Source code for aiida.orm.nodes.node

# -*- coding: utf-8 -*-
###########################################################################
# 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               #
###########################################################################
# pylint: disable=too-many-lines
"""Package for node ORM classes."""
from __future__ import division
from __future__ import print_function
from __future__ import absolute_import

import copy
import importlib
import warnings
import six

from aiida.common import exceptions
from aiida.common.escaping import sql_string_match
from aiida.common.hashing import make_hash, _HASH_EXTRA_KEY
from aiida.common.lang import classproperty, type_check
from aiida.common.links import LinkType
from aiida.common.warnings import AiidaDeprecationWarning
from aiida.manage.manager import get_manager
from aiida.orm.utils.links import LinkManager, LinkTriple
from aiida.orm.utils.repository import Repository
from aiida.orm.utils.node import AbstractNodeMeta, validate_attribute_extra_key

from ..comments import Comment
from ..computers import Computer
from ..entities import Entity
from ..entities import Collection as EntityCollection
from ..querybuilder import QueryBuilder
from ..users import User

__all__ = ('Node',)

_NO_DEFAULT = tuple()


[docs]@six.add_metaclass(AbstractNodeMeta) class Node(Entity): """ Base class for all nodes in AiiDA. Stores attributes starting with an underscore. Caches files and attributes before the first save, and saves everything only on store(). After the call to store(), attributes cannot be changed. Only after storing (or upon loading from uuid) extras can be modified and in this case they are directly set on the db. In the plugin, also set the _plugin_type_string, to be set in the DB in the 'type' field. """ # pylint: disable=too-many-public-methods
[docs] class Collection(EntityCollection): """The collection of AuthInfo entries."""
[docs] def delete(self, node_id): """Delete a `Node` from the collection with the given id :param node_id: the node id """ node = self.get(id=node_id) if not node.is_stored: return if node.get_outgoing().all(): raise exceptions.InvalidOperation('cannot delete Node<{}> because it has output links'.format(node.pk)) repository = node._repository # pylint: disable=protected-access self._backend.nodes.delete(node_id) repository.erase(force=True)
# This will be set by the metaclass call _logger = None # A tuple of attribute names that can be updated even after node is stored # Requires Sealable mixin, but needs empty tuple for base class _updatable_attributes = tuple() # A tuple of attribute names that will be ignored when creating the hash. _hash_ignored_attributes = tuple() # Flag that determines whether the class can be cached. _cachable = True # Base path within the repository where to put objects by default _repository_base_path = 'path' # Flag that determines whether the class can be stored. _storable = False _unstorable_message = 'only Data, WorkflowNode, CalculationNode or their subclasses can be stored' # These are to be initialized in the `initialization` method _incoming_cache = None _repository = None
[docs] @classmethod def from_backend_entity(cls, backend_entity): entity = super(Node, cls).from_backend_entity(backend_entity) return entity
[docs] def __init__(self, backend=None, user=None, computer=None, **kwargs): backend = backend or get_manager().get_backend() if computer and not computer.is_stored: raise ValueError('the computer is not stored') computer = computer.backend_entity if computer else None user = user.backend_entity if user else User.objects(backend).get_default() if user is None: raise ValueError('the user cannot be None') backend_entity = backend.nodes.create( node_type=self.class_node_type, user=user.backend_entity, computer=computer, **kwargs ) super(Node, self).__init__(backend_entity)
[docs] def __repr__(self): return '<{}: {}>'.format(self.__class__.__name__, str(self))
[docs] def __str__(self): if not self.is_stored: return 'uuid: {} (unstored)'.format(self.uuid) return 'uuid: {} (pk: {})'.format(self.uuid, self.pk)
[docs] def __copy__(self): """Copying a Node is not supported in general, but only for the Data sub class.""" raise exceptions.InvalidOperation('copying a base Node is not supported')
[docs] def __deepcopy__(self, memo): """Deep copying a Node is not supported in general, but only for the Data sub class.""" raise exceptions.InvalidOperation('deep copying a base Node is not supported')
[docs] def initialize(self): """ Initialize internal variables for the backend node This needs to be called explicitly in each specific subclass implementation of the init. """ super(Node, self).initialize() # A cache of incoming links represented as a list of LinkTriples instances self._incoming_cache = list() # Calls the initialisation from the RepositoryMixin self._repository = Repository(uuid=self.uuid, is_stored=self.is_stored, base_path=self._repository_base_path)
