aiida.orm.implementation package#

Module containing the backend entity abstracts for storage backends.

Submodules#

Module for the backend implementation of the AuthInfo ORM class.

class aiida.orm.implementation.authinfos.BackendAuthInfo(backend: StorageBackend, **kwargs: Any)[source]#

Bases: aiida.orm.implementation.entities.BackendEntity

Backend implementation for the AuthInfo ORM class.

An authinfo is a set of credentials that can be used to authenticate to a remote computer.

METADATA_WORKDIR = 'workdir'#

__abstractmethods__ = frozenset({'computer', 'enabled', 'get_auth_params', 'get_metadata', 'id', 'is_stored', 'set_auth_params', 'set_metadata', 'store', 'user'})#

__module__ = 'aiida.orm.implementation.authinfos'#

_abc_impl = <_abc_data object>#

abstract property computer: BackendComputer#: Return the computer associated with this instance.

abstract property enabled: bool#

Return whether this instance is enabled.

Returns: boolean, True if enabled, False otherwise

abstract get_auth_params() → Dict[str, Any][source]#

Return the dictionary of authentication parameters

Returns: a dictionary with authentication parameters

abstract get_metadata() → Dict[str, Any][source]#

Return the dictionary of metadata

Returns: a dictionary with metadata

abstract set_auth_params(auth_params: Dict[str, Any]) → None[source]#

Set the dictionary of authentication parameters

Parameters: auth_params – a dictionary with authentication parameters

abstract set_metadata(metadata: Dict[str, Any]) → None[source]#

Set the dictionary of metadata

Parameters: metadata – a dictionary with metadata

abstract property user: BackendUser#: Return the user associated with this instance.

class aiida.orm.implementation.authinfos.BackendAuthInfoCollection(backend: StorageBackend)[source]#

Bases: aiida.orm.implementation.entities.BackendCollection[aiida.orm.implementation.authinfos.BackendAuthInfo]

The collection of backend AuthInfo entries.

ENTITY_CLASS#: alias of aiida.orm.implementation.authinfos.BackendAuthInfo

__module__ = 'aiida.orm.implementation.authinfos'#

__orig_bases__ = (aiida.orm.implementation.entities.BackendCollection[aiida.orm.implementation.authinfos.BackendAuthInfo],)#

__parameters__ = ()#

abstract delete(pk: int) → None[source]#

Delete an entry from the collection.

Parameters: pk – the pk of the entry to delete

Module for comment backend classes.

class aiida.orm.implementation.comments.BackendComment(backend: StorageBackend, **kwargs: Any)[source]#

Bases: aiida.orm.implementation.entities.BackendEntity

Backend implementation for the Comment ORM class.

A comment is a text that can be attached to a node.

__abstractmethods__ = frozenset({'content', 'ctime', 'id', 'is_stored', 'mtime', 'node', 'set_content', 'set_mtime', 'set_user', 'store', 'user', 'uuid'})#

__module__ = 'aiida.orm.implementation.comments'#

_abc_impl = <_abc_data object>#

abstract property content: str#: Return the comment content.

abstract property ctime: datetime.datetime#: Return the creation time of the comment.

abstract property mtime: datetime.datetime#: Return the modified time of the comment.

abstract property node: BackendNode#: Return the comment’s node.

abstract set_content(value: str)[source]#: Set the comment content.

abstract set_mtime(value: datetime.datetime) → None[source]#: Set the modified time of the comment.

abstract set_user(value: BackendUser) → None[source]#: Set the comment owner.

abstract property user: BackendUser#: Return the comment owner.

abstract property uuid: str#: Return the UUID of the comment.

class aiida.orm.implementation.comments.BackendCommentCollection(backend: StorageBackend)[source]#

Bases: aiida.orm.implementation.entities.BackendCollection[aiida.orm.implementation.comments.BackendComment]

The collection of Comment entries.

ENTITY_CLASS#: alias of aiida.orm.implementation.comments.BackendComment

__module__ = 'aiida.orm.implementation.comments'#

__orig_bases__ = (aiida.orm.implementation.entities.BackendCollection[aiida.orm.implementation.comments.BackendComment],)#

__parameters__ = ()#

abstract create(node: BackendNode, user: BackendUser, content: Optional[str] = None, **kwargs)[source]#

Create a Comment for a given node and user

Parameters

node – a Node instance
user – a User instance
content – the comment content

Returns

a Comment object associated to the given node and user

abstract delete(comment_id: int) → None[source]#

Remove a Comment from the collection with the given id

Parameters

comment_id – the id of the comment to delete

Raises

TypeError – if comment_id is not an int
NotExistent – if Comment with ID comment_id is not found

abstract delete_all() → None[source]#

Delete all Comment entries.

Raises: IntegrityError – if all Comments could not be deleted

abstract delete_many(filters: dict) → List[int][source]#

Delete Comments based on filters

Parameters

filters – similar to QueryBuilder filter

Returns

(former) PK s of deleted Comments

Raises

TypeError – if filters is not a dict
ValidationError – if filters is empty

Backend specific computer objects and methods

class aiida.orm.implementation.computers.BackendComputer(backend: StorageBackend, **kwargs: Any)[source]#

Bases: aiida.orm.implementation.entities.BackendEntity

Backend implementation for the Computer ORM class.

A computer is a resource that can be used to run calculations: It has an associated transport_type, which points to a plugin for connecting to the resource and passing data, and a scheduler_type, which points to a plugin for scheduling calculations.

__abstractmethods__ = frozenset({'copy', 'description', 'get_metadata', 'get_scheduler_type', 'get_transport_type', 'hostname', 'id', 'is_stored', 'label', 'set_description', 'set_hostname', 'set_label', 'set_metadata', 'set_scheduler_type', 'set_transport_type', 'store', 'uuid'})#

__module__ = 'aiida.orm.implementation.computers'#

_abc_impl = <_abc_data object>#

_logger = <Logger aiida.orm.implementation.computers (REPORT)>#

abstract copy() → aiida.orm.implementation.computers.BackendComputer[source]#

Create an un-stored clone of an already stored Computer.

