Coverage for python/lsst/daf/butler/registry/collections/_base.py: 91%
180 statements
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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__ = ()
25import itertools
26from abc import abstractmethod
27from collections import namedtuple
28from collections.abc import Iterable, Iterator, Set
29from typing import TYPE_CHECKING, Any, Generic, TypeVar, cast
31import sqlalchemy
33from ...core import DimensionUniverse, Timespan, TimespanDatabaseRepresentation, ddl
34from .._collectionType import CollectionType
35from .._exceptions import MissingCollectionError
36from ..interfaces import ChainedCollectionRecord, CollectionManager, CollectionRecord, RunRecord, VersionTuple
37from ..wildcards import CollectionWildcard
39if TYPE_CHECKING:
40 from ..interfaces import Database, DimensionRecordStorageManager
43def _makeCollectionForeignKey(
44 sourceColumnName: str, collectionIdName: str, **kwargs: Any
45) -> ddl.ForeignKeySpec:
46 """Define foreign key specification that refers to collections table.
48 Parameters
49 ----------
50 sourceColumnName : `str`
51 Name of the column in the referring table.
52 collectionIdName : `str`
53 Name of the column in collections table that identifies it (PK).
54 **kwargs
55 Additional keyword arguments passed directly to `ddl.ForeignKeySpec`.
57 Returns
58 -------
59 spec : `ddl.ForeignKeySpec`
60 Foreign key specification.
62 Notes
63 -----
64 This method assumes fixed name ("collection") of a collections table.
65 There is also a general assumption that collection primary key consists
66 of a single column.
67 """
68 return ddl.ForeignKeySpec("collection", source=(sourceColumnName,), target=(collectionIdName,), **kwargs)
71CollectionTablesTuple = namedtuple("CollectionTablesTuple", ["collection", "run", "collection_chain"])
74def makeRunTableSpec(
75 collectionIdName: str, collectionIdType: type, TimespanReprClass: type[TimespanDatabaseRepresentation]
76) -> ddl.TableSpec:
77 """Define specification for "run" table.
79 Parameters
80 ----------
81 collectionIdName : `str`
82 Name of the column in collections table that identifies it (PK).
83 collectionIdType
84 Type of the PK column in the collections table, one of the
85 `sqlalchemy` types.
86 TimespanReprClass : `type` [ `TimespanDatabaseRepresentation` ]
87 Subclass of `TimespanDatabaseRepresentation` that encapsulates how
88 timespans are stored in this database.
91 Returns
92 -------
93 spec : `ddl.TableSpec`
94 Specification for run table.
96 Notes
97 -----
98 Assumption here and in the code below is that the name of the identifying
99 column is the same in both collections and run tables. The names of
100 non-identifying columns containing run metadata are fixed.
101 """
102 result = ddl.TableSpec(
103 fields=[
104 ddl.FieldSpec(collectionIdName, dtype=collectionIdType, primaryKey=True),
105 ddl.FieldSpec("host", dtype=sqlalchemy.String, length=128),
106 ],
107 foreignKeys=[
108 _makeCollectionForeignKey(collectionIdName, collectionIdName, onDelete="CASCADE"),
109 ],
110 )
111 for fieldSpec in TimespanReprClass.makeFieldSpecs(nullable=True):
112 result.fields.add(fieldSpec)
113 return result
116def makeCollectionChainTableSpec(collectionIdName: str, collectionIdType: type) -> ddl.TableSpec:
117 """Define specification for "collection_chain" table.
119 Parameters
120 ----------
121 collectionIdName : `str`
122 Name of the column in collections table that identifies it (PK).
123 collectionIdType
124 Type of the PK column in the collections table, one of the
125 `sqlalchemy` types.
127 Returns
128 -------
129 spec : `ddl.TableSpec`
130 Specification for collection chain table.
132 Notes
133 -----
134 Collection chain is simply an ordered one-to-many relation between
135 collections. The names of the columns in the table are fixed and
136 also hardcoded in the code below.
137 """
138 return ddl.TableSpec(
139 fields=[
140 ddl.FieldSpec("parent", dtype=collectionIdType, primaryKey=True),
141 ddl.FieldSpec("position", dtype=sqlalchemy.SmallInteger, primaryKey=True),
142 ddl.FieldSpec("child", dtype=collectionIdType, nullable=False),
143 ],
144 foreignKeys=[
145 _makeCollectionForeignKey("parent", collectionIdName, onDelete="CASCADE"),
146 _makeCollectionForeignKey("child", collectionIdName),
147 ],
148 )
151class DefaultRunRecord(RunRecord):
152 """Default `RunRecord` implementation.
