id, selected_filter)
op_inputs = self.project_service.get_operations_for_datatype_group(
selected_dt.id, selected_filter)
op_inputs_in_groups = self.project_service.get_operations_for_datatype_group(
selected_dt.id, selected_filter, only_in_groups=True)
#create graph nodes
dt_inputs, parent_op, dt_outputs, op_inputs = self._create_nodes(
dt_inputs, [], [selected_dt], op_inputs, item_gid)
parent_op = [
graph_structures.OperationGroupNodeStructure(
parent_op_group.gid)
]
op_inputs_in_groups = self._create_operation_group_nodes(
op_inputs_in_groups)
op_inputs.extend(op_inputs_in_groups)
else:
parent_op = self.flow_service.load_operation(
selected_dt.fk_from_operation)
dt_inputs = ProjectService.get_datatype_and_datatypegroup_inputs_for_operation(
parent_op.gid, selected_filter)
op_inputs = self.project_service.get_operations_for_datatype(
selected_dt.gid, selected_filter)
op_inputs_in_groups = self.project_service.get_operations_for_datatype(
selected_dt.gid, selected_filter, only_in_groups=True)
dt_outputs = self.project_service.get_results_for_operation(
parent_op.id, selected_filter)
#create graph nodes
dt_inputs, parent_op, dt_outputs, op_inputs = self._create_nodes(
dt_inputs, [parent_op], dt_outputs, op_inputs, item_gid)
op_inputs_in_groups = self._create_operation_group_nodes(
op_inputs_in_groups)
op_inputs.extend(op_inputs_in_groups)
else:
self.logger.error("Invalid item type: " + str(item_type))
raise Exception("Invalid item type.")
branch = graph_structures.GraphBranch(dt_inputs, parent_op, dt_outputs,
op_inputs)
graph_branches.append(branch)
graph = graph_structures.GraphStructure(graph_branches)
return graph.to_json()
class FlowController(base.BaseController):
"""
This class takes care of executing steps in projects.
"""
def __init__(self):
base.BaseController.__init__(self)
self.context = SelectedAdapterContext()
self.files_helper = FilesHelper()
@cherrypy.expose
@using_template('base_template')
@logged()
@base.settings()
@context_selected()
def step(self, step_key=None):
"""
Choose exact action/adapter for current step.
"""
category = self.flow_service.get_category_by_id(step_key)
if category is None:
message = 'Inconsistent Step Name! Please excuse the wrong link!'
base.set_warning_message(message)
self.logger.warning(message + '- Wrong step:' + str(step_key))
raise cherrypy.HTTPRedirect('/tvb')
step_name = category.displayname.lower()
template_specification = dict(mainContent="header_menu",
section_name=step_name,
controlPage=None,
title="Select an algorithm",
displayControl=False)
adapters_list = []
for algo_group in self.flow_service.get_groups_for_categories(
[category]):
if algo_group.ui_display < 0:
continue
adapter_link = self.get_url_adapter(step_key, algo_group.id)
adapters_list.append({
base.KEY_TITLE: algo_group.displayname,
'link': adapter_link,
'description': algo_group.description,
'subsection': algo_group.subsection_name
})
self.analyze_adapters = adapters_list
template_specification[base.KEY_SUBMENU_LIST] = adapters_list
return self.fill_default_attributes(template_specification)
@cherrypy.expose
@using_template('base_template')
@base.settings()
@logged()
@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
@cherrypy.expose
@base.settings()
@logged()
@context_selected()
@using_template('base_template')
def prepare_group_launch(self, group_gid, step_key, adapter_key, **data):
"""
Recieves 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['range_param_name']
del data['range_param_name']
data[PARAM_RANGE_1] = range_param_name
data[range_param_name] = ','.join([dt.gid for dt in datatypes])
OperationService().group_operation_launch(
base.get_logged_user().id,
base.get_current_project().id, int(adapter_key), int(step_key),
**data)
redirect_url = self._compute_back_link('operations',
base.get_current_project())
raise cherrypy.HTTPRedirect(redirect_url)
@cherrypy.expose
@using_template('base_template')
@base.settings()
@logged()
@context_selected()
def default(self,
step_key,
adapter_key,
cancel=False,
back_page=None,
not_reset=False,
**data):
"""
Render a specific adapter.