Raises: InvalidOperation if the computer is not stored.

abstract property description: str#: Return the description of the computer.

abstract get_metadata() → Dict[str, Any][source]#: Return the metadata for the computer.

abstract get_scheduler_type() → str[source]#: Return the scheduler plugin type.

abstract get_transport_type() → str[source]#: Return the transport plugin type.

abstract property hostname: str#: Return the hostname of the computer (used to associate the connected device).

abstract property label: str#: Return the (unique) label of the computer.

abstract set_description(val: str)[source]#: Set the description of the computer.

abstract set_hostname(val: str) → None[source]#: Set the hostname of this computer :param val: The new hostname

abstract set_label(val: str)[source]#: Set the (unique) label of the computer.

abstract set_metadata(metadata: Dict[str, Any]) → None[source]#: Set the metadata for the computer.

abstract set_scheduler_type(scheduler_type: str) → None[source]#: Set the scheduler plugin type.

abstract set_transport_type(transport_type: str) → None[source]#: Set the transport plugin type.

abstract property uuid: str#: Return the UUID of the computer.

class aiida.orm.implementation.computers.BackendComputerCollection(backend: StorageBackend)[source]#

Bases: aiida.orm.implementation.entities.BackendCollection[aiida.orm.implementation.computers.BackendComputer]

The collection of Computer entries.

ENTITY_CLASS#: alias of aiida.orm.implementation.computers.BackendComputer

__module__ = 'aiida.orm.implementation.computers'#

__orig_bases__ = (aiida.orm.implementation.entities.BackendCollection[aiida.orm.implementation.computers.BackendComputer],)#

__parameters__ = ()#

abstract delete(pk: int) → None[source]#

Delete an entry with the given pk

Parameters: pk – the pk of the entry to delete

Classes and methods for backend non-specific entities

class aiida.orm.implementation.entities.BackendCollection(backend: StorageBackend)[source]#

Bases: Generic[aiida.orm.implementation.entities.EntityType]

Container class that represents a collection of entries of a particular backend entity.

ENTITY_CLASS: ClassVar[Type[aiida.orm.implementation.entities.EntityType]]#

__annotations__ = {'ENTITY_CLASS': typing.ClassVar[typing.Type[~EntityType]]}#

__dict__ = mappingproxy({'__module__': 'aiida.orm.implementation.entities', '__annotations__': {'ENTITY_CLASS': typing.ClassVar[typing.Type[~EntityType]]}, '__doc__': 'Container class that represents a collection of entries of a particular backend entity.', '__init__': <function BackendCollection.__init__>, 'backend': <property object>, 'create': <function BackendCollection.create>, '__orig_bases__': (typing.Generic[~EntityType],), '__dict__': <attribute '__dict__' of 'BackendCollection' objects>, '__weakref__': <attribute '__weakref__' of 'BackendCollection' objects>, '__parameters__': (~EntityType,)})#

__init__(backend: StorageBackend)[source]#

Parameters: backend – the backend this collection belongs to

__module__ = 'aiida.orm.implementation.entities'#

__orig_bases__ = (typing.Generic[~EntityType],)#

__parameters__ = (~EntityType,)#

__weakref__#: list of weak references to the object (if defined)

property backend: StorageBackend#: Return the backend.

create(**kwargs: Any) → aiida.orm.implementation.entities.EntityType[source]#

Create new a entry and set the attributes to those specified in the keyword arguments

Returns: the newly created entry of type ENTITY_CLASS

class aiida.orm.implementation.entities.BackendEntity(backend: StorageBackend, **kwargs: Any)[source]#

Bases: abc.ABC

An first-class entity in the backend

__abstractmethods__ = frozenset({'id', 'is_stored', 'store'})#

__dict__ = mappingproxy({'__module__': 'aiida.orm.implementation.entities', '__doc__': 'An first-class entity in the backend', '__init__': <function BackendEntity.__init__>, 'backend': <property object>, 'id': <property object>, 'pk': <property object>, 'store': <function BackendEntity.store>, 'is_stored': <property object>, '__dict__': <attribute '__dict__' of 'BackendEntity' objects>, '__weakref__': <attribute '__weakref__' of 'BackendEntity' objects>, '__abstractmethods__': frozenset({'id', 'is_stored', 'store'}), '_abc_impl': <_abc_data object>, '__annotations__': {}})#

__init__(backend: StorageBackend, **kwargs: Any)[source]#

__module__ = 'aiida.orm.implementation.entities'#

__weakref__#: list of weak references to the object (if defined)

_abc_impl = <_abc_data object>#

property backend: StorageBackend#

Return the backend this entity belongs to

Returns: the backend instance

abstract property id: int#

Return the id for this entity.

This is unique only amongst entities of this type for a particular backend.

Returns: the entity id

abstract property is_stored: bool#

Return whether the entity is stored.

Returns: True if stored, False otherwise

property pk: int#

Return the id for this entity.

This is unique only amongst entities of this type for a particular backend.

Returns: the entity id

abstract store() → aiida.orm.implementation.entities.EntityType[source]#

Store this entity in the backend.

