# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Framework Package. This package holds all Data Management, and
# Web-UI helpful to run brain-simulations. To use it, you also need to download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also http://www.thevirtualbrain.org
#
# (c) 2012-2023, Baycrest Centre for Geriatric Care ("Baycrest") and others
#
# This program is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software Foundation,
# either version 3 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE. See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this
# program. If not, see <http://www.gnu.org/licenses/>.
#
#
# CITATION:
# When using The Virtual Brain for scientific publications, please cite it as explained here:
# https://www.thevirtualbrain.org/tvb/zwei/neuroscience-publications
#
#
import os
import threading
from cherrypy.lib.static import serve_file
from tvb.adapters.datatypes.db.connectivity import ConnectivityIndex
from tvb.adapters.datatypes.db.simulation_history import SimulationHistoryIndex
from tvb.adapters.exporters.export_manager import ExportManager
from tvb.adapters.forms.coupling_forms import get_form_for_coupling
from tvb.adapters.forms.equation_forms import get_form_for_equation
from tvb.adapters.forms.model_forms import get_form_for_model
from tvb.adapters.forms.monitor_forms import get_form_for_monitor
from tvb.adapters.forms.noise_forms import get_form_for_noise
from tvb.adapters.simulator.range_parameters import RangeParametersCollector
from tvb.adapters.simulator.simulator_adapter import SimulatorAdapterForm, SimulatorAdapter
from tvb.adapters.forms.simulator_fragments import *
from tvb.config.init.introspector_registry import IntrospectionRegistry
from tvb.core.entities.file.simulator.view_model import AdditiveNoiseViewModel, BoldViewModel
from tvb.core.entities.file.simulator.view_model import IntegratorStochasticViewModel
from tvb.core.entities.model.model_burst import BurstConfiguration
from tvb.core.neocom import h5
from tvb.core.services.burst_service import BurstService
from tvb.core.services.exceptions import BurstServiceException, ServicesBaseException
from tvb.core.services.import_service import ImportService
from tvb.core.services.operation_service import OperationService, GROUP_BURST_PENDING
from tvb.core.services.simulator_service import SimulatorService
from tvb.interfaces.web.controllers.autologging import traced
from tvb.interfaces.web.controllers.burst.base_controller import BurstBaseController
from tvb.interfaces.web.controllers.decorators import *
from tvb.interfaces.web.controllers.simulator.monitors_wizard_handler import MonitorsWizardHandler
from tvb.interfaces.web.controllers.simulator.simulator_fragment_rendering_rules import \
SimulatorFragmentRenderingRules, POST_REQUEST
from tvb.interfaces.web.controllers.simulator.simulator_wizzard_urls import SimulatorWizzardURLs
from tvb.interfaces.web.entities.context_simulator import SimulatorContext
from tvb.storage.storage_interface import StorageInterface
[docs]@traced
class SimulatorController(BurstBaseController):
KEY_IS_LOAD_AFTER_REDIRECT = "is_load_after_redirect"
COPY_NAME_FORMAT = "copy_of_{}"
BRANCH_NAME_FORMAT = "{}_branch{}"
KEY_KEEP_SAME_SIM_WIZARD = "keep_same_wizard"
def __init__(self):
BurstBaseController.__init__(self)
self.range_parameters = RangeParametersCollector()
self.burst_service = BurstService()
self.simulator_service = SimulatorService()
self.cached_simulator_algorithm = self.algorithm_service.get_algorithm_by_module_and_class(
IntrospectionRegistry.SIMULATOR_MODULE, IntrospectionRegistry.SIMULATOR_CLASS)
self.context = SimulatorContext()
self.monitors_handler = MonitorsWizardHandler()
[docs] @expose_json
def cancel_or_remove_burst(self, burst_id):
"""
Cancel or Remove the burst entity given by burst_id (and all linked entities: op, DTs)
:returns True: if the op was successfully.
"""
burst_config = BurstService.load_burst_configuration(int(burst_id))
op_id, is_group = burst_config.operation_info_for_burst_removal
return self.cancel_or_remove_operation(op_id, is_group, burst_config.is_finished)
[docs] def cancel_or_remove_operation(self, operation_id, is_group, remove_after_stop=False):
"""
Stop the operation given by operation_id. If is_group is true stop all the
operations from that group.
