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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 

22 

23__all__ = ["SqliteDatabase"] 

24 

25from contextlib import closing 

26import copy 

27from typing import Any, ContextManager, Dict, Iterable, List, Optional 

28from dataclasses import dataclass 

29import os 

30import urllib.parse 

31 

32import sqlite3 

33import sqlalchemy 

34import sqlalchemy.ext.compiler 

35 

36from ..interfaces import Database, StaticTablesContext 

37from ...core import ddl 

38 

39 

40def _onSqlite3Connect(dbapiConnection: sqlite3.Connection, 

41 connectionRecord: sqlalchemy.pool._ConnectionRecord) -> None: 

42 assert isinstance(dbapiConnection, sqlite3.Connection) 

43 # Prevent pysqlite from emitting BEGIN and COMMIT statements. 

44 dbapiConnection.isolation_level = None 

45 # Enable foreign keys 

46 with closing(dbapiConnection.cursor()) as cursor: 

47 cursor.execute("PRAGMA foreign_keys=ON;") 

48 cursor.execute("PRAGMA busy_timeout = 300000;") # in ms, so 5min (way longer than should be needed) 

49 

50 

51def _onSqlite3Begin(connection: sqlalchemy.engine.Connection) -> sqlalchemy.engine.Connection: 

52 assert connection.dialect.name == "sqlite" 

53 # Replace pysqlite's buggy transaction handling that never BEGINs with our 

54 # own that does, and tell SQLite to try to acquire a lock as soon as we 

55 # start a transaction (this should lead to more blocking and fewer 

56 # deadlocks). 

57 connection.execute("BEGIN IMMEDIATE") 

58 return connection 

59 

60 

61class _Replace(sqlalchemy.sql.Insert): 

62 """A SQLAlchemy query that compiles to INSERT ... ON CONFLICT REPLACE 

63 on the primary key constraint for the table. 

64 """ 

65 pass 

66 

67 

68# SQLite and PostgreSQL use similar syntax for their ON CONFLICT extension, 

69# but SQLAlchemy only knows about PostgreSQL's, so we have to compile some 

70# custom text SQL ourselves. 

71 

72# Hard to infer what types these should be from SQLAlchemy docs; just disable 

73# static typing by calling everything "Any". 

74@sqlalchemy.ext.compiler.compiles(_Replace, "sqlite") 

75def _replace(insert: Any, compiler: Any, **kwargs: Any) -> Any: 

76 """Generate an INSERT ... ON CONFLICT REPLACE query. 

77 """ 

78 result = compiler.visit_insert(insert, **kwargs) 

79 preparer = compiler.preparer 

80 pk_columns = ", ".join([preparer.format_column(col) for col in insert.table.primary_key]) 

81 result += f" ON CONFLICT ({pk_columns})" 

82 columns = [preparer.format_column(col) for col in insert.table.columns 

83 if col.name not in insert.table.primary_key] 

84 updates = ", ".join([f"{col} = excluded.{col}" for col in columns]) 

85 result += f" DO UPDATE SET {updates}" 

86 return result 

87 

88 

89class _Ensure(sqlalchemy.sql.Insert): 

90 """A SQLAlchemy query that compiles to INSERT ... ON CONFLICT DO NOTHING. 

91 """ 

92 pass 

93 

94 

95@sqlalchemy.ext.compiler.compiles(_Ensure, "sqlite") 

96def _ensure(insert: Any, compiler: Any, **kwargs: Any) -> Any: 

97 """Generate an INSERT ... ON CONFLICT DO NOTHING query. 

98 """ 

99 result = compiler.visit_insert(insert, **kwargs) 

100 result += " ON CONFLICT DO NOTHING" 

101 return result 

102 

103 

104_AUTOINCR_TABLE_SPEC = ddl.TableSpec( 

105 fields=[ddl.FieldSpec(name="id", dtype=sqlalchemy.Integer, primaryKey=True)] 

106) 

107 

108 

109@dataclass 

110class _AutoincrementCompoundKeyWorkaround: 

111 """A workaround for SQLite's lack of support for compound primary keys that 

112 include an autoincrement field. 