Whether it is possible to call store more than once is delegated to the object itself

class aiida.orm.implementation.entities.BackendEntityExtrasMixin[source]#

Bases: abc.ABC

Mixin class that adds all abstract methods for the extras column to a backend entity

__abstractmethods__ = frozenset({'clear_extras', 'delete_extra', 'extras', 'extras_items', 'extras_keys', 'get_extra', 'reset_extras', 'set_extra'})#

__dict__ = mappingproxy({'__module__': 'aiida.orm.implementation.entities', '__doc__': 'Mixin class that adds all abstract methods for the extras column to a backend entity', 'extras': <property object>, 'get_extra': <function BackendEntityExtrasMixin.get_extra>, 'get_extra_many': <function BackendEntityExtrasMixin.get_extra_many>, 'set_extra': <function BackendEntityExtrasMixin.set_extra>, 'set_extra_many': <function BackendEntityExtrasMixin.set_extra_many>, 'reset_extras': <function BackendEntityExtrasMixin.reset_extras>, 'delete_extra': <function BackendEntityExtrasMixin.delete_extra>, 'delete_extra_many': <function BackendEntityExtrasMixin.delete_extra_many>, 'clear_extras': <function BackendEntityExtrasMixin.clear_extras>, 'extras_items': <function BackendEntityExtrasMixin.extras_items>, 'extras_keys': <function BackendEntityExtrasMixin.extras_keys>, '__dict__': <attribute '__dict__' of 'BackendEntityExtrasMixin' objects>, '__weakref__': <attribute '__weakref__' of 'BackendEntityExtrasMixin' objects>, '__abstractmethods__': frozenset({'delete_extra', 'get_extra', 'set_extra', 'extras', 'clear_extras', 'reset_extras', 'extras_keys', 'extras_items'}), '_abc_impl': <_abc_data object>, '__annotations__': {}})#

__module__ = 'aiida.orm.implementation.entities'#

__weakref__#: list of weak references to the object (if defined)

_abc_impl = <_abc_data object>#

abstract clear_extras() → None[source]#: Delete all extras.

abstract delete_extra(key: str) → None[source]#

Delete an extra.

Parameters: key – name of the extra
Raises: AttributeError – if the extra does not exist

delete_extra_many(keys: Iterable[str]) → None[source]#

Delete multiple extras.

Parameters: keys – names of the extras to delete
Raises: AttributeError – if at least one of the extra does not exist

abstract property extras: Dict[str, Any]#

Return the complete extras dictionary.

Warning

While the entity 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 entity 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.

Returns: the extras as a dictionary

abstract extras_items() → Iterable[Tuple[str, Any]][source]#: Return an iterator over the extras key/value pairs.

abstract extras_keys() → Iterable[str][source]#: Return an iterator over the extra keys.

abstract get_extra(key: str) → Any[source]#

Return the value of an extra.

Warning

While the entity 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 entity 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.

Parameters: key – name of the extra
Returns: the value of the extra
Raises: AttributeError – if the extra does not exist

get_extra_many(keys: Iterable[str]) → List[Any][source]#

Return the values of multiple extras.

Warning

Parameters: keys – a list of extra names
Returns: a list of extra values
Raises: AttributeError – if at least one extra does not exist

abstract reset_extras(extras: Dict[str, Any]) → None[source]#

Reset the extras.

Note

This will completely clear any existing extras and replace them with the new dictionary.

Parameters: extras – a dictionary with the extras to set

abstract set_extra(key: str, value: Any) → None[source]#

Set an extra to the given value.

Parameters

key – name of the extra
value – value of the extra

set_extra_many(extras: Dict[str, Any]) → None[source]#

Set multiple extras.

Note

This will override any existing extras that are present in the new dictionary.

Parameters: extras – a dictionary with the extras to set

Backend group module

class aiida.orm.implementation.groups.BackendGroup(backend: StorageBackend, **kwargs: Any)[source]#

Bases: aiida.orm.implementation.entities.BackendEntity, aiida.orm.implementation.entities.BackendEntityExtrasMixin

Backend implementation for the Group ORM class.

A group is a collection of nodes.

__abstractmethods__ = frozenset({'clear', 'clear_extras', 'count', 'delete_extra', 'description', 'extras', 'extras_items', 'extras_keys', 'get_extra', 'id', 'is_stored', 'label', 'nodes', 'reset_extras', 'set_extra', 'store', 'type_string', 'user', 'uuid'})#

__module__ = 'aiida.orm.implementation.groups'#

__repr__() → str[source]#: Return repr(self).

__str__() → str[source]#: Return str(self).

_abc_impl = <_abc_data object>#

add_nodes(nodes: Sequence[aiida.orm.implementation.nodes.BackendNode], **kwargs)[source]#

Add a set of nodes to the group.

Note: all the nodes and the group itself have to be stored.
Parameters: nodes – a list of BackendNode instances to be added to this group

abstract clear() → None[source]#: Remove all the nodes from this group.

abstract count() → int[source]#

Return the number of entities in this group.

Returns: integer number of entities contained within the group

abstract property description: Optional[str]#: Return the description of the group as a string.

abstract property label: str#: Return the name of the group as a string.

abstract property nodes: aiida.orm.implementation.groups.NodeIterator#: Return a generator/iterator that iterates over all nodes and returns the respective AiiDA subclasses of Node, and also allows to ask for the number of nodes in the group using len().

remove_nodes(nodes: Sequence[aiida.orm.implementation.nodes.BackendNode]) → None[source]#

Remove a set of nodes from the group.

Note: all the nodes and the group itself have to be stored.
Parameters: nodes – a list of BackendNode instances to be removed from this group

abstract property type_string: str#: Return the string defining the type of the group.

abstract property user: BackendUser#: Return a backend user object, representing the user associated to this group.

abstract property uuid: str#: Return the UUID of the group.

class aiida.orm.implementation.groups.BackendGroupCollection(backend: StorageBackend)[source]#

Bases: aiida.orm.implementation.entities.BackendCollection[aiida.orm.implementation.groups.BackendGroup]

The collection of Group entries.