"""
# Load before we remove, to have its data in memory here
burst_config = BurstService.get_burst_for_operation_id(operation_id, is_group)
if burst_config is not None:
self.burst_service.mark_burst_finished(burst_config, BurstConfiguration.BURST_CANCELED, store_h5_file=False)
while GROUP_BURST_PENDING.get(burst_config.id, False):
pass
GROUP_BURST_PENDING.pop(burst_config.id, False)
result = OperationService.stop_operation(operation_id, is_group, remove_after_stop)
if remove_after_stop:
current_burst = self.context.burst_config
if (current_burst is not None and burst_config is not None and current_burst.id == burst_config.id and
((current_burst.fk_simulation == operation_id and not is_group) or
(current_burst.fk_operation_group == operation_id and is_group))):
self.reset_simulator_configuration()
if burst_config is not None:
burst_config = BurstService.load_burst_configuration(burst_config.id)
if burst_config:
BurstService.remove_burst_configuration(burst_config.id)
return result
[docs] @expose_page
@settings
@context_selected
def index(self):
"""Get on burst main page"""
template_specification = dict(mainContent="burst/main_burst", title="Simulation Cockpit",
includedResources='project/included_resources')
if not self.context.last_loaded_fragment_url:
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_CONNECTIVITY_URL)
self.context.set_burst_config()
_, is_simulation_copy, is_simulation_load, is_branch = self.context.get_common_params()
if self.context.burst_config.start_time is not None:
is_simulation_load = True
self.context.add_simulator_load_to_session(True)
template_specification['burstConfig'] = self.context.burst_config
template_specification['burst_list'] = self.burst_service.get_available_bursts(self.context.project.id)
form = self.prepare_first_fragment()
rendering_rules = SimulatorFragmentRenderingRules(
form, SimulatorWizzardURLs.SET_CONNECTIVITY_URL, None, is_simulation_copy, is_simulation_load,
last_form_url=self.context.last_loaded_fragment_url,
last_request_type=cherrypy.request.method, is_first_fragment=True, is_branch=is_branch)
template_specification.update(**rendering_rules.to_dict())
cherrypy.response.headers['Cache-Control'] = 'no-cache, no-store, must-revalidate'
cherrypy.response.headers['Pragma'] = 'no-cache'
cherrypy.response.headers['Expires'] = '0'
return self.fill_default_attributes(template_specification)
[docs] def prepare_first_fragment(self):
self.context.set_simulator()
simulator, _, _, is_branch = self.context.get_common_params()
branch_conditions = self.simulator_service.compute_conn_branch_conditions(is_branch, simulator)
form = self.algorithm_service.prepare_adapter_form(form_instance=SimulatorAdapterForm(),
project_id=self.context.project.id,
extra_conditions=branch_conditions)
self.simulator_service.validate_first_fragment(form, self.context.project.id, ConnectivityIndex)
form.fill_from_trait(self.context.simulator)
return form
[docs] @expose_json
def set_fragment_url(self, **data):
try:
self.context.add_last_loaded_form_url_to_session(data['url'])
except KeyError:
self.logger.error("Cannot set last loaded url to session because the required data was not found.")
[docs] @expose_fragment('simulator_fragment')
def set_connectivity(self, **data):
session_stored_simulator, is_simulation_copy, is_simulation_load, _ = self.context.get_common_params()
if cherrypy.request.method == POST_REQUEST:
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_COUPLING_PARAMS_URL)
form = SimulatorAdapterForm()
form.fill_from_post(data)
self.simulator_service.reset_at_connectivity_change(is_simulation_copy, form, session_stored_simulator)
form.fill_trait(session_stored_simulator)
next_form = self.algorithm_service.prepare_adapter_form(
form_instance=get_form_for_coupling(type(session_stored_simulator.coupling))())
self.range_parameters.range_param_forms[FormWithRanges.COUPLING_FRAGMENT_KEY] = next_form
next_form.fill_from_trait(session_stored_simulator.coupling)
rendering_rules = SimulatorFragmentRenderingRules(
next_form, SimulatorWizzardURLs.SET_COUPLING_PARAMS_URL, SimulatorWizzardURLs.SET_CONNECTIVITY_URL,
is_simulation_copy, is_simulation_load, self.context.last_loaded_fragment_url, cherrypy.request.method)
return rendering_rules.to_dict()
[docs] @expose_fragment('simulator_fragment')
def set_coupling_params(self, **data):
session_stored_simulator, is_simulation_copy, is_simulation_load, is_branch = self.context.get_common_params()