154 This method assumes the same run table definition as produced by
155 `makeRunTableSpec` method. The only non-fixed name in the schema
156 is the PK column name, this needs to be passed in a constructor.
158 Parameters
159 ----------
160 db : `Database`
161 Registry database.
162 key
163 Unique collection ID, can be the same as ``name`` if ``name`` is used
164 for identification. Usually this is an integer or string, but can be
165 other database-specific type.
166 name : `str`
167 Run collection name.
168 table : `sqlalchemy.schema.Table`
169 Table for run records.
170 idColumnName : `str`
171 Name of the identifying column in run table.
172 host : `str`, optional
173 Name of the host where run was produced.
174 timespan : `Timespan`, optional
175 Timespan for this run.
176 """
178 def __init__(
179 self,
180 db: Database,
181 key: Any,
182 name: str,
183 *,
184 table: sqlalchemy.schema.Table,
185 idColumnName: str,
186 host: str | None = None,
187 timespan: Timespan | None = None,
188 ):
189 super().__init__(key=key, name=name, type=CollectionType.RUN)
190 self._db = db
191 self._table = table
192 self._host = host
193 if timespan is None: 193 ↛ 195line 193 didn't jump to line 195, because the condition on line 193 was never false
194 timespan = Timespan(begin=None, end=None)
195 self._timespan = timespan
196 self._idName = idColumnName
198 def update(self, host: str | None = None, timespan: Timespan | None = None) -> None:
199 # Docstring inherited from RunRecord.
200 if timespan is None:
201 timespan = Timespan(begin=None, end=None)
202 row = {
203 self._idName: self.key,
204 "host": host,
205 }
206 self._db.getTimespanRepresentation().update(timespan, result=row)
207 count = self._db.update(self._table, {self._idName: self.key}, row)
208 if count != 1:
209 raise RuntimeError(f"Run update affected {count} records; expected exactly one.")
210 self._host = host
211 self._timespan = timespan
213 @property
214 def host(self) -> str | None:
215 # Docstring inherited from RunRecord.
216 return self._host
218 @property
219 def timespan(self) -> Timespan:
220 # Docstring inherited from RunRecord.
221 return self._timespan
224class DefaultChainedCollectionRecord(ChainedCollectionRecord):
225 """Default `ChainedCollectionRecord` implementation.
227 This method assumes the same chain table definition as produced by
228 `makeCollectionChainTableSpec` method. All column names in the table are
229 fixed and hard-coded in the methods.
231 Parameters
232 ----------
233 db : `Database`
234 Registry database.
235 key
236 Unique collection ID, can be the same as ``name`` if ``name`` is used
237 for identification. Usually this is an integer or string, but can be
238 other database-specific type.
239 name : `str`
240 Collection name.
241 table : `sqlalchemy.schema.Table`
242 Table for chain relationship records.
243 universe : `DimensionUniverse`
244 Object managing all known dimensions.
245 """
247 def __init__(
248 self,
249 db: Database,
250 key: Any,
251 name: str,
252 *,
253 table: sqlalchemy.schema.Table,
254 universe: DimensionUniverse,
255 ):
256 super().__init__(key=key, name=name, universe=universe)
257 self._db = db
258 self._table = table
259 self._universe = universe
261 def _update(self, manager: CollectionManager, children: tuple[str, ...]) -> None:
262 # Docstring inherited from ChainedCollectionRecord.
263 rows = []
264 position = itertools.count()
265 for child in manager.resolve_wildcard(CollectionWildcard.from_names(children), flatten_chains=False):
266 rows.append(
267 {
268 "parent": self.key,
269 "child": child.key,
270 "position": next(position),
271 }
272 )
273 with self._db.transaction():
274 self._db.delete(self._table, ["parent"], {"parent": self.key})
275 self._db.insert(self._table, *rows)
277 def _load(self, manager: CollectionManager) -> tuple[str, ...]:
278 # Docstring inherited from ChainedCollectionRecord.