[docs] def _validate(self): """Check if the attributes and files retrieved from the database are valid. Must be able to work even before storing: therefore, use the `get_attr` and similar methods that automatically read either from the DB or from the internal attribute cache. For the base class, this is always valid. Subclasses will reimplement this. In the subclass, always call the super()._validate() method first! """ # pylint: disable=no-self-use return True
@classproperty def class_node_type(cls): """Returns the node type of this node (sub) class.""" # pylint: disable=no-self-argument,no-member return cls._plugin_type_string @property def logger(self): """Return the logger configured for this Node. :return: Logger object """ return self._logger @property def uuid(self): """Return the node UUID. :return: the string representation of the UUID :rtype: str """ return self.backend_entity.uuid @property def node_type(self): """Return the node type. :return: the node type """ return self.backend_entity.node_type @property def process_type(self): """Return the node process type. :return: the process type """ return self.backend_entity.process_type @process_type.setter def process_type(self, value): """Set the node process type. :param value: the new value to set """ self.backend_entity.process_type = value @property def label(self): """Return the node label. :return: the label """ return self.backend_entity.label @label.setter def label(self, value): """Set the label. :param value: the new value to set """ self.backend_entity.label = value @property def description(self): """Return the node description. :return: the description """ return self.backend_entity.description @description.setter def description(self, value): """Set the description. :param value: the new value to set """ self.backend_entity.description = value @property def computer(self): """Return the computer of this node. :return: the computer or None :rtype: `Computer` or None """ if self.backend_entity.computer: return Computer.from_backend_entity(self.backend_entity.computer) return None @computer.setter def computer(self, computer): """Set the computer of this node. :param computer: a `Computer` """ if self.is_stored: raise exceptions.ModificationNotAllowed('cannot set the computer on a stored node') type_check(computer, Computer, allow_none=True) if computer is not None: computer = computer.backend_entity self.backend_entity.computer = computer @property def user(self): """Return the user of this node. :return: the user :rtype: `User` """ return User.from_backend_entity(self.backend_entity.user) @user.setter def user(self, user): """Set the user of this node. :param user: a `User` """ if self.is_stored: raise exceptions.ModificationNotAllowed('cannot set the user on a stored node') type_check(user, User) self.backend_entity.user = user.backend_entity @property def ctime(self): """Return the node ctime. :return: the ctime """ return self.backend_entity.ctime @property def mtime(self): """Return the node mtime. :return: the mtime """ return self.backend_entity.mtime @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 """ attributes = self.backend_entity.attributes if self.is_stored: attributes = copy.deepcopy(attributes) return attributes
[docs] def get_attribute(self, key, default=_NO_DEFAULT): """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 :param default: return this value instead of raising if the attribute does not exist :return: the value of the attribute :raises AttributeError: if the attribute does not exist and no default is specified """ try: attribute = self.backend_entity.get_attribute(key) except AttributeError: if default is _NO_DEFAULT: raise attribute = default if self.is_stored: attribute = copy.deepcopy(attribute) return attribute
[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 """ attributes = self.backend_entity.get_attribute_many(keys) if self.is_stored: attributes = copy.deepcopy(attributes) return attributes
[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 :raise aiida.common.ValidationError: if the key is invalid, i.e. contains periods :raise aiida.common.ModificationNotAllowed: if the node is stored """ if self.is_stored: raise exceptions.ModificationNotAllowed('the attributes of a stored node are immutable') validate_attribute_extra_key(key) self.backend_entity.set_attribute(key, value)