if cherrypy.request.method == POST_REQUEST:
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_SURFACE_URL)
form = get_form_for_coupling(type(session_stored_simulator.coupling))()
form.fill_from_post(data)
form.fill_trait(session_stored_simulator.coupling)
surface_fragment = self.algorithm_service.prepare_adapter_form(form_instance=SimulatorSurfaceFragment(),
project_id=self.context.project.id)
surface_fragment.fill_from_trait(session_stored_simulator.surface)
rendering_rules = SimulatorFragmentRenderingRules(
surface_fragment, SimulatorWizzardURLs.SET_SURFACE_URL, SimulatorWizzardURLs.SET_COUPLING_PARAMS_URL,
is_simulation_copy, is_simulation_load, self.context.last_loaded_fragment_url, cherrypy.request.method,
is_branch=is_branch)
return rendering_rules.to_dict()
[docs] @expose_fragment('simulator_fragment')
def set_surface(self, **data):
session_stored_simulator, is_simulation_copy, is_simulation_load, is_branch = self.context.get_common_params()
rendering_rules = SimulatorFragmentRenderingRules(
previous_form_action_url=SimulatorWizzardURLs.SET_SURFACE_URL, is_simulation_copy=is_simulation_copy,
is_simulation_readonly_load=is_simulation_load, last_form_url=self.context.last_loaded_fragment_url,
last_request_type=cherrypy.request.method, is_branch=is_branch)
if cherrypy.request.method == POST_REQUEST:
form = SimulatorSurfaceFragment()
form.fill_from_post(data)
self.simulator_service.reset_at_surface_change(is_simulation_copy, form, session_stored_simulator)
self.range_parameters.range_param_forms.pop(FormWithRanges.CORTEX_FRAGMENT_KEY, None)
form.fill_trait(session_stored_simulator)
if session_stored_simulator.surface:
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_CORTEX_URL)
else:
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_STIMULUS_URL)
return SimulatorSurfaceFragment.prepare_next_fragment_after_surface(
session_stored_simulator, rendering_rules, self.context.project.id, SimulatorWizzardURLs.SET_CORTEX_URL,
SimulatorWizzardURLs.SET_STIMULUS_URL)
[docs] @expose_fragment('simulator_fragment')
def set_cortex(self, **data):
session_stored_simulator, is_simulation_copy, is_simulation_load, _ = self.context.get_common_params()
rm_fragment = SimulatorRMFragment()
if cherrypy.request.method == POST_REQUEST:
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_STIMULUS_URL)
rm_fragment.fill_from_post(data)
rm_fragment.fill_trait(session_stored_simulator.surface)
self.range_parameters.range_param_forms[FormWithRanges.CORTEX_FRAGMENT_KEY] = rm_fragment
rendering_rules = SimulatorFragmentRenderingRules(
None, None, SimulatorWizzardURLs.SET_CORTEX_URL, is_simulation_copy, is_simulation_load,
self.context.last_loaded_fragment_url, cherrypy.request.method)
return SimulatorStimulusFragment.prepare_stimulus_fragment(session_stored_simulator, rendering_rules,
True, SimulatorWizzardURLs.SET_STIMULUS_URL,
self.context.project.id)
[docs] @expose_fragment('simulator_fragment')
def set_stimulus(self, **data):
session_stored_simulator, is_simulation_copy, is_simulation_load, is_branch = self.context.get_common_params()
if cherrypy.request.method == POST_REQUEST:
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_MODEL_URL)
stimuli_fragment = SimulatorStimulusFragment(session_stored_simulator.is_surface_simulation)
stimuli_fragment.fill_from_post(data)
stimuli_fragment.fill_trait(session_stored_simulator)
model_fragment = self.algorithm_service.prepare_adapter_form(form_instance=SimulatorModelFragment())
model_fragment.fill_from_trait(session_stored_simulator)
rendering_rules = SimulatorFragmentRenderingRules(
model_fragment, SimulatorWizzardURLs.SET_MODEL_URL, SimulatorWizzardURLs.SET_STIMULUS_URL,
is_simulation_copy, is_simulation_load, self.context.last_loaded_fragment_url, cherrypy.request.method,
is_model_fragment=True, is_surface_simulation=session_stored_simulator.is_surface_simulation,
is_branch=is_branch)
return rendering_rules.to_dict()
[docs] @expose_fragment('simulator_fragment')
def set_model(self, **data):
session_stored_simulator, is_simulation_copy, is_simulation_load, is_branch = self.context.get_common_params()
if cherrypy.request.method == POST_REQUEST:
set_next_wizard = True
if SimulatorController.KEY_KEEP_SAME_SIM_WIZARD in data:
set_next_wizard = False
if set_next_wizard:
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_MODEL_PARAMS_URL)
form = SimulatorModelFragment()
form.fill_from_post(data)
form.fill_trait(session_stored_simulator)
