PostgresqlDatabase¶

class lsst.daf.butler.registry.databases.postgresql.PostgresqlDatabase(*, engine: sqlalchemy.engine.base.Engine, origin: int, namespace: Optional[str, None] = None, writeable: bool = True)¶

Bases: lsst.daf.butler.registry.interfaces.Database

An implementation of the Database interface for PostgreSQL.

Parameters:

connection : sqlalchemy.engine.Connection: An existing connection created by a previous call to connect.
origin : int: An integer ID that should be used as the default for any datasets, quanta, or other entities that use a (autoincrement, origin) compound primary key.
namespace : str, optional: The namespace (schema) this database is associated with. If None, the default schema for the connection is used (which may be None).
writeable : bool, optional: If True, allow write operations on the database, including CREATE TABLE.

Notes

This currently requires the psycopg2 driver to be used as the backend for SQLAlchemy. Running the tests for this class requires the testing.postgresql be installed, which we assume indicates that a PostgreSQL server is installed and can be run locally in userspace.

Some functionality provided by this class (and used by Registry) requires the btree_gist PostgreSQL server extension to be installed an enabled on the database being connected to; this is checked at connection time.

Attributes Summary

dialect The SQLAlchemy dialect for this database engine (sqlalchemy.engine.Dialect).

Methods Summary

`assertTableWriteable`(table, msg)	Raise if the given table is not writeable, either because the database connection is read-write or the table is a temporary table.
`declareStaticTables`(*, create)	Return a context manager in which the database’s static DDL schema can be declared.
`delete`(table, columns, *rows)	Delete one or more rows from a table.
`deleteWhere`(table, where)	Delete rows from a table with pre-constructed WHERE clause.
`ensure`(table, *rows, primary_key_only)	Insert one or more rows into a table, skipping any rows for which insertion would violate a unique constraint.
`ensureTableExists`(name, spec)	Ensure that a table with the given name and specification exists, creating it if necessary.
`expandDatabaseEntityName`(shrunk)	Retrieve the original name for a database entity that was too long to fit within the database engine’s limits.
`fromEngine`(engine, *, origin, namespace, …)	Create a new `Database` from an existing `sqlalchemy.engine.Engine`.
`fromUri`(uri, *, origin, namespace, …)	Construct a database from a SQLAlchemy URI.
`getExistingTable`(name, spec)	Obtain an existing table with the given name and specification.
`getSpatialRegionRepresentation`()	Return a `type` that encapsulates the way `lsst.sphgeom.Region` objects are stored in this database.
`getTimespanRepresentation`()	Return a `type` that encapsulates the way `Timespan` objects are stored in this database.
`insert`(table, *rows, returnIds, select, …)	Insert one or more rows into a table, optionally returning autoincrement primary key values.
`isTableWriteable`(table)	Check whether a table is writeable, either because the database connection is read-write or the table is a temporary table.
`isWriteable`()	Return `True` if this database can be modified by this client.
`makeDefaultUri`(root)	Create a default connection URI appropriate for the given root directory, or `None` if there can be no such default.
`makeEngine`(uri, *, writeable)	Create a `sqlalchemy.engine.Engine` from a SQLAlchemy URI.
`query`(sql, args, *kwargs)	Run a SELECT query against the database.
`replace`(table, *rows)	Insert one or more rows into a table, replacing any existing rows for which insertion of a new row would violate the primary key constraint.
`session`()	Return a context manager that represents a session (persistent connection to a database).
`shrinkDatabaseEntityName`(original)	Return a version of the given name that fits within this database engine’s length limits for table, constraint, indexes, and sequence names.
`sync`(table, *, keys, Any], compared, Any], …)	Insert into a table as necessary to ensure database contains values equivalent to the given ones.
`transaction`(*, interrupting, savepoint, lock)	Return a context manager that represents a transaction.
`update`(table, where, str], *rows)	Update one or more rows in a table.

Attributes Documentation

dialect¶: The SQLAlchemy dialect for this database engine (sqlalchemy.engine.Dialect).

Methods Documentation

assertTableWriteable(table: sqlalchemy.sql.schema.Table, msg: str) → None¶

Raise if the given table is not writeable, either because the database connection is read-write or the table is a temporary table.

