def mountServer(path, database=None, fuseOptions=None, quiet=False, plugins=None):
"""
Perform the mount.
:param path: the mount location.
:param database: a database connection URI, if it contains '://'.
Otherwise, the default database is used.
:param fuseOptions: a comma-separated string of options to pass to the FUSE
mount. A key without a value is taken as True. Boolean values are
case insensitive. For instance, 'foreground' or 'foreground=True' will
keep this program running until the SIGTERM or unmounted.
:param quiet: if True, suppress Girder logs.
:param plugins: an optional list of plugins to enable. If None, use the
plugins that are configured.
"""
if quiet:
curConfig = config.getConfig()
curConfig.setdefault('logging', {})['log_quiet'] = True
curConfig.setdefault('logging', {})['log_level'] = 'FATAL'
girder._setupLogger()
if database and '://' in database:
cherrypy.config['database']['uri'] = database
if plugins is not None:
plugins = plugins.split(',')
webroot, appconf = configureServer(plugins=plugins)
girder._setupCache()
opClass = ServerFuse(stat=os.stat(path))
options = {
# By default, we run in the background so the mount command returns
# immediately. If we run in the foreground, a SIGTERM will shut it
# down
'foreground': False,
# Cache files if their size and timestamp haven't changed.
# This lets the OS buffer files efficiently.
'auto_cache': True,
# We aren't specifying our own inos
'use_ino': False,
# read-only file system
'ro': True,
}
if sys.platform != 'darwin':
# Automatically unmount when we try to mount again
options['auto_unmount'] = True
if fuseOptions:
for opt in fuseOptions.split(','):
if '=' in opt:
key, value = opt.split('=', 1)
value = (False if value.lower() == 'false' else
True if value.lower() == 'true' else value)
else:
key, value = opt, True
if key in ('use_ino', 'ro', 'rw') and options.get(key) != value:
logprint.warning('Ignoring the %s=%r option' % (key, value))
continue
options[key] = value
Setting().set(SettingKey.GIRDER_MOUNT_INFORMATION,
{'path': path, 'mounttime': time.time()})
FUSELogError(opClass, path, **options)
def mountServer(path, database=None, fuseOptions=None, quiet=False, plugins=None):
"""
Perform the mount.
:param path: the mount location.
:param database: a database connection URI, if it contains '://'.
Otherwise, the default database is used.
:param fuseOptions: a comma-separated string of options to pass to the FUSE
mount. A key without a value is taken as True. Boolean values are
case insensitive. For instance, 'foreground' or 'foreground=True' will
keep this program running until the SIGTERM or unmounted.
:param quiet: if True, suppress Girder logs.
:param plugins: an optional list of plugins to enable. If None, use the
plugins that are configured.
"""
if quiet:
curConfig = config.getConfig()
curConfig.setdefault('logging', {})['log_quiet'] = True
curConfig.setdefault('logging', {})['log_level'] = 'FATAL'
girder._attachFileLogHandlers()
if database and '://' in database:
cherrypy.config['database']['uri'] = database
if plugins is not None:
plugins = plugins.split(',')
webroot, appconf = configureServer(plugins=plugins)
girder._setupCache()
opClass = ServerFuse(stat=os.stat(path))