[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 :raise aiida.common.ValidationError: if any of the keys are invalid, i.e. contain periods :raise aiida.common.ModificationNotAllowed: if the node is stored """ if self.is_stored: raise exceptions.ModificationNotAllowed('the attributes of a stored node are immutable') for key in attributes: validate_attribute_extra_key(key) self.backend_entity.set_attribute_many(attributes)
[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 :raise aiida.common.ValidationError: if any of the keys are invalid, i.e. contain periods :raise aiida.common.ModificationNotAllowed: if the node is stored """ if self.is_stored: raise exceptions.ModificationNotAllowed('the attributes of a stored node are immutable') for key in attributes: validate_attribute_extra_key(key) self.backend_entity.reset_attributes(attributes)
[docs] def delete_attribute(self, key): """Delete an attribute. :param key: name of the attribute :raises AttributeError: if the attribute does not exist :raise aiida.common.ModificationNotAllowed: if the node is stored """ if self.is_stored: raise exceptions.ModificationNotAllowed('the attributes of a stored node are immutable') self.backend_entity.delete_attribute(key)
[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 :raise aiida.common.ModificationNotAllowed: if the node is stored """ if self.is_stored: raise exceptions.ModificationNotAllowed('the attributes of a stored node are immutable') self.backend_entity.delete_attribute_many(keys)
[docs] def clear_attributes(self): """Delete all attributes.""" if self.is_stored: raise exceptions.ModificationNotAllowed('the attributes of a stored node are immutable') self.backend_entity.clear_attributes()
[docs] def attributes_items(self): """Return an iterator over the attributes. :return: an iterator with attribute key value pairs """ return self.backend_entity.attributes_items()
[docs] def attributes_keys(self): """Return an iterator over the attribute keys. :return: an iterator with attribute keys """ return self.backend_entity.attributes_keys()
@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 """ extras = self.backend_entity.extras if self.is_stored: extras = copy.deepcopy(extras) return extras
[docs] def get_extra(self, key, default=_NO_DEFAULT): """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 :param default: return this value instead of raising if the attribute does not exist :return: the value of the extra :raises AttributeError: if the extra does not exist and no default is specified """ try: extra = self.backend_entity.get_extra(key) except AttributeError: if default is _NO_DEFAULT: raise extra = default if self.is_stored: extra = copy.deepcopy(extra) return extra
[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 """ extras = self.backend_entity.get_extra_many(keys) if self.is_stored: extras = copy.deepcopy(extras) return extras
[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 :raise aiida.common.ValidationError: if the key is invalid, i.e. contains periods """ validate_attribute_extra_key(key) self.backend_entity.set_extra(key, value)
[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 :raise aiida.common.ValidationError: if any of the keys are invalid, i.e. contain periods """ for key in extras: validate_attribute_extra_key(key) self.backend_entity.set_extra_many(extras)
[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 :raise aiida.common.ValidationError: if any of the keys are invalid, i.e. contain periods """ for key in extras: validate_attribute_extra_key(key) self.backend_entity.reset_extras(extras)
[docs] def delete_extra(self, key): """Delete an extra. :param key: name of the extra :raises AttributeError: if the extra does not exist """ self.backend_entity.delete_extra(key)
[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 """ self.backend_entity.delete_extra_many(keys)
[docs] def clear_extras(self): """Delete all extras.""" self.backend_entity.clear_extras()
[docs] def extras_items(self): """Return an iterator over the extras. :return: an iterator with extra key value pairs """ return self.backend_entity.extras_items()
[docs] def extras_keys(self): """Return an iterator over the extra keys. :return: an iterator with extra keys """ return self.backend_entity.extras_keys()
[docs] def list_objects(self, key=None): """Return a list of the objects contained in this repository, optionally in the given sub directory. :param key: fully qualified identifier for the object within the repository :return: a list of `File` named tuples representing the objects present in directory with the given key """ return self._repository.list_objects(key)
[docs] def list_object_names(self, key=None): """Return a list of the object names contained in this repository, optionally in the given sub directory. :param key: fully qualified identifier for the object within the repository :return: a list of `File` named tuples representing the objects present in directory with the given key """ return self._repository.list_object_names(key)