Parameters:	table : `sqlalchemy.schema.Table` SQLAlchemy table object to check. msg : `str`, optional If provided, raise `ReadOnlyDatabaseError` instead of returning `False`, with this message.

declareStaticTables(*, create: bool) → Iterator[lsst.daf.butler.registry.interfaces._database.StaticTablesContext]¶

Return a context manager in which the database’s static DDL schema can be declared.

Parameters:	create : `bool` If `True`, attempt to create all tables at the end of the context. If `False`, they will be assumed to already exist.
Returns:	schema : `StaticTablesContext` A helper object that is used to add new tables.
Raises:	ReadOnlyDatabaseError Raised if `create` is `True`, `Database.isWriteable` is `False`, and one or more declared tables do not already exist.

Notes

A database’s static DDL schema must be declared before any dynamic tables are managed via calls to ensureTableExists or getExistingTable. The order in which static schema tables are added inside the context block is unimportant; they will automatically be sorted and added in an order consistent with their foreign key relationships.

Examples

Given a Database instance db:

with db.declareStaticTables(create=True) as schema:
    schema.addTable("table1", TableSpec(...))
    schema.addTable("table2", TableSpec(...))

delete(table: sqlalchemy.sql.schema.Table, columns: Iterable[str], *rows) → int¶

Delete one or more rows from a table.

Parameters:	table : `sqlalchemy.schema.Table` Table that rows should be deleted from. columns: `~collections.abc.Iterable` of `str` The names of columns that will be used to constrain the rows to be deleted; these will be combined via `AND` to form the `WHERE` clause of the delete query. *rows Positional arguments are the keys of rows to be deleted, as dictionaries mapping column name to value. The keys in all dictionaries must be exactly the names in `columns`.
Returns:	count : `int` Number of rows deleted.
Raises:	ReadOnlyDatabaseError Raised if `isWriteable` returns `False` when this method is called.

Notes

May be used inside transaction contexts, so implementations may not perform operations that interrupt transactions.

The default implementation should be sufficient for most derived classes.

deleteWhere(table: sqlalchemy.sql.schema.Table, where: sqlalchemy.sql.elements.ClauseElement) → int¶

Delete rows from a table with pre-constructed WHERE clause.

Parameters:	table : `sqlalchemy.schema.Table` Table that rows should be deleted from. where: `sqlalchemy.sql.ClauseElement` The names of columns that will be used to constrain the rows to be deleted; these will be combined via `AND` to form the `WHERE` clause of the delete query.
Returns:	count : `int` Number of rows deleted.
Raises:	ReadOnlyDatabaseError Raised if `isWriteable` returns `False` when this method is called.

Notes

May be used inside transaction contexts, so implementations may not perform operations that interrupt transactions.

The default implementation should be sufficient for most derived classes.

ensure(table: sqlalchemy.sql.schema.Table, *rows, primary_key_only: bool = False) → int¶

Insert one or more rows into a table, skipping any rows for which insertion would violate a unique constraint.

Parameters:	table : `sqlalchemy.schema.Table` Table rows should be inserted into. rows Positional arguments are the rows to be inserted, as dictionaries mapping column name to value. The keys in all dictionaries must be the same. primary_key_only* : `bool`, optional If `True` (`False` is default), only skip rows that violate the primary key constraint, and raise an exception (and rollback transactions) for other constraint violations.
Returns:	count : `int` The number of rows actually inserted.
Raises:	ReadOnlyDatabaseError Raised if `isWriteable` returns `False` when this method is called. This is raised even if the operation would do nothing even on a writeable database.

Notes

May be used inside transaction contexts, so implementations may not perform operations that interrupt transactions.

Implementations are not required to support ensure on tables with autoincrement keys.

ensureTableExists(name: str, spec: lsst.daf.butler.core.ddl.TableSpec) → sqlalchemy.sql.schema.Table¶

Ensure that a table with the given name and specification exists, creating it if necessary.

Parameters:	name : `str` Name of the table (not including namespace qualifiers). spec : `TableSpec` Specification for the table. This will be used when creating the table, and may be used when obtaining an existing table to check for consistency, but no such check is guaranteed.
Returns:	table : `sqlalchemy.schema.Table` SQLAlchemy representation of the table.
Raises:	ReadOnlyDatabaseError Raised if `isWriteable` returns `False`, and the table does not already exist. DatabaseConflictError Raised if the table exists but `spec` is inconsistent with its definition.