options = {
# By default, we run in the background so the mount command returns
# immediately. If we run in the foreground, a SIGTERM will shut it
# down
'foreground': False,
# Cache files if their size and timestamp haven't changed.
# This lets the OS buffer files efficiently.
'auto_cache': True,
# We aren't specifying our own inos
'use_ino': False,
# read-only file system
'ro': True,
}
if sys.platform != 'darwin':
# Automatically unmount when we try to mount again
options['auto_unmount'] = True
if fuseOptions:
for opt in fuseOptions.split(','):
if '=' in opt:
key, value = opt.split('=', 1)
value = (False if value.lower() == 'false' else
True if value.lower() == 'true' else value)
else:
key, value = opt, True
if key in ('use_ino', 'ro', 'rw') and options.get(key) != value:
logprint.warning('Ignoring the %s=%r option' % (key, value))
continue
options[key] = value
Setting().set(SettingKey.GIRDER_MOUNT_INFORMATION,
{'path': path, 'mounttime': time.time()})
FUSELogError(opClass, path, **options)
def main(plugins):
if plugins is not None:
plugins = plugins.split(',')
webroot, appconf = configureServer(plugins=plugins)
_launchShell({
'webroot': webroot,
'appconf': appconf
})
def main(plugins, script, args):
if plugins is not None:
plugins = plugins.split(',')
webroot, appconf = configureServer(plugins=plugins)
if script is None:
_launchShell({
'webroot': webroot,
'appconf': appconf
})
else:
globals_ = {k: v for k, v in six.viewitems(globals()) if k not in {'__file__', '__name__'}}
sys.argv = [script] + list(args)
six.exec_(open(script, 'rb').read(), dict(
webroot=webroot, appconf=appconf, __name__='__main__',
__file__=script, **globals_))
def main(plugins, script, args):
if plugins is not None:
plugins = plugins.split(',')
webroot, appconf = configureServer(plugins=plugins)
if script is None:
_launchShell({
'webroot': webroot,
'appconf': appconf
})
else:
globals_ = {k: v for k, v in six.viewitems(globals()) if k not in {'__file__', '__name__'}}
sys.argv = [script] + list(args)
exec(open(script, 'rb').read(), dict(
webroot=webroot, appconf=appconf, __name__='__main__',
__file__=script, **globals_))
# This ensures that:
# - Worker settings are correct
# - there is at least one admin user
# - there is a default task folder
# - there is at least one assetstore
from girder.models.assetstore import Assetstore
from girder.models.collection import Collection
from girder.models.folder import Folder
from girder.models.setting import Setting
from girder.models.user import User
from girder.utility.server import configureServer
# This loads plugins, allowing setting validation
configureServer()
# Ensure worker settings are correct
Setting().set('worker.broker', 'amqp://*****:*****@rabbitmq/')
Setting().set('worker.backend', 'rpc://*****:*****@rabbitmq/')
Setting().set('worker.api_url', 'http://*****:*****@nowhere.nil')
adminUser = User().findOne({'admin': True})
# Make sure we have an assetstore
if Assetstore().findOne() is None:
Assetstore().createFilesystemAssetstore('Assetstore', '/assetstore')
# If we don't have a default task folder, make a task collection and folder
if not Setting().get('slicer_cli_web.task_folder'):
from girder.utility import server as girder_server
girder_server.configureServer()
from girder.models.file import File # noqa: E402, I100
from girder.models.folder import Folder # noqa: E402
from girder.models.item import Item # noqa: E402
from girder.plugins.isic_archive.models.dataset import Dataset # noqa: E402
for dataset in Dataset().find():
print(dataset['name'])
for registration in dataset['metadataFiles']:
metadataFile = File().load(registration['fileId'], force=True)
item = Item().load(metadataFile['itemId'], force=True)
folder = Folder().load(item['folderId'], force=True)
print(' ', metadataFile['name'])
del metadataFile['itemId']
metadataFile['attachedToType'] = ['dataset', 'isic_archive']
metadataFile = File().save(metadataFile)
File().propagateSizeChange(item, -metadataFile['size'])
Item().remove(item)
Folder().remove(folder)
def setup(config, store):
config = {"server": {"api_root": "/plugin/girder/girder/api/v1",
"static_root": "/plugin/girder/girder/static"}}
girder_app, config = configureServer(curConfig=config)
return {"apps": [(girder_app, config, "girder")]}
import pprint
import re
from bson.objectid import ObjectId
from girder.utility import server as girder_server # noqa
girder_server.configureServer() # noqa
from girder.models.file import File # noqa
from girder.models.item import Item # noqa
from isic_archive.models.dataset import Dataset # noqa: E402
for image in Item().find(
{'baseParentId': ObjectId('55943cff9fc3c13155bcad5e')}
):
dataset = Dataset().find({'_id': image['meta']['datasetId']})
print(f'{image["name"]}, {image["_id"]}, {next(dataset)["name"]}')
files = list(File().find({'itemId': image['_id']}))
taken_file_ids = set()
# already migrated
if [f for f in files if 'imageRole' in f]:
continue
superpixel_file_ids = [
f['_id']
for f in files
if 'superpixels' in f['name']
and f['size'] > 0
and f['_id'] not in taken_file_ids
from girder.utility import server as girder_server
girder_server.configureServer()
from girder.models.file import File # noqa: E402, I100
from girder.models.folder import Folder # noqa: E402
from girder.models.item import Item # noqa: E402
from isic_archive.models.dataset import Dataset # noqa: E402
for dataset in Dataset().find():
print(dataset['name'])
for registration in dataset['metadataFiles']:
metadataFile = File().load(registration['fileId'], force=True)
item = Item().load(metadataFile['itemId'], force=True)
folder = Folder().load(item['folderId'], force=True)
print(' ', metadataFile['name'])
del metadataFile['itemId']
metadataFile['attachedToType'] = ['dataset', 'isic_archive']
metadataFile = File().save(metadataFile)
File().propagateSizeChange(item, -metadataFile['size'])
Item().remove(item)
Folder().remove(folder)