[docs] def open(self, key, mode='r'): """Open a file handle to an object stored under the given key. :param key: fully qualified identifier for the object within the repository :param mode: the mode under which to open the handle """ return self._repository.open(key, mode)
[docs] def get_object(self, key): """Return the object identified by key. :param key: fully qualified identifier for the object within the repository :return: a `File` named tuple representing the object located at key """ return self._repository.get_object(key)
[docs] def get_object_content(self, key, mode='r'): """Return the content of a object identified by key. :param key: fully qualified identifier for the object within the repository """ return self._repository.get_object_content(key, mode)
[docs] def put_object_from_tree(self, path, key=None, contents_only=True, force=False): """Store a new object under `key` with the contents of the directory located at `path` on this file system. .. warning:: If the repository belongs to a stored node, a `ModificationNotAllowed` exception will be raised. This check can be avoided by using the `force` flag, but this should be used with extreme caution! :param path: absolute path of directory whose contents to copy to the repository :param key: fully qualified identifier for the object within the repository :param contents_only: boolean, if True, omit the top level directory of the path and only copy its contents. :param force: boolean, if True, will skip the mutability check :raises aiida.common.ModificationNotAllowed: if repository is immutable and `force=False` """ self._repository.put_object_from_tree(path, key, contents_only, force)
[docs] def put_object_from_file(self, path, key, mode=None, encoding=None, force=False): """Store a new object under `key` with contents of the file located at `path` on this file system. .. warning:: If the repository belongs to a stored node, a `ModificationNotAllowed` exception will be raised. This check can be avoided by using the `force` flag, but this should be used with extreme caution! :param path: absolute path of file whose contents to copy to the repository :param key: fully qualified identifier for the object within the repository :param mode: the file mode with which the object will be written Deprecated: will be removed in `v2.0.0` :param encoding: the file encoding with which the object will be written Deprecated: will be removed in `v2.0.0` :param force: boolean, if True, will skip the mutability check :raises aiida.common.ModificationNotAllowed: if repository is immutable and `force=False` """ # Note that the defaults of `mode` and `encoding` had to be change to `None` from `w` and `utf-8` resptively, in # order to detect when they were being passed such that the deprecation warning can be emitted. The defaults did # not make sense and so ignoring them is justified, since the side-effect of this function, a file being copied, # will continue working the same. if mode is not None: warnings.warn('the `mode` argument is deprecated and will be removed in `v2.0.0`', AiidaDeprecationWarning) # pylint: disable=no-member if encoding is not None: warnings.warn( # pylint: disable=no-member 'the `encoding` argument is deprecated and will be removed in `v2.0.0`', AiidaDeprecationWarning ) self._repository.put_object_from_file(path, key, mode, encoding, force)
[docs] def put_object_from_filelike(self, handle, key, mode='w', encoding='utf8', force=False): """Store a new object under `key` with contents of filelike object `handle`. .. warning:: If the repository belongs to a stored node, a `ModificationNotAllowed` exception will be raised. This check can be avoided by using the `force` flag, but this should be used with extreme caution! :param handle: filelike object with the content to be stored :param key: fully qualified identifier for the object within the repository :param mode: the file mode with which the object will be written :param encoding: the file encoding with which the object will be written :param force: boolean, if True, will skip the mutability check :raises aiida.common.ModificationNotAllowed: if repository is immutable and `force=False` """ self._repository.put_object_from_filelike(handle, key, mode, encoding, force)
[docs] def delete_object(self, key, force=False): """Delete the object from the repository. .. warning:: If the repository belongs to a stored node, a `ModificationNotAllowed` exception will be raised. This check can be avoided by using the `force` flag, but this should be used with extreme caution! :param key: fully qualified identifier for the object within the repository :param force: boolean, if True, will skip the mutability check :raises aiida.common.ModificationNotAllowed: if repository is immutable and `force=False` """ self._repository.delete_object(key, force)