279 sql = (
280 sqlalchemy.sql.select(
281 self._table.columns.child,
282 )
283 .select_from(self._table)
284 .where(self._table.columns.parent == self.key)
285 .order_by(self._table.columns.position)
286 )
287 with self._db.query(sql) as sql_result:
288 return tuple(manager[row[self._table.columns.child]].name for row in sql_result.mappings())
291K = TypeVar("K")
294class DefaultCollectionManager(Generic[K], CollectionManager):
295 """Default `CollectionManager` implementation.
297 This implementation uses record classes defined in this module and is
298 based on the same assumptions about schema outlined in the record classes.
300 Parameters
301 ----------
302 db : `Database`
303 Interface to the underlying database engine and namespace.
304 tables : `CollectionTablesTuple`
305 Named tuple of SQLAlchemy table objects.
306 collectionIdName : `str`
307 Name of the column in collections table that identifies it (PK).
308 dimensions : `DimensionRecordStorageManager`
309 Manager object for the dimensions in this `Registry`.
311 Notes
312 -----
313 Implementation uses "aggressive" pre-fetching and caching of the records
314 in memory. Memory cache is synchronized from database when `refresh`
315 method is called.
316 """
318 def __init__(
319 self,
320 db: Database,
321 tables: CollectionTablesTuple,
322 collectionIdName: str,
323 *,
324 dimensions: DimensionRecordStorageManager,
325 registry_schema_version: VersionTuple | None = None,
326 ):
327 super().__init__(registry_schema_version=registry_schema_version)
328 self._db = db
329 self._tables = tables
330 self._collectionIdName = collectionIdName
331 self._records: dict[K, CollectionRecord] = {} # indexed by record ID
332 self._dimensions = dimensions
334 def refresh(self) -> None:
335 # Docstring inherited from CollectionManager.
336 sql = sqlalchemy.sql.select(
337 *(list(self._tables.collection.columns) + list(self._tables.run.columns))
338 ).select_from(self._tables.collection.join(self._tables.run, isouter=True))
339 # Put found records into a temporary instead of updating self._records
340 # in place, for exception safety.
341 records = []
342 chains = []
343 TimespanReprClass = self._db.getTimespanRepresentation()
344 with self._db.query(sql) as sql_result:
345 sql_rows = sql_result.mappings().fetchall()
346 for row in sql_rows:
347 collection_id = row[self._tables.collection.columns[self._collectionIdName]]
348 name = row[self._tables.collection.columns.name]
349 type = CollectionType(row["type"])
350 record: CollectionRecord
351 if type is CollectionType.RUN:
352 record = DefaultRunRecord(
353 key=collection_id,
354 name=name,
355 db=self._db,
356 table=self._tables.run,
357 idColumnName=self._collectionIdName,
358 host=row[self._tables.run.columns.host],
359 timespan=TimespanReprClass.extract(row),
360 )
361 elif type is CollectionType.CHAINED:
362 record = DefaultChainedCollectionRecord(
363 db=self._db,
364 key=collection_id,
365 table=self._tables.collection_chain,
366 name=name,
367 universe=self._dimensions.universe,
368 )
369 chains.append(record)
370 else:
371 record = CollectionRecord(key=collection_id, name=name, type=type)
372 records.append(record)
373 self._setRecordCache(records)
374 for chain in chains:
375 try:
376 chain.refresh(self)
377 except MissingCollectionError:
378 # This indicates a race condition in which some other client
379 # created a new collection and added it as a child of this
380 # (pre-existing) chain between the time we fetched all
381 # collections and the time we queried for parent-child
382 # relationships.
383 # Because that's some other unrelated client, we shouldn't care
384 # about that parent collection anyway, so we just drop it on
385 # the floor (a manual refresh can be used to get it back).
386 self._removeCachedRecord(chain)
388 def register(
389 self, name: str, type: CollectionType, doc: str | None = None
390 ) -> tuple[CollectionRecord, bool]:
391 # Docstring inherited from CollectionManager.