'data' are arguments for POST
"""
project = base.get_current_project()
algo_group = self.flow_service.get_algo_group_by_identifier(
adapter_key)
back_page_link = self._compute_back_link(back_page, project)
if algo_group 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)
if cherrypy.request.method == 'POST':
back_indicator = back_page if back_page == 'burst' else 'operations'
success_url = self._compute_back_link(back_indicator, project)
data[base.KEY_ADAPTER] = adapter_key
template_specification = self.execute_post(project.id, submit_link,
success_url, step_key,
algo_group, **data)
else:
if (('Referer' not in cherrypy.request.headers or
('Referer' in cherrypy.request.headers
and 'step' not in cherrypy.request.headers['Referer']))
and 'View' in algo_group.group_category.displayname):
# Avoid reset in case of Visualizers, as a supplementary GET
# might be enforced by MPLH5 on FF.
not_reset = True
template_specification = self.get_template_for_adapter(
project.id, step_key, algo_group, submit_link, not not_reset)
if template_specification is None:
raise cherrypy.HTTPRedirect('/tvb')
if KEY_CONTROLLS not in template_specification:
template_specification[KEY_CONTROLLS] = None
if base.KEY_SUBMIT_LINK not in template_specification:
template_specification[base.KEY_SUBMIT_LINK] = submit_link
if KEY_CONTENT not in template_specification:
template_specification[KEY_CONTENT] = "flow/full_adapter_interface"
template_specification[base.KEY_DISPLAY_MENU] = False
else:
template_specification[base.KEY_DISPLAY_MENU] = True
template_specification[base.KEY_BACK_PAGE] = back_page_link
template_specification[base.KEY_ADAPTER] = adapter_key
template_specification[ABCDisplayer.KEY_IS_ADAPTER] = True
self.fill_default_attributes(template_specification, algo_group)
if (back_page is not None and back_page in ['operations', 'data']
and not (base.KEY_SECTION in template_specification
and template_specification[base.KEY_SECTION]
== 'connectivity')):
template_specification[base.KEY_SECTION] = 'project'
return template_specification
@cherrypy.expose
@using_template("flow/reduce_dimension_select")
@logged()
def gettemplatefordimensionselect(self,
entity_gid=None,
select_name="",
reset_session='False',
parameters_prefix="dimensions",
required_dimension=1,
expected_shape="",
operations=""):
"""
Returns the HTML which contains the selects components which allows the user
to reduce the dimension of a multi-dimensional array.
We try to obtain the aggregation_functions from the entity, which is a list of lists.
For each dimension should be a list with the supported aggregation functions. We
create a DICT for each of those lists. The key will be the name of the function and
the value will be its label.
