def init_test_env():
"""
This method prepares all necessary data for tests execution
"""
# Set a default test profile, for when running tests from dev-env.
from tvb.basic.profile import TvbProfile
if TvbProfile.CURRENT_PROFILE_NAME is None:
profile = TvbProfile.TEST_SQLITE_PROFILE
if len(sys.argv) > 1:
for i in range(1, len(sys.argv) - 1):
if "--profile=" in sys.argv[i]:
profile = sys.argv[i].split("=")[1]
TvbProfile.set_profile(profile)
print("Not expected to happen except from PyCharm: setting profile",
TvbProfile.CURRENT_PROFILE_NAME)
db_file = TvbProfile.current.db.DB_URL.replace('sqlite:///', '')
if os.path.exists(db_file):
os.remove(db_file)
from tvb.config.init.model_manager import reset_database
from tvb.config.init.initializer import initialize
reset_database()
initialize(skip_import=True)
# Add Dummy DataType
REGISTRY.register_datatype(DummyDataType, DummyDataTypeH5,
DummyDataTypeIndex)
REGISTRY.register_datatype(None, None, DummyDataType2Index)
def setup_test_env():
from tvb.basic.profile import TvbProfile
if len(sys.argv) > 1:
profile = sys.argv[1]
else:
profile = TvbProfile.TEST_SQLITE_PROFILE
TvbProfile.set_profile(profile)
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
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)
def setup_test_console_env():
import sys
# Remove anything pointing to the framework, to make sure that only one direct dependency exists
# TVB-Framework --> TVB Scientific Library
# We should have nothing inverse.
sys.path = [
path for path in sys.path if not path.endswith('framework_tvb')
]
from tvb.basic.profile import TvbProfile
TvbProfile.set_profile(TvbProfile.TEST_LIBRARY_PROFILE)
def command_initializer(persist_settings=True, skip_import=False):
if persist_settings and TvbProfile.is_first_run():
settings_service = SettingsService()
settings = {}
# Save default settings
for key, setting in settings_service.configurable_keys.items():
settings[key] = setting['value']
settings_service.save_settings(**settings)
TvbProfile.set_profile(TvbProfile.COMMAND_PROFILE)
# Build new db engine in case DB URL value changed
new_db_engine = build_db_engine()
SA_SESSIONMAKER.configure(bind=new_db_engine)
# Initialize application
initialize(skip_import)
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)
def init_test_env():
"""
This method prepares all necessary data for tests execution
"""
# Set a default test profile, for when running tests from dev-env.
if TvbProfile.CURRENT_PROFILE_NAME is None:
TvbProfile.set_profile(TvbProfile.TEST_SQLITE_PROFILE)
print "Not expected to happen except from PyCharm: setting profile", TvbProfile.CURRENT_PROFILE_NAME
db_file = TvbProfile.current.db.DB_URL.replace('sqlite:///', '')
if os.path.exists(db_file):
os.remove(db_file)
from tvb.core.entities.model_manager import reset_database
from tvb.core.services.initializer import initialize
reset_database()
initialize(["tvb.config", "tvb.tests.framework"], skip_import=True)
def init_test_env():
"""
This method prepares all necessary data for tests execution
"""
# Set a default test profile, for when running tests from dev-env.
if TvbProfile.CURRENT_PROFILE_NAME is None:
TvbProfile.set_profile(TvbProfile.TEST_SQLITE_PROFILE)
print "Not expected to happen except from PyCharm: setting profile", TvbProfile.CURRENT_PROFILE_NAME
db_file = TvbProfile.current.db.DB_URL.replace("sqlite:///", "")
if os.path.exists(db_file):
os.remove(db_file)
from tvb.core.entities.model_manager import reset_database
from tvb.core.services.initializer import initialize
reset_database()
initialize(["tvb.config", "tvb.tests.framework"], skip_import=True)
def setup():
if sys.platform != 'darwin':
unsupport_module('h5py')
import logging
logging.basicConfig(level=logging.DEBUG, stream=sys.stdout)
from tvb.basic.profile import TvbProfile
TvbProfile.set_profile(TvbProfile.MATLAB_PROFILE)
# MATLAB states the module doesn't exist if not importable and provides no traceback
# to diagnose the import error, so we'll need to workaround this in the future. For now,
# just try to import the simlab and report if it worked or not.
try:
import tvb.simulator.lab
print('TVB modules available.')
