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Source code for tvb.basic.config.profile_settings

# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Scientific Package. This package holds all simulators, and
# analysers necessary to run brain-simulations. You can use it stand alone or
# in conjunction with TheVirtualBrain-Framework Package. See content of the
# documentation-folder for more details. See also http://www.thevirtualbrain.org
#
# (c) 2012-2022, 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 follows:
#
#   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)
#
#

"""
Prepare TVB settings to be grouped under various profile classes.

.. moduleauthor:: Lia Domide <lia.domide@codemart.ro>
"""
import os
import sys

from tvb.basic.config import stored
from tvb.basic.config.environment import Environment
from tvb.basic.config.settings import ClusterSettings, DBSettings, VersionSettings, WebSettings, HPCSettings


[docs]class BaseSettingsProfile(object): TVB_USER_HOME = os.environ.get('TVB_USER_HOME', '~') TVB_CONFIG_FILE = os.path.expanduser(os.path.join(TVB_USER_HOME, '.tvb.configuration')) DEFAULT_STORAGE = os.path.expanduser(os.path.join(TVB_USER_HOME, 'TVB' + os.sep)) FIRST_RUN_STORAGE = os.path.expanduser(os.path.join(TVB_USER_HOME, '.tvb-temp')) LOGGER_CONFIG_FILE_NAME = "logger_config.conf" # Access rights for TVB generated files/folders. ACCESS_MODE_TVB_FILES = 0o744 # Number used for estimation of TVB used storage space MAGIC_NUMBER = 9 def __init__(self): self.manager = stored.SettingsManager(self.TVB_CONFIG_FILE) # Actual storage of all TVB related files self.KEYCLOAK_CONFIG = self.manager.get_attribute(stored.KEY_KC_CONFIGURATION, '') self.KEYCLOAK_LOGIN_ENABLED = self.manager.get_attribute(stored.KEY_ENABLE_KC_LOGIN, False, eval) self.KEYCLOAK_WEB_CONFIG = self.manager.get_attribute(stored.KEY_KC_WEB_CONFIGURATION, '') self.TVB_STORAGE = self.manager.get_attribute(stored.KEY_STORAGE, self.FIRST_RUN_STORAGE, str) self.UPLOAD_KEY_PATH = self.manager.get_attribute(stored.KEY_UPLOAD_PRIVATE_KEY_PATH, None, str) self.TRACE_USER_ACTIONS = self.manager.get_attribute(stored.KEY_TRACE_USER_ACTIONS, False, eval) self.TVB_LOG_FOLDER = os.path.join(self.TVB_STORAGE, "logs") self.TVB_TEMP_FOLDER = os.path.join(self.TVB_STORAGE, "TEMP") self.env = Environment() self.cluster = ClusterSettings(self.manager) self.hpc = HPCSettings(self.manager) self.web = WebSettings(self.manager) self.db = DBSettings(self.manager, self.DEFAULT_STORAGE, self.TVB_STORAGE) self.version = VersionSettings(self.manager, self.BIN_FOLDER) self.file_storage = self.manager.get_attribute(stored.KEY_FILE_STORAGE, 'h5', str) self.EXTERNALS_FOLDER_PARENT = os.path.dirname(self.BIN_FOLDER) if not self.env.is_distribution(): self.EXTERNALS_FOLDER_PARENT = os.path.dirname(self.EXTERNALS_FOLDER_PARENT) # The path to the matlab executable (if existent). Otherwise just return an empty string. value = self.manager.get_attribute(stored.KEY_MATLAB_EXECUTABLE, '', str) or '' if value == 'None': value = '' self.MATLAB_EXECUTABLE = value # Maximum number of vertices acceptable o be part of a surface at import time. self.MAX_SURFACE_VERTICES_NUMBER = self.manager.get_attribute(stored.KEY_MAX_NR_SURFACE_VERTEX, 300000, int) # Max number of ops that can be scheduled from UI in a PSE. To be correlated with the oarsub limitations self.MAX_RANGE_NUMBER = self.manager.get_attribute(stored.KEY_MAX_RANGE_NR, 2000, int) # Max number of threads in the pool of ops running in parallel. TO be correlated with CPU cores self.MAX_THREADS_NUMBER = self.manager.get_attribute(stored.KEY_MAX_THREAD_NR, 4, int) self.OPERATIONS_BACKGROUND_JOB_INTERVAL = self.manager.get_attribute(stored.KEY_OP_BACKGROUND_INTERVAL, 60, int) # The maximum disk space that can be used by one single user, in KB. self.MAX_DISK_SPACE = self.manager.get_attribute(stored.KEY_MAX_DISK_SPACE_USR, 5 * 1024 * 1024, int) @property