entity_gid - the GID of the entity for which is displayed the component
select_name - the name of the parent select. The select in which
is displayed the entity with the given GID
parameters_prefix - a string which will be used for computing the names of the component
required_dimension - the expected dimension for the resulted array
expected_shape and operations - used for applying conditions on the resulted array
e.g.: If the resulted array is a 3D array and we want that the length of the second
dimension to be smaller then 512 then the expected_shape and operations should be:
expected_shape='x,512,x' and operations='x,<,x'
"""
template_params = dict()
template_params["select_name"] = ""
template_params["data"] = []
template_params["parameters_prefix"] = parameters_prefix
template_params["array_shape"] = ""
template_params["required_dimension"] = required_dimension
template_params["currentDim"] = ""
template_params["required_dim_msg"] = ""
template_params["expected_shape"] = expected_shape
template_params["operations"] = operations
#if reload => populate the selected values
session_dict = self.context.get_current_default()
dimensions = {1: [0], 3: [0]}
selected_agg_functions = {}
if not eval(str(reset_session)) and session_dict is not None:
starts_with_str = select_name + "_" + parameters_prefix + "_"
ui_sel_items = dict((k, v) for k, v in session_dict.items()
if k.startswith(starts_with_str))
dimensions, selected_agg_functions, required_dimension, _ = MappedArray(
).parse_selected_items(ui_sel_items)
template_params["selected_items"] = dimensions
template_params["selected_functions"] = selected_agg_functions
aggregation_functions = []
default_agg_functions = self.accepted__aggregation_functions()
labels_set = ["Time", "Channel", "Line"]
if entity_gid is not None:
actual_entity = ABCAdapter.load_entity_by_gid(entity_gid)
if hasattr(actual_entity, 'shape'):
array_shape = actual_entity.shape
new_shape, current_dim = self._compute_current_dimension(
list(array_shape), dimensions, selected_agg_functions)
if required_dimension is not None and current_dim != int(
required_dimension):
template_params[
"required_dim_msg"] = "Please select a " + str(
required_dimension) + "D array"
if not current_dim:
template_params["currentDim"] = "1 element"
else:
template_params["currentDim"] = str(
current_dim) + "D array"
template_params["array_shape"] = json.dumps(new_shape)
if hasattr(actual_entity, 'dimensions_labels'
) and actual_entity.dimensions_labels is not None:
labels_set = actual_entity.dimensions_labels
#make sure there exists labels for each dimension
while len(labels_set) < len(array_shape):
labels_set.append("Undefined")
if (hasattr(actual_entity, 'aggregation_functions')
and actual_entity.aggregation_functions is not None
and len(actual_entity.aggregation_functions)
== len(array_shape)):
#will be a list of lists of aggregation functions
defined_functions = actual_entity.aggregation_functions
for function in defined_functions:
if not len(function):
aggregation_functions.append({})
else:
func_dict = dict()
for function_key in function:
func_dict[
function_key] = default_agg_functions[
function_key]
aggregation_functions.append(func_dict)
else:
for _ in array_shape:
aggregation_functions.append(default_agg_functions)
result = []
for i, shape in enumerate(array_shape):
labels = []
values = []
for j in xrange(shape):
labels.append(labels_set[i] + " " + str(j))
values.append(entity_gid + "_" + str(i) + "_" + str(j))
result.append([labels, values, aggregation_functions[i]])
template_params["select_name"] = select_name
template_params["data"] = result
return template_params
return template_params
@staticmethod
def _compute_current_dimension(array_shape, selected_items,
selected_functions):
"""
If the user reloads an operation we have to compute the current dimension of the array
and also the shape of the array based on his selections
"""
current_dim = len(array_shape)
for i in xrange(len(array_shape)):
if i in selected_items and len(selected_items[i]) > 0:
array_shape[i] = len(selected_items[i])
if len(selected_items[i]) == 1:
current_dim -= 1
if i in selected_functions and selected_functions[i] != 'none':
array_shape[i] = 1
if i not in selected_items or len(selected_items[i]) > 1:
current_dim -= 1
return array_shape, current_dim
@staticmethod
def accepted__aggregation_functions():
"""
Returns the list of aggregation functions that may be
applied on arrays.
"""
return {"sum": "Sum", "average": "Average"}
@cherrypy.expose
@using_template("flow/type2component/datatype2select_simple")
@logged()
def getfiltereddatatypes(self, name, parent_div, tree_session_key,
filters):
"""
Given the name from the input tree, the dataType required and a number of
filters, return the available dataType that satisfy the conditions imposed.
