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Source code for galaxy.managers.folders

"""
Manager and Serializer for Library Folders.
"""
import logging

from sqlalchemy.orm.exc import (
    MultipleResultsFound,
    NoResultFound
)

from galaxy.exceptions import (
    AuthenticationRequired,
    InconsistentDatabase,
    InsufficientPermissionsException,
    InternalServerError,
    ItemAccessibilityException,
    MalformedId,
    RequestParameterInvalidException
)

log = logging.getLogger(__name__)


# =============================================================================
[docs]class FolderManager(object): """ Interface/service object for interacting with folders. """
[docs] def get(self, trans, decoded_folder_id, check_manageable=False, check_accessible=True): """ Get the folder from the DB. :param decoded_folder_id: decoded folder id :type decoded_folder_id: int :param check_manageable: flag whether the check that user can manage item :type check_manageable: bool :param check_accessible: flag whether to check that user can access item :type check_accessible: bool :returns: the requested folder :rtype: LibraryFolder :raises: InconsistentDatabase, RequestParameterInvalidException, InternalServerError """ try: folder = trans.sa_session.query(trans.app.model.LibraryFolder).filter(trans.app.model.LibraryFolder.table.c.id == decoded_folder_id).one() except MultipleResultsFound: raise InconsistentDatabase('Multiple folders found with the same id.') except NoResultFound: raise RequestParameterInvalidException('No folder found with the id provided.') except Exception as e: raise InternalServerError('Error loading from the database.' + str(e)) folder = self.secure(trans, folder, check_manageable, check_accessible) return folder
[docs] def secure(self, trans, folder, check_manageable=True, check_accessible=True): """ Check if (a) user can manage folder or (b) folder is accessible to user. :param folder: folder item :type folder: LibraryFolder :param check_manageable: flag whether to check that user can manage item :type check_manageable: bool :param check_accessible: flag whether to check that user can access item :type check_accessible: bool :returns: the original folder :rtype: LibraryFolder """ # all folders are accessible to an admin if trans.user_is_admin: return folder if check_manageable: folder = self.check_manageable(trans, folder) if check_accessible: folder = self.check_accessible(trans, folder) return folder
[docs] def check_manageable(self, trans, folder): """ Check whether the user can manage the folder. :returns: the original folder :rtype: LibraryFolder :raises: AuthenticationRequired, InsufficientPermissionsException """ if not trans.user: raise AuthenticationRequired("Must be logged in to manage Galaxy items.", type='error') current_user_roles = trans.get_current_user_roles() if not trans.app.security_agent.can_manage_library_item(current_user_roles, folder): raise InsufficientPermissionsException("You don't have permissions to manage this folder.", type='error') else: return folder
[docs] def check_accessible(self, trans, folder): """ Check whether the folder is accessible to current user. By default every folder is accessible (contents have their own permissions). """ return folder
[docs] def get_folder_dict(self, trans, folder): """ Return folder data in the form of a dictionary. :param folder: folder item :type folder: LibraryFolder :returns: dict with data about the folder :rtype: dictionary """ folder_dict = folder.to_dict(view='element') folder_dict = trans.security.encode_all_ids(folder_dict, True) folder_dict['id'] = 'F' + folder_dict['id'] if folder_dict['parent_id'] is not None: folder_dict['parent_id'] = 'F' + folder_dict['parent_id'] folder_dict['update_time'] = folder.update_time.strftime("%Y-%m-%d %I:%M %p") return folder_dict
[docs] def create(self, trans, parent_folder_id, new_folder_name, new_folder_description=''): """ Create a new folder under the given folder. :param parent_folder_id: decoded id :type parent_folder_id: int :param new_folder_name: name of the new folder :type new_folder_name: str :param new_folder_description: description of the folder (optional, defaults to empty string) :type new_folder_description: str :returns: the new folder :rtype: LibraryFolder :raises: InsufficientPermissionsException """ parent_folder = self.get(trans, parent_folder_id) current_user_roles = trans.get_current_user_roles() if not (trans.user_is_admin or trans.app.security_agent.can_add_library_item(current_user_roles, parent_folder)): raise InsufficientPermissionsException('You do not have proper permission to create folders under given folder.') new_folder = trans.app.model.LibraryFolder(name=new_folder_name, description=new_folder_description) # We are associating the last used genome build with folders, so we will always # initialize a new folder with the first dbkey in genome builds list which is currently # ? unspecified (?) new_folder.genome_build = trans.app.genome_builds.default_value parent_folder.add_folder(new_folder) trans.sa_session.add(new_folder) trans.sa_session.flush() # New folders default to having the same permissions as their parent folder trans.app.security_agent.copy_library_permissions(trans, parent_folder, new_folder) return new_folder
