✨ NEW: Add Backend bulk methods

.pre-commit-config.yaml

@@ -75,6 +75,10 @@ repos:
                 aiida/manage/manager.py|
                 aiida/manage/database/delete/nodes.py|
                 aiida/orm/querybuilder.py|
+                aiida/orm/implementation/backends.py|
+                aiida/orm/implementation/sql/backends.py|
+                aiida/orm/implementation/django/backend.py|
+                aiida/orm/implementation/sqlalchemy/backend.py|
                 aiida/orm/implementation/querybuilder.py|
                 aiida/orm/implementation/sqlalchemy/querybuilder/.*py|
                 aiida/orm/nodes/data/jsonable.py|

aiida/backends/sqlalchemy/models/group.py

@@ -31,6 +31,11 @@
 )
 
 
+class DbGroupNode(Base):
+    """Class to store group to nodes relation using SQLA backend."""
+    __table__ = table_groups_nodes
+
+
 class DbGroup(Base):
     """Class to store groups using SQLA backend."""
 

aiida/backends/sqlalchemy/utils.py

@@ -11,34 +11,6 @@
 """Utility functions specific to the SqlAlchemy backend."""
 
 
-def delete_nodes_and_connections_sqla(pks_to_delete):  # pylint: disable=invalid-name
-    """
-    Delete all nodes corresponding to pks in the input.
-    :param pks_to_delete: A list, tuple or set of pks that should be deleted.
-    """
-    # pylint: disable=no-value-for-parameter
-    from aiida.backends.sqlalchemy.models.group import table_groups_nodes
-    from aiida.backends.sqlalchemy.models.node import DbLink, DbNode
-    from aiida.manage.manager import get_manager
-
-    backend = get_manager().get_backend()
-
-    with backend.transaction() as session:
-        # I am first making a statement to delete the membership of these nodes to groups.
-        # Since table_groups_nodes is a sqlalchemy.schema.Table, I am using expression language to compile
-        # a stmt to be executed by the session. It works, but it's not nice that two different ways are used!
-        # Can this be changed?
-        stmt = table_groups_nodes.delete().where(table_groups_nodes.c.dbnode_id.in_(list(pks_to_delete)))
-        session.execute(stmt)
-        # First delete links, then the Nodes, since we are not cascading deletions.
-        # Here I delete the links coming out of the nodes marked for deletion.
-        session.query(DbLink).filter(DbLink.input_id.in_(list(pks_to_delete))).delete(synchronize_session='fetch')
-        # Here I delete the links pointing to the nodes marked for deletion.
-        session.query(DbLink).filter(DbLink.output_id.in_(list(pks_to_delete))).delete(synchronize_session='fetch')
-        # Now I am deleting the nodes
-        session.query(DbNode).filter(DbNode.id.in_(list(pks_to_delete))).delete(synchronize_session='fetch')
-
-
 def flag_modified(instance, key):
     """Wrapper around `sqlalchemy.orm.attributes.flag_modified` to correctly dereference utils.ModelWrapper
 

aiida/backends/utils.py

@@ -8,9 +8,6 @@
 # For further information please visit http://www.aiida.net               #
 ###########################################################################
 """Backend-agnostic utility functions"""
-from aiida.backends import BACKEND_DJANGO, BACKEND_SQLA
-from aiida.manage import configuration
-
 AIIDA_ATTRIBUTE_SEP = '.'
 
 
@@ -47,15 +44,3 @@ def create_scoped_session_factory(engine, **kwargs):
     """Create scoped SQLAlchemy session factory"""
     from sqlalchemy.orm import scoped_session, sessionmaker
     return scoped_session(sessionmaker(bind=engine, future=True, **kwargs))
-
-
-def delete_nodes_and_connections(pks):
-    """Backend-agnostic function to delete Nodes and connections"""
-    if configuration.PROFILE.database_backend == BACKEND_DJANGO:
-        from aiida.backends.djsite.utils import delete_nodes_and_connections_django as delete_nodes_backend
-    elif configuration.PROFILE.database_backend == BACKEND_SQLA:
-        from aiida.backends.sqlalchemy.utils import delete_nodes_and_connections_sqla as delete_nodes_backend
-    else:
-        raise Exception(f'unknown backend {configuration.PROFILE.database_backend}')
-
-    delete_nodes_backend(pks)

aiida/orm/entities.py

@@ -10,6 +10,7 @@
 """Module for all common top level AiiDA entity classes and methods"""
 import abc
 import copy
+from enum import Enum
 import typing
 
 from plumpy.base.utils import call_with_super_check, super_check
@@ -25,6 +26,19 @@
 _NO_DEFAULT = tuple()
 