"""
previous_tree = self.context.get_session_tree_for_key(tree_session_key)
if previous_tree is None:
base.set_error_message(
"Adapter Interface not in session for filtering!")
raise cherrypy.HTTPRedirect("/tvb?error=True")
current_node = self._get_node(previous_tree, name)
if current_node is None:
raise Exception("Could not find node :" + name)
datatype = current_node[ABCAdapter.KEY_DATATYPE]
filters = json.loads(filters)
availablefilter = json.loads(
FilterChain.get_filters_for_type(datatype))
for i, filter_ in enumerate(filters[FILTER_FIELDS]):
#Check for filter input of type 'date' as these need to be converted
if filter_ in availablefilter and availablefilter[filter_][
FILTER_TYPE] == 'date':
try:
filter_ = string2date(filter_, False)
filters[FILTER_VALUES][i] = filter_
except ValueError, excep:
raise excep
#In order for the filter object not to "stack up" on multiple calls to
#this method, create a deepCopy to work with
if ABCAdapter.KEY_CONDITION in current_node:
new_filter = copy.deepcopy(current_node[ABCAdapter.KEY_CONDITION])
else:
new_filter = FilterChain()
new_filter.fields.extend(filters[FILTER_FIELDS])
new_filter.operations.extend(filters[FILTER_OPERATIONS])
new_filter.values.extend(filters[FILTER_VALUES])
#Get dataTypes that match the filters from DB then populate with values
datatypes = self.flow_service.get_available_datatypes(
base.get_current_project().id, datatype, new_filter)
values = self.flow_service.populate_values(
datatypes, datatype, self.context.get_current_step())
#Create a dictionary that matches what the template expects
parameters = dict()
parameters[ABCAdapter.KEY_NAME] = name
if ABCAdapter.KEY_REQUIRED in current_node:
parameters[ABCAdapter.KEY_REQUIRED] = current_node[
ABCAdapter.KEY_REQUIRED]
if len(values) > 0 and eval(
str(parameters[ABCAdapter.KEY_REQUIRED])):
parameters[ABCAdapter.KEY_DEFAULT] = str(
values[-1][ABCAdapter.KEY_VALUE])
previous_selected = self.context.get_current_default(name)
if previous_selected is not None and previous_selected in [
str(vv['value']) for vv in values
]:
parameters[ABCAdapter.KEY_DEFAULT] = previous_selected
parameters[ABCAdapter.KEY_FILTERABLE] = availablefilter
parameters[ABCAdapter.KEY_TYPE] = ABCAdapter.TYPE_SELECT
parameters[ABCAdapter.KEY_OPTIONS] = values
parameters[ABCAdapter.KEY_DATATYPE] = datatype
template_specification = {
"inputRow": parameters,
"disabled": False,
"parentDivId": parent_div,
base.KEY_SESSION_TREE: tree_session_key
}
return self.fill_default_attributes(template_specification)
def get_datatype_details(self,
entity_gid,
back_page='burst',
exclude_tabs=None):
"""
Returns the HTML which contains the details for the given dataType.
"""
if exclude_tabs is None:
exclude_tabs = []
selected_project = bc.get_current_project()
datatype_details, states, entity = self.project_service.get_datatype_details(
entity_gid)
### Load DataType categories
current_type = datatype_details.data_type
datatype_gid = datatype_details.gid
categories = {}
if not entity.invalid:
categories = self.getalgorithmsfordatatype(str(current_type),
str(datatype_gid))
categories = json.loads(categories)
datatype_id = datatype_details.data_type_id
is_group = False
if datatype_details.operation_group_id is not None:
## Is a DataTypeGroup
datatype_id = datatype_details.operation_group_id
is_group = True
### Retrieve links
linkable_projects_dict = self._get_linkable_projects_dict(datatype_id)
### Load all exporters
exporters = {}
if not entity.invalid:
exporters = ExportManager().get_exporters_for_data(entity)
is_relevant = entity.visible
template_specification = dict()
template_specification["entity_gid"] = entity_gid
template_specification["nodeFields"] = datatype_details.get_ui_fields()
template_specification["allStates"] = states
template_specification["project"] = selected_project