113 """ 

114 

115 table: sqlalchemy.schema.Table 

116 """A single-column internal table that can be inserted into to yield 

117 autoincrement values (`sqlalchemy.schema.Table`). 

118 """ 

119 

120 column: str 

121 """The name of the column in the original table that needs to be populated 

122 with values from the internal table (`str`). 

123 """ 

124 

125 

126class SqliteDatabase(Database): 

127 """An implementation of the `Database` interface for SQLite3. 

128 

129 Parameters 

130 ---------- 

131 connection : `sqlalchemy.engine.Connection` 

132 An existing connection created by a previous call to `connect`. 

133 origin : `int` 

134 An integer ID that should be used as the default for any datasets, 

135 quanta, or other entities that use a (autoincrement, origin) compound 

136 primary key. 

137 namespace : `str`, optional 

138 The namespace (schema) this database is associated with. If `None`, 

139 the default schema for the connection is used (which may be `None`). 

140 writeable : `bool`, optional 

141 If `True`, allow write operations on the database, including 

142 ``CREATE TABLE``. 

143 

144 Notes 

145 ----- 

146 The case where ``namespace is not None`` is not yet tested, and may be 

147 broken; we need an API for attaching to different databases in order to 

148 write those tests, but haven't yet worked out what is common/different 

149 across databases well enough to define it. 

150 """ 

151 

152 def __init__(self, *, connection: sqlalchemy.engine.Connection, origin: int, 

153 namespace: Optional[str] = None, writeable: bool = True): 

154 super().__init__(origin=origin, connection=connection, namespace=namespace) 

155 # Get the filename from a call to 'PRAGMA database_list'. 

156 with closing(connection.connection.cursor()) as cursor: 

157 dbList = list(cursor.execute("PRAGMA database_list").fetchall()) 

158 if len(dbList) == 0: 

159 raise RuntimeError("No database in connection.") 

160 if namespace is None: 

161 namespace = "main" 

162 for _, dbname, filename in dbList: 

163 if dbname == namespace: 

164 break 

165 else: 

166 raise RuntimeError(f"No '{namespace}' database in connection.") 

167 if not filename: 

168 self.filename = None 

169 else: 

170 self.filename = filename 

171 self._writeable = writeable 

172 self._autoincr: Dict[str, _AutoincrementCompoundKeyWorkaround] = {} 

173 

174 @classmethod 

175 def makeDefaultUri(cls, root: str) -> Optional[str]: 

176 return "sqlite:///" + os.path.join(root, "gen3.sqlite3") 

177 

178 @classmethod 

179 def connect(cls, uri: Optional[str] = None, *, filename: Optional[str] = None, 

180 writeable: bool = True) -> sqlalchemy.engine.Connection: 

181 """Create a `sqlalchemy.engine.Connection` from a SQLAlchemy URI or 

182 filename. 

183 

184 Parameters 

185 ---------- 

186 uri : `str` 

187 A SQLAlchemy URI connection string. 

188 filename : `str` 

189 Name of the SQLite database file, or `None` to use an in-memory 

190 database. Ignored if ``uri is not None``. 

191 origin : `int` 

192 An integer ID that should be used as the default for any datasets, 

193 quanta, or other entities that use a (autoincrement, origin) 

194 compound primary key. 

195 writeable : `bool`, optional 

196 If `True`, allow write operations on the database, including 

197 ``CREATE TABLE``. 

198 

199 Returns 

200 ------- 

201 cs : `sqlalchemy.engine.Connection` 

202 A database connection and transaction state. 

203 """ 

204 # In order to be able to tell SQLite that we want a read-only or 

205 # read-write connection, we need to make the SQLite DBAPI connection 

206 # with a "URI"-based connection string. SQLAlchemy claims it can do 

207 # this 

208 # (https://docs.sqlalchemy.org/en/13/dialects/sqlite.html#uri-connections), 

209 # but it doesn't seem to work as advertised. To work around this, we 

210 # use the 'creator' argument to sqlalchemy.engine.create_engine, which 

211 # lets us pass a callable that creates the DBAPI connection. 

