def load(info):
registerAccessFlag(constants.ACCESS_FLAG_EXECUTE_TASK,
name='Execute analyses',
admin=True)
TokenScope.describeScope(constants.TOKEN_SCOPE_EXECUTE_TASK,
name='Execute tasks',
description='Execute item tasks.')
TokenScope.describeScope(constants.TOKEN_SCOPE_AUTO_CREATE_CLI,
'Item task auto-creation',
'Create new CLIs via automatic introspection.',
admin=True)
ModelImporter.model('item').ensureIndex(
['meta.isItemTask', {
'sparse': True
}])
ModelImporter.model('item').exposeFields(level=AccessType.READ,
fields='createdByJob')
ModelImporter.model('job', 'jobs').exposeFields(
level=AccessType.READ, fields={'itemTaskId', 'itemTaskBindings'})
events.bind('jobs.job.update', info['name'], _onJobSave)
events.bind('data.process', info['name'], _onUpload)
info['apiRoot'].item_task = ItemTask()
def load(info):
registerAccessFlag(constants.ACCESS_FLAG_EXECUTE_TASK, name='Execute analyses', admin=True)
TokenScope.describeScope(
constants.TOKEN_SCOPE_EXECUTE_TASK, name='Execute tasks', description='Execute item tasks.')
TokenScope.describeScope(
constants.TOKEN_SCOPE_AUTO_CREATE_CLI, 'Item task auto-creation',
'Create new CLIs via automatic introspection.', admin=True)
ModelImporter.model('item').ensureIndex(['meta.isItemTask', {'sparse': True}])
ModelImporter.model('item').exposeFields(level=AccessType.READ, fields='createdByJob')
ModelImporter.model('job', 'jobs').exposeFields(level=AccessType.READ, fields={
'itemTaskId', 'itemTaskBindings'})
events.bind('jobs.job.update', info['name'], _onJobSave)
events.bind('data.process', info['name'], _onUpload)
info['apiRoot'].item_task = ItemTask()
info['apiRoot'].item.route('POST', (':id', 'item_task_slicer_cli_description'),
runSlicerCliTasksDescriptionForItem)
info['apiRoot'].item.route('PUT', (':id', 'item_task_slicer_cli_xml'),
configureItemTaskFromSlicerCliXml)
info['apiRoot'].item.route('POST', (':id', 'item_task_json_description'),
runJsonTasksDescriptionForItem)
info['apiRoot'].item.route('PUT', (':id', 'item_task_json_specs'),
configureItemTaskFromJson)
info['apiRoot'].folder.route('POST', (':id', 'item_task_slicer_cli_description'),
runSlicerCliTasksDescriptionForFolder)
info['apiRoot'].folder.route('POST', (':id', 'item_task_slicer_cli_xml'),
createItemTasksFromSlicerCliXml)
info['apiRoot'].folder.route('POST', (':id', 'item_task_json_description'),
runJsonTasksDescriptionForFolder)
info['apiRoot'].folder.route('POST', (':id', 'item_task_json_specs'),
createItemTasksFromJson)
def __init__(self):
self.resourceName = 'smqtk'
self.route('GET', ('settings',), self.settings)
self.route('POST', ('process_images',), self.processImages)
TokenScope.describeScope(SMQTK_SETTING_READ, 'Read SMQTK settings',
'Allow clients to look up the SMQTK settings, including private '
'fields such as database credentials.')
def __init__(self):
self.resourceName = 'smqtk'
self.route('GET', ('settings', ), self.settings)
self.route('POST', ('process_images', ), self.processImages)
TokenScope.describeScope(
SMQTK_SETTING_READ, 'Read SMQTK settings',
'Allow clients to look up the SMQTK settings, including private '
'fields such as database credentials.')
def validate(self, doc):
from .token import Token
from .user import User
if doc['tokenDuration']:
doc['tokenDuration'] = float(doc['tokenDuration'])
else:
doc['tokenDuration'] = None
doc['name'] = doc['name'].strip()
doc['active'] = bool(doc.get('active', True))
if doc['scope'] is not None:
if not isinstance(doc['scope'], (list, tuple)):
raise ValidationException('Scope must be a list, or None.')
if not doc['scope']:
raise ValidationException(
'Custom scope list must not be empty.')
# Ensure only registered scopes are being set
admin = User().load(doc['userId'], force=True)['admin']
scopes = TokenScope.scopeIds(admin)
unknownScopes = set(doc['scope']) - scopes
if unknownScopes:
raise ValidationException('Invalid scopes: %s.' %
','.join(unknownScopes))
# Deactivating an already existing token
if '_id' in doc and not doc['active']:
Token().clearForApiKey(doc)
return doc
def validate(self, doc):
from .token import Token
from .user import User
if doc['tokenDuration']:
doc['tokenDuration'] = float(doc['tokenDuration'])
else:
doc['tokenDuration'] = None
doc['name'] = doc['name'].strip()
doc['active'] = bool(doc.get('active', True))
if doc['scope'] is not None:
if not isinstance(doc['scope'], (list, tuple)):
raise ValidationException('Scope must be a list, or None.')
if not doc['scope']:
raise ValidationException('Custom scope list must not be empty.')