except Exception as exc:
#print 'failed to import all TVB modules, not all functionality may be .'
pass
def setup():
if sys.platform != 'darwin':
unsupport_module('h5py')
import logging
logging.basicConfig(level=logging.DEBUG, stream=sys.stdout)
from tvb.basic.profile import TvbProfile
TvbProfile.set_profile(TvbProfile.MATLAB_PROFILE)
# MATLAB states the module doesn't exist if not importable and provides no traceback
# to diagnose the import error, so we'll need to workaround this in the future. For now,
# just try to import the simlab and report if it worked or not.
try:
import tvb.simulator.lab
print('TVB modules available.')
except Exception as exc:
#print 'failed to import all TVB modules, not all functionality may be .'
pass
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
def init_test_env():
"""
This method prepares all necessary data for tests execution
"""
# Set a default test profile, for when running tests from dev-env.
if TvbProfile.CURRENT_PROFILE_NAME is None:
profile = TvbProfile.TEST_SQLITE_PROFILE
if len(sys.argv) > 1:
for i in range(1,len(sys.argv)-1):
if "--profile=" in sys.argv[i]:
profile = sys.argv[i].split("=")[1]
TvbProfile.set_profile(profile)
print("Not expected to happen except from PyCharm: setting profile", TvbProfile.CURRENT_PROFILE_NAME)
db_file = TvbProfile.current.db.DB_URL.replace('sqlite:///', '')
if os.path.exists(db_file):
os.remove(db_file)
from tvb.core.entities.model_manager import reset_database
from tvb.core.services.initializer import initialize
reset_database()
initialize(["tvb.config", "tvb.tests.framework"], skip_import=True)
# -*- coding: utf-8 -*-
import time
import numpy as np
from tvb.basic.profile import TvbProfile
TvbProfile.set_profile(TvbProfile.LIBRARY_PROFILE)
from tvb_multiscale.examples.plot_results import plot_results
from tvb_multiscale.config import CONFIGURED
from tvb_multiscale.tvb.simulator_builder import SimulatorBuilder
from tvb_multiscale.plot.plotter import Plotter
from tvb.simulator.models.reduced_wong_wang_exc_io_inh_i import ReducedWongWangExcIOInhI
from tvb.simulator.models.spiking_wong_wang_exc_io_inh_i import SpikingWongWangExcIOInhI
from tvb.simulator.models.multiscale_wong_wang_exc_io_inh_i import MultiscaleWongWangExcIOInhI
from tvb.simulator.models.wilson_cowan_constraint import WilsonCowan
from tvb.simulator.models.generic_2d_oscillator_multiscale import Generic2dOscillator
def main_example(tvb_sim_model=ReducedWongWangExcIOInhI,
connectivity=CONFIGURED.DEFAULT_CONNECTIVITY_ZIP,
simulation_length=100.0,
config=CONFIGURED,
**model_params):
plotter = Plotter(config)
# ----------------------1. Define a TVB simulator (model, integrator, monitors...)----------------------------------
simulator_builder = SimulatorBuilder()
# Optionally modify the default configuration:
simulator_builder.model = tvb_sim_model
def profile(request):
profile = request.config.getoption("--profile")
TvbProfile.set_profile(profile)
return profile
def applicationWillTerminate_(self, notification):
""" Make sure no TVB subprocess is left behind running """
execute_stop()
app = AppKit.NSApplication.sharedApplication()
delegate = ApplicationDelegate.alloc().init()
app.setDelegate_(delegate)
AppHelper.runEventLoop()
if __name__ == "__main__":
ARGS = parse_commandline()
# Do not run BaseSettingsProfile.initialize_profile(..) as we do not want artefacts
TvbProfile.set_profile(ARGS.profile, run_init=False)
PYTHON_EXE_PATH = TvbProfile.current.PYTHON_INTERPRETER_PATH
tvb_storage = TvbProfile.current.TVB_STORAGE
TVB_PID_FILE = os.path.join(tvb_storage, "pid.tvb")
if not os.path.exists(tvb_storage):
try:
os.makedirs(tvb_storage)
except Exception:
sys.exit(
"You do not have enough rights to use TVB storage folder:" +
str(tvb_storage))
if ARGS.subcommand == 'start':
# Start one of TVB interfaces
from tvb.adapters.simulator.hpc_simulator_adapter import HPCSimulatorAdapter
from tvb.basic.logger.builder import get_logger
from tvb.basic.profile import TvbProfile
from tvb.config.init.datatypes_registry import populate_datatypes_registry
from tvb.core.entities.model.model_operation import STATUS_STARTED, STATUS_FINISHED, STATUS_ERROR
from tvb.core.neocom import h5
from tvb.core.services.authorization import AuthorizationManager
from tvb.core.services.backend_clients.hpc_scheduler_client import HPCSchedulerClient
from tvb.storage.storage_interface import StorageInterface
log = get_logger(__name__)