[docs] def add_comment(self, content, user=None): """Add a new comment. :param content: string with comment :param user: the user to associate with the comment, will use default if not supplied :return: the newly created comment """ user = user or User.objects.get_default() return Comment(node=self, user=user, content=content).store()
[docs] def get_comment(self, identifier): """Return a comment corresponding to the given identifier. :param identifier: the comment pk :raise aiida.common.NotExistent: if the comment with the given id does not exist :raise aiida.common.MultipleObjectsError: if the id cannot be uniquely resolved to a comment :return: the comment """ return Comment.objects.get(dbnode_id=self.pk, pk=identifier)
[docs] def get_comments(self): """Return a sorted list of comments for this node. :return: the list of comments, sorted by pk """ return Comment.objects.find(filters={'dbnode_id': self.pk}, order_by=[{'id': 'asc'}])
[docs] def update_comment(self, identifier, content): """Update the content of an existing comment. :param identifier: the comment pk :param content: the new comment content :raise aiida.common.NotExistent: if the comment with the given id does not exist :raise aiida.common.MultipleObjectsError: if the id cannot be uniquely resolved to a comment """ comment = Comment.objects.get(dbnode_id=self.pk, pk=identifier) comment.set_content(content)
[docs] def remove_comment(self, identifier): """Delete an existing comment. :param identifier: the comment pk """ Comment.objects.delete(dbnode_id=self.pk, comment=identifier)
[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 :raise TypeError: if `source` is not a Node instance or `link_type` is not a `LinkType` enum :raise ValueError: if the proposed link is invalid """ self.validate_incoming(source, link_type, link_label) source.validate_outgoing(self, link_type, link_label) if self.is_stored and source.is_stored: self.backend_entity.add_incoming(source.backend_entity, link_type, link_label) else: self._add_incoming_cache(source, link_type, link_label)
[docs] def validate_incoming(self, source, link_type, link_label): """Validate adding a link of the given type from a given node to ourself. This function will first validate the types of the inputs, followed by the node and link types and validate whether in principle a link of that type between the nodes of these types is allowed.the Subsequently, the validity of the "degree" of the proposed link is validated, which means validating the number of links of the given type from the given node type is allowed. :param source: the node from which the link is coming :param link_type: the link type :param link_label: the link label :raise TypeError: if `source` is not a Node instance or `link_type` is not a `LinkType` enum :raise ValueError: if the proposed link is invalid """ from aiida.orm.utils.links import validate_link validate_link(source, self, link_type, link_label) # Check if the proposed link would introduce a cycle in the graph following ancestor/descendant rules if link_type in [LinkType.CREATE, LinkType.INPUT_CALC, LinkType.INPUT_WORK]: builder = QueryBuilder().append( Node, filters={'id': self.pk}, tag='parent').append( Node, filters={'id': source.pk}, tag='child', with_ancestors='parent') # yapf:disable if builder.count() > 0: raise ValueError('the link you are attempting to create would generate a cycle in the graph')
[docs] def validate_outgoing(self, target, link_type, link_label): # pylint: disable=unused-argument,no-self-use """Validate adding a link of the given type from ourself to a given node. The validity of the triple (source, link, target) should be validated in the `validate_incoming` call. This method will be called afterwards and can be overriden by subclasses to add additional checks that are specific to that subclass. :param target: the node to which the link is going :param link_type: the link type :param link_label: the link label :raise TypeError: if `target` is not a Node instance or `link_type` is not a `LinkType` enum :raise ValueError: if the proposed link is invalid """ type_check(link_type, LinkType, 'link_type should be a LinkType enum but got: {}'.format(type(link_type))) type_check(target, Node, 'target should be a `Node` instance but got: {}'.format(type(target)))
