Coverage for python/lsst/daf/butler/registry/databases/sqlite.py : 18%

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1# This file is part of daf_butler.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (http://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <http://www.gnu.org/licenses/>.
21from __future__ import annotations
23__all__ = ["SqliteDatabase"]
25from contextlib import closing
26import copy
27from typing import ContextManager, List, Optional
28from dataclasses import dataclass
29import os
30import urllib.parse
32import sqlite3
33import sqlalchemy
34import sqlalchemy.ext.compiler
36from ..interfaces import Database, ReadOnlyDatabaseError, StaticTablesContext
37from ...core import ddl
40def _onSqlite3Connect(dbapiConnection, connectionRecord):
41 assert isinstance(dbapiConnection, sqlite3.Connection)
42 # Prevent pysqlite from emitting BEGIN and COMMIT statements.
43 dbapiConnection.isolation_level = None
44 # Enable foreign keys
45 with closing(dbapiConnection.cursor()) as cursor:
46 cursor.execute("PRAGMA foreign_keys=ON;")
47 cursor.execute("PRAGMA busy_timeout = 300000;") # in ms, so 5min (way longer than should be needed)
50def _onSqlite3Begin(connection):
51 assert connection.dialect.name == "sqlite"
52 # Replace pysqlite's buggy transaction handling that never BEGINs with our
53 # own that does, and tell SQLite to try to acquire a lock as soon as we
54 # start a transaction (this should lead to more blocking and fewer
55 # deadlocks).
56 connection.execute("BEGIN IMMEDIATE")
57 return connection
60class _Replace(sqlalchemy.sql.Insert):
61 """A SQLAlchemy query that compiles to INSERT ... ON CONFLICT REPLACE
62 on the primary key constraint for the table.
63 """
64 pass
67@sqlalchemy.ext.compiler.compiles(_Replace, "sqlite")
68def _replace(insert, compiler, **kw):
69 """Generate an INSERT ... ON CONFLICT REPLACE query.
70 """
71 # SQLite and PostgreSQL use similar syntax for their ON CONFLICT extension,
72 # but SQLAlchemy only knows about PostgreSQL's, so we have to compile some
73 # custom text SQL ourselves.
74 result = compiler.visit_insert(insert, **kw)
75 preparer = compiler.preparer
76 pk_columns = ", ".join([preparer.format_column(col) for col in insert.table.primary_key])
77 result += f" ON CONFLICT ({pk_columns})"
78 columns = [preparer.format_column(col) for col in insert.table.columns
79 if col.name not in insert.table.primary_key]
80 updates = ", ".join([f"{col} = excluded.{col}" for col in columns])
81 result += f" DO UPDATE SET {updates}"
82 return result
85_AUTOINCR_TABLE_SPEC = ddl.TableSpec(
86 fields=[ddl.FieldSpec(name="id", dtype=sqlalchemy.Integer, primaryKey=True)]
87)
90@dataclass
91class _AutoincrementCompoundKeyWorkaround:
92 """A workaround for SQLite's lack of support for compound primary keys that
93 include an autoincrement field.
94 """
96 table: sqlalchemy.schema.Table
97 """A single-column internal table that can be inserted into to yield
98 autoincrement values (`sqlalchemy.schema.Table`).
99 """
101 column: str
102 """The name of the column in the original table that needs to be populated
103 with values from the internal table (`str`).
104 """
107class SqliteDatabase(Database):
108 """An implementation of the `Database` interface for SQLite3.
110 Parameters
111 ----------
112 connection : `sqlalchemy.engine.Connection`
113 An existing connection created by a previous call to `connect`.
114 origin : `int`
115 An integer ID that should be used as the default for any datasets,
116 quanta, or other entities that use a (autoincrement, origin) compound
117 primary key.
118 namespace : `str`, optional
119 The namespace (schema) this database is associated with. If `None`,
120 the default schema for the connection is used (which may be `None`).
121 writeable : `bool`, optional
122 If `True`, allow write operations on the database, including
123 ``CREATE TABLE``.