form = self.algorithm_service.prepare_adapter_form(
form_instance=get_form_for_model(type(session_stored_simulator.model))(is_branch))
self.range_parameters.range_param_forms[FormWithRanges.MODEL_FRAGMENT_KEY] = form
form.fill_from_trait(session_stored_simulator.model)
rendering_rules = SimulatorFragmentRenderingRules(
form, SimulatorWizzardURLs.SET_MODEL_PARAMS_URL, SimulatorWizzardURLs.SET_MODEL_URL, is_simulation_copy,
is_simulation_load, self.context.last_loaded_fragment_url, cherrypy.request.method)
return rendering_rules.to_dict()
[docs] @expose_fragment('simulator_fragment')
def set_model_params(self, **data):
session_stored_simulator, is_simulation_copy, is_simulation_load, is_branch = self.context.get_common_params()
if cherrypy.request.method == POST_REQUEST:
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_INTEGRATOR_URL)
form = get_form_for_model(type(session_stored_simulator.model))(is_branch)
if is_branch:
data['variables_of_interest'] = list(session_stored_simulator.model.variables_of_interest)
form.fill_from_post(data)
form.fill_trait(session_stored_simulator.model)
integrator_fragment = self.algorithm_service.prepare_adapter_form(form_instance=SimulatorIntegratorFragment())
integrator_fragment.integrator.display_subform = False
integrator_fragment.fill_from_trait(session_stored_simulator)
rendering_rules = SimulatorFragmentRenderingRules(
integrator_fragment, SimulatorWizzardURLs.SET_INTEGRATOR_URL,
SimulatorWizzardURLs.SET_MODEL_PARAMS_URL, is_simulation_copy, is_simulation_load,
self.context.last_loaded_fragment_url, cherrypy.request.method, is_branch=is_branch)
return rendering_rules.to_dict()
[docs] @expose_fragment('simulator_fragment')
def set_integrator(self, **data):
session_stored_simulator, is_simulation_copy, is_simulation_load, is_branch = self.context.get_common_params()
if cherrypy.request.method == POST_REQUEST:
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_INTEGRATOR_PARAMS_URL)
fragment = SimulatorIntegratorFragment()
fragment.fill_from_post(data)
fragment.fill_trait(session_stored_simulator)
form = self.algorithm_service.prepare_adapter_form(form_instance=get_form_for_integrator(
type(session_stored_simulator.integrator))(is_branch))
if hasattr(form, 'noise'):
form.noise.display_subform = False
form.fill_from_trait(session_stored_simulator.integrator)
rendering_rules = SimulatorFragmentRenderingRules(
form, SimulatorWizzardURLs.SET_INTEGRATOR_PARAMS_URL, SimulatorWizzardURLs.SET_INTEGRATOR_URL,
is_simulation_copy, is_simulation_load, self.context.last_loaded_fragment_url, cherrypy.request.method)
return rendering_rules.to_dict()
[docs] @expose_fragment('simulator_fragment')
def set_integrator_params(self, **data):
session_stored_simulator, is_simulation_copy, is_simulation_load, is_branch = self.context.get_common_params()
if cherrypy.request.method == POST_REQUEST:
form = get_form_for_integrator(type(session_stored_simulator.integrator))(is_branch)
if is_branch:
data['dt'] = str(session_stored_simulator.integrator.dt)
form.fill_from_post(data)
form.fill_trait(session_stored_simulator.integrator)
if isinstance(session_stored_simulator.integrator, IntegratorStochasticViewModel):
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_NOISE_PARAMS_URL)
else:
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_MONITORS_URL)
self.range_parameters.range_param_forms.pop(FormWithRanges.NOISE_FRAGMENT_KEY, None)
rendering_rules = SimulatorFragmentRenderingRules(
None, None, SimulatorWizzardURLs.SET_INTEGRATOR_PARAMS_URL, is_simulation_copy,
is_simulation_load, self.context.last_loaded_fragment_url, cherrypy.request.method,
is_noise_fragment=False)
if not isinstance(session_stored_simulator.integrator, IntegratorStochasticViewModel):
return self.monitors_handler.prepare_monitor_fragment(session_stored_simulator, rendering_rules,
SimulatorWizzardURLs.SET_MONITORS_URL)
integrator_noise_fragment = get_form_for_noise(type(session_stored_simulator.integrator.noise))()
if hasattr(integrator_noise_fragment, 'equation'):
integrator_noise_fragment.equation.display_subform = False
self.range_parameters.range_param_forms[FormWithRanges.NOISE_FRAGMENT_KEY] = integrator_noise_fragment
integrator_noise_fragment.fill_from_trait(session_stored_simulator.integrator.noise)
rendering_rules.form = integrator_noise_fragment
rendering_rules.form_action_url = SimulatorWizzardURLs.SET_NOISE_PARAMS_URL
rendering_rules.is_noise_fragment = True
return rendering_rules.to_dict()