[docs] def _add_incoming_cache(self, source, link_type, link_label): """Add an incoming link to the cache. .. note: the proposed link is not validated in this function, so this should not be called directly but it should only be called by `Node.add_incoming`. :param source: the node from which the link is coming :param link_type: the link type :param link_label: the link label :raise aiida.common.UniquenessError: if the given link triple already exists in the cache """ link_triple = LinkTriple(source, link_type, link_label) if link_triple in self._incoming_cache: raise exceptions.UniquenessError('the link triple {} is already present in the cache'.format(link_triple)) self._incoming_cache.append(link_triple)
[docs] def get_incoming(self, node_class=None, link_type=(), link_label_filter=None, only_uuid=False): """Return a list of link triples that are (directly) incoming into this node. :param node_class: If specified, should be a class or tuple of classes, and it filters only elements of that specific type (or a subclass of 'type') :param link_type: If specified should be a string or tuple to get the inputs of this link type, if None then returns all inputs of all link types. :param link_label_filter: filters the incoming nodes by its link label. Here wildcards (% and _) can be passed in link label filter as we are using "like" in QB. :param only_uuid: project only the node UUID instead of the instance onto the `NodeTriple.node` entries """ if not isinstance(link_type, tuple): link_type = (link_type,) if self.is_stored: link_triples = self.get_stored_link_triples( node_class, link_type, link_label_filter, 'incoming', only_uuid=only_uuid ) else: link_triples = [] # Get all cached link triples for link_triple in self._incoming_cache: if only_uuid: link_triple = LinkTriple(link_triple.node.uuid, link_triple.link_type, link_triple.link_label) if link_triple in link_triples: raise exceptions.InternalError( 'Node<{}> has both a stored and cached link triple {}'.format(self.pk, link_triple) ) if not link_type or link_triple.link_type in link_type: if link_label_filter is not None: if sql_string_match(string=link_triple.link_label, pattern=link_label_filter): link_triples.append(link_triple) else: link_triples.append(link_triple) return LinkManager(link_triples)
[docs] def get_outgoing(self, node_class=None, link_type=(), link_label_filter=None, only_uuid=False): """Return a list of link triples that are (directly) outgoing of this node. :param node_class: If specified, should be a class or tuple of classes, and it filters only elements of that specific type (or a subclass of 'type') :param link_type: If specified should be a string or tuple to get the inputs of this link type, if None then returns all outputs of all link types. :param link_label_filter: filters the outgoing nodes by its link label. Here wildcards (% and _) can be passed in link label filter as we are using "like" in QB. :param only_uuid: project only the node UUID instead of the instance onto the `NodeTriple.node` entries """ link_triples = self.get_stored_link_triples(node_class, link_type, link_label_filter, 'outgoing', only_uuid) return LinkManager(link_triples)
[docs] def store_all(self, with_transaction=True, use_cache=None): """Store the node, together with all input links. Unstored nodes from cached incoming linkswill also be stored. :parameter with_transaction: if False, do not use a transaction because the caller will already have opened one. """ if use_cache is not None: warnings.warn( # pylint: disable=no-member 'the `use_cache` argument is deprecated and will be removed in `v2.0.0`', AiidaDeprecationWarning ) if self.is_stored: raise exceptions.ModificationNotAllowed('Node<{}> is already stored'.format(self.id)) # For each node of a cached incoming link, check that all its incoming links are stored for link_triple in self._incoming_cache: link_triple.node.verify_are_parents_stored() for link_triple in self._incoming_cache: if not link_triple.node.is_stored: link_triple.node.store(with_transaction=with_transaction) return self.store(with_transaction)
[docs] def store(self, with_transaction=True, use_cache=None): """Store the node in the database while saving its attributes and repository directory. After being called attributes cannot be changed anymore! Instead, extras can be changed only AFTER calling this store() function. :note: After successful storage, those links that are in the cache, and for which also the parent node is already stored, will be automatically stored. The others will remain unstored. :parameter with_transaction: if False, do not use a transaction because the caller will already have opened one. """ # pylint: disable=arguments-differ from aiida.manage.caching import get_use_cache if use_cache is not None: warnings.warn( # pylint: disable=no-member 'the `use_cache` argument is deprecated and will be removed in `v2.0.0`', AiidaDeprecationWarning ) if not self._storable: raise exceptions.StoringNotAllowed(self._unstorable_message) if not self.is_stored: self._validate() # Verify