Source code for aiida.orm.implementation.sqlalchemy.groups

# -*- coding: utf-8 -*-
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# Copyright (c), The AiiDA team. All rights reserved.                     #
# This file is part of the AiiDA code.                                    #
#                                                                         #
# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
# For further information on the license, see the LICENSE.txt file        #
# For further information please visit http://www.aiida.net               #
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"""SQLA groups"""

import collections
import logging

from aiida.backends import sqlalchemy as sa
from aiida.backends.sqlalchemy.models.group import DbGroup, table_groups_nodes
from aiida.backends.sqlalchemy.models.node import DbNode
from aiida.common.exceptions import UniquenessError
from aiida.common.lang import type_check
from aiida.orm.implementation.groups import BackendGroup, BackendGroupCollection
from . import entities
from . import users
from . import utils

__all__ = ('SqlaGroup', 'SqlaGroupCollection')

_LOGGER = logging.getLogger(__name__)


# Unfortunately the linter doesn't seem to be able to pick up on the fact that the abstract property 'id'
# of BackendGroup is actually implemented in SqlaModelEntity so disable the abstract check
[docs]class SqlaGroup(entities.SqlaModelEntity[DbGroup], BackendGroup): # pylint: disable=abstract-method """The SQLAlchemy Group object""" MODEL_CLASS = DbGroup
[docs] def __init__(self, backend, label, user, description='', type_string=''): """ Construct a new SQLA group :param backend: the backend to use :param label: the group label :param user: the owner of the group :param description: an optional group description :param type_string: an optional type for the group to contain """ type_check(user, users.SqlaUser) super().__init__(backend) dbgroup = DbGroup(label=label, description=description, user=user.dbmodel, type_string=type_string) self._dbmodel = utils.ModelWrapper(dbgroup)
@property def label(self): return self._dbmodel.label @label.setter def label(self, label): """ Attempt to change the label of the group instance. If the group is already stored and the another group of the same type already exists with the desired label, a UniquenessError will be raised :param label: the new group label :raises aiida.common.UniquenessError: if another group of same type and label already exists """ self._dbmodel.label = label if self.is_stored: try: self._dbmodel.save() except Exception: raise UniquenessError('a group of the same type with the label {} already exists'.format(label)) @property def description(self): return self._dbmodel.description @description.setter def description(self, value): self._dbmodel.description = value # Update the entry in the DB, if the group is already stored if self.is_stored: self._dbmodel.save() @property def type_string(self): return self._dbmodel.type_string @property def user(self): return self._backend.users.from_dbmodel(self._dbmodel.user) @user.setter def user(self, new_user): type_check(new_user, users.SqlaUser) self._dbmodel.user = new_user.dbmodel @property def pk(self): return self._dbmodel.id @property def uuid(self): return str(self._dbmodel.uuid)
[docs] def __int__(self): if not self.is_stored: return None return self._dbnode.id
@property def is_stored(self): return self.pk is not None
[docs] def store(self): self._dbmodel.save() return self
[docs] def count(self): """Return the number of entities in this group. :return: integer number of entities contained within the group """ from aiida.backends.sqlalchemy import get_scoped_session session = get_scoped_session() return session.query(self.MODEL_CLASS).join(self.MODEL_CLASS.dbnodes).filter(DbGroup.id == self.pk).count()
[docs] def clear(self): """Remove all the nodes from this group.""" from aiida.backends.sqlalchemy import get_scoped_session session = get_scoped_session() # Note we have to call `dbmodel` and `_dbmodel` to circumvent the `ModelWrapper` self.dbmodel.dbnodes = [] session.commit()
@property def nodes(self): """Get an iterator to all the nodes in the group""" class Iterator: """Nodes iterator""" def __init__(self, dbnodes, backend): self._backend = backend self._dbnodes = dbnodes self.generator = self._genfunction() def _genfunction(self): for node in self._dbnodes: yield self._backend.get_backend_entity(node) def __iter__(self): return self def __len__(self): return self._dbnodes.count() def __getitem__(self, value): if isinstance(value, slice): return [self._backend.get_backend_entity(n) for n in self._dbnodes[value]] return self._backend.get_backend_entity(self._dbnodes[value]) def __next__(self): return next(self.generator) return Iterator(self._dbmodel.dbnodes, self._backend)