ENTITY_CLASS#: alias of aiida.orm.implementation.groups.BackendGroup

__module__ = 'aiida.orm.implementation.groups'#

__orig_bases__ = (aiida.orm.implementation.entities.BackendCollection[aiida.orm.implementation.groups.BackendGroup],)#

__parameters__ = ()#

abstract delete(id: int) → None[source]#

Delete a group with the given id

Parameters: id – the id of the group to delete

class aiida.orm.implementation.groups.NodeIterator(*args, **kwargs)[source]#

Bases: Protocol

Protocol for iterating over nodes in a group

__abstractmethods__ = frozenset({})#

__dict__ = mappingproxy({'__module__': 'aiida.orm.implementation.groups', '__doc__': 'Protocol for iterating over nodes in a group', '__iter__': <function NodeIterator.__iter__>, '__next__': <function NodeIterator.__next__>, '__getitem__': <function NodeIterator.__getitem__>, '__len__': <function NodeIterator.__len__>, '__dict__': <attribute '__dict__' of 'NodeIterator' objects>, '__weakref__': <attribute '__weakref__' of 'NodeIterator' objects>, '__parameters__': (), '_is_protocol': True, '__subclasshook__': <function Protocol.__init_subclass__.<locals>._proto_hook>, '__init__': <function _no_init>, '__abstractmethods__': frozenset(), '_abc_impl': <_abc_data object>, '__annotations__': {}})#

__getitem__(value: Union[int, slice]) → Union[aiida.orm.implementation.nodes.BackendNode, List[aiida.orm.implementation.nodes.BackendNode]][source]#: Index node(s) from the group.

__init__(*args, **kwargs)#

__iter__() → aiida.orm.implementation.groups.NodeIterator[source]#: Return an iterator over the nodes in the group.

__len__() → int[source]#: Return the number of nodes in the group.

__module__ = 'aiida.orm.implementation.groups'#

__next__() → aiida.orm.implementation.nodes.BackendNode[source]#: Return the next node in the group.

__parameters__ = ()#

__subclasshook__()#

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__#: list of weak references to the object (if defined)

_abc_impl = <_abc_data object>#

_is_protocol = True#

Backend group module

class aiida.orm.implementation.logs.BackendLog(backend: StorageBackend, **kwargs: Any)[source]#

Bases: aiida.orm.implementation.entities.BackendEntity

Backend implementation for the Log ORM class.

A log is a record of logging call for a particular node.

__abstractmethods__ = frozenset({'dbnode_id', 'id', 'is_stored', 'levelname', 'loggername', 'message', 'metadata', 'store', 'time', 'uuid'})#

__module__ = 'aiida.orm.implementation.logs'#

_abc_impl = <_abc_data object>#

abstract property dbnode_id: int#: Return the id of the object that created the log entry.

abstract property levelname: str#: Return the name of the log level.

abstract property loggername: str#: Return the name of the logger that created this entry.

abstract property message: str#: Return the message corresponding to the log entry.

abstract property metadata: Dict[str, Any]#: Return the metadata corresponding to the log entry.

abstract property time: datetime.datetime#: Return the time corresponding to the log entry.

abstract property uuid: str#: Return the UUID of the log entry.

class aiida.orm.implementation.logs.BackendLogCollection(backend: StorageBackend)[source]#

Bases: aiida.orm.implementation.entities.BackendCollection[aiida.orm.implementation.logs.BackendLog]

The collection of Log entries.

ENTITY_CLASS#: alias of aiida.orm.implementation.logs.BackendLog

__module__ = 'aiida.orm.implementation.logs'#

__orig_bases__ = (aiida.orm.implementation.entities.BackendCollection[aiida.orm.implementation.logs.BackendLog],)#

__parameters__ = ()#

abstract delete(log_id: int) → None[source]#

Remove a Log entry from the collection with the given id

Parameters

log_id – id of the Log to delete

Raises

TypeError – if log_id is not an int
NotExistent – if Log with ID log_id is not found

abstract delete_all() → None[source]#

Delete all Log entries.

Raises: IntegrityError – if all Logs could not be deleted

abstract delete_many(filters: dict) → List[int][source]#

Delete Logs based on filters

Parameters

filters – similar to QueryBuilder filter

Returns

(former) PK s of deleted Logs

Raises

TypeError – if filters is not a dict
ValidationError – if filters is empty

Abstract BackendNode and BackendNodeCollection implementation.

class aiida.orm.implementation.nodes.BackendNode(backend: StorageBackend, **kwargs: Any)[source]#

Bases: aiida.orm.implementation.entities.BackendEntity, aiida.orm.implementation.entities.BackendEntityExtrasMixin

Backend implementation for the Node ORM class.

A node stores data input or output from a computation.

__abstractmethods__ = frozenset({'add_incoming', 'attributes', 'attributes_items', 'attributes_keys', 'clean_values', 'clear_attributes', 'clear_extras', 'clone', 'computer', 'ctime', 'delete_attribute', 'delete_extra', 'description', 'extras', 'extras_items', 'extras_keys', 'get_attribute', 'get_extra', 'id', 'is_stored', 'label', 'mtime', 'node_type', 'process_type', 'repository_metadata', 'reset_attributes', 'reset_extras', 'set_attribute', 'set_extra', 'store', 'user', 'uuid'})#

__module__ = 'aiida.orm.implementation.nodes'#

_abc_impl = <_abc_data object>#

abstract add_incoming(source: aiida.orm.implementation.nodes.BackendNode, link_type, link_label)[source]#

Add a link of the given type from a given node to ourself.

Parameters

source – the node from which the link is coming
link_type – the link type
link_label – the link label

Returns

True if the proposed link is allowed, False otherwise

Raises

TypeError – if source is not a Node instance or link_type is not a LinkType enum
ValueError – if the proposed link is invalid
aiida.common.ModificationNotAllowed – if either source or target node is not stored

abstract property attributes: Dict[str, Any]#

Return the complete attributes dictionary.

Warning

While the entity 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 entity 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.

Returns: the attributes as a dictionary

abstract attributes_items() → Iterable[Tuple[str, Any]][source]#

Return an iterator over the attributes.

Returns: an iterator with attribute key value pairs

abstract attributes_keys() → Iterable[str][source]#

Return an iterator over the attribute keys.

Returns: an iterator with attribute keys

abstract clean_values()[source]#

Clean the values of the node fields.

This method is called before storing the node. The purpose of this method is to convert data to a type which can be serialized and deserialized for storage in the DB without its value changing.

abstract clear_attributes()[source]#: Delete all attributes.

abstract clone() → aiida.orm.implementation.nodes.BackendNodeType[source]#

Return an unstored clone of ourselves.

