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

# -*- 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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"""SqlAlchemy implementation of the `BackendNode` and `BackendNodeCollection` classes."""
from __future__ import division
from __future__ import print_function
from __future__ import absolute_import

# pylint: disable=no-name-in-module,import-error
from datetime import datetime
from sqlalchemy.orm.exc import NoResultFound
from sqlalchemy.exc import SQLAlchemyError

from aiida.backends.sqlalchemy import get_scoped_session
from aiida.backends.sqlalchemy.models import node as models
from aiida.common import exceptions
from aiida.common.lang import type_check
from aiida.orm.utils.node import clean_value

from .. import BackendNode, BackendNodeCollection
from . import entities
from . import utils as sqla_utils
from .computers import SqlaComputer
from .users import SqlaUser


[docs]class SqlaNode(entities.SqlaModelEntity[models.DbNode], BackendNode): """SQLA Node backend entity""" # pylint: disable=too-many-public-methods MODEL_CLASS = models.DbNode
[docs] def __init__( self, backend, node_type, user, computer=None, process_type=None, label='', description='', ctime=None, mtime=None ): """Construct a new `BackendNode` instance wrapping a new `DbNode` instance. :param backend: the backend :param node_type: the node type string :param user: associated `BackendUser` :param computer: associated `BackendComputer` :param label: string label :param description: string description :param ctime: The creation time as datetime object :param mtime: The modification time as datetime object """ # pylint: disable=too-many-arguments super(SqlaNode, self).__init__(backend) arguments = { 'node_type': node_type, 'process_type': process_type, 'user': user.dbmodel, 'label': label, 'description': description, } type_check(user, SqlaUser) if computer: type_check(computer, SqlaComputer, 'computer is of type {}'.format(type(computer))) arguments['dbcomputer'] = computer.dbmodel if ctime: type_check(ctime, datetime, 'the given ctime is of type {}'.format(type(ctime))) arguments['ctime'] = ctime if mtime: type_check(mtime, datetime, 'the given mtime is of type {}'.format(type(mtime))) arguments['mtime'] = mtime self._dbmodel = sqla_utils.ModelWrapper(models.DbNode(**arguments))
[docs] def clone(self): """Return an unstored clone of ourselves. :return: an unstored `BackendNode` with the exact same attributes and extras as self """ arguments = { 'node_type': self._dbmodel.node_type, 'process_type': self._dbmodel.process_type, 'user': self._dbmodel.user, 'dbcomputer': self._dbmodel.dbcomputer, 'label': self._dbmodel.label, 'description': self._dbmodel.description, 'attributes': self._dbmodel.attributes, 'extras': self._dbmodel.extras, } clone = self.__class__.__new__(self.__class__) # pylint: disable=no-value-for-parameter clone.__init__(self.backend, self.node_type, self.user) clone._dbmodel = sqla_utils.ModelWrapper(models.DbNode(**arguments)) # pylint: disable=protected-access return clone
@property def computer(self): """Return the computer of this node. :return: the computer or None :rtype: `BackendComputer` or None """ try: return self.backend.computers.from_dbmodel(self._dbmodel.dbcomputer) except TypeError: return None @computer.setter def computer(self, computer): """Set the computer of this node. :param computer: a `BackendComputer` """ type_check(computer, SqlaComputer, allow_none=True) if computer is not None: computer = computer.dbmodel self._dbmodel.dbcomputer = computer @property def user(self): """Return the user of this node. :return: the user :rtype: `BackendUser` """ return self.backend.users.from_dbmodel(self._dbmodel.user) @user.setter def user(self, user): """Set the user of this node. :param user: a `BackendUser` """ type_check(user, SqlaUser) self._dbmodel.user = user.dbmodel @property def attributes(self): """Return the complete attributes dictionary. .. warning:: While the node is unstored, this will return references of the attributes on the database model, meaning that changes on the returned values (if they are mutable themselves, e.g. a list or dictionary) will automatically be reflected on the database model as well. As soon as the node is stored, the returned attributes will be a deep copy and mutations of the database attributes will have to go through the appropriate set methods. Therefore, once stored, retrieving a deep copy can be a heavy operation. If you only need the keys or some values, use the iterators `attributes_keys` and `attributes_items`, or the getters `get_attribute` and `get_attribute_many` instead. :return: the attributes as a dictionary """ return self._dbmodel.attributes
[docs] def get_attribute(self, key): """Return the value of an attribute. .. warning:: While the node is unstored, this will return a reference of the attribute on the database model, meaning that changes on the returned value (if they are mutable themselves, e.g. a list or dictionary) will automatically be reflected on the database model as well. As soon as the node is stored, the returned attribute will be a deep copy and mutations of the database attributes will have to go through the appropriate set methods. :param key: name of the attribute :return: the value of the attribute :raises AttributeError: if the attribute does not exist and no default is specified """ try: return self._dbmodel.attributes[key] except KeyError as exception: raise AttributeError('attribute `{}` does not exist'.format(exception))