UPDATE_STATUS_KEY = "NEW_STATUS"
if __name__ == '__main__':
TvbProfile.set_profile(TvbProfile.WEB_PROFILE, True)
TvbProfile.current.hpc.IS_HPC_RUN = True
def _encrypt_results(adapter_instance, storage_interface, dir_gid):
output_plain_dir = adapter_instance._get_output_path()
output_plain_files = os.listdir(output_plain_dir)
output_plain_files = [
os.path.join(output_plain_dir, plain_file)
for plain_file in output_plain_files
]
log.info("Encrypt files: {}".format(output_plain_files))
storage_interface.encrypt_inputs(dir_gid, output_plain_files,
HPCSchedulerClient.OUTPUT_FOLDER)
4 is the operation id stored in the DataBase in the table "OPERATIONS" It gets the algorithm, and the adapter with its parameters from database. And finally launches the computation. The results of the computation will be stored by the adapter itself. .. moduleauthor:: Bogdan Neacsa <*****@*****.**> .. moduleauthor:: Lia Domide <*****@*****.**> .. moduleauthor:: Yann Gordon <*****@*****.**> """ ## Make sure selected profile is propagated when launching an operation. import sys from tvb.basic.profile import TvbProfile as tvb_profile tvb_profile.set_profile(sys.argv) ### Overwrite PostgreSQL number of connections when executed in the context of a node from tvb.basic.config.settings import TVBSettings TVBSettings.MAX_DB_CONNECTIONS = TVBSettings.MAX_DB_ASYNC_CONNECTIONS TVBSettings.OPERATION_EXECUTION_PROCESS = True import matplotlib from tvb.basic.logger.builder import get_logger from tvb.core.adapters.abcadapter import ABCAdapter from tvb.core.entities.storage import dao from tvb.core.utils import parse_json_parameters from tvb.core.traits import db_events from tvb.core.services.operationservice import OperationService from tvb.core.services.workflowservice import WorkflowService
# Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
# The Virtual Brain: a simulator of primate brain network dynamics.
# Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
#
#
"""
Find a TS in current project (by Subject) and later run an analyzer on it.
__main__ will contain the code.
.. moduleauthor:: Lia Domide <*****@*****.**>
"""
if __name__ == "__main__":
from tvb.basic.profile import TvbProfile
TvbProfile.set_profile(TvbProfile.COMMAND_PROFILE)
from time import sleep
from tvb.basic.logger.builder import get_logger
from tvb.core.adapters.abcadapter import ABCAdapter
from tvb.core.entities import model
from tvb.core.entities.storage import dao
from tvb.core.entities.transient.structure_entities import DataTypeMetaData
from tvb.core.services.flow_service import FlowService
from tvb.core.services.operation_service import OperationService
from tvb.adapters.analyzers.fourier_adapter import FourierAdapter
from tvb.datatypes.time_series import TimeSeriesRegion
from tvb.datatypes.spectral import FourierSpectrum
LOG = get_logger(__name__)
"""
import importlib
import time
from subprocess import Popen, PIPE
STARTUP_TIC = time.time()
import os
import sys
import cherrypy
import webbrowser
from cherrypy import Tool
from tvb.basic.profile import TvbProfile
if __name__ == '__main__':
TvbProfile.set_profile(sys.argv[1])
from tvb.basic.logger.builder import get_logger
from tvb.core.adapters.abcdisplayer import ABCDisplayer
from tvb.core.decorators import user_environment_execution
from tvb.config.init.initializer import initialize, reset
from tvb.core.services.exceptions import InvalidSettingsException
from tvb.interfaces.web.request_handler import RequestHandler
from tvb.interfaces.web.controllers.base_controller import BaseController
from tvb.interfaces.web.controllers.users_controller import UserController
from tvb.interfaces.web.controllers.help.help_controller import HelpController
from tvb.interfaces.web.controllers.project.project_controller import ProjectController
from tvb.interfaces.web.controllers.project.figure_controller import FigureController
from tvb.interfaces.web.controllers.flow_controller import FlowController
from tvb.interfaces.web.controllers.settings_controller import SettingsController
from tvb.interfaces.web.controllers.burst.region_model_parameters_controller import RegionsModelParametersController
import sys
import ctypes
mex = ctypes.CDLL('libmex')
class mexOut(object):
def write(self, s):
mex.mexPrintf(s)
def flush(self):
mex.mexEvalString('drawnow;')
mex_out = mexOut()
if False:
sys.stdout = sys.stderr = mexOut()
print 'Python stdout/err -> mexPrintf enabled.'