Notes

This method may not be called within transactions. It may be called on read-only databases if and only if the table does in fact already exist.

Subclasses may override this method, but usually should not need to.

expandDatabaseEntityName(shrunk: str) → str¶

Retrieve the original name for a database entity that was too long to fit within the database engine’s limits.

Parameters:	original : `str` The original name.
Returns:	shrunk : `str` The new, possibly shortened name.

classmethod fromEngine(engine: sqlalchemy.engine.base.Engine, *, origin: int, namespace: Optional[str, None] = None, writeable: bool = True) → lsst.daf.butler.registry.interfaces._database.Database¶

Create a new Database from an existing sqlalchemy.engine.Engine.

Parameters:

engine : sqlalchemy.engine.Engine: The engine for the database. May be shared between Database instances.
origin : int: An integer ID that should be used as the default for any datasets, quanta, or other entities that use a (autoincrement, origin) compound primary key.
namespace : str, optional: A different database namespace (i.e. schema) the new instance should be associated with. If None (default), the namespace (if any) is inferred from the connection.
writeable : bool, optional: If True, allow write operations on the database, including CREATE TABLE.

Returns:

db : Database: A new Database instance.

Notes

This method allows different Database instances to share the same engine, which is desirable when they represent different namespaces can be queried together.

classmethod fromUri(uri: str, *, origin: int, namespace: Optional[str, None] = None, writeable: bool = True) → lsst.daf.butler.registry.interfaces._database.Database¶

Construct a database from a SQLAlchemy URI.

Parameters:

uri : str: A SQLAlchemy URI connection string.
origin : int: An integer ID that should be used as the default for any datasets, quanta, or other entities that use a (autoincrement, origin) compound primary key.
namespace : str, optional: A database namespace (i.e. schema) the new instance should be associated with. If None (default), the namespace (if any) is inferred from the URI.
writeable : bool, optional: If True, allow write operations on the database, including CREATE TABLE.

Returns:

db : Database: A new Database instance.

getExistingTable(name: str, spec: lsst.daf.butler.core.ddl.TableSpec) → Optional[sqlalchemy.sql.schema.Table, None]¶

Obtain an existing table with the given name and specification.

Parameters:	name : `str` Name of the table (not including namespace qualifiers). spec : `TableSpec` Specification for the table. This will be used when creating the SQLAlchemy representation of the table, and it is used to check that the actual table in the database is consistent.
Returns:	table : `sqlalchemy.schema.Table` or `None` SQLAlchemy representation of the table, or `None` if it does not exist.
Raises:	DatabaseConflictError Raised if the table exists but `spec` is inconsistent with its definition.

Notes

This method can be called within transactions and never modifies the database.

Subclasses may override this method, but usually should not need to.

classmethod getSpatialRegionRepresentation() → Type[lsst.daf.butler.core._topology.SpatialRegionDatabaseRepresentation]¶

Return a type that encapsulates the way lsst.sphgeom.Region objects are stored in this database.

Database does not automatically use the return type of this method anywhere else; calling code is responsible for making sure that DDL and queries are consistent with it.

Returns:	RegionReprClass : `type` (`SpatialRegionDatabaseRepresention` subclass) A type that encapsulates the way `lsst.sphgeom.Region` objects should be stored in this database.

Notes

See getTimespanRepresentation for comments on why this method is not more tightly integrated with the rest of the Database interface.

classmethod getTimespanRepresentation() → Type[lsst.daf.butler.core.timespan.TimespanDatabaseRepresentation]¶

Return a type that encapsulates the way Timespan objects are stored in this database.

Database does not automatically use the return type of this method anywhere else; calling code is responsible for making sure that DDL and queries are consistent with it.

Returns:	TimespanReprClass : `type` (`TimespanDatabaseRepresention` subclass) A type that encapsulates the way `Timespan` objects should be stored in this database.

Notes

There are two big reasons we’ve decided to keep timespan-mangling logic outside the Database implementations, even though the choice of representation is ultimately up to a Database implementation:

Timespans appear in relatively few tables and queries in our typical usage, and the code that operates on them is already aware that it is working with timespans. In contrast, a timespan-representation-aware implementation of, say, insert, would need to have extra logic to identify when timespan-mangling needed to occur, which would usually be useless overhead.