[docs] def update(self, trans, folder, name=None, description=None): """ Update the given folder's name or description. :param folder: the model object :type folder: LibraryFolder :param name: new name for the library folder :type name: str :param description: new description for the library folder :type description: str :returns: the folder :rtype: LibraryFolder :raises: ItemAccessibilityException, InsufficientPermissionsException """ changed = False if not trans.user_is_admin: if not self.check_manageable(trans, folder): raise InsufficientPermissionsException("You do not have proper permission to update the library folder.") if folder.deleted is True: raise ItemAccessibilityException("You cannot update a deleted library folder. Undelete it first.") if name is not None and name != folder.name: folder.name = name changed = True if description is not None and description != folder.description: folder.description = description changed = True if changed: trans.sa_session.add(folder) trans.sa_session.flush() return folder
[docs] def delete(self, trans, folder, undelete=False): """ Mark given folder deleted/undeleted based on the flag. :param folder: the model object :type folder: LibraryFolder :param undelete: flag whether to delete (when False) or undelete :type undelete: Bool :returns: the folder :rtype: LibraryFolder :raises: ItemAccessibilityException """ if not trans.user_is_admin: folder = self.check_manageable(trans, folder) if undelete: folder.deleted = False else: folder.deleted = True trans.sa_session.add(folder) trans.sa_session.flush() return folder
[docs] def get_current_roles(self, trans, folder): """ Find all roles currently connected to relevant permissions on the folder. :param folder: the model object :type folder: LibraryFolder :returns: dict of current roles for all available permission types :rtype: dictionary """ # Omit duplicated roles by converting to set modify_roles = set(trans.app.security_agent.get_roles_for_action(folder, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY)) manage_roles = set(trans.app.security_agent.get_roles_for_action(folder, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE)) add_roles = set(trans.app.security_agent.get_roles_for_action(folder, trans.app.security_agent.permitted_actions.LIBRARY_ADD)) modify_folder_role_list = [(modify_role.name, trans.security.encode_id(modify_role.id)) for modify_role in modify_roles] manage_folder_role_list = [(manage_role.name, trans.security.encode_id(manage_role.id)) for manage_role in manage_roles] add_library_item_role_list = [(add_role.name, trans.security.encode_id(add_role.id)) for add_role in add_roles] return dict(modify_folder_role_list=modify_folder_role_list, manage_folder_role_list=manage_folder_role_list, add_library_item_role_list=add_library_item_role_list)
[docs] def can_add_item(self, trans, folder): """ Return true if the user has permissions to add item to the given folder. """ if trans.user_is_admin: return True current_user_roles = trans.get_current_user_roles() add_roles = set(trans.app.security_agent.get_roles_for_action(folder, trans.app.security_agent.permitted_actions.LIBRARY_ADD)) for role in current_user_roles: if role in add_roles: return True return False
[docs] def cut_the_prefix(self, encoded_folder_id): """ Remove the prefix from the encoded folder id. :param encoded_folder_id: encoded id of the Folder object with 'F' prepended :type encoded_folder_id: string :returns: encoded Folder id without the 'F' prefix :rtype: string :raises: MalformedId """ if ((len(encoded_folder_id) % 16 == 1) and encoded_folder_id.startswith('F')): cut_id = encoded_folder_id[1:] else: raise MalformedId('Malformed folder id ( %s ) specified, unable to decode.' % str(encoded_folder_id)) return cut_id
[docs] def decode_folder_id(self, trans, encoded_folder_id): """ Decode the folder id given that it has already lost the prefixed 'F'. :param encoded_folder_id: encoded id of the Folder object :type encoded_folder_id: string :returns: decoded Folder id :rtype: int :raises: MalformedId """ try: decoded_id = trans.security.decode_id(encoded_folder_id) except ValueError: raise MalformedId("Malformed folder id ( %s ) specified, unable to decode" % (str(encoded_folder_id))) return decoded_id
[docs] def cut_and_decode(self, trans, encoded_folder_id): """ Cuts the folder prefix (the prepended 'F') and returns the decoded id. :param encoded_folder_id: encoded id of the Folder object :type encoded_folder_id: string :returns: decoded Folder id :rtype: int """ return self.decode_folder_id(trans, self.cut_the_prefix(encoded_folder_id))