template_specification["categories"] = categories
template_specification["exporters"] = exporters
template_specification["datatype_id"] = datatype_id
template_specification["isGroup"] = is_group
template_specification["isRelevant"] = is_relevant
template_specification["nodeType"] = 'datatype'
template_specification["backPageIdentifier"] = back_page
template_specification.update(linkable_projects_dict)
overlay_class = "can-browse editor-node node-type-" + str(
current_type).lower()
if is_relevant:
overlay_class += " node-relevant"
else:
overlay_class += " node_irrelevant"
overlay_title = current_type
if datatype_details.datatype_tag_1:
overlay_title += " " + datatype_details.datatype_tag_1
tabs = []
overlay_indexes = []
if "Metadata" not in exclude_tabs:
tabs.append(OverlayTabDefinition("Metadata", "metadata"))
overlay_indexes.append(0)
if "Analyzers" not in exclude_tabs:
tabs.append(
OverlayTabDefinition("Analyzers",
"analyzers",
enabled=categories
and 'Analyze' in categories))
overlay_indexes.append(1)
if "Visualizers" not in exclude_tabs:
tabs.append(
OverlayTabDefinition("Visualizers",
"visualizers",
enabled=categories
and 'View' in categories))
overlay_indexes.append(2)
enable_link_tab = False
if (not entity.invalid) and (linkable_projects_dict is not None):
if self.PRROJECTS_FOR_LINK_KEY in linkable_projects_dict:
projects_for_link = linkable_projects_dict[
self.PRROJECTS_FOR_LINK_KEY]
if projects_for_link is not None and len(
projects_for_link) > 0:
enable_link_tab = True
if self.PRROJECTS_LINKED_KEY in linkable_projects_dict:
projects_linked = linkable_projects_dict[
self.PRROJECTS_LINKED_KEY]
if projects_linked is not None and len(projects_linked) > 0:
enable_link_tab = True
if "Links" not in exclude_tabs:
tabs.append(
OverlayTabDefinition("Links",
"link_to",
enabled=enable_link_tab))
overlay_indexes.append(3)
if "Export" not in exclude_tabs:
tabs.append(
OverlayTabDefinition("Export",
"export",
enabled=(exporters
and len(exporters) > 0)))
overlay_indexes.append(4)
if "Resulted Datatypes" not in exclude_tabs:
tabs.append(
OverlayTabDefinition(
"Resulted Datatypes",
"result_dts",
enabled=self.project_service.
count_datatypes_generated_from(entity_gid)))
overlay_indexes.append(5)
template_specification = self.fill_overlay_attributes(
template_specification, "DataType Details", overlay_title,
"project/details_datatype_overlay", overlay_class, tabs,
overlay_indexes)
template_specification['baseUrl'] = cfg.BASE_URL
#template_specification[bc.KEY_OVERLAY_PAGINATION] = True
#template_specification[bc.KEY_OVERLAY_PREVIOUS] = "alert(1);"
#template_specification[bc.KEY_OVERLAY_NEXT] = "alert(2);"
return FlowController().fill_default_attributes(template_specification)
data[upload_param],
bc.get_logged_user().id)
except ServicesBaseException, excep:
self.logger.warning(excep.message)
bc.set_error_message(excep.message)
raise cherrypy.HTTPRedirect('/project/viewall')
def _remove_project(self, project_id):
"""Private method for removing project."""
try:
self.project_service.remove_project(project_id)
except ServicesBaseException, exc:
self.logger.error("Could not delete project!")
self.logger.exception(exc)
bc.set_error_message(exc.message)
prj = bc.get_current_project()
if prj is not None and prj.id == int(project_id):
bc.remove_from_session(bc.KEY_PROJECT)
def _persist_project(self, data, project_id, is_create, current_user):
"""Private method to persist"""
data = EditForm().to_python(data)
saved_project = self.project_service.store_project(
current_user, is_create, project_id, **data)
selected_project = bc.get_current_project()
if len(
self.project_service.retrieve_projects_for_user(
current_user.id, 1)) == 1:
selected_project = saved_project
if selected_project is None or (saved_project.id
== selected_project.id):