# -*- 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 json
import os
import sys
import requests
from requests import HTTPError
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, encryption_handler):
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))
encryption_handler.encrypt_inputs(output_plain_files, HPCSchedulerClient.OUTPUT_FOLDER)
[docs]def do_operation_launch(simulator_gid, available_disk_space, is_group_launch, base_url, operation_id, plain_dir='/root/plain'):
try:
log.info("Preparing HPC launch for simulation with id={}".format(simulator_gid))
populate_datatypes_registry()
log.info("Current TVB profile has HPC run=: {}".format(TvbProfile.current.hpc.IS_HPC_RUN))
encryption_handler = StorageInterface.get_encryption_handler(simulator_gid)
_request_passfile(simulator_gid, operation_id, base_url, encryption_handler.get_password_file())
encryption_handler.decrypt_results_to_dir(plain_dir)
log.info("Current wdir is: {}".format(plain_dir))
view_model = h5.load_view_model(simulator_gid, plain_dir)
adapter_instance = HPCSimulatorAdapter(plain_dir, is_group_launch)
_update_operation_status(STATUS_STARTED, simulator_gid, operation_id, base_url)
adapter_instance._prelaunch(None, view_model, available_disk_space)
_encrypt_results(adapter_instance, encryption_handler)
_update_operation_status(STATUS_FINISHED, simulator_gid, operation_id, base_url)
except Exception as excep:
log.error("Could not execute operation {}".format(str(sys.argv[1])))
log.exception(excep)
_update_operation_status(STATUS_ERROR, simulator_gid, operation_id, base_url)
raise excep
# TODO: extract common rest api parts
CHUNK_SIZE = 128
def _save_file(file_path, response):
with open(file_path, 'wb') as local_file:
for chunk in response.iter_content(chunk_size=CHUNK_SIZE):
if chunk:
local_file.write(chunk)
return file_path
def _request_passfile(simulator_gid, operation_id, base_url, destination_path):
# type: (str, str, str, str) -> str
try:
req_params = "{}/hpc/encryption_config/{}/{}".format(base_url, simulator_gid, operation_id)
log.info('URL is: {}'.format(req_params))
response = _build_secured_request().get(req_params)
log.info('Response is: {}'.format(response))
if response.ok:
log.info('Passfile downloaded at: {}'.format(destination_path))
path = _save_file(destination_path, response)
if not os.path.exists(path):
raise Exception("Cannot find password file.")
return path
except HTTPError:
log.warning(
"Failed to request passfile from TVB server {} for simulator {}".format(base_url, simulator_gid))
def _update_operation_status(status, simulator_gid, operation_id, base_url):
# type: (str, str, str, str) -> None
try:
req_params = "{}/hpc/update_status/{}/{}".format(base_url, simulator_gid, operation_id)
log.info('URL is: {}'.format(req_params))
response = _build_secured_request().put(req_params, data={
UPDATE_STATUS_KEY: status,
})
if not response.ok:
log.warning("Failed to update status. {}".format(response.json()))
except Exception:
log.warning(
"Failed to notify TVB server {} for simulator {} status update {}".format(base_url, simulator_gid, status))
def _build_secured_request():
token_file_path = os.path.join(HPCSchedulerClient.HOME_FOLDER_MOUNT, ".token")
kc_config_file_path = os.path.join(HPCSchedulerClient.HOME_FOLDER_MOUNT, ".kc_config")
token = ""
if os.path.exists(token_file_path) and os.path.exists(kc_config_file_path):
try:
with open(token_file_path, "r") as file:
refresh_token = file.read()
kc_instance = AuthorizationManager(kc_config_file_path).get_keycloak_instance()
response = kc_instance.refresh_token(refresh_token.replace('\n', ''))
token = response['access_token']
except Exception as e:
log.error(e, exc_info=True)
else:
log.warning("Token file was not found.")
with requests.Session() as request:
auth_header = {"Authorization": "Bearer {}".format(token)}
request.headers.update(auth_header)
return request
if __name__ == '__main__':
simulator_gid = sys.argv[1]
available_disk_space = sys.argv[2]
is_group_launch = json.loads(sys.argv[3].lower())
base_url = sys.argv[4]
operation_id = sys.argv[5]
do_operation_launch(simulator_gid, available_disk_space, is_group_launch, base_url, operation_id)
