aiida.storage.psql_dos package#

Module with implementation of the storage backend using PostGreSQL and the disk-objectstore.

Subpackages#

aiida.storage.psql_dos.migrations package
- Subpackages
  - aiida.storage.psql_dos.migrations.utils package
    - Submodules
- Submodules
aiida.storage.psql_dos.models package
- Submodules
aiida.storage.psql_dos.orm package
- Subpackages
  - aiida.storage.psql_dos.orm.querybuilder package
    - Submodules
- Submodules

Submodules#

Simple wrapper around the alembic command line tool that first loads an AiiDA profile.

class aiida.storage.psql_dos.alembic_cli.AlembicRunner[source]#

Bases: object

Wrapper around the alembic command line tool that first loads an AiiDA profile.

__dict__ = mappingproxy({'__module__': 'aiida.storage.psql_dos.alembic_cli', '__doc__': 'Wrapper around the alembic command line tool that first loads an AiiDA profile.', '__init__': <function AlembicRunner.__init__>, 'execute_alembic_command': <function AlembicRunner.execute_alembic_command>, '__dict__': <attribute '__dict__' of 'AlembicRunner' objects>, '__weakref__': <attribute '__weakref__' of 'AlembicRunner' objects>, '__annotations__': {}})#

__init__() → None[source]#

__module__ = 'aiida.storage.psql_dos.alembic_cli'#

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

execute_alembic_command(command_name, connect=True, **kwargs)[source]#

Execute an Alembic CLI command.

Parameters

command_name – the sub command name
kwargs – parameters to pass to the command

SqlAlchemy implementation of aiida.orm.implementation.backends.Backend.

class aiida.storage.psql_dos.backend.PsqlDosBackend(profile: aiida.manage.configuration.profile.Profile)[source]#

Bases: aiida.orm.implementation.storage_backend.StorageBackend

An AiiDA storage backend that stores data in a PostgreSQL database and disk-objectstore repository.

Note, there were originally two such backends, sqlalchemy and django. The django backend was removed, to consolidate access to this storage.

__abstractmethods__ = frozenset({})#

__init__(profile: aiida.manage.configuration.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.storage.psql_dos.backend'#

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

_abc_impl = <_abc_data object>#

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

Warning

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

_default_user: Optional[User]#

static _get_mapper_from_entity(entity_type: aiida.orm.entities.EntityTypes, with_pk: bool)[source]#

Return the Sqlalchemy mapper and fields corresponding to the given entity.

Parameters: with_pk – if True, the fields returned will include the primary key

_initialise_session()[source]#

Initialise the SQLAlchemy session factory.

Only one session factory is ever associated with a given class instance, i.e. once the instance is closed, it cannot be reopened.

The session factory, returns a session that is bound to the current thread. Multi-thread support is currently required by the REST API. Although, in the future, we may want to move the multi-thread handling to higher in the AiiDA stack.

property authinfos#: Return the collection of authorisation information objects

bulk_insert(entity_type: aiida.orm.entities.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

bulk_update(entity_type: aiida.orm.entities.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

close() → None[source]#: Close the storage access.

property comments#: Return the collection of comments

property computers#: Return the collection of computers

delete_nodes_and_connections(pks_to_delete: Sequence[int]) → None[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

get_backend_entity(model: sqlalchemy.orm.decl_api.Model) → aiida.orm.implementation.entities.BackendEntity[source]#

Return the backend entity that corresponds to the given Model instance

Parameters: model – the ORM model instance to promote to a backend instance
Returns: the backend entity corresponding to the given model

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_repository() → DiskObjectStoreRepositoryBackend[source]#: Return the object repository configured for this backend.

get_session() → sqlalchemy.orm.session.Session[source]#: Return an SQLAlchemy session bound to the current thread.

get_unreferenced_keyset(check_consistency: bool = True) → Set[str][source]#

Returns the keyset of objects that exist in the repository but are not tracked by AiiDA.

This should be all the soft-deleted files.

Parameters: check_consistency – toggle for a check that raises if there are references in the database with no actual object in the underlying repository.
Returns: a set with all the objects in the underlying repository that are not referenced in the database.

property groups#: Return the collection of groups

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

classmethod initialise(profile: aiida.manage.configuration.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.

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

property logs#: Return the collection of logs

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.

classmethod migrate(profile: aiida.manage.configuration.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.

migrator#: alias of aiida.storage.psql_dos.migrator.PsqlDosMigrator

classmethod migrator_context(profile: aiida.manage.configuration.profile.Profile)[source]#

property nodes#: Return the collection of nodes

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

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

transaction() → Iterator[sqlalchemy.orm.session.Session][source]#

Open a transaction to be used as a context manager.

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.

property users#: Return the collection of users

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

classmethod version_profile(profile: aiida.manage.configuration.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

aiida.storage.psql_dos.backend.get_filepath_container(profile: aiida.manage.configuration.profile.Profile) → pathlib.Path[source]#: Return the filepath of the disk-object store container.

Schema validation and migration utilities.

This code interacts directly with the database, outside of the ORM, taking a Profile as input for the connection configuration.