# Ensure only registered scopes are being set
admin = User().load(doc['userId'], force=True)['admin']
scopes = TokenScope.scopeIds(admin)
unknownScopes = set(doc['scope']) - scopes
if unknownScopes:
raise ValidationException('Invalid scopes: %s.' % ','.join(unknownScopes))
# Deactivating an already existing token
if '_id' in doc and not doc['active']:
Token().clearForApiKey(doc)
return doc
def load(info):
registerAccessFlag(constants.ACCESS_FLAG_EXECUTE_TASK,
name='Execute analyses',
admin=True)
TokenScope.describeScope(constants.TOKEN_SCOPE_EXECUTE_TASK,
name='Execute tasks',
description='Execute item tasks.')
TokenScope.describeScope(constants.TOKEN_SCOPE_AUTO_CREATE_CLI,
'Item task auto-creation',
'Create new CLIs via automatic introspection.',
admin=True)
ModelImporter.model('item').ensureIndex(
['meta.isItemTask', {
'sparse': True
}])
ModelImporter.model('item').exposeFields(level=AccessType.READ,
fields='createdByJob')
ModelImporter.model('job', 'jobs').exposeFields(
level=AccessType.READ, fields={'itemTaskId', 'itemTaskBindings'})
events.bind('jobs.job.update', info['name'], _onJobSave)
events.bind('data.process', info['name'], _onUpload)
info['apiRoot'].item_task = ItemTask()
info['apiRoot'].item.route('POST',
(':id', 'item_task_slicer_cli_description'),
runSlicerCliTasksDescriptionForItem)
info['apiRoot'].item.route('PUT', (':id', 'item_task_slicer_cli_xml'),
configureItemTaskFromSlicerCliXml)
info['apiRoot'].item.route('POST', (':id', 'item_task_json_description'),
runJsonTasksDescriptionForItem)
info['apiRoot'].item.route('PUT', (':id', 'item_task_json_specs'),
configureItemTaskFromJson)
info['apiRoot'].folder.route('POST',
(':id', 'item_task_slicer_cli_description'),
runSlicerCliTasksDescriptionForFolder)
info['apiRoot'].folder.route('POST', (':id', 'item_task_slicer_cli_xml'),
createItemTasksFromSlicerCliXml)
info['apiRoot'].folder.route('POST', (':id', 'item_task_json_description'),
runJsonTasksDescriptionForFolder)
info['apiRoot'].folder.route('POST', (':id', 'item_task_json_specs'),
createItemTasksFromJson)
def testListScopes(server):
resp = server.request('/token/scopes')
assertStatusOk(resp)
assert resp.json == TokenScope.listScopes()
assert 'custom' in resp.json
assert isinstance(resp.json['custom'], list)
assert 'adminCustom' in resp.json
assert isinstance(resp.json['adminCustom'], list)
for scope in resp.json['custom'] + resp.json['adminCustom']:
assert 'id' in scope
assert 'name' in scope
assert 'description' in scope
def testListScopes(server):
resp = server.request('/token/scopes')
assertStatusOk(resp)
assert resp.json == TokenScope.listScopes()
assert 'custom' in resp.json
assert isinstance(resp.json['custom'], list)
assert 'adminCustom' in resp.json
assert isinstance(resp.json['adminCustom'], list)
for scope in resp.json['custom'] + resp.json['adminCustom']:
assert 'id' in scope
assert 'name' in scope
assert 'description' in scope
def testListScopes(self):
resp = self.request('/token/scopes')
self.assertStatusOk(resp)
self.assertEqual(resp.json, TokenScope.listScopes())
self.assertIn('custom', resp.json)
self.assertIsInstance(resp.json['custom'], list)
self.assertIn('adminCustom', resp.json)
self.assertIsInstance(resp.json['adminCustom'], list)
for scope in resp.json['custom'] + resp.json['adminCustom']:
self.assertIn('id', scope)
self.assertIn('name', scope)
self.assertIn('description', scope)
def testListScopes(self):
resp = self.request('/token/scopes')
self.assertStatusOk(resp)
self.assertEqual(resp.json, TokenScope.listScopes())
self.assertIn('custom', resp.json)
self.assertIsInstance(resp.json['custom'], list)
self.assertIn('adminCustom', resp.json)
self.assertIsInstance(resp.json['adminCustom'], list)
for scope in resp.json['custom'] + resp.json['adminCustom']:
self.assertIn('id', scope)
self.assertIn('name', scope)
self.assertIn('description', scope)
def listScopes(self):
return TokenScope.listScopes()
from girder_worker.docker.tasks import docker_run
from girder_worker.docker.transforms import VolumePath
from girder_worker.docker.transforms.girder import (
GirderFolderIdToVolume, GirderUploadVolumePathToFolder,
GirderFileIdToVolume, ProgressPipe)
from PIL import Image
CLEANUP_TOKEN_SCOPE = 'stroke_ct.cleanup'
DATE_FMT = '%A %B %-d, %Y'
DAYS_UNTIL_EMAIL = 7
DAYS_UNTIL_DELETION = 14
DELETE_SUBJECT = 'Warning: your timelapse data will be deleted soon!'
TokenScope.describeScope(
CLEANUP_TOKEN_SCOPE,
'Delete expired timelapse data',
description='Delete expired timelapses and send emails for pending ones.',
admin=True)
# [[x1, y2], [x2, y2]] in pixel coordinates
_MASK_RECT_SCHEMA = {
'type': 'array',
'maxItems': 2,
'minItems': 2,
'items': {
'type': 'array',
'maxItems': 2,
'minItems': 2,
'items': {
'type': 'integer',
'minimum': 0
def listScopes(self, params):
return TokenScope.listScopes()