Returns: an unstored BackendNode with the exact same attributes and extras as self

abstract property computer: Optional[BackendComputer]#

Return the computer of this node.

Returns: the computer or None

abstract property ctime: datetime.datetime#

Return the node ctime.

Returns: the ctime

abstract delete_attribute(key: str) → None[source]#

Delete an attribute.

Parameters: key – name of the attribute
Raises: AttributeError – if the attribute does not exist

delete_attribute_many(keys: Iterable[str]) → None[source]#

Delete multiple attributes.

Parameters: keys – names of the attributes to delete
Raises: AttributeError – if at least one of the attribute does not exist

abstract property description: str#

Return the node description.

Returns: the description

abstract get_attribute(key: str) → Any[source]#

Return the value of an attribute.

Warning

While the entity 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 entity 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.

Parameters: key – name of the attribute
Returns: the value of the attribute
Raises: AttributeError – if the attribute does not exist

get_attribute_many(keys: Iterable[str]) → List[Any][source]#

Return the values of multiple attributes.

Warning

Parameters: keys – a list of attribute names
Returns: a list of attribute values
Raises: AttributeError – if at least one attribute does not exist

abstract property label: str#

Return the node label.

Returns: the label

abstract property mtime: datetime.datetime#

Return the node mtime.

Returns: the mtime

abstract property node_type: str#

Return the node type.

Returns: the node type

abstract property process_type: Optional[str]#

Return the node process type.

Returns: the process type

abstract property repository_metadata: Dict[str, Any]#

Return the node repository metadata.

Returns: the repository metadata

abstract reset_attributes(attributes: Dict[str, Any]) → None[source]#

Reset the attributes.

Note

This will completely clear any existing attributes and replace them with the new dictionary.

Parameters: attributes – a dictionary with the attributes to set

abstract set_attribute(key: str, value: Any) → None[source]#

Set an attribute to the given value.

Parameters

key – name of the attribute
value – value of the attribute

set_attribute_many(attributes: Dict[str, Any]) → None[source]#

Set multiple attributes.

Note

This will override any existing attributes that are present in the new dictionary.

Parameters: attributes – a dictionary with the attributes to set

abstract store(links: Optional[Sequence[LinkTriple]] = None, with_transaction: bool = True, clean: bool = True) → aiida.orm.implementation.nodes.BackendNodeType[source]#

Store the node in the database.

Parameters

links – optional links to add before storing
with_transaction – if False, do not use a transaction because the caller will already have opened one.
clean – boolean, if True, will clean the attributes and extras before attempting to store

abstract property user: BackendUser#

Return the user of this node.

Returns: the user

abstract property uuid: str#

Return the node UUID.

Returns: the string representation of the UUID

class aiida.orm.implementation.nodes.BackendNodeCollection(backend: StorageBackend)[source]#

Bases: aiida.orm.implementation.entities.BackendCollection[aiida.orm.implementation.nodes.BackendNode]

The collection of BackendNode entries.

ENTITY_CLASS#: alias of aiida.orm.implementation.nodes.BackendNode

__module__ = 'aiida.orm.implementation.nodes'#

__orig_bases__ = (aiida.orm.implementation.entities.BackendCollection[aiida.orm.implementation.nodes.BackendNode],)#

__parameters__ = ()#

abstract delete(pk: int) → None[source]#

Remove a Node entry from the collection with the given id

Parameters: pk – id of the node to delete

abstract get(pk: int)[source]#

Return a Node entry from the collection with the given id

Parameters: pk – id of the node

Abstract QueryBuilder definition.

class aiida.orm.implementation.querybuilder.BackendQueryBuilder(backend: StorageBackend)[source]#

Bases: abc.ABC

Backend query builder interface

__abstractmethods__ = frozenset({'count', 'first', 'get_creation_statistics', 'iterall', 'iterdict'})#

__dict__ = mappingproxy({'__module__': 'aiida.orm.implementation.querybuilder', '__doc__': 'Backend query builder interface', '__init__': <function BackendQueryBuilder.__init__>, 'count': <function BackendQueryBuilder.count>, 'first': <function BackendQueryBuilder.first>, 'iterall': <function BackendQueryBuilder.iterall>, 'iterdict': <function BackendQueryBuilder.iterdict>, 'as_sql': <function BackendQueryBuilder.as_sql>, 'analyze_query': <function BackendQueryBuilder.analyze_query>, 'get_creation_statistics': <function BackendQueryBuilder.get_creation_statistics>, '__dict__': <attribute '__dict__' of 'BackendQueryBuilder' objects>, '__weakref__': <attribute '__weakref__' of 'BackendQueryBuilder' objects>, '__abstractmethods__': frozenset({'first', 'iterall', 'get_creation_statistics', 'count', 'iterdict'}), '_abc_impl': <_abc_data object>, '__annotations__': {}})#

__init__(backend: StorageBackend)[source]#

Parameters: backend – the backend

__module__ = 'aiida.orm.implementation.querybuilder'#

__weakref__#: list of weak references to the object (if defined)

_abc_impl = <_abc_data object>#

analyze_query(data: aiida.orm.implementation.querybuilder.QueryDictType, execute: bool = True, verbose: bool = False) → str[source]#

Return the query plan, i.e. a list of SQL statements that will be executed.

See: https://www.postgresql.org/docs/11/sql-explain.html

Params execute: Carry out the command and show actual run times and other statistics.
Params verbose: Display additional information regarding the plan.

as_sql(data: aiida.orm.implementation.querybuilder.QueryDictType, inline: bool = False) → str[source]#

Convert the query to an SQL string representation.

Warning

This method should be used for debugging purposes only, since normally sqlalchemy will handle this process internally.

Params inline: Inline bound parameters (this is normally handled by the Python DBAPI).

abstract count(data: aiida.orm.implementation.querybuilder.QueryDictType) → int[source]#: Return the number of results of the query

abstract first(data: aiida.orm.implementation.querybuilder.QueryDictType) → Optional[List[Any]][source]#

Executes query, asking for one instance.

