SqliteDatabase

class lsst.daf.butler.registry.databases.sqlite.SqliteDatabase(*, connection: sqlalchemy.engine.base.Connection, origin: int, namespace: Optional[str] = None, writeable: bool = True)

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

An implementation of the Database interface for SQLite3.

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

The case where namespace is not None is not yet tested, and may be broken; we need an API for attaching to different databases in order to write those tests, but haven’t yet worked out what is common/different across databases well enough to define it.

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.
connect(uri, *, filename, writeable) Create a sqlalchemy.engine.Connection from a SQLAlchemy URI or filename.
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.
dropTemporaryTable(table) Drop a temporary table.
ensure(table, *rows) Insert one or more rows into a table, skipping any rows for which insertion would violate any 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.
fromConnection(connection, *, origin, …) Create a new Database from an existing sqlalchemy.engine.Connection.
fromUri(uri, *, origin, namespace, writeable) 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, names) 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.
makeTemporaryTable(spec, name) Create a temporary table.
query(sql, *args, **kwds) 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.
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, …) 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.
classmethod connect(uri: Optional[str] = None, *, filename: Optional[str] = None, writeable: bool = True) → sqlalchemy.engine.base.Connection

Create a sqlalchemy.engine.Connection from a SQLAlchemy URI or filename.

Parameters:
uri : str

A SQLAlchemy URI connection string.

filename : str

Name of the SQLite database file, or None to use an in-memory database. Ignored if uri is not None.

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.

writeable : bool, optional

If True, allow write operations on the database, including CREATE TABLE.
Returns:
cs : sqlalchemy.engine.Connection

A database connection and transaction state.
declareStaticTables(*, create: bool) → AbstractContextManager[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 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.

dropTemporaryTable(table: sqlalchemy.sql.schema.Table) → None

Drop a temporary table.

Parameters:
table : sqlalchemy.schema.Table

A SQLAlchemy object returned by a previous call to makeTemporaryTable.
ensure(table: sqlalchemy.sql.schema.Table, *rows) → int

Insert one or more rows into a table, skipping any rows for which insertion would violate any 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.
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 fromConnection(connection: sqlalchemy.engine.base.Connection, *, origin: int, namespace: Optional[str] = None, writeable: bool = True) → lsst.daf.butler.registry.interfaces._database.Database

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

Parameters:
connection : sqllachemy.engine.Connection

The connection for the 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 connection, which is desirable when they represent different namespaces can be queried together. This also ties their transaction state, however; starting a transaction in any database automatically starts on in all other databases.

classmethod fromUri(uri: str, *, origin: int, namespace: Optional[str] = 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]

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, names: Optional[Iterable[str]] = None) → Optional[List[int]]

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]

Create a default connection URI appropriate for the given root directory, or None if there can be no such default.

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

Create a temporary table.

Parameters:
spec : TableSpec

Specification for the table.

name : str, optional

A unique (within this session/connetion) name for the table. Subclasses may override to modify the actual name used. If not provided, a unique name will be generated.
Returns:
table : sqlalchemy.schema.Table

SQLAlchemy representation of the table.

Notes

Temporary tables may be created, dropped, and written to even in read-only databases - at least according to the Python-level protections in the Database classes. Server permissions may say otherwise, but in that case they probably need to be modified to support the full range of expected read-only butler behavior.

Temporary table rows are guaranteed to be dropped when a connection is closed. Database implementations are permitted to allow the table to remain as long as this is transparent to the user (i.e. “creating” the temporary table in a new session should not be an error, even if it does nothing).

It may not be possible to use temporary tables within transactions with some database engines (or configurations thereof).

query(sql: sqlalchemy.sql.selectable.FromClause, *args, **kwds) → sqlalchemy.engine.result.ResultProxy

Run a SELECT query against the database.

Parameters:
sql : sqlalchemy.sql.FromClause

A SQLAlchemy representation of a SELECT query.

*args

Additional positional arguments are forwarded to sqlalchemy.engine.Connection.execute.

**kwds

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.

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, extra: Optional[Dict[str, Any]] = None, returning: Optional[Sequence[str]] = None) → Tuple[Optional[Dict[str, Any]], bool]

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.
Returns:
row : dict, optional

The value of the fields indicated by returning, or None if returning is None.

inserted : bool

If True, a new row was inserted.
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[T_co]

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.