[docs] @expose_fragment('simulator_fragment')
def set_noise_params(self, **data):
session_stored_simulator, is_simulation_copy, is_simulation_load, is_branch = self.context.get_common_params()
if cherrypy.request.method == POST_REQUEST:
form = get_form_for_noise(type(session_stored_simulator.integrator.noise))()
form.fill_from_post(data)
form.fill_trait(session_stored_simulator.integrator.noise)
if isinstance(session_stored_simulator.integrator.noise, AdditiveNoiseViewModel):
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_MONITORS_URL)
else:
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_NOISE_EQUATION_PARAMS_URL)
rendering_rules = SimulatorFragmentRenderingRules(
None, None, SimulatorWizzardURLs.SET_NOISE_PARAMS_URL, is_simulation_copy, is_simulation_load,
self.context.last_loaded_fragment_url, cherrypy.request.method)
return self.monitors_handler.prepare_next_fragment_after_noise(
session_stored_simulator, is_branch, rendering_rules, SimulatorWizzardURLs.SET_MONITORS_URL,
SimulatorWizzardURLs.SET_NOISE_EQUATION_PARAMS_URL)
[docs] @expose_fragment('simulator_fragment')
def set_noise_equation_params(self, **data):
session_stored_simulator, is_simulation_copy, is_simulation_load, _ = self.context.get_common_params()
if cherrypy.request.method == POST_REQUEST:
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_MONITORS_URL)
form = get_form_for_equation(type(session_stored_simulator.integrator.noise.b))()
form.fill_from_post(data)
form.fill_trait(session_stored_simulator.integrator.noise.b)
rendering_rules = SimulatorFragmentRenderingRules(
None, None, SimulatorWizzardURLs.SET_NOISE_EQUATION_PARAMS_URL, is_simulation_copy, is_simulation_load,
self.context.last_loaded_fragment_url, cherrypy.request.method)
return self.monitors_handler.prepare_monitor_fragment(session_stored_simulator, rendering_rules,
SimulatorWizzardURLs.SET_MONITORS_URL)
[docs] @staticmethod
def build_monitor_url(fragment_url, monitor):
url_regex = '{}/{}'
url = url_regex.format(fragment_url, monitor)
return url
[docs] def get_first_monitor_fragment_url(self, simulator, monitors_url):
first_monitor = simulator.first_monitor
if first_monitor is not None:
monitor_vm_name = type(first_monitor).__name__
return self.build_monitor_url(monitors_url, monitor_vm_name)
return SimulatorWizzardURLs.SETUP_PSE_URL
[docs] @expose_fragment('simulator_fragment')
def set_monitors(self, **data):
session_stored_simulator, is_simulation_copy, is_simulation_load, is_branch = self.context.get_common_params()
if cherrypy.request.method == POST_REQUEST:
fragment = SimulatorMonitorFragment(is_surface_simulation=session_stored_simulator.is_surface_simulation)
fragment.fill_from_post(data)
self.monitors_handler.set_monitors_list_on_simulator(session_stored_simulator, fragment.monitors.value)
last_loaded_fragment_url = self.get_first_monitor_fragment_url(
session_stored_simulator, SimulatorWizzardURLs.SET_MONITOR_PARAMS_URL)
if cherrypy.request.method == POST_REQUEST:
self.context.add_last_loaded_form_url_to_session(last_loaded_fragment_url)
rendering_rules = SimulatorFragmentRenderingRules(
is_simulation_copy=is_simulation_copy, is_simulation_readonly_load=is_simulation_load,
last_request_type=cherrypy.request.method, form_action_url=last_loaded_fragment_url,
previous_form_action_url=SimulatorWizzardURLs.SET_MONITORS_URL)
return self.monitors_handler.get_fragment_after_monitors(
session_stored_simulator, self.context.burst_config, self.context.project.id,
is_branch, rendering_rules, SimulatorWizzardURLs.SETUP_PSE_URL)
[docs] def get_url_after_monitors(self, current_monitor, monitor_name, next_monitor):
if isinstance(current_monitor, BoldViewModel):
return self.build_monitor_url(SimulatorWizzardURLs.SET_MONITOR_EQUATION_URL, monitor_name)
if next_monitor is not None:
return self.build_monitor_url(SimulatorWizzardURLs.SET_MONITOR_PARAMS_URL, type(next_monitor).__name__)
return SimulatorWizzardURLs.SETUP_PSE_URL
[docs] @staticmethod
def get_url_for_final_fragment(burst_config):
if burst_config.is_pse_burst():
return SimulatorWizzardURLs.LAUNCH_PSE_URL
return SimulatorWizzardURLs.SETUP_PSE_URL
[docs] def get_urls_for_next_monitor_fragment(self, next_monitor, current_monitor):
form_action_url = self.build_monitor_url(SimulatorWizzardURLs.SET_MONITOR_PARAMS_URL,
type(next_monitor).__name__)
if_bold_url = self.build_monitor_url(SimulatorWizzardURLs.SET_MONITOR_EQUATION_URL,
type(current_monitor).__name__)
return form_action_url, if_bold_url