Returns: One row of aiida results

abstract get_creation_statistics(user_pk: Optional[int] = None) → Dict[str, Any][source]#

Return a dictionary with the statistics of node creation, summarized by day.

Note

Days when no nodes were created are not present in the returned ctime_by_day dictionary.

Parameters

user_pk – If None (default), return statistics for all users. If user pk is specified, return only the statistics for the given user.

Returns

a dictionary as follows:

{
   "total": TOTAL_NUM_OF_NODES,
   "types": {TYPESTRING1: count, TYPESTRING2: count, ...},
   "ctime_by_day": {'YYYY-MMM-DD': count, ...}
}

where in ctime_by_day the key is a string in the format ‘YYYY-MM-DD’ and the value is an integer with the number of nodes created that day.

abstract iterall(data: aiida.orm.implementation.querybuilder.QueryDictType, batch_size: Optional[int]) → Iterable[List[Any]][source]#: Return an iterator over all the results of a list of lists.

abstract iterdict(data: aiida.orm.implementation.querybuilder.QueryDictType, batch_size: Optional[int]) → Iterable[Dict[str, Dict[str, Any]]][source]#: Return an iterator over all the results of a list of dictionaries.

class aiida.orm.implementation.querybuilder.PathItemType(*args, **kwargs)[source]#

Bases: dict

An item on the query path

__annotations__ = {'edge_tag': <class 'str'>, 'entity_type': typing.Union[str, typing.List[str]], 'joining_keyword': <class 'str'>, 'joining_value': <class 'str'>, 'orm_base': typing.Literal['node', 'group', 'authinfo', 'comment', 'computer', 'log', 'user'], 'outerjoin': <class 'bool'>, 'tag': <class 'str'>}#

__dict__ = mappingproxy({'__module__': 'aiida.orm.implementation.querybuilder', '__annotations__': {'entity_type': typing.Union[str, typing.List[str]], 'orm_base': typing.Literal['node', 'group', 'authinfo', 'comment', 'computer', 'log', 'user'], 'tag': <class 'str'>, 'joining_keyword': <class 'str'>, 'joining_value': <class 'str'>, 'outerjoin': <class 'bool'>, 'edge_tag': <class 'str'>}, '__doc__': 'An item on the query path', '__new__': <staticmethod object>, '__dict__': <attribute '__dict__' of 'PathItemType' objects>, '__weakref__': <attribute '__weakref__' of 'PathItemType' objects>, '__total__': True})#

__module__ = 'aiida.orm.implementation.querybuilder'#

static __new__(cls, /, *args, **kwargs)#

__total__ = True#

__weakref__#: list of weak references to the object (if defined)

edge_tag: str#

entity_type: Union[str, List[str]]#

joining_keyword: str#

joining_value: str#

orm_base: Literal['node', 'group', 'authinfo', 'comment', 'computer', 'log', 'user']#

outerjoin: bool#

tag: str#

class aiida.orm.implementation.querybuilder.QueryDictType(*args, **kwargs)[source]#

Bases: dict

A JSON serialisable representation of a QueryBuilder instance

__annotations__ = {'distinct': <class 'bool'>, 'filters': typing.Dict[str, typing.Dict[str, typing.Union[typing.Dict[str, typing.List[typing.Dict[str, typing.Any]]], typing.Dict[str, typing.Any]]]], 'limit': typing.Union[int, NoneType], 'offset': typing.Union[int, NoneType], 'order_by': typing.List[typing.Dict[str, typing.List[typing.Dict[str, typing.Dict[str, str]]]]], 'path': typing.List[aiida.orm.implementation.querybuilder.PathItemType], 'project': typing.Dict[str, typing.List[typing.Dict[str, typing.Dict[str, typing.Any]]]]}#

__dict__ = mappingproxy({'__module__': 'aiida.orm.implementation.querybuilder', '__annotations__': {'path': typing.List[aiida.orm.implementation.querybuilder.PathItemType], 'filters': typing.Dict[str, typing.Dict[str, typing.Union[typing.Dict[str, typing.List[typing.Dict[str, typing.Any]]], typing.Dict[str, typing.Any]]]], 'project': typing.Dict[str, typing.List[typing.Dict[str, typing.Dict[str, typing.Any]]]], 'order_by': typing.List[typing.Dict[str, typing.List[typing.Dict[str, typing.Dict[str, str]]]]], 'offset': typing.Union[int, NoneType], 'limit': typing.Union[int, NoneType], 'distinct': <class 'bool'>}, '__doc__': 'A JSON serialisable representation of a ``QueryBuilder`` instance', '__new__': <staticmethod object>, '__dict__': <attribute '__dict__' of 'QueryDictType' objects>, '__weakref__': <attribute '__weakref__' of 'QueryDictType' objects>, '__total__': True})#

__module__ = 'aiida.orm.implementation.querybuilder'#

static __new__(cls, /, *args, **kwargs)#

__total__ = True#

__weakref__#: list of weak references to the object (if defined)

distinct: bool#

filters: Dict[str, Dict[str, Union[Dict[str, List[Dict[str, Any]]], Dict[str, Any]]]]#

limit: Optional[int]#

offset: Optional[int]#

order_by: List[Dict[str, List[Dict[str, Dict[str, str]]]]]#

path: List[aiida.orm.implementation.querybuilder.PathItemType]#

project: Dict[str, List[Dict[str, Dict[str, Any]]]]#

Generic backend related objects

class aiida.orm.implementation.storage_backend.StorageBackend(profile: Profile)[source]#

Bases: abc.ABC

Abstraction for a backend to read/write persistent data for a profile’s provenance graph.

AiiDA splits data storage into two sources:

Searchable data, which is stored in the database and can be queried using the QueryBuilder
Non-searchable (binary) data, which is stored in the repository and can be loaded using the RepositoryBackend

The two sources are inter-linked by the Node.base.repository.metadata. Once stored, the leaf values of this dictionary must be valid pointers to object keys in the repository.