125 Notes
126 -----
127 The case where ``namespace is not None`` is not yet tested, and may be
128 broken; we need an API for attaching to different databases in order to
129 write those tests, but haven't yet worked out what is common/different
130 across databases well enough to define it.
131 """
133 def __init__(self, *, connection: sqlalchemy.engine.Connection, origin: int,
134 namespace: Optional[str] = None, writeable: bool = True):
135 super().__init__(origin=origin, connection=connection, namespace=namespace)
136 # Get the filename from a call to 'PRAGMA database_list'.
137 with closing(connection.connection.cursor()) as cursor:
138 dbList = list(cursor.execute("PRAGMA database_list").fetchall())
139 if len(dbList) == 0:
140 raise RuntimeError("No database in connection.")
141 if namespace is None:
142 namespace = "main"
143 for _, dbname, filename in dbList:
144 if dbname == namespace:
145 break
146 else:
147 raise RuntimeError(f"No '{namespace}' database in connection.")
148 if not filename:
149 self.filename = None
150 else:
151 self.filename = filename
152 self._writeable = writeable
153 self._autoincr = {}
155 @classmethod
156 def makeDefaultUri(cls, root: str) -> Optional[str]:
157 return "sqlite:///" + os.path.join(root, "gen3.sqlite3")
159 @classmethod
160 def connect(cls, uri: Optional[str] = None, *, filename: Optional[str] = None,
161 writeable: bool = True) -> sqlalchemy.engine.Connection:
162 """Create a `sqlalchemy.engine.Connection` from a SQLAlchemy URI or
163 filename.
165 Parameters
166 ----------
167 uri : `str`
168 A SQLAlchemy URI connection string.
169 filename : `str`
170 Name of the SQLite database file, or `None` to use an in-memory
171 database. Ignored if ``uri is not None``.
172 origin : `int`
173 An integer ID that should be used as the default for any datasets,
174 quanta, or other entities that use a (autoincrement, origin)
175 compound primary key.
176 writeable : `bool`, optional
177 If `True`, allow write operations on the database, including
178 ``CREATE TABLE``.
180 Returns
181 -------
182 cs : `sqlalchemy.engine.Connection`
183 A database connection and transaction state.
184 """
185 # In order to be able to tell SQLite that we want a read-only or
186 # read-write connection, we need to make the SQLite DBAPI connection
187 # with a "URI"-based connection string. SQLAlchemy claims it can do
188 # this
189 # (https://docs.sqlalchemy.org/en/13/dialects/sqlite.html#uri-connections),
190 # but it doesn't seem to work as advertised. To work around this, we
191 # use the 'creator' argument to sqlalchemy.engine.create_engine, which
192 # lets us pass a callable that creates the DBAPI connection.
193 if uri is None:
194 if filename is None:
195 target = ":memory:"
196 uri = "sqlite://"
197 else:
198 target = f"file:{filename}"
199 uri = f"sqlite:///{filename}"
200 else:
201 parsed = urllib.parse.urlparse(uri)
202 queries = parsed.query.split("&")
203 if "uri=true" in queries:
204 # This is a SQLAlchemy URI that is already trying to make a
205 # SQLite connection via a SQLite URI, and hence there may
206 # be URI components for both SQLite and SQLAlchemy. We
207 # don't need to support that, and it'd be a
208 # reimplementation of all of the (broken) logic in
209 # SQLAlchemy for doing this, so we just don't.
210 raise NotImplementedError("SQLite connection strings with 'uri=true' are not supported.")
211 # This is just a SQLAlchemy URI with a non-URI SQLite
212 # connection string inside it. Pull that out so we can use it
213 # in the creator call.
214 if parsed.path.startswith("/"):
215 filename = parsed.path[1:]
216 target = f"file:{filename}"
217 else:
218 filename = None
219 target = ":memory:"
220 if filename is None:
221 if not writeable:
222 raise NotImplementedError("Read-only :memory: databases are not supported.")