212 if uri is None: 

213 if filename is None: 

214 target = ":memory:" 

215 uri = "sqlite://" 

216 else: 

217 target = f"file:{filename}" 

218 uri = f"sqlite:///{filename}" 

219 else: 

220 parsed = urllib.parse.urlparse(uri) 

221 queries = parsed.query.split("&") 

222 if "uri=true" in queries: 

223 # This is a SQLAlchemy URI that is already trying to make a 

224 # SQLite connection via a SQLite URI, and hence there may 

225 # be URI components for both SQLite and SQLAlchemy. We 

226 # don't need to support that, and it'd be a 

227 # reimplementation of all of the (broken) logic in 

228 # SQLAlchemy for doing this, so we just don't. 

229 raise NotImplementedError("SQLite connection strings with 'uri=true' are not supported.") 

230 # This is just a SQLAlchemy URI with a non-URI SQLite 

231 # connection string inside it. Pull that out so we can use it 

232 # in the creator call. 

233 if parsed.path.startswith("/"): 

234 filename = parsed.path[1:] 

235 target = f"file:{filename}" 

236 else: 

237 filename = None 

238 target = ":memory:" 

239 if filename is None: 

240 if not writeable: 

241 raise NotImplementedError("Read-only :memory: databases are not supported.") 

242 else: 

243 if writeable: 

244 target += '?mode=rwc&uri=true' 

245 else: 

246 target += '?mode=ro&uri=true' 

247 

248 def creator() -> sqlite3.Connection: 

249 return sqlite3.connect(target, check_same_thread=False, uri=True) 

250 

251 engine = sqlalchemy.engine.create_engine(uri, poolclass=sqlalchemy.pool.NullPool, 

252 creator=creator) 

253 

254 sqlalchemy.event.listen(engine, "connect", _onSqlite3Connect) 

255 sqlalchemy.event.listen(engine, "begin", _onSqlite3Begin) 

256 try: 

257 return engine.connect() 

258 except sqlalchemy.exc.OperationalError as err: 

259 raise RuntimeError(f"Error creating connection with uri='{uri}', filename='{filename}', " 

260 f"target={target}.") from err 

261 

262 @classmethod 

263 def fromConnection(cls, connection: sqlalchemy.engine.Connection, *, origin: int, 

264 namespace: Optional[str] = None, writeable: bool = True) -> Database: 

265 return cls(connection=connection, origin=origin, writeable=writeable, namespace=namespace) 

266 

267 def isWriteable(self) -> bool: 

268 return self._writeable 

269 

270 def __str__(self) -> str: 

271 if self.filename: 

272 return f"SQLite3@{self.filename}" 

273 else: 

274 return "SQLite3@:memory:" 

275 

276 def _lockTables(self, tables: Iterable[sqlalchemy.schema.Table] = ()) -> None: 

277 # Docstring inherited. 

278 # Our SQLite database always acquires full-database locks at the 

279 # beginning of a transaction, so there's no need to acquire table-level 

280 # locks - which is good, because SQLite doesn't have table-level 

281 # locking. 

282 pass 

283 

284 # MyPy claims that the return type here isn't covariant with the return 

285 # type of the base class method, which is formally correct but irrelevant 

286 # - the base class return type is _GeneratorContextManager, but only 

287 # because it's generated by the contextmanager decorator. 

288 def declareStaticTables(self, *, create: bool) -> ContextManager[StaticTablesContext]: # type: ignore 

289 # If the user asked for an in-memory, writeable database, then we may 

290 # need to re-create schema even if create=False because schema can be 

291 # lost on re-connect. This is only really relevant for tests, and it's 

292 # convenient there. 

