# -*- 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
#
#
"""
A convenience module for the command interface
.. moduleauthor:: Mihai Andrei <mihai.andrei@codemart.ro>
"""
import os
from datetime import datetime
from time import sleep
from tvb.adapters.uploaders.tvb_importer import TVBImporter
from tvb.adapters.uploaders.zip_connectivity_importer import ZIPConnectivityImporter, ZIPConnectivityImporterModel
from tvb.basic.logger.builder import get_logger
from tvb.basic.profile import TvbProfile
from tvb.config.init.initializer import command_initializer
from tvb.config.init.introspector_registry import IntrospectionRegistry
from tvb.core.adapters.abcadapter import ABCAdapter
from tvb.core.entities.file.simulator.view_model import SimulatorAdapterModel
from tvb.core.entities.model.model_burst import BurstConfiguration
from tvb.core.entities.model.model_operation import STATUS_FINISHED
from tvb.core.entities.storage import dao
from tvb.core.neocom import h5
from tvb.core.services.algorithm_service import AlgorithmService
from tvb.core.services.operation_service import OperationService
from tvb.core.services.project_service import ProjectService
from tvb.core.services.simulator_service import SimulatorService
from tvb.core.services.user_service import UserService
from tvb.storage.storage_interface import StorageInterface
command_initializer()
LOG = get_logger(__name__)
[docs]def list_projects():
fmt = "%24s %5s"
print(fmt % ('name', 'id'))
for p in dao.get_all_projects():
print(fmt % (p.name, p.id))
[docs]def list_datatypes(project_id):
fmt = "%24s %16s %5s %32s %12s"
print(fmt % ('type', 'tag', 'id', 'gid', 'date'))
for dt in dao.get_datatypes_in_project(project_id):
print(fmt % (dt.type, dt.user_tag_1, dt.id, dt.gid, dt.create_date))
[docs]def datatype_details(dt_id):
dt = dao.get_datatype_by_id(dt_id)
print(ProjectService().get_datatype_details(dt.gid))
[docs]def load_dt(dt_id=None, dt_gid=None):
if dt_id:
dt = dao.get_datatype_by_id(dt_id)
dt_idx = dao.get_generic_entity(dt.module + '.' + dt.type, dt_id)[0]
elif dt_gid:
dt = dao.get_datatype_by_gid(dt_gid)
dt_idx = dao.get_generic_entity(dt.module + '.' + dt.type, dt_gid, select_field='gid')[0]
else:
return None
dt_ht = h5.load_from_index(dt_idx)
return dt_ht
[docs]def new_project(name):
usr = UserService.get_administrators()[0]
proj = ProjectService().store_project(usr, True, None, name=name, description=name, users=[usr], max_operation_size=1024, disable_imports=False)
return proj
[docs]def import_conn_zip(project_id, zip_path):
TvbProfile.set_profile(TvbProfile.COMMAND_PROFILE)
project = dao.get_project_by_id(project_id)
importer = ABCAdapter.build_adapter_from_class(ZIPConnectivityImporter)
view_model = ZIPConnectivityImporterModel()
view_model.uploaded = zip_path
return OperationService().fire_operation(importer, project.administrator, project_id, view_model=view_model)
[docs]def import_conn_h5(project_id, h5_path):
project = dao.get_project_by_id(project_id)
TvbProfile.set_profile(TvbProfile.COMMAND_PROFILE)
now = datetime.now()
date_str = "%d-%d-%d_%d-%d-%d_%d" % (now.year, now.month, now.day, now.hour,
now.minute, now.second, now.microsecond)
uq_name = "%s-Connectivity" % date_str
new_path = os.path.join(TvbProfile.current.TVB_TEMP_FOLDER, uq_name)
StorageInterface.copy_file(h5_path, new_path)
importer = ABCAdapter.build_adapter_from_class(TVBImporter)
view_model = importer.get_view_model_class()()
view_model.data_file = new_path
return OperationService().fire_operation(importer, project.administrator, project_id, view_model=view_model)
[docs]def fire_simulation(project_id, simulator_model):
TvbProfile.set_profile(TvbProfile.COMMAND_PROFILE)
project = dao.get_project_by_id(project_id)
assert isinstance(simulator_model, SimulatorAdapterModel)
# Load the SimulatorAdapter algorithm from DB
cached_simulator_algorithm = AlgorithmService().get_algorithm_by_module_and_class(
IntrospectionRegistry.SIMULATOR_MODULE,
IntrospectionRegistry.SIMULATOR_CLASS)
# Instantiate a SimulatorService and launch the configured simulation
simulator_service = SimulatorService()
burst = BurstConfiguration(project.id)
burst.name = "Sim " + str(datetime.now())
burst.start_time = datetime.now()
dao.store_entity(burst)
launched_operation = simulator_service.async_launch_and_prepare_simulation(burst, project.administrator, project,
cached_simulator_algorithm,
simulator_model)
LOG.info("Operation launched ....")
return launched_operation
[docs]def fire_operation(project_id, adapter_instance, view_model):
TvbProfile.set_profile(TvbProfile.COMMAND_PROFILE)
project = dao.get_project_by_id(project_id)
# launch an operation and have the results stored both in DB and on disk
launched_operation = OperationService().fire_operation(adapter_instance, project.administrator,
project.id, view_model=view_model)
LOG.info("Operation launched....")
return launched_operation
[docs]def wait_to_finish(operation):
# Wait for the operation to finish
while not operation.has_finished:
sleep(1)
operation = dao.get_operation_by_id(operation.id)
if operation.status == STATUS_FINISHED:
LOG.info("Operation finished successfully")
else:
LOG.warning("Operation ended with problems [%s]: [%s]" % (operation.status, operation.additional_info))
return operation
[docs]def list_operation_results(operation_id):
fmt = "%16s %24s %32s %12s"
print(fmt % ('id', 'type', 'gid', 'date'))
for dt in dao.get_results_for_operation(operation_id):
print(fmt % (dt.id, dt.type, dt.gid, dt.create_date))
[docs]def get_operation_results(operation_id):
return dao.get_results_for_operation(operation_id)
