# -*- coding: utf-8 -*-
# This software and supporting documentation are distributed by
# Institut Federatif de Recherche 49
# CEA/NeuroSpin, Batiment 145,
# 91191 Gif-sur-Yvette cedex
# France
#
# This software is governed by the CeCILL license version 2 under
# French law and abiding by the rules of distribution of free software.
# You can use, modify and/or redistribute the software under the
# terms of the CeCILL license version 2 as circulated by CEA, CNRS
# and INRIA at the following URL "http://www.cecill.info".
#
# As a counterpart to the access to the source code and rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
# liability.
#
# In this respect, the user's attention is drawn to the risks associated
# with loading, using, modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean that it is complicated to manipulate, and that also
# therefore means that it is reserved for developers and experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
# requirements in conditions enabling the security of their systems and/or
# data to be ensured and, more generally, to use and operate it in the
# same conditions as regards security.
#
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license version 2 and that you accept its terms.
'''
@author: Yann Cointepas
@organization: U{NeuroSpin<http://www.neurospin.org>} and U{IFR 49<http://www.ifr49.org>}
@license: U{CeCILL version 2<http://www.cecill.info/licences/Licence_CeCILL_V2-en.html>}
'''
from __future__ import print_function
from __future__ import absolute_import
import os
import sys
from soma.configuration import ConfigurationGroup
from soma.signature.api import HasSignature, Signature, FileName, \
Boolean, OpenedChoice, Sequence, Unicode, \
Choice, Any
from soma.minf.api import readMinf
import six
#------------------------------------------------------------------------------
[docs]class DatabasesConfiguration(ConfigurationGroup):
label = 'Databases'
icon = 'database_read.png'
[docs] class FileSystemOntology(HasSignature):
signature = Signature(
'directory', FileName, dict(defaultValue=''),
'selected', Boolean, dict(defaultValue=True),
'read_only', Boolean, dict(defaultValue=False),
)
def __init__(self, directory='', selected=True, read_only=False):
super(DatabasesConfiguration.FileSystemOntology, self).__init__()
self.directory = directory
self.selected = bool(selected)
self.read_only = bool(read_only)
self.onAttributeChange('directory', self._directoryChanged)
def _directoryChanged(self, newDirectory):
if newDirectory and not os.path.exists(newDirectory):
self.selected = False
signature = Signature(
'fso', Sequence(FileSystemOntology), dict(defaultValue=[]),
)
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------
[docs]class ExpertDatabaseSettings(HasSignature):
signature = Signature(
'ontology', OpenedChoice(), dict(defaultValue='brainvisa-3.2.0',
writeIfDefault=True),
'sqliteFileName', FileName, dict(defaultValue=''),
'activate_history', Boolean, dict(defaultValue=False),
'fedji_backend', Boolean, dict(defaultValue=False),
'uuid', Unicode(), dict(defaultValue='', visible=False),
# for compatibility only
'lastIncrementalUpdate', Unicode(), dict(defaultValue='', visible=False),
# no type dict defined in signature types, using Any
'lastIncrementalUpdates', Any(), dict(defaultValue={}, visible=False),
'preferred_formats_order', FormatsSequence(),
dict(defaultValue=[], collapsed=True),
)
def __init__(self):
# The list of ontolgies is never empty, so this test cannot to update this list and new ontology such as freesurfer are not added
# in the expert_settings
# if not ExpertDatabaseSettings.signature[ 'ontology' ].type.values:
# ExpertDatabaseSettings.signature[ 'ontology' ].type.setChoices(
# *ExpertDatabaseSettings.availableOntologies() )
ExpertDatabaseSettings.signature['ontology'].type.setChoices(
*ExpertDatabaseSettings.availableOntologies())
super(ExpertDatabaseSettings, self).__init__()
try:
self.signature['preferred_formats_order'].defaultValue \
= FormatsSequence.all_formats()
except ImportError:
# may happen at startup:
# neuroConfig is using DatabaseSettings and ExpertDatabaseSettings
# in its initialization, and here we cannot import neuroConfig which
# is currently initializing.
pass
def __eq__(self, other):
if not isinstance(other, ExpertDatabaseSettings):
return False
return ((self.ontology == other.ontology)
and (self.sqliteFileName == other.sqliteFileName)
and (self.activate_history == other.activate_history)
and (self.preferred_formats_order
== other.preferred_formats_order))
@staticmethod
def availableOntologies():
ontologies = ['brainvisa-3.2.0', 'brainvisa-3.1.0', 'brainvisa-3.0',
'shared']
moreOntologies = set()
try:
from brainvisa.configuration import neuroConfig
for path in neuroConfig.fileSystemOntologiesPath:
if os.path.exists(path):
for ontology in os.listdir(path):
if ontology == 'flat':
continue
if ontology not in ontologies and ontology not in moreOntologies:
moreOntologies.add(ontology)
except ImportError:
# may happen at startup:
# neuroConfig is using DatabaseSettings and ExpertDatabaseSettings
# in its initialization, and here we cannot import neuroConfig which
# is currently initializing.
pass
ontologies += sorted(moreOntologies)
return ontologies
#------------------------------------------------------------------------------
[docs]class DatabaseSettings(HasSignature):
signature = Signature(
'directory', FileName(
readOnly=True, directoryOnly=True), # dict( defaultValue='' ),
'read_only', Boolean(),
'expert_settings', ExpertDatabaseSettings, dict(collapsed=True),
)
def __init__(self, directory=None, selected=True, read_only=False):
HasSignature.__init__(self)
self.expert_settings = ExpertDatabaseSettings()
if directory:
if os.path.exists(directory):
self.directory = os.path.normpath(directory)
self._selected = selected
if not os.access(directory, os.R_OK + os.W_OK + os.X_OK):
read_only = True
else:
self._selected = False
else:
self._selected = selected
self.builtin = False
self.read_only = read_only
self.onAttributeChange('directory', self._directoryChanged)
self._directoryChanged(directory)
def __eq__(self, other):
return ((self.directory == other.directory)
and (self.expert_settings == other.expert_settings)
and self.read_only == other.read_only)
def _directoryChanged(self, newDirectory):
if newDirectory:
minf = os.path.join(newDirectory, 'database_settings.minf')
if os.path.exists(minf):
#self.expert_settings.preferred_formats_order = []
readMinf(minf, targets=(self.expert_settings, ))
else:
it = six.iteritems(self.expert_settings.signature)
next(it)
for n, v in it:
if n == 'ontology':
self.expert_settings.ontology = 'brainvisa-3.2.0'
else:
setattr(self.expert_settings, n, v.defaultValue)