293 if self.filename is None and self.isWriteable(): 

294 inspector = sqlalchemy.engine.reflection.Inspector(self._connection) 

295 tables = inspector.get_table_names(schema=self.namespace) 

296 if not tables: 

297 create = True 

298 return super().declareStaticTables(create=create) 

299 

300 def _convertFieldSpec(self, table: str, spec: ddl.FieldSpec, metadata: sqlalchemy.MetaData, 

301 **kwargs: Any) -> sqlalchemy.schema.Column: 

302 if spec.autoincrement: 

303 if not spec.primaryKey: 

304 raise RuntimeError(f"Autoincrement field {table}.{spec.name} that is not a " 

305 f"primary key is not supported.") 

306 if spec.dtype != sqlalchemy.Integer: 

307 # SQLite's autoincrement is really limited; it only works if 

308 # the column type is exactly "INTEGER". But it also doesn't 

309 # care about the distinctions between different integer types, 

310 # so it's safe to change it. 

311 spec = copy.copy(spec) 

312 spec.dtype = sqlalchemy.Integer 

313 return super()._convertFieldSpec(table, spec, metadata, **kwargs) 

314 

315 def _makeColumnConstraints(self, table: str, spec: ddl.FieldSpec) -> List[sqlalchemy.CheckConstraint]: 

316 # For sqlite we force constraints on all string columns since sqlite 

317 # ignores everything otherwise and this leads to problems with 

318 # other databases. 

319 

320 constraints = [] 

321 if spec.isStringType(): 

322 name = self.shrinkDatabaseEntityName("_".join([table, "len", spec.name])) 

323 constraints.append(sqlalchemy.CheckConstraint(f"length({spec.name})<={spec.length}" 

324 # Oracle converts 

325 # empty strings to 

326 # NULL so check 

327 f" AND length({spec.name})>=1", 

328 name=name)) 

329 

330 constraints.extend(super()._makeColumnConstraints(table, spec)) 

331 return constraints 

332 

333 def _convertTableSpec(self, name: str, spec: ddl.TableSpec, metadata: sqlalchemy.MetaData, 

334 **kwargs: Any) -> sqlalchemy.schema.Table: 

335 primaryKeyFieldNames = set(field.name for field in spec.fields if field.primaryKey) 

336 autoincrFieldNames = set(field.name for field in spec.fields if field.autoincrement) 

337 if len(autoincrFieldNames) > 1: 

338 raise RuntimeError("At most one autoincrement field per table is allowed.") 

339 if len(primaryKeyFieldNames) > 1 and len(autoincrFieldNames) > 0: 

340 # SQLite's default rowid-based autoincrement doesn't work if the 

341 # field is just one field in a compound primary key. As a 

342 # workaround, we create an extra table with just one column that 

343 # we'll insert into to generate those IDs. That's only safe if 

344 # that single-column table's records are already unique with just 

345 # the autoincrement field, not the rest of the primary key. In 

346 # practice, that means the single-column table's records are those 

347 # for which origin == self.origin. 

348 autoincrFieldName, = autoincrFieldNames 

349 otherPrimaryKeyFieldNames = primaryKeyFieldNames - autoincrFieldNames 

350 if otherPrimaryKeyFieldNames != {"origin"}: 

351 # We need the only other field in the key to be 'origin'. 

352 raise NotImplementedError( 

353 "Compound primary keys with an autoincrement are only supported in SQLite " 

354 "if the only non-autoincrement primary key field is 'origin'." 

355 ) 

356 self._autoincr[name] = _AutoincrementCompoundKeyWorkaround( 

357 table=self._convertTableSpec(f"_autoinc_{name}", _AUTOINCR_TABLE_SPEC, metadata, **kwargs), 

358 column=autoincrFieldName 

359 ) 

360 if not spec.recycleIds: 

361 kwargs = dict(kwargs, sqlite_autoincrement=True) 

362 return super()._convertTableSpec(name, spec, metadata, **kwargs) 

363 

364 def insert(self, table: sqlalchemy.schema.Table, *rows: dict, returnIds: bool = False, 

365 select: Optional[sqlalchemy.sql.Select] = None, 

366 names: Optional[Iterable[str]] = None, 

367 ) -> Optional[List[int]]: 

368 self.assertTableWriteable(table, f"Cannot insert into read-only table {table}.") 

