Source code for galaxy.managers.lddas

import logging

from galaxy import model, util
from galaxy.managers import base as manager_base
from galaxy.managers.datasets import DatasetAssociationManager

log = logging.getLogger(__name__)


[docs]class LDDAManager(DatasetAssociationManager): """ A fairly sparse manager for LDDAs. """ model_class = model.LibraryDatasetDatasetAssociation
[docs] def __init__(self, app): """ Set up and initialize other managers needed by lddas. """ pass
[docs] def get(self, trans, id, check_accessible=True): return manager_base.get_object(trans, id, 'LibraryDatasetDatasetAssociation', check_ownership=False, check_accessible=check_accessible)
def _set_permissions(self, trans, library_dataset, role_ids_dict): dataset = library_dataset.library_dataset_dataset_association.dataset new_access_roles_ids = role_ids_dict["DATASET_ACCESS"] new_manage_roles_ids = role_ids_dict["DATASET_MANAGE_PERMISSIONS"] new_modify_roles_ids = role_ids_dict["LIBRARY_MODIFY"] # ACCESS DATASET ROLES valid_access_roles = [] invalid_access_roles_ids = [] valid_roles_for_dataset, total_roles = trans.app.security_agent.get_valid_roles(trans, dataset) if new_access_roles_ids is None: trans.app.security_agent.make_dataset_public(dataset) else: for role_id in new_access_roles_ids: role = self.role_manager.get(trans, self.app, role_id) if role in valid_roles_for_dataset: valid_access_roles.append(role) else: invalid_access_roles_ids.append(role_id) if len(invalid_access_roles_ids) > 0: log.warning("The following roles could not be added to the dataset access permission: " + str(invalid_access_roles_ids)) access_permission = dict(access=valid_access_roles) trans.app.security_agent.set_dataset_permission(dataset, access_permission) # MANAGE DATASET ROLES valid_manage_roles = [] invalid_manage_roles_ids = [] new_manage_roles_ids = util.listify(new_manage_roles_ids) for role_id in new_manage_roles_ids: role = self.role_manager.get(trans, self.app, role_id) if role in valid_roles_for_dataset: valid_manage_roles.append(role) else: invalid_manage_roles_ids.append(role_id) if len(invalid_manage_roles_ids) > 0: log.warning("The following roles could not be added to the dataset manage permission: " + str(invalid_manage_roles_ids)) manage_permission = {trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS: valid_manage_roles} trans.app.security_agent.set_dataset_permission(dataset, manage_permission) # MODIFY LIBRARY ITEM ROLES valid_modify_roles = [] invalid_modify_roles_ids = [] new_modify_roles_ids = util.listify(new_modify_roles_ids) for role_id in new_modify_roles_ids: role = self.role_manager.get(trans, self.app, role_id) if role in valid_roles_for_dataset: valid_modify_roles.append(role) else: invalid_modify_roles_ids.append(role_id) if len(invalid_modify_roles_ids) > 0: log.warning("The following roles could not be added to the dataset modify permission: " + str(invalid_modify_roles_ids)) modify_permission = {trans.app.security_agent.permitted_actions.LIBRARY_MODIFY: valid_modify_roles} trans.app.security_agent.set_library_item_permission(library_dataset, modify_permission)