def is_distribution():
"""
Return True when TVB is used with Python installed natively (with GitHub clone, SVN, pip or conda)
"""
svn_variable = 'SVN_REVISION'
if svn_variable in os.environ:
# Usage in Hudson build
return False
try:
import tvb_bin
except ImportError:
# No tvb_bin, it means usage from pip or conda
return False
try:
_proc = Popen(["git", "status"], stdout=PIPE, stderr=PIPE)
if "On branch " in str(_proc.communicate()):
# usage from git
return False
except Exception:
pass
try:
_proc = Popen(["svnversion", "."], stdout=PIPE, stderr=PIPE)
version = VersionSettings.parse_svn_version(_proc.communicate()[0])
if version:
# usage from SVN
return False
except Exception:
# Usage from tvb_distribution
return True
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)
def ensure_svn_current_version():
"""
Enforce later revision number is written in 'tvb.version' file
"""
import tvb.basic.config
from tvb.basic.config.settings import VersionSettings
config_folder = os.path.dirname(os.path.abspath(tvb.basic.config.__file__))
svn_variable = 'SVN_REVISION'
if svn_variable in os.environ:
real_svn_number = int(os.environ[svn_variable])
else:
_proc = Popen(["svnversion", "."], stdout=PIPE)
real_svn_number = VersionSettings.parse_svn_version(
str(_proc.communicate()[0]))
with open(os.path.join(config_folder, 'tvb.version'), 'r') as version_file:
version_line = version_file.read()
try:
written_svn_number = VersionSettings.parse_svn_version(
version_line)
except ValueError:
written_svn_number = 0
if written_svn_number == real_svn_number:
print("We will not change file tvb.version")
return
with open(os.path.join(config_folder, 'tvb.version'), 'w') as version_file:
new_text = "Revision: " + str(real_svn_number + 1)
version_file.write(new_text)
print("Updating tvb.version content to: %s because %d != %d" %
(new_text, written_svn_number, real_svn_number))
# Update SVN_REVISION in the current build, as we are creating a new commit
os.environ[svn_variable] = str(real_svn_number + 1)
_proc = Popen([
"svn", "commit", "../scientific_library/tvb/basic/config/tvb.version",
"-m", "Update SVN revision number automatically from Hudson",
"--trust-server-cert"
],
stdout=PIPE)
print(_proc.communicate()[0])
def ensure_tvb_current_revision(branch=None):
"""
Enforce later revision number is written in 'tvb.version' file
"""
import tvb.basic.config
from tvb.basic.config.settings import VersionSettings
config_folder = os.path.dirname(os.path.abspath(tvb.basic.config.__file__))
if branch is None:
branch = "master"
print('Current branch {}'.format(branch))
real_version_number = VersionSettings.fetch_current_revision(branch)
with open(os.path.join(config_folder, 'tvb.version'), 'r') as version_file:
version_line = version_file.read()
try:
written_tvb_number = VersionSettings.parse_revision_number(
version_line)
except ValueError:
written_tvb_number = 0
if written_tvb_number == real_version_number:
print("We will not change file tvb.version")
return
tvb_version_path = "../scientific_library/tvb/basic/config/tvb.version"
print("Tvb version file path: {}".format(tvb_version_path))
paths = [tvb_version_path, os.path.join(config_folder, 'tvb.version')]
for path in paths:
with open(path, 'w') as version_file:
new_text = "Revision: " + str(real_version_number + 1)
version_file.write(new_text)
print(
"Updating tvb.version content in %s to: %s because %d != %d" %
(path, new_text, written_tvb_number, real_version_number))
def __init__(self, web_enabled=True):
self.manager = stored.SettingsManager(self.TVB_CONFIG_FILE)
## Actual storage of all TVB related files
self.TVB_STORAGE = self.manager.get_attribute(stored.KEY_STORAGE,
self.FIRST_RUN_STORAGE,
unicode)
self.TVB_LOG_FOLDER = os.path.join(self.TVB_STORAGE, "logs")
self.TVB_TEMP_FOLDER = os.path.join(self.TVB_STORAGE, "TEMP")
self.TVB_PATH = self.manager.get_attribute(stored.KEY_TVB_PATH, '')
self.env = Environment()
self.cluster = ClusterSettings(self.manager)
self.web = WebSettings(self.manager, web_enabled)
self.db = DBSettings(self.manager, self.DEFAULT_STORAGE,
self.TVB_STORAGE)
self.version = VersionSettings(self.manager, self.BIN_FOLDER)
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)
# 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)
## Configure Traits
self.TRAITS_CONFIGURATION = EnhancedDictionary()
self.TRAITS_CONFIGURATION.interface_method_name = 'interface'
self.TRAITS_CONFIGURATION.use_storage = True
def is_distribution():
"""
Return True when TVB_Distribution package, False when used from a GitHub clone, Pypi, Conda or Docker
"""
try:
import tvb_bin
except ImportError:
# No tvb_bin, it means usage from Pypi or Conda Forge
return False
try:
_proc = Popen(["git", "status"], stdout=PIPE, stderr=PIPE)
if "On branch " in str(_proc.communicate()):
# usage from GitHub clone directly
return False
except Exception:
pass
if os.path.join(
os.path.dirname(
os.path.dirname(
os.path.dirname(os.path.abspath(tvb_bin.__file__)))),
"externals"):
# usage from GitHub clone without got cmd or inside a Docker container (as a mounted volume)
return False
try:
_proc = Popen(["svnversion", "."], stdout=PIPE, stderr=PIPE)
version = VersionSettings.parse_svn_version(_proc.communicate()[0])
if version:
# usage from SVN (deprecated)
return False
except Exception:
pass
# We default as usage from TVB_Distribution
return True