[docs] def get_attribute_many(self, keys): """Return the values of multiple attributes. .. warning:: While the node is unstored, this will return references of the attributes on the database model, meaning that changes on the returned values (if they are mutable themselves, e.g. a list or dictionary) will automatically be reflected on the database model as well. As soon as the node is stored, the returned attributes will be a deep copy and mutations of the database attributes will have to go through the appropriate set methods. Therefore, once stored, retrieving a deep copy can be a heavy operation. If you only need the keys or some values, use the iterators `attributes_keys` and `attributes_items`, or the getters `get_attribute` and `get_attribute_many` instead. :param keys: a list of attribute names :return: a list of attribute values :raises AttributeError: if at least one attribute does not exist """ try: return [self.get_attribute(key) for key in keys] except KeyError as exception: raise AttributeError('attribute `{}` does not exist'.format(exception))
[docs] def set_attribute(self, key, value): """Set an attribute to the given value. :param key: name of the attribute :param value: value of the attribute """ if self.is_stored: value = clean_value(value) self._dbmodel.attributes[key] = value self._flag_field('attributes') self._flush_if_stored()
[docs] def set_attribute_many(self, attributes): """Set multiple attributes. .. note:: This will override any existing attributes that are present in the new dictionary. :param attributes: a dictionary with the attributes to set """ if self.is_stored: attributes = {key: clean_value(value) for key, value in attributes.items()} for key, value in attributes.items(): self.dbmodel.attributes[key] = value self._flag_field('attributes') self._flush_if_stored()
[docs] def reset_attributes(self, attributes): """Reset the attributes. .. note:: This will completely clear any existing attributes and replace them with the new dictionary. :param attributes: a dictionary with the attributes to set """ if self.is_stored: attributes = clean_value(attributes) self.dbmodel.attributes = attributes self._flag_field('attributes') self._flush_if_stored()
[docs] def delete_attribute(self, key): """Delete an attribute. :param key: name of the attribute :raises AttributeError: if the attribute does not exist """ try: self._dbmodel.attributes.pop(key) except KeyError as exception: raise AttributeError('attribute `{}` does not exist'.format(exception)) else: self._flag_field('attributes') self._flush_if_stored()
[docs] def delete_attribute_many(self, keys): """Delete multiple attributes. :param keys: names of the attributes to delete :raises AttributeError: if at least one of the attribute does not exist """ non_existing_keys = [key for key in keys if key not in self._dbmodel.attributes] if non_existing_keys: raise AttributeError('attributes `{}` do not exist'.format(', '.join(non_existing_keys))) for key in keys: self.dbmodel.attributes.pop(key) self._flag_field('attributes') self._flush_if_stored()
[docs] def clear_attributes(self): """Delete all attributes.""" self._dbmodel.attributes = {}
[docs] def attributes_items(self): """Return an iterator over the attributes. :return: an iterator with attribute key value pairs """ for key, value in self._dbmodel.attributes.items(): yield key, value
[docs] def attributes_keys(self): """Return an iterator over the attribute keys. :return: an iterator with attribute keys """ for key in self._dbmodel.attributes.keys(): yield key
@property def extras(self): """Return the complete extras dictionary. .. warning:: While the node is unstored, this will return references of the extras on the database model, meaning that changes on the returned values (if they are mutable themselves, e.g. a list or dictionary) will automatically be reflected on the database model as well. As soon as the node is stored, the returned extras will be a deep copy and mutations of the database extras will have to go through the appropriate set methods. Therefore, once stored, retrieving a deep copy can be a heavy operation. If you only need the keys or some values, use the iterators `extras_keys` and `extras_items`, or the getters `get_extra` and `get_extra_many` instead. :return: the extras as a dictionary """ return self._dbmodel.extras
[docs] def get_extra(self, key): """Return the value of an extra. .. warning:: While the node is unstored, this will return a reference of the extra on the database model, meaning that changes on the returned value (if they are mutable themselves, e.g. a list or dictionary) will automatically be reflected on the database model as well. As soon as the node is stored, the returned extra will be a deep copy and mutations of the database extras will have to go through the appropriate set methods. :param key: name of the extra :return: the value of the extra :raises AttributeError: if the extra does not exist and no default is specified """ try: return self._dbmodel.extras[key] except KeyError as exception: raise AttributeError('extra `{}` does not exist'.format(exception))