For a completely new storage, the initialise method should be called first. This will automatically initialise the repository and the database with the current schema. The class methods,`version_profile` and migrate should be able to be called for existing storage, at any supported schema version. But an instance of this class should be created only for the latest schema version.

__abstractmethods__ = frozenset({'__init__', '__str__', '_clear', 'authinfos', 'bulk_insert', 'bulk_update', 'close', 'comments', 'computers', 'delete_nodes_and_connections', 'get_global_variable', 'get_repository', 'groups', 'in_transaction', 'initialise', 'is_closed', 'logs', 'maintain', 'migrate', 'nodes', 'query', 'set_global_variable', 'transaction', 'users', 'version_head', 'version_profile'})#

__dict__ = mappingproxy({'__module__': 'aiida.orm.implementation.storage_backend', '__doc__': "Abstraction for a backend to read/write persistent data for a profile's provenance graph.\n\n AiiDA splits data storage into two sources:\n\n - Searchable data, which is stored in the database and can be queried using the QueryBuilder\n - Non-searchable (binary) data, which is stored in the repository and can be loaded using the RepositoryBackend\n\n The two sources are inter-linked by the ``Node.base.repository.metadata``.\n Once stored, the leaf values of this dictionary must be valid pointers to object keys in the repository.\n\n For a completely new storage, the ``initialise`` method should be called first. This will automatically initialise\n the repository and the database with the current schema. The class methods,`version_profile` and `migrate` should be\n able to be called for existing storage, at any supported schema version. But an instance of this class should be\n created only for the latest schema version.\n ", 'version_head': <classmethod object>, 'version_profile': <classmethod object>, 'initialise': <classmethod object>, 'migrate': <classmethod object>, '__init__': <function StorageBackend.__init__>, '__str__': <function StorageBackend.__str__>, 'profile': <property object>, 'autogroup': <property object>, 'version': <function StorageBackend.version>, 'close': <function StorageBackend.close>, 'is_closed': <property object>, '_clear': <function StorageBackend._clear>, 'authinfos': <property object>, 'comments': <property object>, 'computers': <property object>, 'groups': <property object>, 'logs': <property object>, 'nodes': <property object>, 'users': <property object>, 'default_user': <property object>, 'query': <function StorageBackend.query>, 'transaction': <function StorageBackend.transaction>, 'in_transaction': <property object>, 'bulk_insert': <function StorageBackend.bulk_insert>, 'bulk_update': <function StorageBackend.bulk_update>, 'delete_nodes_and_connections': <function StorageBackend.delete_nodes_and_connections>, 'get_repository': <function StorageBackend.get_repository>, 'set_global_variable': <function StorageBackend.set_global_variable>, 'get_global_variable': <function StorageBackend.get_global_variable>, 'maintain': <function StorageBackend.maintain>, 'get_info': <function StorageBackend.get_info>, 'get_orm_entities': <function StorageBackend.get_orm_entities>, '__dict__': <attribute '__dict__' of 'StorageBackend' objects>, '__weakref__': <attribute '__weakref__' of 'StorageBackend' objects>, '__abstractmethods__': frozenset({'maintain', 'migrate', 'nodes', 'users', 'delete_nodes_and_connections', '__str__', 'close', '_clear', 'authinfos', 'is_closed', 'get_global_variable', 'bulk_insert', 'comments', 'initialise', 'in_transaction', 'get_repository', 'computers', 'transaction', 'groups', 'version_head', 'bulk_update', 'set_global_variable', '__init__', 'logs', 'version_profile', 'query'}), '_abc_impl': <_abc_data object>, '__annotations__': {'_default_user': "Optional['User']"}})#

abstract __init__(profile: Profile) → None[source]#

Initialize the backend, for this profile.

Raises

~aiida.common.exceptions.UnreachableStorage if the storage cannot be accessed

Raises

~aiida.common.exceptions.IncompatibleStorageSchema if the profile’s storage schema is not at the latest version (and thus should be migrated)

Raises

raises: aiida.common.exceptions.CorruptStorage if the storage is internally inconsistent

__module__ = 'aiida.orm.implementation.storage_backend'#

abstract __str__() → str[source]#: Return a string showing connection details for this instance.

__weakref__#: list of weak references to the object (if defined)

_abc_impl = <_abc_data object>#

abstract _clear() → None[source]#: Clear the storage, removing all data.

Warning

This is a destructive operation, and should only be used for testing purposes.

abstract property authinfos: BackendAuthInfoCollection#: Return the collection of authorisation information objects

property autogroup: AutogroupManager#: Return the autogroup manager for this backend.

abstract bulk_insert(entity_type: EntityTypes, rows: List[dict], allow_defaults: bool = False) → List[int][source]#

Insert a list of entities into the database, directly into a backend transaction.

Parameters

entity_type – The type of the entity
data – A list of dictionaries, containing all fields of the backend model, except the id field (a.k.a primary key), which will be generated dynamically
allow_defaults – If False, assert that each row contains all fields (except primary key(s)), otherwise, allow default values for missing fields.

Raises

IntegrityError if the keys in a row are not a subset of the columns in the table

Returns

The list of generated primary keys for the entities

abstract bulk_update(entity_type: EntityTypes, rows: List[dict]) → None[source]#

Update a list of entities in the database, directly with a backend transaction.

Parameters

entity_type – The type of the entity
data – A list of dictionaries, containing fields of the backend model to update, and the id field (a.k.a primary key)

Raises

IntegrityError if the keys in a row are not a subset of the columns in the table

abstract close()[source]#: Close the storage access.

abstract property comments: BackendCommentCollection#: Return the collection of comments

abstract property computers: BackendComputerCollection#: Return the collection of computers

property default_user: Optional[User]#

Return the default user for the profile, if it has been created.

This is cached, since it is a frequently used operation, for creating other entities.

abstract delete_nodes_and_connections(pks_to_delete: Sequence[int])[source]#

Delete all nodes corresponding to pks in the input and any links to/from them.

This method is intended to be used within a transaction context.