369 autoincr = self._autoincr.get(table.name) 

370 if autoincr is not None: 

371 if select is not None: 

372 raise NotImplementedError( 

373 "Cannot do INSERT INTO ... SELECT on a SQLite table with a simulated autoincrement " 

374 "compound primary key" 

375 ) 

376 # This table has a compound primary key that includes an 

377 # autoincrement. That doesn't work natively in SQLite, so we 

378 # insert into a single-column table and use those IDs. 

379 if not rows: 

380 return [] if returnIds else None 

381 if autoincr.column in rows[0]: 

382 # Caller passed the autoincrement key values explicitly in the 

383 # first row. They had better have done the same for all rows, 

384 # or SQLAlchemy would have a problem, even if we didn't. 

385 assert all(autoincr.column in row for row in rows) 

386 # We need to insert only the values that correspond to 

387 # ``origin == self.origin`` into the single-column table, to 

388 # make sure we don't generate conflicting keys there later. 

389 rowsForAutoincrTable = [dict(id=row[autoincr.column]) 

390 for row in rows if row["origin"] == self.origin] 

391 # Insert into the autoincr table and the target table inside 

392 # a transaction. The main-table insertion can take care of 

393 # returnIds for us. 

394 with self.transaction(): 

395 self._connection.execute(autoincr.table.insert(), *rowsForAutoincrTable) 

396 return super().insert(table, *rows, returnIds=returnIds) 

397 else: 

398 # Caller did not pass autoincrement key values on the first 

399 # row. Make sure they didn't ever do that, and also make 

400 # sure the origin that was passed in is always self.origin, 

401 # because we can't safely generate autoincrement values 

402 # otherwise. 

403 assert all(autoincr.column not in row and row["origin"] == self.origin for row in rows) 

404 # Insert into the autoincr table one by one to get the 

405 # primary key values back, then insert into the target table 

406 # in the same transaction. 

407 with self.transaction(): 

408 newRows = [] 

409 ids = [] 

410 for row in rows: 

411 newRow = row.copy() 

412 id = self._connection.execute(autoincr.table.insert()).inserted_primary_key[0] 

413 newRow[autoincr.column] = id 

414 newRows.append(newRow) 

415 ids.append(id) 

416 # Don't ever ask to returnIds here, because we've already 

417 # got them. 

418 super().insert(table, *newRows) 

419 if returnIds: 

420 return ids 

421 else: 

422 return None 

423 else: 

424 return super().insert(table, *rows, select=select, names=names, returnIds=returnIds) 

425 

426 def replace(self, table: sqlalchemy.schema.Table, *rows: dict) -> None: 

427 self.assertTableWriteable(table, f"Cannot replace into read-only table {table}.") 

428 if not rows: 

429 return 

430 if table.name in self._autoincr: 

431 raise NotImplementedError( 

432 "replace does not support compound primary keys with autoincrement fields." 

433 ) 

434 self._connection.execute(_Replace(table), *rows) 

435 

436 def ensure(self, table: sqlalchemy.schema.Table, *rows: dict) -> int: 

437 self.assertTableWriteable(table, f"Cannot ensure into read-only table {table}.") 

438 if not rows: 

439 return 0 

440 if table.name in self._autoincr: 

441 raise NotImplementedError( 

442 "ensure does not support compound primary keys with autoincrement fields." 

443 ) 

444 return self._connection.execute(_Ensure(table), *rows).rowcount 

445 

446 filename: Optional[str] 

447 """Name of the file this database is connected to (`str` or `None`). 

448 

449 Set to `None` for in-memory databases. 

450 """