[docs] def get_extra_many(self, keys): """Return the values of multiple extras. .. warning:: While the node is unstored, this will return references of the extras on the database model, meaning that changes on the returned values (if they are mutable themselves, e.g. a list or dictionary) will automatically be reflected on the database model as well. As soon as the node is stored, the returned extras will be a deep copy and mutations of the database extras will have to go through the appropriate set methods. Therefore, once stored, retrieving a deep copy can be a heavy operation. If you only need the keys or some values, use the iterators `extras_keys` and `extras_items`, or the getters `get_extra` and `get_extra_many` instead. :param keys: a list of extra names :return: a list of extra values :raises AttributeError: if at least one extra does not exist """ try: return [self.get_extra(key) for key in keys] except KeyError as exception: raise AttributeError('extra `{}` does not exist'.format(exception))
[docs] def set_extra(self, key, value): """Set an extra to the given value. :param key: name of the extra :param value: value of the extra """ if self.is_stored: value = clean_value(value) self._dbmodel.extras[key] = value self._flag_field('extras') self._flush_if_stored()
[docs] def set_extra_many(self, extras): """Set multiple extras. .. note:: This will override any existing extras that are present in the new dictionary. :param extras: a dictionary with the extras to set """ if self.is_stored: extras = {key: clean_value(value) for key, value in extras.items()} for key, value in extras.items(): self.dbmodel.extras[key] = value self._flag_field('extras') self._flush_if_stored()
[docs] def reset_extras(self, extras): """Reset the extras. .. note:: This will completely clear any existing extras and replace them with the new dictionary. :param extras: a dictionary with the extras to set """ self.dbmodel.extras = extras self._flag_field('extras') self._flush_if_stored()
[docs] def delete_extra(self, key): """Delete an extra. :param key: name of the extra :raises AttributeError: if the extra does not exist """ try: self._dbmodel.extras.pop(key) except KeyError as exception: raise AttributeError('extra `{}` does not exist'.format(exception)) else: self._flag_field('extras') self._flush_if_stored()
[docs] def delete_extra_many(self, keys): """Delete multiple extras. :param keys: names of the extras to delete :raises AttributeError: if at least one of the extra does not exist """ non_existing_keys = [key for key in keys if key not in self._dbmodel.extras] if non_existing_keys: raise AttributeError('extras `{}` do not exist'.format(', '.join(non_existing_keys))) for key in keys: self.dbmodel.extras.pop(key) self._flag_field('extras') self._flush_if_stored()
[docs] def clear_extras(self): """Delete all extras.""" self._dbmodel.extras = {}
[docs] def extras_items(self): """Return an iterator over the extras. :return: an iterator with extra key value pairs """ for key, value in self._dbmodel.extras.items(): yield key, value
[docs] def extras_keys(self): """Return an iterator over the extra keys. :return: an iterator with extra keys """ for key in self._dbmodel.extras.keys(): yield key
[docs] def _flag_field(self, field): from aiida.backends.sqlalchemy.utils import flag_modified flag_modified(self._dbmodel, field)
[docs] def _flush_if_stored(self): if self._dbmodel.is_saved(): self._dbmodel.save()
[docs] def add_incoming(self, source, link_type, link_label): """Add a link of the given type from a given node to ourself. :param source: the node from which the link is coming :param link_type: the link type :param link_label: the link label :return: True if the proposed link is allowed, False otherwise :raise aiida.common.ModificationNotAllowed: if either source or target node is not stored """ session = get_scoped_session() type_check(source, SqlaNode) if not self.is_stored: raise exceptions.ModificationNotAllowed('node has to be stored when adding an incoming link') if not source.is_stored: raise exceptions.ModificationNotAllowed('source node has to be stored when adding a link from it') self._add_link(source, link_type, link_label) session.commit()
[docs] def clean_values(self): self._dbmodel.attributes = clean_value(self._dbmodel.attributes) self._dbmodel.extras = clean_value(self._dbmodel.extras)
[docs] def store(self, links=None, with_transaction=True, clean=True): """Store the node in the database. :param links: optional links to add before storing :param with_transaction: if False, do not use a transaction because the caller will already have opened one. :param clean: boolean, if True, will clean the attributes and extras before attempting to store """ session = get_scoped_session() if clean: self.clean_values() session.add(self._dbmodel) if links: for link_triple in links: self._add_link(*link_triple) if with_transaction: try: session.commit() except SQLAlchemyError: session.rollback() raise return self
[docs]class SqlaNodeCollection(BackendNodeCollection): """The collection of Node entries.""" ENTITY_CLASS = SqlaNode
[docs] def get(self, pk): """Return a Node entry from the collection with the given id :param pk: id of the node """ session = get_scoped_session() try: return self.ENTITY_CLASS.from_dbmodel(session.query(models.DbNode).filter_by(id=pk).one(), self.backend) except NoResultFound: raise exceptions.NotExistent("Node with pk '{}' not found".format(pk))
[docs] def delete(self, pk): """Remove a Node entry from the collection with the given id :param pk: id of the node to delete """ session = get_scoped_session() try: session.query(models.DbNode).filter_by(id=pk).one().delete() session.commit() except NoResultFound: raise exceptions.NotExistent("Node with pk '{}' not found".format(pk))