 
+class EntityTypes(Enum):
+    """Enum for referring to ORM entities in a backend-agnostic manner."""
+    AUTHINFO = 'authinfo'
+    COMMENT = 'comment'
+    COMPUTER = 'computer'
+    GROUP = 'group'
+    LOG = 'log'
+    NODE = 'node'
+    USER = 'user'
+    LINK = 'link'
+    GROUP_NODE = 'group_node'
+
+
 class Collection(typing.Generic[EntityType]):
     """Container class that represents the collection of objects of a particular type."""
 

aiida/orm/implementation/backends.py

@@ -9,11 +9,12 @@
 ###########################################################################
 """Generic backend related objects"""
 import abc
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Any, ContextManager, List, Sequence, TypeVar
 
 if TYPE_CHECKING:
     from sqlalchemy.orm.session import Session
 
+    from aiida.orm.entities import EntityTypes
     from aiida.orm.implementation import (
         BackendAuthInfoCollection,
         BackendCommentCollection,
@@ -27,12 +28,14 @@
 
 __all__ = ('Backend',)
 
+TransactionType = TypeVar('TransactionType')
+
 
 class Backend(abc.ABC):
     """The public interface that defines a backend factory that creates backend specific concrete objects."""
 
     @abc.abstractmethod
-    def migrate(self):
+    def migrate(self) -> None:
         """Migrate the database to the latest schema generation or version."""
 
     @property
@@ -65,17 +68,24 @@ def logs(self) -> 'BackendLogCollection':
     def nodes(self) -> 'BackendNodeCollection':
         """Return the collection of nodes"""
 
+    @property
+    @abc.abstractmethod
+    def users(self) -> 'BackendUserCollection':
+        """Return the collection of users"""
+
     @abc.abstractmethod
     def query(self) -> 'BackendQueryBuilder':
         """Return an instance of a query builder implementation for this backend"""
 
-    @property
     @abc.abstractmethod
-    def users(self) -> 'BackendUserCollection':
-        """Return the collection of users"""
+    def get_session(self) -> 'Session':
+        """Return a database session that can be used by the `QueryBuilder` to perform its query.
+
+        :return: an instance of :class:`sqlalchemy.orm.session.Session`
+        """
 
     @abc.abstractmethod
-    def transaction(self):
+    def transaction(self) -> ContextManager[Any]:
         """
         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
@@ -84,9 +94,44 @@ def transaction(self):
         :return: a context manager to group database operations
         """
 
+    @property
     @abc.abstractmethod
-    def get_session(self) -> 'Session':
-        """Return a database session that can be used by the `QueryBuilder` to perform its query.
+    def in_transaction(self) -> bool:
+        """Return whether a transaction is currently active."""
 
-        :return: an instance of :class:`sqlalchemy.orm.session.Session`
+    @abc.abstractmethod
+    def bulk_insert(self, entity_type: 'EntityTypes', rows: List[dict], allow_defaults: bool = False) -> List[int]:
+        """Insert a list of entities into the database, directly into a backend transaction.
+
+        :param entity_type: The type of the entity
+        :param 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
+        :param 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
+        """
+
+    @abc.abstractmethod
+    def bulk_update(self, entity_type: 'EntityTypes', rows: List[dict]) -> None:
+        """Update a list of entities in the database, directly with a backend transaction.
+
+        :param entity_type: The type of the entity
+        :param 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
+        """
+
+    @abc.abstractmethod
+    def delete_nodes_and_connections(self, pks_to_delete: Sequence[int]):
+        """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.
+
+        :param pks_to_delete: a sequence of node pks to delete
+
+        :raises: ``AssertionError`` if a transaction is not active
         """

aiida/orm/implementation/django/backend.py

@@ -9,11 +9,18 @@
 ###########################################################################
 """Django implementation of `aiida.orm.implementation.backends.Backend`."""
 from contextlib import contextmanager
+import functools
+from typing import Any, ContextManager, List, Sequence
 
 # pylint: disable=import-error,no-name-in-module
-from django.db import models, transaction
+from django.apps import apps
+from django.db import models
+from django.db import transaction as django_transaction
 
+from aiida.backends.djsite.db import models as dbm
 from aiida.backends.djsite.manager import DjangoBackendManager
+from aiida.common.exceptions import IntegrityError
+from aiida.orm.entities import EntityTypes
 
 from . import authinfos, comments, computers, convert, groups, logs, nodes, querybuilder, users
 from ..sql.backends import SqlBackend
@@ -69,11 +76,6 @@ def query(self):
     def users(self):
         return self._users
 
-    @staticmethod
-    def transaction():
-        """Open a transaction to be used as a context manager."""
-        return transaction.atomic()
-
     @staticmethod
     def get_session():
         """Return a database session that can be used by the `QueryBuilder` to perform its query.
@@ -86,6 +88,92 @@ def get_session():
         from aiida.backends.djsite import get_scoped_session
         return get_scoped_session()
 