[docs] def BIN_FOLDER(self): """ Return path towards tvb_bin location. It will be used in some environment for determining the starting point """ try: import tvb_bin return os.path.dirname(os.path.abspath(tvb_bin.__file__)) except ImportError: return "."
@property
[docs] def PYTHON_INTERPRETER_PATH(self): """ Get Python path, based on current environment. """ if self.env.is_mac_deployment(): return os.path.join(os.path.dirname(sys.executable), "python") return sys.executable
[docs] def prepare_for_operation_mode(self): """ Overwrite PostgreSQL number of connections when executed in the context of a node. """ self.db.MAX_CONNECTIONS = self.db.MAX_ASYNC_CONNECTIONS self.cluster.IN_OPERATION_EXECUTION_PROCESS = True self.hpc.IN_OPERATION_EXECUTION_PROCESS = True
[docs] def initialize_profile(self): """ Make sure tvb folders are created. """ if not os.path.exists(self.TVB_LOG_FOLDER): os.makedirs(self.TVB_LOG_FOLDER) if not os.path.exists(self.TVB_TEMP_FOLDER): os.makedirs(self.TVB_TEMP_FOLDER) if not os.path.exists(self.TVB_STORAGE): os.makedirs(self.TVB_STORAGE)
[docs] def initialize_for_deployment(self): library_folder = self.env.get_library_folder(self.BIN_FOLDER) if self.env.is_windows_deployment(): self.env.setup_python_path(library_folder, os.path.join(library_folder, 'lib-tk')) self.env.append_to_path(library_folder) self.env.setup_tk_tcl_environ(library_folder) if self.env.is_mac_deployment(): # MacOS package structure is in the form: # Contents/Resorces/lib/python2.7/tvb . PYTHONPATH needs to be set # at the level Contents/Resources/lib/python2.7/ and the root path # from where to start looking for TK and TCL up to Contents/ tcl_root = os.path.dirname(os.path.dirname(os.path.dirname(library_folder))) self.env.setup_tk_tcl_environ(tcl_root) self.env.setup_python_path(library_folder, os.path.join(library_folder, 'site-packages.zip'), os.path.join(library_folder, 'lib-dynload')) if self.env.is_linux_deployment(): # Note that for the Linux package some environment variables like LD_LIBRARY_PATH, # LD_RUN_PATH, PYTHONPATH and PYTHONHOME are set also in the startup scripts. self.env.setup_python_path(library_folder, os.path.join(library_folder, 'lib-tk')) self.env.setup_tk_tcl_environ(library_folder) # Correctly set MatplotLib Path, before start. mpl_data_path_maybe = os.path.join(library_folder, 'mpl-data') try: os.stat(mpl_data_path_maybe) os.environ['MATPLOTLIBDATA'] = mpl_data_path_maybe except: pass
[docs]class LibrarySettingsProfile(BaseSettingsProfile): """ Profile used when scientific library is used without storage and without web UI. """ TVB_STORAGE = os.path.expanduser(os.path.join("~", "TVB" + os.sep)) LOGGER_CONFIG_FILE_NAME = "library_logger.conf" def __init__(self): super(LibrarySettingsProfile, self).__init__()
[docs]class TestLibraryProfile(LibrarySettingsProfile): """ Profile for library unit-tests. """ LOGGER_CONFIG_FILE_NAME = "library_logger_test.conf" def __init__(self): super(TestLibraryProfile, self).__init__() self.TVB_LOG_FOLDER = "TEST_OUTPUT"
[docs]class MATLABLibraryProfile(LibrarySettingsProfile): """ Profile use library use from MATLAB. """ LOGGER_CONFIG_FILE_NAME = None