SQLAlchemy’s rich SELECT query expression system has no way to wrap multiple columns in a single expression object (the ORM does, but we are not using the ORM). So we would have to wrap _much_ more of that code in our own interfaces to encapsulate timespan representations there.

insert(table: sqlalchemy.sql.schema.Table, *rows, returnIds: bool = False, select: Optional[sqlalchemy.sql.selectable.Select, None] = None, names: Optional[Iterable[str], None] = None) → Optional[List[int], None]¶

Insert one or more rows into a table, optionally returning autoincrement primary key values.

Parameters:	table : `sqlalchemy.schema.Table` Table rows should be inserted into. returnIds: `bool` If `True` (`False` is default), return the values of the table’s autoincrement primary key field (which much exist). select : `sqlalchemy.sql.Select`, optional A SELECT query expression to insert rows from. Cannot be provided with either `rows` or `returnIds=True`. names : `Iterable` [ `str` ], optional Names of columns in `table` to be populated, ordered to match the columns returned by `select`. Ignored if `select` is `None`. If not provided, the columns returned by `select` must be named to match the desired columns of `table`. *rows Positional arguments are the rows to be inserted, as dictionaries mapping column name to value. The keys in all dictionaries must be the same.
Returns:	ids : `None`, or `list` of `int` If `returnIds` is `True`, a `list` containing the inserted values for the table’s autoincrement primary key.
Raises:	ReadOnlyDatabaseError Raised if `isWriteable` returns `False` when this method is called.

Notes

The default implementation uses bulk insert syntax when returnIds is False, and a loop over single-row insert operations when it is True.

Derived classes should reimplement when they can provide a more efficient implementation (especially for the latter case).

May be used inside transaction contexts, so implementations may not perform operations that interrupt transactions.

isTableWriteable(table: sqlalchemy.sql.schema.Table) → bool¶

Check whether a table is writeable, either because the database connection is read-write or the table is a temporary table.

Parameters:	table : `sqlalchemy.schema.Table` SQLAlchemy table object to check.
Returns:	writeable : `bool` Whether this table is writeable.

isWriteable() → bool¶: Return True if this database can be modified by this client.

classmethod makeDefaultUri(root: str) → Optional[str, None]¶: Create a default connection URI appropriate for the given root directory, or None if there can be no such default.

classmethod makeEngine(uri: str, *, writeable: bool = True) → sqlalchemy.engine.base.Engine¶

Create a sqlalchemy.engine.Engine from a SQLAlchemy URI.

Parameters:	uri : `str` A SQLAlchemy URI connection string. writeable : `bool`, optional If `True`, allow write operations on the database, including `CREATE TABLE`.
Returns:	engine : `sqlalchemy.engine.Engine` A database engine.

Notes

Subclasses that support other ways to connect to a database are encouraged to add optional arguments to their implementation of this method, as long as they maintain compatibility with the base class call signature.

query(sql: sqlalchemy.sql.selectable.Selectable, *args, **kwargs) → sqlalchemy.engine.cursor.LegacyCursorResult¶

Run a SELECT query against the database.

Parameters:	sql : `sqlalchemy.sql.Selectable` A SQLAlchemy representation of a `SELECT` query. args Additional positional arguments are forwarded to `sqlalchemy.engine.Connection.execute`. *kwargs Additional keyword arguments are forwarded to `sqlalchemy.engine.Connection.execute`.
Returns:	result : `sqlalchemy.engine.ResultProxy` Query results.

Notes

The default implementation should be sufficient for most derived classes.

replace(table: sqlalchemy.sql.schema.Table, *rows) → None¶

Insert one or more rows into a table, replacing any existing rows for which insertion of a new row would violate the primary key constraint.

Parameters:	table : `sqlalchemy.schema.Table` Table rows should be inserted into. *rows Positional arguments are the rows to be inserted, as dictionaries mapping column name to value. The keys in all dictionaries must be the same.
Raises:	ReadOnlyDatabaseError Raised if `isWriteable` returns `False` when this method is called.

Notes

May be used inside transaction contexts, so implementations may not perform operations that interrupt transactions.

Implementations should raise a sqlalchemy.exc.IntegrityError exception when a constraint other than the primary key would be violated.

Implementations are not required to support replace on tables with autoincrement keys.

session() → Iterator¶: Return a context manager that represents a session (persistent connection to a database).

shrinkDatabaseEntityName(original: str) → str¶

Return a version of the given name that fits within this database engine’s length limits for table, constraint, indexes, and sequence names.