Parameters: pks_to_delete – a sequence of node pks to delete
Raises: AssertionError if a transaction is not active

abstract get_global_variable(key: str) → Union[None, str, int, float][source]#

Return a global variable from the storage.

Parameters: key – the key of the setting
Raises: KeyError if the setting does not exist

get_info(detailed: bool = False) → dict[source]#

Return general information on the storage.

Parameters: detailed – flag to request more detailed information about the content of the storage.
Returns: a nested dict with the relevant information.

get_orm_entities(detailed: bool = False) → dict[source]#

Return a mapping with an overview of the storage contents regarding ORM entities.

Parameters: detailed – flag to request more detailed information about the content of the storage.
Returns: a nested dict with the relevant information.

abstract get_repository() → AbstractRepositoryBackend[source]#: Return the object repository configured for this backend.

abstract property groups: BackendGroupCollection#: Return the collection of groups

abstract property in_transaction: bool#: Return whether a transaction is currently active.

abstract classmethod initialise(profile: Profile, reset: bool = False) → bool[source]#

Initialise the storage backend.

This is typically used once when a new storage backed is created. If this method returns without exceptions the storage backend is ready for use. If the backend already seems initialised, this method is a no-op.

Parameters: reset – If true, destroy the backend if it already exists including all of its data before recreating and initialising it. This is useful for example for test profiles that need to be reset before or after tests having run.
Returns: True if the storage was initialised by the function call, False if it was already initialised.

abstract property is_closed: bool#: Return whether the storage is closed.

abstract property logs: BackendLogCollection#: Return the collection of logs

abstract maintain(full: bool = False, dry_run: bool = False, **kwargs) → None[source]#

Perform maintenance tasks on the storage.

If full == True, then this method may attempt to block the profile associated with the storage to guarantee the safety of its procedures. This will not only prevent any other subsequent process from accessing that profile, but will also first check if there is already any process using it and raise if that is the case. The user will have to manually stop any processes that is currently accessing the profile themselves or wait for it to finish on its own.

Parameters

full – flag to perform operations that require to stop using the profile to be maintained.
dry_run – flag to only print the actions that would be taken without actually executing them.

abstract classmethod migrate(profile: Profile) → None[source]#

Migrate the storage of a profile to the latest schema version.

If the schema version is already the latest version, this method does nothing. If the storage is uninitialised, this method will raise an exception.

Raises: :class`~aiida.common.exceptions.UnreachableStorage` if the storage cannot be accessed.
Raises: StorageMigrationError if the storage is not initialised.

abstract property nodes: BackendNodeCollection#: Return the collection of nodes

property profile: Profile#: Return the profile for this backend.

abstract query() → BackendQueryBuilder[source]#: Return an instance of a query builder implementation for this backend

abstract set_global_variable(key: str, value: Union[None, str, int, float], description: Optional[str] = None, overwrite=True) → None[source]#

Set a global variable in the storage.

Parameters

key – the key of the setting
value – the value of the setting
description – the description of the setting (optional)
overwrite – if True, overwrite the setting if it already exists

Raises

ValueError if the key already exists and overwrite is False

abstract transaction() → AbstractContextManager[Any][source]#

Get a context manager that can be used as a transaction context for a series of backend operations. If there is an exception within the context then the changes will be rolled back and the state will be as before entering. Transactions can be nested.

Returns: a context manager to group database operations

abstract property users: BackendUserCollection#: Return the collection of users

version() → str[source]#: Return the schema version of the profile’s storage.

abstract classmethod version_head() → str[source]#: Return the head schema version of this storage backend type.

abstract classmethod version_profile(profile: Profile) → Optional[str][source]#

Return the schema version of the given profile’s storage, or None for empty/uninitialised storage.

Raises: ~aiida.common.exceptions.UnreachableStorage if the storage cannot be accessed

Backend user

class aiida.orm.implementation.users.BackendUser(backend: StorageBackend, **kwargs: Any)[source]#

Bases: aiida.orm.implementation.entities.BackendEntity

Backend implementation for the User ORM class.

A user can be assigned as the creator of a variety of other entities.

__abstractmethods__ = frozenset({'email', 'first_name', 'id', 'institution', 'is_stored', 'last_name', 'store'})#

__module__ = 'aiida.orm.implementation.users'#

_abc_impl = <_abc_data object>#

abstract property email: str#

Get the email address of the user

Returns: the email address

abstract property first_name: str#

Get the user’s first name

Returns: the first name

abstract property institution: str#

Get the user’s institution

Returns: the institution

abstract property last_name: str#

Get the user’s last name

Returns: the last name

class aiida.orm.implementation.users.BackendUserCollection(backend: StorageBackend)[source]#

Bases: aiida.orm.implementation.entities.BackendCollection[aiida.orm.implementation.users.BackendUser]

ENTITY_CLASS#: alias of aiida.orm.implementation.users.BackendUser

__module__ = 'aiida.orm.implementation.users'#

__orig_bases__ = (aiida.orm.implementation.entities.BackendCollection[aiida.orm.implementation.users.BackendUser],)#

__parameters__ = ()#

Utility methods for backend non-specific implementations.

aiida.orm.implementation.utils.clean_value(value)[source]#

Get value from input and (recursively) replace, if needed, all occurrences of BaseType AiiDA data nodes with their value, and List with a standard list. It also makes a deep copy of everything The purpose of this function is to convert data to a type which can be serialized and deserialized for storage in the DB without its value changing.

Note however that there is no logic to avoid infinite loops when the user passes some perverse recursive dictionary or list. In any case, however, this would not be storable by AiiDA…

Parameters: value – A value to be set as an attribute or an extra
Returns: a “cleaned” value, potentially identical to value, but with values replaced where needed.

aiida.orm.implementation.utils.validate_attribute_extra_key(key)[source]#

Validate the key for an entity attribute or extra.

Raises: aiida.common.ValidationError – if the key is not a string or contains reserved separator character

aiida.orm package

aiida.orm.nodes package