Important

This code should only be accessed via the storage backend class, not directly!

class aiida.storage.psql_dos.migrator.PsqlDosMigrator(profile: aiida.manage.configuration.profile.Profile)[source]#

Bases: object

Class for validating and migrating psql_dos storage instances.

Important

This class should only be accessed via the storage backend class (apart from for test purposes)

__dict__ = mappingproxy({'__module__': 'aiida.storage.psql_dos.migrator', '__doc__': 'Class for validating and migrating `psql_dos` storage instances.\n\n .. important:: This class should only be accessed via the storage backend class (apart from for test purposes)\n ', 'alembic_version_tbl_name': 'alembic_version', 'django_version_table': <sqlalchemy.sql.selectable.TableClause at 0x7f9c708c4610; django_migrations>, '__init__': <function PsqlDosMigrator.__init__>, 'close': <function PsqlDosMigrator.close>, 'connection': <property object>, 'get_schema_versions': <classmethod object>, 'get_schema_version_head': <classmethod object>, 'get_schema_version_profile': <function PsqlDosMigrator.get_schema_version_profile>, 'validate_storage': <function PsqlDosMigrator.validate_storage>, 'get_container': <function PsqlDosMigrator.get_container>, 'get_repository_uuid': <function PsqlDosMigrator.get_repository_uuid>, 'initialise': <function PsqlDosMigrator.initialise>, 'is_initialised': <property object>, 'is_repository_initialised': <property object>, 'is_database_initialised': <property object>, 'reset_repository': <function PsqlDosMigrator.reset_repository>, 'reset_database': <function PsqlDosMigrator.reset_database>, 'initialise_repository': <function PsqlDosMigrator.initialise_repository>, 'initialise_database': <function PsqlDosMigrator.initialise_database>, 'delete_all_tables': <function PsqlDosMigrator.delete_all_tables>, 'migrate': <function PsqlDosMigrator.migrate>, 'migrate_up': <function PsqlDosMigrator.migrate_up>, 'migrate_down': <function PsqlDosMigrator.migrate_down>, '_alembic_config': <staticmethod object>, '_alembic_script': <classmethod object>, '_alembic_connect': <function PsqlDosMigrator._alembic_connect>, '_migration_context': <function PsqlDosMigrator._migration_context>, 'session': <function PsqlDosMigrator.session>, 'get_current_table': <function PsqlDosMigrator.get_current_table>, '__dict__': <attribute '__dict__' of 'PsqlDosMigrator' objects>, '__weakref__': <attribute '__weakref__' of 'PsqlDosMigrator' objects>, '__annotations__': {}})#

__init__(profile: aiida.manage.configuration.profile.Profile) → None[source]#

__module__ = 'aiida.storage.psql_dos.migrator'#

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

static _alembic_config()[source]#: Return an instance of an Alembic Config.

_alembic_connect() → Iterator[alembic.config.Config][source]#

Context manager to return an instance of an Alembic configuration.

The profiles’s database connection is added in the attributes property, through which it can then also be retrieved, also in the env.py file, which is run when the database is migrated.

classmethod _alembic_script()[source]#: Return an instance of an Alembic ScriptDirectory.

_migration_context() → Iterator[alembic.runtime.migration.MigrationContext][source]#

Context manager to return an instance of an Alembic migration context.

This migration context will have been configured with the current database connection, which allows this context to be used to inspect the contents of the database, such as the current revision.

alembic_version_tbl_name = 'alembic_version'#

close() → None[source]#: Close the connection if it was opened and dispose of the engine.

property connection#

Return the connection to the database.

Will automatically create the engine and open an connection if not already opened in a previous call.

Returns: Open connection to the database.
Raises: aiida.common.exceptions.UnreachableStorage if connecting to the database fails.

delete_all_tables(*, exclude_tables: list[str] | None = None) → None[source]#

Delete all tables of the current database schema.

The tables are determined dynamically through reflection of the current schema version. Any other tables in the database that are not part of the schema should remain unaffected.

Parameters: exclude_tables – Optional list of table names that should not be deleted.

django_version_table = <sqlalchemy.sql.selectable.TableClause at 0x7f9c708c4610; django_migrations>#

get_container() → disk_objectstore.container.Container[source]#

Return the disk-object store container.

Returns: The disk-object store container configured for the repository path of the current profile.

get_current_table(table_name: str) → Any[source]#

Return a table instantiated at the correct migration.

Note that this is obtained by inspecting the database and not by looking into the models file. So, special methods possibly defined in the models files/classes are not present.

get_repository_uuid() → str[source]#

Return the UUID of the repository.

Returns: The repository UUID.
Raises: UnreachableStorage if the UUID cannot be retrieved, which probably means that the repository is not initialised.

classmethod get_schema_version_head() → str[source]#: Return the head schema version for this storage, i.e. the latest schema this storage can be migrated to.

get_schema_version_profile(check_legacy=False) → Optional[str][source]#

Return the schema version of the backend instance for this profile.

Note, the version will be None if the database is empty or is a legacy django database.

classmethod get_schema_versions() → Dict[str, str][source]#

Return all available schema versions (oldest to latest).