import logging
logging.basicConfig(level=logging.DEBUG, stream=mex_out)
LOG = logging.getLogger('helpers')
LOG.info('ready')
from tvb.basic.profile import TvbProfile
TvbProfile.set_profile(TvbProfile.MATLAB_PROFILE)
.. moduleauthor:: Lia Domide <*****@*****.**>
"""
import os
import sys
import cherrypy
import webbrowser
from copy import copy
from cherrypy import Tool
from sys import platform, argv
### Set running profile from arguments.
from tvb.basic.profile import TvbProfile
TvbProfile.set_profile(argv, True)
from tvb.basic.config.settings import TVBSettings
### For Linux Distribution, correctly set MatplotLib Path, before start.
if TVBSettings().is_linux():
os.environ['MATPLOTLIBDATA'] = os.path.join(
os.path.dirname(sys.executable), 'mpl-data')
# sys.path = ['', os.path.dirname(sys.executable)]
### Import MPLH5 to have the back-end Thread started.
from tvb.interfaces.web.mplh5 import mplh5server
from tvb.basic.logger.builder import get_logger
LOGGER = get_logger('tvb.interfaces.web.mplh5.mplh5server')
mplh5server.start_server(LOGGER)
Example: python operation_async_launcher.py 4 user_name_label
4 is the operation id stored in the DataBase in the table "OPERATIONS"
It gets the algorithm, and the adapter with its parameters from database.
And finally launches the computation.
The results of the computation will be stored by the adapter itself.
.. moduleauthor:: Bogdan Neacsa <*****@*****.**>
.. moduleauthor:: Lia Domide <*****@*****.**>
.. moduleauthor:: Yann Gordon <*****@*****.**>
"""
import sys
from tvb.basic.profile import TvbProfile
if __name__ == '__main__':
TvbProfile.set_profile(sys.argv[2], True)
from tvb.basic.logger.builder import get_logger
from tvb.core.adapters.abcadapter import ABCAdapter
from tvb.core.entities.storage import dao
from tvb.core.utils import parse_json_parameters
from tvb.core.services.operation_service import OperationService
from tvb.core.services.workflow_service import WorkflowService
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')
if __name__ == "__main__":
#Start all TVB tests (if in Coverage mode)
if KEY_COVERAGE in sys.argv:
import tvb.interfaces as intf
SOURCE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(intf.__file__)))
COVERAGE = coverage(source=[SOURCE_DIR], omit=generage_excludes([SOURCE_DIR]), cover_pylib=False)
COVERAGE.start()
## This needs to be executed before any TVB import.
import unittest
import datetime
from tvb.basic.profile import TvbProfile
TvbProfile.set_profile(sys.argv[1])
from tvb.tests.framework.xml_runner import XMLTestRunner
from tvb.tests.framework.core import core_tests_main
from tvb.tests.framework.adapters import adapters_tests_main
from tvb.tests.framework.analyzers import bct_test
from tvb.tests.framework.interfaces.web import web_tests_main
def suite():
"""
Gather all the tests in a test suite.
"""
test_suite = unittest.TestSuite()
test_suite.addTest(core_tests_main.suite())
#
# Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
# Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
# The Virtual Brain: a simulator of primate brain network dynamics.
# Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
#
#
"""
This is intended to be a Benchmarking and Validator script.
