Fixes for LDDA manager - clearly that didn't work at all.

import logging

from galaxy import model, util

from galaxy import model

from galaxy.managers import base as manager_base

from galaxy.managers.datasets import DatasetAssociationManager

from galaxy.structured_app import MinimalManagerApp

        """

        Set up and initialize other managers needed by lddas.

        """

        super().__init__(app)

    def get(self, trans, id, check_accessible=True):

        return manager_base.get_object(trans, id,

                                       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)

        # Check Git history for an older broken implementation, but it was broken

        # and security related and had not test coverage so it was deleted.

        raise NotImplementedError()