Returns: schema version -> description

initialise(reset: bool = False) → bool[source]#

Initialise the storage backend.

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.

initialise_database() → None[source]#

Initialise the database.

This assumes that the database has no schema whatsoever and so the initial schema is created directly from the models at the current head version without migrating through all of them one by one.

initialise_repository() → None[source]#: Initialise the repository.

property is_database_initialised: bool#

Return whether the database is initialised.

This is the case if it contains the table that holds the schema version for alembic or Django.

Returns: True if the database is initialised, False otherwise.

property is_initialised: bool#

Return whether the storage is initialised.

This is the case if both the database and the repository are initialised.

Returns: True if the storage is initialised, False otherwise.

property is_repository_initialised: bool#

Return whether the repository is initialised.

Returns: True if the repository is initialised, False otherwise.

migrate() → None[source]#

Migrate the storage for this profile to the head version.

Raises: UnreachableStorage if the storage cannot be accessed.
Raises: StorageMigrationError if the storage is not initialised.

migrate_down(version: str) → None[source]#

Migrate the database down to a specific version.

Parameters: version – string with schema version to migrate to

migrate_up(version: str) → None[source]#

Migrate the database up to a specific version.

Parameters: version – string with schema version to migrate to

reset_database() → None[source]#

Reset the database by deleting all content from all tables.

This will also destroy the settings table and so in order to use it again, it will have to be reinitialised.

reset_repository() → None[source]#

Reset the repository by deleting all of its contents.

This will also destroy the configuration and so in order to use it again, it will have to be reinitialised.

session() → Iterator[sqlalchemy.orm.session.Session][source]#: Context manager to return a session for the database.

validate_storage() → None[source]#

Validate that the storage for this profile

That the database schema is at the head version, i.e. is compatible with the code API.
That the repository ID is equal to the UUID set in the database

Raises: aiida.common.exceptions.UnreachableStorage if the storage cannot be connected to
Raises: aiida.common.exceptions.IncompatibleStorageSchema if the storage is not compatible with the code API.
Raises: aiida.common.exceptions.CorruptStorage if the repository ID is not equal to the UUID set in thedatabase.

Utility functions specific to the SqlAlchemy backend.

class aiida.storage.psql_dos.utils.PsqlConfig(*args, **kwargs)[source]#

Bases: dict

Configuration to connect to a PostgreSQL database.

__annotations__ = {'database_hostname': <class 'str'>, 'database_name': <class 'str'>, 'database_password': <class 'str'>, 'database_port': <class 'int'>, 'database_username': <class 'str'>, 'engine_kwargs': <class 'dict'>}#

__dict__ = mappingproxy({'__module__': 'aiida.storage.psql_dos.utils', '__annotations__': {'database_hostname': <class 'str'>, 'database_port': <class 'int'>, 'database_username': <class 'str'>, 'database_password': <class 'str'>, 'database_name': <class 'str'>, 'engine_kwargs': <class 'dict'>}, '__doc__': 'Configuration to connect to a PostgreSQL database.', '__new__': <staticmethod object>, '__dict__': <attribute '__dict__' of 'PsqlConfig' objects>, '__weakref__': <attribute '__weakref__' of 'PsqlConfig' objects>, '__total__': False})#

__module__ = 'aiida.storage.psql_dos.utils'#

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

__total__ = False#

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

database_hostname: str#

database_name: str#

database_password: str#

database_port: int#

database_username: str#

engine_kwargs: dict#: keyword argument that will be passed on to the SQLAlchemy engine.

aiida.storage.psql_dos.utils.create_scoped_session_factory(engine, **kwargs)[source]#: Create scoped SQLAlchemy session factory

aiida.storage.psql_dos.utils.create_sqlalchemy_engine(config: aiida.storage.psql_dos.utils.PsqlConfig)[source]#

Create SQLAlchemy engine (to be used for QueryBuilder queries)

Parameters: kwargs – keyword arguments that will be passed on to sqlalchemy.create_engine. See https://docs.sqlalchemy.org/en/13/core/engines.html?highlight=create_engine#sqlalchemy.create_engine for more info.

aiida.storage.psql_dos.utils.flag_modified(instance, key)[source]#

Wrapper around sqlalchemy.orm.attributes.flag_modified to correctly dereference utils.ModelWrapper

Since SqlAlchemy 1.2.12 (and maybe earlier but not in 1.0.19) the flag_modified function will check that the key is actually present in the instance or it will except. If we pass a model instance, wrapped in the ModelWrapper the call will raise an InvalidRequestError. In this function that wraps the flag_modified of SqlAlchemy, we derefence the model instance if the passed instance is actually wrapped in the ModelWrapper.

aiida.storage.psql_dos.utils.get_pg_tc(links_table_name, links_table_input_field, links_table_output_field, closure_table_name, closure_table_parent_field, closure_table_child_field)[source]#: Return the transitive closure table template

aiida.storage.psql_dos.utils.install_tc(session)[source]#: Install the transitive closure table with SqlAlchemy.

aiida.storage package

aiida.storage.psql_dos.migrations package