[docs] @expose_fragment('simulator_fragment')
def set_monitor_params(self, current_monitor_name, **data):
session_stored_simulator, is_simulation_copy, is_simulator_load, is_branch = self.context.get_common_params()
current_monitor, next_monitor = self.monitors_handler.get_current_and_next_monitor_form(
current_monitor_name, session_stored_simulator)
if cherrypy.request.method == POST_REQUEST:
form = get_form_for_monitor(type(current_monitor))(session_stored_simulator, is_branch)
if is_branch:
data['period'] = str(current_monitor.period)
data['variables_of_interest'] = [session_stored_simulator.model.variables_of_interest[i] for i
in current_monitor.variables_of_interest]
form.fill_from_post(data)
form.fill_trait(current_monitor)
last_loaded_form_url = self.get_url_after_monitors(
current_monitor, current_monitor_name, next_monitor)
self.context.add_last_loaded_form_url_to_session(last_loaded_form_url)
previous_form_action_url = self.build_monitor_url(SimulatorWizzardURLs.SET_MONITOR_PARAMS_URL,
current_monitor_name)
rendering_rules = SimulatorFragmentRenderingRules(
is_simulation_copy=is_simulation_copy, is_simulation_readonly_load=is_simulator_load,
last_request_type=cherrypy.request.method, last_form_url=self.context.last_loaded_fragment_url,
previous_form_action_url=previous_form_action_url)
form_action_url, if_bold_url = self.get_urls_for_next_monitor_fragment(next_monitor, current_monitor)
self.monitors_handler.update_monitor(current_monitor, session_stored_simulator)
return self.monitors_handler.handle_next_fragment_for_monitors(self.context, rendering_rules, current_monitor,
next_monitor, False, form_action_url,
if_bold_url)
[docs] def get_url_after_monitor_equation(self, next_monitor):
if next_monitor is None:
return SimulatorWizzardURLs.SETUP_PSE_URL
last_loaded_fragment_url = self.build_monitor_url(SimulatorWizzardURLs.SET_MONITOR_PARAMS_URL,
type(next_monitor).__name__)
return last_loaded_fragment_url
[docs] @expose_fragment('simulator_fragment')
def set_monitor_equation(self, current_monitor_name, **data):
session_stored_simulator, is_simulation_copy, is_simulator_load, is_branch = self.context.get_common_params()
current_monitor, next_monitor = self.monitors_handler.get_current_and_next_monitor_form(
current_monitor_name, session_stored_simulator)
if cherrypy.request.method == POST_REQUEST:
form = get_form_for_equation(type(current_monitor.hrf_kernel))()
form.fill_from_post(data)
form.fill_trait(current_monitor.hrf_kernel)
last_loaded_fragment_url = self.get_url_after_monitor_equation(next_monitor)
self.context.add_last_loaded_form_url_to_session(last_loaded_fragment_url)
previous_form_action_url = self.build_monitor_url(
SimulatorWizzardURLs.SET_MONITOR_EQUATION_URL, current_monitor_name)
rendering_rules = SimulatorFragmentRenderingRules(
None, None, previous_form_action_url, is_simulation_copy, is_simulator_load,
self.context.last_loaded_fragment_url, cherrypy.request)
form_action_url, if_bold_url = self.get_urls_for_next_monitor_fragment(next_monitor, current_monitor)
return self.monitors_handler.handle_next_fragment_for_monitors(self.context, rendering_rules, current_monitor,
next_monitor, True, form_action_url, if_bold_url)
[docs] @expose_fragment('simulator_fragment')
def setup_pse(self, **data):
session_stored_simulator, is_simulation_copy, is_simulator_load, _ = self.context.get_common_params()
burst_config = self.context.burst_config
all_range_parameters = self.range_parameters.get_all_range_parameters()
next_form = self.algorithm_service.prepare_adapter_form(
form_instance=SimulatorPSEConfigurationFragment(all_range_parameters))
if cherrypy.request.method == POST_REQUEST:
session_stored_simulator.simulation_length = float(data['simulation_length'])
burst_config.name = data['input_simulation_name_id']
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_PSE_PARAMS_URL)
param1, param2 = self.burst_service.handle_range_params_at_loading(burst_config, all_range_parameters)
if param1:
param_dict = {'pse_param1': param1.name}
if param2 is not None:
param_dict['pse_param2'] = param2.name
next_form.fill_from_post(param_dict)
rendering_rules = SimulatorFragmentRenderingRules(next_form, SimulatorWizzardURLs.SET_PSE_PARAMS_URL,
SimulatorWizzardURLs.SETUP_PSE_URL, is_simulation_copy,
is_simulator_load, self.context.last_loaded_fragment_url,
cherrypy.request.method)
return rendering_rules.to_dict()
[docs] @expose_fragment('simulator_fragment')
def set_pse_params(self, **data):