that parents are already stored. Raises if this is not the case. self.verify_are_parents_stored() # Determine whether the cache should be used for the process type of this node. use_cache = get_use_cache(identifier=self.process_type) # Clean the values on the backend node *before* computing the hash in `_get_same_node`. This will allow # us to set `clean=False` if we are storing normally, since the values will already have been cleaned self._backend_entity.clean_values() # Retrieve the cached node. same_node = self._get_same_node() if use_cache else None if same_node is not None: self._store_from_cache(same_node, with_transaction=with_transaction) else: self._store(with_transaction=with_transaction, clean=True) # Set up autogrouping used by verdi run from aiida.orm.autogroup import current_autogroup, Autogroup, VERDIAUTOGROUP_TYPE from aiida.orm import Group if current_autogroup is not None: if not isinstance(current_autogroup, Autogroup): raise exceptions.ValidationError('`current_autogroup` is not of type `Autogroup`') if current_autogroup.is_to_be_grouped(self): group_label = current_autogroup.get_group_name() if group_label is not None: group = Group.objects.get_or_create(label=group_label, type_string=VERDIAUTOGROUP_TYPE)[0] group.add_nodes(self) return self
[docs] def _store(self, with_transaction=True, clean=True): """Store the node in the database while saving its attributes and repository directory. :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 """ # First store the repository folder such that if this fails, there won't be an incomplete node in the database. # On the flipside, in the case that storing the node does fail, the repository will now have an orphaned node # directory which will have to be cleaned manually sometime. self._repository.store() try: links = self._incoming_cache self._backend_entity.store(links, with_transaction=with_transaction, clean=clean) except Exception: # I put back the files in the sandbox folder since the transaction did not succeed self._repository.restore() raise self._incoming_cache = list() self._backend_entity.set_extra(_HASH_EXTRA_KEY, self.get_hash()) return self
[docs] def verify_are_parents_stored(self): """Verify that all `parent` nodes are already stored. :raise aiida.common.ModificationNotAllowed: if one of the source nodes of incoming links is not stored. """ for link_triple in self._incoming_cache: if not link_triple.node.is_stored: raise exceptions.ModificationNotAllowed( 'Cannot store because source node of link triple {} is not stored'.format(link_triple) )
[docs] def _store_from_cache(self, cache_node, with_transaction): """Store this node from an existing cache node.""" from aiida.orm.utils.mixins import Sealable assert self.node_type == cache_node.node_type # Make sure the node doesn't have any RETURN links if cache_node.get_outgoing(link_type=LinkType.RETURN).all(): raise ValueError('Cannot use cache from nodes with RETURN links.') self.label = cache_node.label self.description = cache_node.description for key, value in cache_node.attributes.items(): if key != Sealable.SEALED_KEY: self.set_attribute(key, value) self.put_object_from_tree(cache_node._repository._get_base_folder().abspath) # pylint: disable=protected-access self._store(with_transaction=with_transaction, clean=False) self._add_outputs_from_cache(cache_node) self.set_extra('_aiida_cached_from', cache_node.uuid)
[docs] def _add_outputs_from_cache(self, cache_node): """Replicate the output links and nodes from the cached node onto this node.""" for entry in cache_node.get_outgoing(link_type=LinkType.CREATE): new_node = entry.node.clone() new_node.add_incoming(self, link_type=LinkType.CREATE, link_label=entry.link_label) new_node.store()
[docs] def get_hash(self, ignore_errors=True, **kwargs): """Return the hash for this node based on its attributes.""" if not self.is_stored: raise exceptions.InvalidOperation('You can get the hash only after having stored the node') return self._get_hash(ignore_errors=ignore_errors, **kwargs)
[docs] def _get_hash(self, ignore_errors=True, **kwargs): """ Return the hash for this node based on its attributes. This will always work, even before storing. """ try: return make_hash(self._get_objects_to_hash(), **kwargs) except Exception: # pylint: disable=broad-except if not ignore_errors: raise
[docs] def _get_objects_to_hash(self): """Return a list of objects which should be included in the hash.""" objects = [ importlib.import_module(self.__module__.split('.', 1)[0]).__version__, { key: val for key, val in self.attributes_items() if key not in self._hash_ignored_attributes and key not in self._updatable_attributes # pylint: disable=unsupported-membership-test }, self._repository._get_base_folder(), # pylint: disable=protected-access self.computer.uuid if self.computer is not None else None ] return objects