.. moduleauthor:: bogdan.neacsa
"""
from tvb.basic.profile import TvbProfile as tvb_profile
tvb_profile.set_profile(["-profile", "CONSOLE_PROFILE"], try_reload=False)
import sys
from time import sleep
from tvb.config import SIMULATOR_MODULE, SIMULATOR_CLASS
from tvb.core.services.flow_service import FlowService
from tvb.core.services.operation_service import OperationService
from tvb.core.entities.storage import dao
from tvb.core.entities.model import STATUS_STARTED, STATUS_FINISHED, STATUS_ERROR, PARAM_RANGE_PREFIX
KEY_PROJECT = 'project'
class ModelValidator(object):
overwrites = {}
#
#
"""
Make use of the correlation_coefficient analyzer to compute functional connectivity, using
the demo data at the region level.
``Run time``:
``Memory requirement``:
.. moduleauthor:: Paula Sanz Leon <*****@*****.**>
"""
from tvb.basic.profile import TvbProfile
TvbProfile.set_profile(["-profile", "LIBRARY_PROFILE"], try_reload=False)
import numpy
import tvb.datatypes.connectivity as connectivity
import tvb.analyzers.correlation_coefficient as corr_coeff
from tvb.datatypes.time_series import TimeSeriesRegion
from tvb.basic.logger.builder import get_logger
from tvb.simulator.plot.tools import *
LOG = get_logger(__name__)
#Load the demo region timeseries dataset
try:
data = numpy.load("demo_data_region_16s_2048Hz.npy")
except IOError:
Launches the web server and configure the controllers for UI.
.. moduleauthor:: Lia Domide <*****@*****.**>
"""
import os
import sys
import cherrypy
import webbrowser
from copy import copy
from cherrypy import Tool
from sys import platform, argv
### This will set running profile from arguments.
from tvb.basic.profile import TvbProfile
TvbProfile.set_profile(argv, True)
from tvb.basic.config.settings import TVBSettings
### For Linux Distribution, correctly set MatplotLib Path, before start.
if TVBSettings().is_linux():
os.environ['MATPLOTLIBDATA'] = os.path.join(TVBSettings().get_library_folder(), 'mpl-data')
### Import MPLH5 to have the back-end Thread started.
from tvb.interfaces.web.mplh5 import mplh5_server
from tvb.basic.logger.builder import get_logger
LOGGER = get_logger('tvb.interfaces.web.mplh5.mplh5_server')
mplh5_server.start_server(LOGGER)
from tvb.core.adapters.abcdisplayer import ABCDisplayer
from tvb.core.decorators import user_environment_execution
from tvb.core.services.settings_service import SettingsService
# Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
# Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
# The Virtual Brain: a simulator of primate brain network dynamics.
# Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
#
#
"""
This is intended to be a Benchmarking and Validator script.
.. moduleauthor:: bogdan.neacsa
"""
if __name__ == '__main__':
from tvb.basic.profile import TvbProfile
TvbProfile.set_profile(TvbProfile.COMMAND_PROFILE)
import sys
from time import sleep
from tvb.config import SIMULATOR_MODULE, SIMULATOR_CLASS
from tvb.core.adapters.abcadapter import ABCAdapter
from tvb.core.services.flow_service import FlowService
from tvb.core.services.operation_service import OperationService
from tvb.core.entities.storage import dao
from tvb.core.entities.model import STATUS_STARTED, STATUS_FINISHED, STATUS_ERROR, PARAM_RANGE_PREFIX
KEY_PROJECT = 'project'
class ModelValidator(object):
"""
tvb.simulator.lab is a umbrella module designed to make console and scripting
work easier by importing all the simulator pieces at once.