Implementations should not assume that simple truncation is safe, because multiple long names often begin with the same prefix.

The default implementation simply returns the given name.

Parameters:	original : `str` The original name.
Returns:	shrunk : `str` The new, possibly shortened name.

sync(table: sqlalchemy.sql.schema.Table, *, keys: Dict[str, Any], compared: Optional[Dict[str, Any], None] = None, extra: Optional[Dict[str, Any], None] = None, returning: Optional[Sequence[str], None] = None, update: bool = False) → Tuple[Optional[Dict[str, Any], None], Union[bool, Dict[str, Any]]]¶

Insert into a table as necessary to ensure database contains values equivalent to the given ones.

Parameters:	table : `sqlalchemy.schema.Table` Table to be queried and possibly inserted into. keys : `dict` Column name-value pairs used to search for an existing row; must be a combination that can be used to select a single row if one exists. If such a row does not exist, these values are used in the insert. compared : `dict`, optional Column name-value pairs that are compared to those in any existing row. If such a row does not exist, these rows are used in the insert. extra : `dict`, optional Column name-value pairs that are ignored if a matching row exists, but used in an insert if one is necessary. returning : `Sequence` of `str`, optional The names of columns whose values should be returned. update : `bool`, optional If `True` (`False` is default), update the existing row with the values in `compared` instead of raising `DatabaseConflictError`.
Returns:	row : `dict`, optional The value of the fields indicated by `returning`, or `None` if `returning` is `None`. inserted_or_updated : `bool` or `dict` If `True`, a new row was inserted; if `False`, a matching row already existed. If a `dict` (only possible if `update=True`), then an existing row was updated, and the dict maps the names of the updated columns to their old values (new values can be obtained from `compared`).
Raises:	DatabaseConflictError Raised if the values in `compared` do not match the values in the database. ReadOnlyDatabaseError Raised if `isWriteable` returns `False`, and no matching record already exists.

Notes

May be used inside transaction contexts, so implementations may not perform operations that interrupt transactions.

It may be called on read-only databases if and only if the matching row does in fact already exist.

transaction(*, interrupting: bool = False, savepoint: bool = False, lock: Iterable[sqlalchemy.sql.schema.Table] = ()) → Iterator[None]¶

Return a context manager that represents a transaction.

Parameters:

interrupting : bool, optional: If True (False is default), this transaction block may not be nested without an outer one, and attempting to do so is a logic (i.e. assertion) error.
savepoint : bool, optional: If True (False is default), create a SAVEPOINT, allowing exceptions raised by the database (e.g. due to constraint violations) during this transaction’s context to be caught outside it without also rolling back all operations in an outer transaction block. If False, transactions may still be nested, but a rollback may be generated at any level and affects all levels, and commits are deferred until the outermost block completes. If any outer transaction block was created with savepoint=True, all inner blocks will be as well (regardless of the actual value passed). This has no effect if this is the outermost transaction.
lock : Iterable [ sqlalchemy.schema.Table ], optional: A list of tables to lock for the duration of this transaction. These locks are guaranteed to prevent concurrent writes and allow this transaction (only) to acquire the same locks (others should block), but only prevent concurrent reads if the database engine requires that in order to block concurrent writes.

Notes

All transactions on a connection managed by one or more Database instances _must_ go through this method, or transaction state will not be correctly managed.

update(table: sqlalchemy.sql.schema.Table, where: Dict[str, str], *rows) → int¶

Update one or more rows in a table.

Parameters:	table : `sqlalchemy.schema.Table` Table containing the rows to be updated. where : `dict` [`str`, `str`] A mapping from the names of columns that will be used to search for existing rows to the keys that will hold these values in the `rows` dictionaries. Note that these may not be the same due to SQLAlchemy limitations. *rows Positional arguments are the rows to be updated. The keys in all dictionaries must be the same, and may correspond to either a value in the `where` dictionary or the name of a column to be updated.
Returns:	count : `int` Number of rows matched (regardless of whether the update actually modified them).
Raises:	ReadOnlyDatabaseError Raised if `isWriteable` returns `False` when this method is called.

Notes

May be used inside transaction contexts, so implementations may not perform operations that interrupt transactions.

The default implementation should be sufficient for most derived classes.

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PostgresqlDatabase¶