[docs] def rehash(self): """Regenerate the stored hash of the Node.""" self.set_extra(_HASH_EXTRA_KEY, self.get_hash())
[docs] def clear_hash(self): """Sets the stored hash of the Node to None.""" self.set_extra(_HASH_EXTRA_KEY, None)
[docs] def get_cache_source(self): """Return the UUID of the node that was used in creating this node from the cache, or None if it was not cached. :return: source node UUID or None """ return self.get_extra('_aiida_cached_from', None)
@property def is_created_from_cache(self): """Return whether this node was created from a cached node. :return: boolean, True if the node was created by cloning a cached node, False otherwise """ return self.get_cache_source() is not None
[docs] def _get_same_node(self): """Returns a stored node from which the current Node can be cached or None if it does not exist If a node is returned it is a valid cache, meaning its `_aiida_hash` extra matches `self.get_hash()`. If there are multiple valid matches, the first one is returned. If no matches are found, `None` is returned. :return: a stored `Node` instance with the same hash as this code or None Note: this should be only called on stored nodes, or internally from .store() since it first calls clean_value() on the attributes to normalise them. """ try: return next(self._iter_all_same_nodes(allow_before_store=True)) except StopIteration: return None
[docs] def get_all_same_nodes(self): """Return a list of stored nodes which match the type and hash of the current node. All returned nodes are valid caches, meaning their `_aiida_hash` extra matches `self.get_hash()`. Note: this can be called only after storing a Node (since at store time attributes will be cleaned with `clean_value` and the hash should become idempotent to the action of serialization/deserialization) """ return list(self._iter_all_same_nodes())
[docs] def _iter_all_same_nodes(self, allow_before_store=False): """ Returns an iterator of all same nodes. Note: this should be only called on stored nodes, or internally from .store() since it first calls clean_value() on the attributes to normalise them. """ if not allow_before_store and not self.is_stored: raise exceptions.InvalidOperation('You can get the hash only after having stored the node') node_hash = self._get_hash() if not node_hash or not self._cachable: return iter(()) builder = QueryBuilder() builder.append(self.__class__, filters={'extras._aiida_hash': node_hash}, project='*', subclassing=False) nodes_identical = (n[0] for n in builder.iterall()) return (node for node in nodes_identical if node.is_valid_cache)
@property def is_valid_cache(self): """Hook to exclude certain `Node` instances from being considered a valid cache.""" # pylint: disable=no-self-use return True
[docs] def get_description(self): """Return a string with a description of the node. :return: a description string :rtype: str """ # pylint: disable=no-self-use return ''
[docs] @staticmethod def get_schema(): """ Every node property contains: - display_name: display name of the property - help text: short help text of the property - is_foreign_key: is the property foreign key to other type of the node - type: type of the property. e.g. str, dict, int :return: get schema of the node """ return { 'attributes': { 'display_name': 'Attributes', 'help_text': 'Attributes of the node', 'is_foreign_key': False, 'type': 'dict' }, 'attributes.state': { 'display_name': 'State', 'help_text': 'AiiDA state of the calculation', 'is_foreign_key': False, 'type': '' }, 'ctime': { 'display_name': 'Creation time', 'help_text': 'Creation time of the node', 'is_foreign_key': False, 'type': 'datetime.datetime' }, 'extras': { 'display_name': 'Extras', 'help_text': 'Extras of the node', 'is_foreign_key': False, 'type': 'dict' }, 'id': { 'display_name': 'Id', 'help_text': 'Id of the object', 'is_foreign_key': False, 'type': 'int' }, 'label': { 'display_name': 'Label', 'help_text': 'User-assigned label', 'is_foreign_key': False, 'type': 'str' }, 'mtime': { 'display_name': 'Last Modification time', 'help_text': 'Last modification time', 'is_foreign_key': False, 'type': 'datetime.datetime' }, 'node_type': { 'display_name': 'Type', 'help_text': 'Node type', 'is_foreign_key': False, 'type': 'str' }, 'user_id': { 'display_name': 'Id of creator', 'help_text': 'Id of the user that created the node', 'is_foreign_key': True, 'related_column': 'id', 'related_resource': '_dbusers', 'type': 'int' }, 'uuid': { 'display_name': 'Unique ID', 'help_text': 'Universally Unique Identifier', 'is_foreign_key': False, 'type': 'unicode' }, 'process_type': { 'display_name': 'Process type', 'help_text': 'Process type', 'is_foreign_key': False, 'type': 'str' } }