223 else:
224 if writeable:
225 target += '?mode=rwc&uri=true'
226 else:
227 target += '?mode=ro&uri=true'
229 def creator():
230 return sqlite3.connect(target, check_same_thread=False, uri=True)
232 engine = sqlalchemy.engine.create_engine(uri, poolclass=sqlalchemy.pool.NullPool,
233 creator=creator)
235 sqlalchemy.event.listen(engine, "connect", _onSqlite3Connect)
236 sqlalchemy.event.listen(engine, "begin", _onSqlite3Begin)
237 try:
238 return engine.connect()
239 except sqlalchemy.exc.OperationalError as err:
240 raise RuntimeError(f"Error creating connection with uri='{uri}', filename='{filename}', "
241 f"target={target}.") from err
243 @classmethod
244 def fromConnection(cls, connection: sqlalchemy.engine.Connection, *, origin: int,
245 namespace: Optional[str] = None, writeable: bool = True) -> Database:
246 return cls(connection=connection, origin=origin, writeable=writeable, namespace=namespace)
248 def isWriteable(self) -> bool:
249 return self._writeable
251 def __str__(self) -> str:
252 if self.filename:
253 return f"SQLite3@{self.filename}"
254 else:
255 return "SQLite3@:memory:"
257 def declareStaticTables(self, *, create: bool) -> ContextManager[StaticTablesContext]:
258 # If the user asked for an in-memory, writeable database, assume
259 # create=True. This is only really relevant for tests, and it's
260 # convenient there.
261 return super().declareStaticTables(create=(create if self.filename else self.isWriteable()))
263 def _convertFieldSpec(self, table: str, spec: ddl.FieldSpec, metadata: sqlalchemy.MetaData,
264 **kwds) -> sqlalchemy.schema.Column:
265 if spec.autoincrement:
266 if not spec.primaryKey:
267 raise RuntimeError(f"Autoincrement field {table}.{spec.name} that is not a "
268 f"primary key is not supported.")
269 if spec.dtype != sqlalchemy.Integer:
270 # SQLite's autoincrement is really limited; it only works if
271 # the column type is exactly "INTEGER". But it also doesn't
272 # care about the distinctions between different integer types,
273 # so it's safe to change it.
274 spec = copy.copy(spec)
275 spec.dtype = sqlalchemy.Integer
276 return super()._convertFieldSpec(table, spec, metadata, **kwds)
278 def _makeColumnConstraints(self, table: str, spec: ddl.FieldSpec) -> List[sqlalchemy.CheckConstraint]:
279 # For sqlite we force constraints on all string columns since sqlite
280 # ignores everything otherwise and this leads to problems with
281 # other databases.
283 constraints = []
284 if spec.dtype == sqlalchemy.String:
285 name = self.shrinkDatabaseEntityName("_".join([table, "len", spec.name]))
286 constraints.append(sqlalchemy.CheckConstraint(f"length({spec.name})<={spec.length}"
287 # Oracle converts
288 # empty strings to
289 # NULL so check
290 f" AND length({spec.name})>=1",
291 name=name))
293 constraints.extend(super()._makeColumnConstraints(table, spec))
294 return constraints
296 def _convertTableSpec(self, name: str, spec: ddl.TableSpec, metadata: sqlalchemy.MetaData,
297 **kwds) -> sqlalchemy.schema.Table:
298 primaryKeyFieldNames = set(field.name for field in spec.fields if field.primaryKey)
299 autoincrFieldNames = set(field.name for field in spec.fields if field.autoincrement)
300 if len(autoincrFieldNames) > 1:
301 raise RuntimeError("At most one autoincrement field per table is allowed.")
302 if len(primaryKeyFieldNames) > 1 and len(autoincrFieldNames) > 0:
303 # SQLite's default rowid-based autoincrement doesn't work if the
304 # field is just one field in a compound primary key. As a
305 # workaround, we create an extra table with just one column that
306 # we'll insert into to generate those IDs. That's only safe if
307 # that single-column table's records are already unique with just
308 # the autoincrement field, not the rest of the primary key. In
309 # practice, that means the single-column table's records are those
310 # for which origin == self.origin.