session_stored_simulator, is_simulation_copy, is_simulation_load, _ = self.context.get_common_params()
burst_config = self.context.burst_config
form = SimulatorPSEConfigurationFragment(self.range_parameters.get_all_range_parameters())
if cherrypy.request.method == POST_REQUEST:
self.context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.LAUNCH_PSE_URL)
form.fill_from_post(data)
param1 = form.pse_param1.value
burst_config.range1 = param1.to_json()
param2 = None
if form.pse_param2.value:
param2 = form.pse_param2.value
burst_config.range2 = param2.to_json()
else:
all_range_parameters = self.range_parameters.get_all_range_parameters()
param1, param2 = self.burst_service.handle_range_params_at_loading(burst_config, all_range_parameters)
next_form = self.algorithm_service.prepare_adapter_form(form_instance=SimulatorPSERangeFragment(param1, param2))
rendering_rules = SimulatorFragmentRenderingRules(
next_form, SimulatorWizzardURLs.LAUNCH_PSE_URL, SimulatorWizzardURLs.SET_PSE_PARAMS_URL, is_simulation_copy,
is_simulation_load, last_form_url=self.context.last_loaded_fragment_url, is_launch_pse_fragment=True)
return rendering_rules.to_dict()
[docs] @expose_json
def launch_pse(self, **data):
session_stored_simulator = self.context.simulator
all_range_parameters = self.range_parameters.get_all_range_parameters()
range_param1, range_param2 = SimulatorPSERangeFragment.fill_from_post(all_range_parameters, **data)
burst_config = self.context.burst_config
burst_config.start_time = datetime.now()
burst_config.range1 = range_param1.to_json()
len_range = len(range_param1.get_range_values())
if range_param2:
burst_config.range2 = range_param2.to_json()
len_range *= len(range_param2.get_range_values())
if not self.simulator_service.operation_service.fits_max_operation_size(SimulatorAdapter(), session_stored_simulator,
self.context.project.id, len_range):
return {'error': self.MAX_SIZE_ERROR_MSG}
burst_config = self.burst_service.prepare_burst_for_pse(burst_config)
session_stored_simulator.operation_group_gid = uuid.UUID(burst_config.operation_group.gid)
session_stored_simulator.ranges = json.dumps(burst_config.ranges)
try:
thread = threading.Thread(target=self.simulator_service.async_launch_and_prepare_pse,
kwargs={'burst_config': burst_config,
'user': self.context.logged_user,
'project': self.context.project,
'simulator_algo': self.cached_simulator_algorithm,
'range_param1': range_param1,
'range_param2': range_param2,
'session_stored_simulator': session_stored_simulator})
thread.start()
return {'id': burst_config.id}
except BurstServiceException as e:
self.logger.exception("Could not launch burst!")
return {'error': e.message}
[docs] @expose_json
def launch_simulation(self, launch_mode, **data):
current_form = SimulatorFinalFragment()
burst_config = self.context.burst_config
burst_config.range1 = None
burst_config.range2 = None
try:
current_form.fill_from_post(data)
except Exception as exc:
self.logger.exception(exc)
return {'error': str(exc)}
burst_name = current_form.simulation_name.value
session_stored_simulator = self.context.simulator
session_stored_simulator.simulation_length = current_form.simulation_length.value
if burst_name != 'none_undefined':
burst_config.name = burst_name
if launch_mode == self.burst_service.LAUNCH_BRANCH:
simulation_state_index = self.simulator_service.get_simulation_state_index(burst_config,
SimulationHistoryIndex)
session_stored_simulator.history_gid = simulation_state_index[0].gid
if not self.simulator_service.operation_service.fits_max_operation_size(SimulatorAdapter(), session_stored_simulator,
self.context.project.id):
return {'error': self.MAX_SIZE_ERROR_MSG}
burst_config.start_time = datetime.now()
session_burst_config = self.burst_service.store_burst(burst_config)
try:
thread = threading.Thread(target=self.simulator_service.async_launch_and_prepare_simulation,
kwargs={'burst_config': session_burst_config,
'user': self.context.logged_user,
'project': self.context.project,
'simulator_algo': self.cached_simulator_algorithm,
'simulator': session_stored_simulator})
thread.start()
return {'id': session_burst_config.id}
except BurstServiceException as e:
self.logger.exception('Could not launch burst!')
return {'error': e.message}
[docs] @expose_fragment('burst/burst_history')
def load_burst_history(self, initBurst=None):
"""
Load the available burst that are stored in the database at this time.
This is one alternative to 'chrome-back problem'.