[docs] def add_nodes(self, nodes, **kwargs): """Add a node or a set of nodes to the group. :note: all the nodes *and* the group itself have to be stored. :param nodes: a list of `BackendNode` instance to be added to this group :param kwargs: skip_orm: When the flag is on, the SQLA ORM is skipped and SQLA is used to create a direct SQL INSERT statement to the group-node relationship table (to improve speed). """ from sqlalchemy.exc import IntegrityError # pylint: disable=import-error, no-name-in-module from sqlalchemy.dialects.postgresql import insert # pylint: disable=import-error, no-name-in-module from aiida.orm.implementation.sqlalchemy.nodes import SqlaNode from aiida.backends.sqlalchemy import get_scoped_session from aiida.backends.sqlalchemy.models.base import Base super().add_nodes(nodes) skip_orm = kwargs.get('skip_orm', False) def check_node(given_node): """ Check if given node is of correct type and stored """ if not isinstance(given_node, SqlaNode): raise TypeError('invalid type {}, has to be {}'.format(type(given_node), SqlaNode)) if not given_node.is_stored: raise ValueError('At least one of the provided nodes is unstored, stopping...') with utils.disable_expire_on_commit(get_scoped_session()) as session: if not skip_orm: # Get dbnodes here ONCE, otherwise each call to dbnodes will re-read the current value in the database dbnodes = self._dbmodel.dbnodes for node in nodes: check_node(node) # Use pattern as suggested here: # http://docs.sqlalchemy.org/en/latest/orm/session_transaction.html#using-savepoint try: with session.begin_nested(): dbnodes.append(node.dbmodel) session.flush() except IntegrityError: # Duplicate entry, skip pass else: ins_dict = list() for node in nodes: check_node(node) ins_dict.append({'dbnode_id': node.id, 'dbgroup_id': self.id}) my_table = Base.metadata.tables['db_dbgroup_dbnodes'] ins = insert(my_table).values(ins_dict) session.execute(ins.on_conflict_do_nothing(index_elements=['dbnode_id', 'dbgroup_id'])) # Commit everything as up till now we've just flushed session.commit()
[docs] def remove_nodes(self, nodes, **kwargs): """Remove a node or a set of nodes from the group. :note: all the nodes *and* the group itself have to be stored. :param nodes: a list of `BackendNode` instance to be added to this group :param kwargs: skip_orm: When the flag is set to `True`, the SQLA ORM is skipped and SQLA is used to create a direct SQL DELETE statement to the group-node relationship table in order to improve speed. """ from sqlalchemy import and_ from aiida.backends.sqlalchemy import get_scoped_session from aiida.backends.sqlalchemy.models.base import Base from aiida.orm.implementation.sqlalchemy.nodes import SqlaNode super().remove_nodes(nodes) # Get dbnodes here ONCE, otherwise each call to dbnodes will re-read the current value in the database dbnodes = self._dbmodel.dbnodes skip_orm = kwargs.get('skip_orm', False) def check_node(node): if not isinstance(node, SqlaNode): raise TypeError('invalid type {}, has to be {}'.format(type(node), SqlaNode)) if node.id is None: raise ValueError('At least one of the provided nodes is unstored, stopping...') list_nodes = [] with utils.disable_expire_on_commit(get_scoped_session()) as session: if not skip_orm: for node in nodes: check_node(node) # Check first, if SqlA issues a DELETE statement for an unexisting key it will result in an error if node.dbmodel in dbnodes: list_nodes.append(node.dbmodel) for node in list_nodes: dbnodes.remove(node) else: table = Base.metadata.tables['db_dbgroup_dbnodes'] for node in nodes: check_node(node) clause = and_(table.c.dbnode_id == node.id, table.c.dbgroup_id == self.id) statement = table.delete().where(clause) session.execute(statement) session.commit()
[docs]class SqlaGroupCollection(BackendGroupCollection): """The SLQA collection of groups""" ENTITY_CLASS = SqlaGroup
[docs] def query( self, label=None, type_string=None, pk=None, uuid=None, nodes=None, user=None, node_attributes=None, past_days=None, label_filters=None, **kwargs ): # pylint: disable=too-many-arguments # pylint: disable=too-many-branches from aiida.orm.implementation.sqlalchemy.nodes import SqlaNode session = sa.get_scoped_session() filters = [] if label is not None: filters.append(DbGroup.label == label) if type_string is not None: filters.append(DbGroup.type_string == type_string) if pk is not None: filters.append(DbGroup.id == pk) if uuid is not None: filters.append(DbGroup.uuid == uuid) if past_days is not None: filters.append(DbGroup.time >= past_days) if nodes: if not isinstance(nodes, collections.Iterable): nodes = [nodes] if not all(isinstance(n, (SqlaNode, DbNode)) for n in nodes): raise TypeError( 'At least one of the elements passed as ' 'nodes for the query on Group is neither ' 'a Node nor a DbNode' ) # In the case of the Node orm from Sqlalchemy, there is an id # property on it. sub_query = ( session.query(table_groups_nodes).filter( table_groups_nodes.c['dbnode_id'].in_([n.id for n in nodes]), table_groups_nodes.c['dbgroup_id'] == DbGroup.id ).exists() ) filters.append(sub_query) if user: if isinstance(user, str): filters.append(DbGroup.user.has(email=user.email)) else: type_check(user, users.SqlaUser) filters.append(DbGroup.user == user.dbmodel) if label_filters: for key, value in label_filters.items(): if not value: continue if key == 'startswith': filters.append(DbGroup.label.like('{}%'.format(value))) elif key == 'endswith': filters.append(DbGroup.label.like('%{}'.format(value))) elif key == 'contains': filters.append(DbGroup.label.like('%{}%'.format(value))) if node_attributes: _LOGGER.warning("SQLA query doesn't support node attribute filters, ignoring '%s'", node_attributes) if kwargs: _LOGGER.warning("SQLA query doesn't support additional filters, ignoring '%s'", kwargs) groups = (session.query(DbGroup).filter(*filters).order_by(DbGroup.id).distinct().all()) return [SqlaGroup.from_dbmodel(group, self._backend) for group in groups]
[docs] def delete(self, id): # pylint: disable=redefined-builtin session = sa.get_scoped_session() session.query(DbGroup).get(id).delete() session.commit()