.. moduleauthor:: Marmaduke Woodman <*****@*****.**>
"""
import os
import pdb
from time import time
from numpy import * # for load & save not available in pylab
import numpy as np
from tvb.basic.profile import TvbProfile
TvbProfile.set_profile(["-profile", "LIBRARY_PROFILE"], try_reload=False)
from tvb.simulator import (simulator, models, coupling, integrators, monitors,
noise)
from tvb.datatypes import connectivity, surfaces, equations, patterns
from tvb.simulator.common import get_logger
LOG = get_logger(__name__)
PDB = lambda: pdb.set_trace()
def file_exists(fname):
"""
file_exists(fname) is a convenience function to test whether a file
already exists or not. Returns True if we can stat the file, otherwise
4 is the operation id stored in the DataBase in the table "OPERATIONS" It gets the algorithm, and the adapter with its parameters from database. And finally launches the computation. The results of the computation will be stored by the adapter itself. .. moduleauthor:: Bogdan Neacsa <*****@*****.**> .. moduleauthor:: Lia Domide <*****@*****.**> .. moduleauthor:: Yann Gordon <*****@*****.**> """ ## Make sure selected profile is propagated when launching an operation. import sys from tvb.basic.profile import TvbProfile as tvb_profile tvb_profile.set_profile(sys.argv) ### Overwrite PostgreSQL number of connections when executed in the context of a node from tvb.basic.config.settings import TVBSettings TVBSettings.MAX_DB_CONNECTIONS = TVBSettings.MAX_DB_ASYNC_CONNECTIONS TVBSettings.OPERATION_EXECUTION_PROCESS = True import matplotlib from tvb.basic.logger.builder import get_logger from tvb.core.adapters.abcadapter import ABCAdapter from tvb.core.entities.storage import dao from tvb.core.utils import parse_json_parameters from tvb.core.traits import db_events from tvb.core.services.operation_service import OperationService from tvb.core.services.workflow_service import WorkflowService
4 is the operation id stored in the DataBase in the table "OPERATIONS"
It gets the algorithm, and the adapter with its parameters from database.
And finally launches the computation.
The results of the computation will be stored by the adapter itself.
.. moduleauthor:: Bogdan Neacsa <*****@*****.**>
.. moduleauthor:: Lia Domide <*****@*****.**>
.. moduleauthor:: Yann Gordon <*****@*****.**>
"""
import sys
from tvb.basic.profile import TvbProfile
if __name__ == '__main__':
TvbProfile.set_profile(sys.argv[2], True)
from tvb.basic.logger.builder import get_logger
from tvb.core.adapters.abcadapter import ABCAdapter
from tvb.core.entities.storage import dao
from tvb.core.utils import parse_json_parameters
from tvb.core.services.operation_service import OperationService
from tvb.core.services.workflow_service import WorkflowService
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')
# Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
# The Virtual Brain: a simulator of primate brain network dynamics.
# Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
#
#
"""
Based on the Brunel and Wang model.
.. moduleauthor:: Paula Sanz Leon <*****@*****.**>
.. moduleauthor:: Marmaduke Woodman <*****@*****.**>
.. moduleauthor:: Stuart A. Knock <*****@*****.**>
"""
from tvb.basic.profile import TvbProfile
TvbProfile.set_profile(TvbProfile.TEST_LIBRARY_PROFILE)
import inspect
import numpy
from tvb.basic.neotraits.api import NArray, Range, List, Final
import tvb.datatypes.lookup_tables as lookup_tables
import tvb.simulator.models as models
from tvb.simulator.common import get_logger
LOG = get_logger(__name__)
class BrunelWang(models.Model):
"""
.. [DJ_2012] Deco G and Jirsa V. *Ongoing Cortical
Activity at Rest: Criticality, Multistability, and Ghost Attractors*.
import shutil
import os
import sys
from tvb.basic.profile import TvbProfile
from tvb.config.init.initializer import initialize
from tvb.core.entities.file.files_update_manager import FilesUpdateManager
if __name__ == '__main__':
"""
Script written for testing the migration from version 1.5.8 to 2.1.0.
"""
# set web profile
TvbProfile.set_profile(TvbProfile.WEB_PROFILE)
# migrate the database and h5 files
h5_migrating_thread = initialize()
# wait for thread to finish before processing
h5_migrating_thread.join()
# copy files in tvb_root folder so Jenkins can find them
shutil.copytree(
TvbProfile.current.TVB_LOG_FOLDER,
os.path.join(TvbProfile.current.EXTERNALS_FOLDER_PARENT, 'logs'))
# test if there are any files which were not migrated
number_of_unmigrated_files = len(FilesUpdateManager.get_all_h5_paths())
if number_of_unmigrated_files != 0:
sys.exit(-1)