"""
bursts = self.burst_service.get_available_bursts(self.context.project.id)
self.burst_service.populate_burst_disk_usage(bursts)
fromInit = False
if initBurst is not None:
fromInit = True
return {'burst_list': bursts,
'fromInit': fromInit,
'selectedBurst': self.context.burst_config.id,
'first_fragment_url': SimulatorFragmentRenderingRules.FIRST_FORM_URL}
[docs] @cherrypy.expose
def get_last_fragment_url(self, burst_config_id):
burst_config = self.burst_service.load_burst_configuration(burst_config_id)
return self.get_url_for_final_fragment(burst_config)
[docs] @expose_fragment('simulator_fragment')
def load_burst_read_only(self, burst_config_id):
try:
burst_config = self.burst_service.load_burst_configuration(burst_config_id)
storage_path = StorageInterface().get_project_folder(self.context.project.name,
str(burst_config.fk_simulation))
simulator = h5.load_view_model(burst_config.simulator_gid, storage_path)
last_loaded_form_url = self.get_url_for_final_fragment(burst_config)
self.context.init_session_at_burst_loading(burst_config, simulator, last_loaded_form_url)
form = self.prepare_first_fragment()
rendering_rules = SimulatorFragmentRenderingRules(form, SimulatorWizzardURLs.SET_CONNECTIVITY_URL,
is_simulation_readonly_load=True, is_first_fragment=True)
return rendering_rules.to_dict()
except Exception:
# Most probably Burst was removed. Delete it from session, so that client
# has a good chance to get a good response on refresh
self.logger.exception("Error loading burst")
self.context.remove_burst_config_from_session()
raise
def _prepare_first_fragment_for_burst_copy(self, burst_config_id, burst_name_format):
simulator, burst_config_copy = self.burst_service.prepare_data_for_burst_copy(
burst_config_id, burst_name_format, self.context.project)
last_loaded_form_url = self.get_url_for_final_fragment(burst_config_copy)
self.context.init_session_at_copy_preparation(burst_config_copy, simulator, last_loaded_form_url)
return self.prepare_first_fragment()
[docs] @expose_fragment('simulator_fragment')
def copy_simulator_configuration(self, burst_config_id):
self.context.add_branch_and_copy_to_session(False, True)
form = self._prepare_first_fragment_for_burst_copy(burst_config_id, self.COPY_NAME_FORMAT)
rendering_rules = SimulatorFragmentRenderingRules(form, SimulatorWizzardURLs.SET_CONNECTIVITY_URL,
is_simulation_copy=True, is_simulation_readonly_load=True,
is_first_fragment=True)
return rendering_rules.to_dict()
[docs] @expose_fragment('simulator_fragment')
def branch_simulator_configuration(self, burst_config_id):
self.context.add_branch_and_copy_to_session(True, False)
form = self._prepare_first_fragment_for_burst_copy(burst_config_id, self.BRANCH_NAME_FORMAT)
rendering_rules = SimulatorFragmentRenderingRules(form, SimulatorWizzardURLs.SET_CONNECTIVITY_URL,
is_simulation_copy=True, is_simulation_readonly_load=True,
is_first_fragment=True)
return rendering_rules.to_dict()
[docs] @expose_fragment('simulator_fragment')
def reset_simulator_configuration(self):
burst_config = BurstConfiguration(self.context.project.id)
self.context.init_session_at_sim_reset(burst_config, SimulatorWizzardURLs.SET_CONNECTIVITY_URL)
form = self.prepare_first_fragment()
rendering_rules = SimulatorFragmentRenderingRules(form, SimulatorWizzardURLs.SET_CONNECTIVITY_URL,
is_first_fragment=True)
return rendering_rules.to_dict()
[docs] @expose_json
def rename_burst(self, burst_id, burst_name):
"""
Rename the burst given by burst_id, setting it's new name to
burst_name.
"""
validation_result = SimulatorFinalFragment.is_burst_name_ok(burst_name)
if validation_result is True:
self.burst_service.rename_burst(burst_id, burst_name)
return {'success': "Simulation successfully renamed!"}
else:
self.logger.exception(validation_result)
return {'error': validation_result}
[docs] @expose_json
def get_history_status(self, **data):
"""
For each burst id received, get the status and return it.
"""
return self.burst_service.update_history_status(json.loads(data['burst_ids']))
[docs] @cherrypy.expose
@handle_error(redirect=False)
@check_user
def export(self, burst_id):
export_manager = ExportManager()
export_zip = export_manager.export_simulator_configuration(burst_id)
result_name = "tvb_simulation_" + str(burst_id) + ".zip"
return serve_file(export_zip, "application/x-download", "attachment", result_name)
[docs] @expose_fragment("overlay")
def get_upload_overlay(self):
template_specification = self.fill_overlay_attributes(None, "Upload", "Simulation ZIP",
"burst/upload_burst_overlay", "dialog-upload")
template_specification['first_fragment_url'] = SimulatorWizzardURLs.SET_CONNECTIVITY_URL
return self.fill_default_attributes(template_specification)
[docs] @cherrypy.expose
@handle_error(redirect=True)
@check_user
@settings
def load_simulator_configuration_from_zip(self, **data):
"""Upload Simulator from previously exported ZIP file"""
self.logger.debug("Uploading ..." + str(data))
last_loaded_form_url = SimulatorWizzardURLs.SETUP_PSE_URL
try:
upload_param = "uploadedfile"
if upload_param in data and data[upload_param]:
simulator, burst_config, sim_folder = self.burst_service.load_simulation_from_zip(data[upload_param],
self.context.project)
dts_folder = os.path.join(sim_folder, StorageInterface.EXPORTED_SIMULATION_DTS_DIR)
ImportService().import_list_of_operations(self.context.project, dts_folder, False, None)
if burst_config.is_pse_burst():
last_loaded_form_url = SimulatorWizzardURLs.LAUNCH_PSE_URL
self.context.init_session_at_sim_config_from_zip(burst_config, simulator, last_loaded_form_url)
except IOError as ioexcep:
self.logger.exception(ioexcep)
self.context.set_warning_message("This ZIP does not contain a complete simulator configuration")
except ServicesBaseException as excep:
self.logger.warning(excep.message)
self.context.set_warning_message(excep.message)
self.redirect('/burst/')