+    @staticmethod
+    def transaction() -> ContextManager[Any]:
+        """Open a transaction to be used as a context manager."""
+        return django_transaction.atomic()
+
+    @property
+    def in_transaction(self) -> bool:
+        return not django_transaction.get_autocommit()
+
+    @staticmethod
+    @functools.lru_cache(maxsize=18)
+    def _get_model_from_entity(entity_type: EntityTypes, with_pk: bool):
+        """Return the Django model and fields corresponding to the given entity.
+
+        :param with_pk: if True, the fields returned will include the primary key
+        """
+        from sqlalchemy import inspect
+
+        model = {
+            EntityTypes.AUTHINFO: dbm.DbAuthInfo,
+            EntityTypes.COMMENT: dbm.DbComment,
+            EntityTypes.COMPUTER: dbm.DbComputer,
+            EntityTypes.GROUP: dbm.DbGroup,
+            EntityTypes.LOG: dbm.DbLog,
+            EntityTypes.NODE: dbm.DbNode,
+            EntityTypes.USER: dbm.DbUser,
+            EntityTypes.LINK: dbm.DbLink,
+            EntityTypes.GROUP_NODE:
+            {model._meta.db_table: model for model in apps.get_models(include_auto_created=True)}['db_dbgroup_dbnodes']
+        }[entity_type]
+        mapper = inspect(model.sa).mapper  # here aldjemy provides us the SQLAlchemy model
+        keys = {key for key, col in mapper.c.items() if with_pk or col not in mapper.primary_key}
+        return model, keys
+
+    def bulk_insert(self, entity_type: EntityTypes, rows: List[dict], allow_defaults: bool = False) -> List[int]:
+        model, keys = self._get_model_from_entity(entity_type, False)
+        if allow_defaults:
+            for row in rows:
+                if not keys.issuperset(row):
+                    raise IntegrityError(f'Incorrect fields given for {entity_type}: {set(row)} not subset of {keys}')
+        else:
+            for row in rows:
+                if set(row) != keys:
+                    raise IntegrityError(f'Incorrect fields given for {entity_type}: {set(row)} != {keys}')
+        objects = [model(**row) for row in rows]
+        # if there is an mtime field, disable the automatic update, so as not to change it
+        if entity_type in (EntityTypes.NODE, EntityTypes.COMMENT):
+            with dbm.suppress_auto_now([(model, ['mtime'])]):
+                model.objects.bulk_create(objects)
+        else:
+            model.objects.bulk_create(objects)
+        return [obj.id for obj in objects]
+
+    def bulk_update(self, entity_type: EntityTypes, rows: List[dict]) -> None:
+        model, keys = self._get_model_from_entity(entity_type, True)
+        id_entries = {}
+        fields = None
+        for row in rows:
+            if not keys.issuperset(row):
+                raise IntegrityError(f'Incorrect fields given for {entity_type}: {set(row)} not subset of {keys}')
+            try:
+                id_entries[row['id']] = {k: v for k, v in row.items() if k != 'id'}
+                fields = fields or list(id_entries[row['id']])
+                assert fields == list(id_entries[row['id']])
+            except KeyError:
+                raise IntegrityError(f"'id' field not given for {entity_type}: {set(row)}")
+            except AssertionError:
+                # this is handled in sqlalchemy, but would require more complex logic here
+                raise NotImplementedError(f'Cannot bulk update {entity_type} with different fields')
+        if fields is None:
+            return
+        objects = []
+        for pk, obj in model.objects.in_bulk(list(id_entries), field_name='id').items():
+            for name, value in id_entries[pk].items():
+                setattr(obj, name, value)
+            objects.append(obj)
+        model.objects.bulk_update(objects, fields)
+
+    def delete_nodes_and_connections(self, pks_to_delete: Sequence[int]) -> None:
+        if not self.in_transaction:
+            raise AssertionError('Cannot delete nodes and links outside a transaction')
+        # Delete all links pointing to or from a given node
+        dbm.DbLink.objects.filter(models.Q(input__in=pks_to_delete) | models.Q(output__in=pks_to_delete)).delete()
+        # now delete nodes
+        dbm.DbNode.objects.filter(pk__in=pks_to_delete).delete()
+
     # Below are abstract methods inherited from `aiida.orm.implementation.sql.backends.SqlBackend`
 
     def get_backend_entity(self, model):
@@ -100,7 +188,7 @@ def cursor(self):
         :rtype: :class:`psycopg2.extensions.cursor`
         """
         try:
-            yield self.get_connection().cursor()
+            yield self._get_connection().cursor()
         finally:
             pass
 
@@ -117,7 +205,7 @@ def execute_raw(self, query):
         return results
 
     @staticmethod
-    def get_connection():
+    def _get_connection():
         """
         Get the Django connection