Source code for brainvisa.data.neuroHierarchy
# -*- coding: utf-8 -*-
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"""
This module defines functions to load Brainvisa **databases**.
The databases objects are stored in a global variable:
.. py:data:: databases
:py:class:`brainvisa.data.sqlFSODatabase.SQLDatabases` object which contains the loaded Brainvisa databases.
This object is created with the function :py:func:`initializeDatabases`.
Then each each database can be loaded with the function :py:func:`openDatabases`.
An object :py:class:`brainvisa.data.sqlFSODatabase.SQLDatabase` is created for each database selected in Brainvisa options.
The function :py:func:`hierarchies` enables to get the list of databases objects.
"""
from __future__ import print_function
from __future__ import absolute_import
import os
from brainvisa.data.sqlFSODatabase import SQLDatabase, SQLDatabases, DatabaseError, databaseVersion, databaseVersions
from brainvisa.processing.neuroException import showException, showWarning
from brainvisa.configuration import neuroConfig
# Import read and write diskitem because neuroHierarchy.ReadDiskItem and
# neuroHierarchy.WriteDiskItem is used in some processes
from brainvisa.data.readdiskitem import ReadDiskItem
from brainvisa.data.writediskitem import WriteDiskItem
databases = None
[docs]def initializeDatabases():
"""
Creates the object :py:data:`databases` which is an instance of :py:class:`brainvisa.data.sqlFSODatabase.SQLDatabases`.
It will contain all loaded databases.
"""
global databases
databases = SQLDatabases()
[docs]def openDatabases():
"""
Loads databases which are selected in Brainvisa options.
For each database, an object :py:class:`brainvisa.data.sqlFSODatabase.SQLDatabase` is created.
The new database objects are added to :py:data:`databases`, any existing database in this object is previously removed.
Warning messages may be displayed if a database is readonly or uses a deprecated ontology (*brainvisa-3.0*).
"""
from brainvisa.processes import defaultContext
global databases
newDatabases = []
for dbSettings in neuroConfig.dataPath:
try:
if getattr(dbSettings, "builtin", False) and databases.hasDatabase(dbSettings.directory): # builtin databases are not re created
newDatabases.append(databases.database(dbSettings.directory))
else:
databases.remove(dbSettings.directory)
if dbSettings.expert_settings.fedji_backend:
from fedji.axon_frontend import AxonFedjiDatabase
base = AxonFedjiDatabase(
dbSettings.directory, fom_name=dbSettings.expert_settings.ontology)
newDatabases.append(base)
else:
remoteAccessURI = os.path.join(
dbSettings.directory, 'remoteAccessURI')
if os.path.exists(remoteAccessURI):
raise NotImplementedError(
'Remote database access has been removed from '
'BrainVISA, it was an experimental feature. '
'Please remove {0} and check your database '
'configuration.'.format(remoteAccessURI)
)
else:
otherSqliteFiles = []
if dbSettings.expert_settings.sqliteFileName != ":memory:" and dbSettings.expert_settings.sqliteFileName != ":temporary:":
if dbSettings.expert_settings.sqliteFileName:
path, ext = os.path.splitext(
dbSettings.expert_settings.sqliteFileName)
else:
path = os.path.join(
dbSettings.directory, 'database')
ext = '.sqlite'
sqlite = path + "-" + databaseVersion + ext
# other versions of sqlite file
other = path + ext
if os.path.exists(other):
otherSqliteFiles.append(other)
for version in databaseVersions.keys():
if version != databaseVersion:
other = path + "-" + version + ext
if os.path.exists(other):
otherSqliteFiles.append(
path + "-" + version + ext)
else:
sqlite = dbSettings.expert_settings.sqliteFileName
base = SQLDatabase(
sqlite, dbSettings.directory, fso=dbSettings.expert_settings.ontology,
context=defaultContext(), otherSqliteFiles=otherSqliteFiles, settings=dbSettings)
newDatabases.append(base)
# Usually users do not have to modify a builtin
# database. Therefore no warning is shown for these
# databases.
if ((not dbSettings.builtin) and (not os.access(dbSettings.directory, os.W_OK) or (os.path.exists(sqlite) and not os.access(sqlite, os.W_OK)))):
showWarning(
_t_("The database " + base.name + " is read only, you will not be able to add new items in this database."))
if base.fso.name == "brainvisa-3.0":
showWarning(
_t_("The database " + base.name + " uses brainvisa-3.0 ontology which is deprecated. You should convert this database to the new ontology using the process Data management -> Convert Old database."))
except Exception:
showException()
# update SQLDatabases object
databases.removeDatabases()
for db in newDatabases:
databases.add(db)
[docs]def hierarchies():
"""
Returns a list of :py:class:`brainvisa.data.sqlFSODatabase.SQLDatabase` objects representing the databases currently loaded in Brainvisa.
"""
return list(databases._databases.values())
def update_soma_workflow_translations():
if not neuroConfig.fastStart:
translation_file = open(
os.path.join(neuroConfig.homeBrainVISADir, 'soma-workflow.translation'), 'w')
for db in databases.iterDatabases():
uuid = getattr(db, 'uuid', None)
if uuid:
print(uuid, db.name, file=translation_file)
else:
print("warning: " + repr(db.name) + " has no uuid")
translation_file.close()