311 autoincrFieldName, = autoincrFieldNames
312 otherPrimaryKeyFieldNames = primaryKeyFieldNames - autoincrFieldNames
313 if otherPrimaryKeyFieldNames != {"origin"}:
314 # We need the only other field in the key to be 'origin'.
315 raise NotImplementedError(
316 "Compound primary keys with an autoincrement are only supported in SQLite "
317 "if the only non-autoincrement primary key field is 'origin'."
318 )
319 self._autoincr[name] = _AutoincrementCompoundKeyWorkaround(
320 table=self._convertTableSpec(f"_autoinc_{name}", _AUTOINCR_TABLE_SPEC, metadata, **kwds),
321 column=autoincrFieldName
322 )
323 if not spec.recycleIds:
324 kwds = dict(kwds, sqlite_autoincrement=True)
325 return super()._convertTableSpec(name, spec, metadata, **kwds)
327 def insert(self, table: sqlalchemy.schema.Table, *rows: dict, returnIds: bool = False,
328 ) -> Optional[List[int]]:
329 autoincr = self._autoincr.get(table.name)
330 if autoincr is not None:
331 # This table has a compound primary key that includes an
332 # autoincrement. That doesn't work natively in SQLite, so we
333 # insert into a single-column table and use those IDs.
334 if not rows:
335 return [] if returnIds else None
336 if autoincr.column in rows[0]:
337 # Caller passed the autoincrement key values explicitly in the
338 # first row. They had better have done the same for all rows,
339 # or SQLAlchemy would have a problem, even if we didn't.
340 assert all(autoincr.column in row for row in rows)
341 # We need to insert only the values that correspond to
342 # ``origin == self.origin`` into the single-column table, to
343 # make sure we don't generate conflicting keys there later.
344 rowsForAutoincrTable = [dict(id=row[autoincr.column])
345 for row in rows if row["origin"] == self.origin]
346 # Insert into the autoincr table and the target table inside
347 # a transaction. The main-table insertion can take care of
348 # returnIds for us.
349 with self.transaction():
350 self._connection.execute(autoincr.table.insert(), *rowsForAutoincrTable)
351 return super().insert(table, *rows, returnIds=returnIds)
352 else:
353 # Caller did not pass autoincrement key values on the first
354 # row. Make sure they didn't ever do that, and also make
355 # sure the origin that was passed in is always self.origin,
356 # because we can't safely generate autoincrement values
357 # otherwise.
358 assert all(autoincr.column not in row and row["origin"] == self.origin for row in rows)
359 # Insert into the autoincr table one by one to get the
360 # primary key values back, then insert into the target table
361 # in the same transaction.
362 with self.transaction():
363 newRows = []
364 ids = []
365 for row in rows:
366 newRow = row.copy()
367 id = self._connection.execute(autoincr.table.insert()).inserted_primary_key[0]
368 newRow[autoincr.column] = id
369 newRows.append(newRow)
370 ids.append(id)
371 # Don't ever ask to returnIds here, because we've already
372 # got them.
373 super().insert(table, *newRows)
374 if returnIds:
375 return ids
376 else:
377 return None
378 else:
379 return super().insert(table, *rows, returnIds=returnIds)
381 def replace(self, table: sqlalchemy.schema.Table, *rows: dict):
382 if not self.isWriteable():
383 raise ReadOnlyDatabaseError(f"Attempt to replace into read-only database '{self}'.")
384 if table.name in self._autoincr:
385 raise NotImplementedError(
386 "replace does not support compound primary keys with autoincrement fields."
387 )
388 self._connection.execute(_Replace(table), *rows)
390 filename: Optional[str]
391 """Name of the file this database is connected to (`str` or `None`).
393 Set to `None` for in-memory databases.
394 """