392 registered = False
393 record = self._getByName(name)
394 if record is None:
395 row, inserted_or_updated = self._db.sync(
396 self._tables.collection,
397 keys={"name": name},
398 compared={"type": int(type)},
399 extra={"doc": doc},
400 returning=[self._collectionIdName],
401 )
402 assert isinstance(inserted_or_updated, bool)
403 registered = inserted_or_updated
404 assert row is not None
405 collection_id = row[self._collectionIdName]
406 if type is CollectionType.RUN:
407 TimespanReprClass = self._db.getTimespanRepresentation()
408 row, _ = self._db.sync(
409 self._tables.run,
410 keys={self._collectionIdName: collection_id},
411 returning=("host",) + TimespanReprClass.getFieldNames(),
412 )
413 assert row is not None
414 record = DefaultRunRecord(
415 db=self._db,
416 key=collection_id,
417 name=name,
418 table=self._tables.run,
419 idColumnName=self._collectionIdName,
420 host=row["host"],
421 timespan=TimespanReprClass.extract(row),
422 )
423 elif type is CollectionType.CHAINED:
424 record = DefaultChainedCollectionRecord(
425 db=self._db,
426 key=collection_id,
427 name=name,
428 table=self._tables.collection_chain,
429 universe=self._dimensions.universe,
430 )
431 else:
432 record = CollectionRecord(key=collection_id, name=name, type=type)
433 self._addCachedRecord(record)
434 return record, registered
436 def remove(self, name: str) -> None:
437 # Docstring inherited from CollectionManager.
438 record = self._getByName(name)
439 if record is None: 439 ↛ 440line 439 didn't jump to line 440, because the condition on line 439 was never true
440 raise MissingCollectionError(f"No collection with name '{name}' found.")
441 # This may raise
442 self._db.delete(
443 self._tables.collection, [self._collectionIdName], {self._collectionIdName: record.key}
444 )
445 self._removeCachedRecord(record)
447 def find(self, name: str) -> CollectionRecord:
448 # Docstring inherited from CollectionManager.
449 result = self._getByName(name)
450 if result is None:
451 raise MissingCollectionError(f"No collection with name '{name}' found.")
452 return result
454 def __getitem__(self, key: Any) -> CollectionRecord:
455 # Docstring inherited from CollectionManager.
456 try:
457 return self._records[key]
458 except KeyError as err:
459 raise MissingCollectionError(f"Collection with key '{key}' not found.") from err
461 def resolve_wildcard(
462 self,
463 wildcard: CollectionWildcard,
464 *,
465 collection_types: Set[CollectionType] = CollectionType.all(),
466 done: set[str] | None = None,
467 flatten_chains: bool = True,
468 include_chains: bool | None = None,
469 ) -> list[CollectionRecord]:
470 # Docstring inherited
471 if done is None: 471 ↛ 473line 471 didn't jump to line 473, because the condition on line 471 was never false
472 done = set()
473 include_chains = include_chains if include_chains is not None else not flatten_chains
475 def resolve_nested(record: CollectionRecord, done: set[str]) -> Iterator[CollectionRecord]:
476 if record.name in done:
477 return
478 if record.type in collection_types:
479 done.add(record.name)
480 if record.type is not CollectionType.CHAINED or include_chains:
481 yield record
482 if flatten_chains and record.type is CollectionType.CHAINED:
483 done.add(record.name)
484 for name in cast(ChainedCollectionRecord, record).children:
485 # flake8 can't tell that we only delete this closure when
486 # we're totally done with it.
487 yield from resolve_nested(self.find(name), done) # noqa: F821
489 result: list[CollectionRecord] = []
491 if wildcard.patterns is ...:
492 for record in self._records.values():
493 result.extend(resolve_nested(record, done))
494 del resolve_nested
495 return result
496 for name in wildcard.strings:
497 result.extend(resolve_nested(self.find(name), done))
498 if wildcard.patterns:
499 for record in self._records.values():
500 if any(p.fullmatch(record.name) for p in wildcard.patterns):
501 result.extend(resolve_nested(record, done))
502 del resolve_nested
503 return result
505 def getDocumentation(self, key: Any) -> str | None:
506 # Docstring inherited from CollectionManager.
507 sql = (
508 sqlalchemy.sql.select(self._tables.collection.columns.doc)
509 .select_from(self._tables.collection)
510 .where(self._tables.collection.columns[self._collectionIdName] == key)
511 )
512 with self._db.query(sql) as sql_result:
513 return sql_result.scalar()
515 def setDocumentation(self, key: Any, doc: str | None) -> None:
516 # Docstring inherited from CollectionManager.
517 self._db.update(self._tables.collection, {self._collectionIdName: "key"}, {"key": key, "doc": doc})
519 def _setRecordCache(self, records: Iterable[CollectionRecord]) -> None:
520 """Set internal record cache to contain given records,
521 old cached records will be removed.
522 """
523 self._records = {}
524 for record in records:
525 self._records[record.key] = record
527 def _addCachedRecord(self, record: CollectionRecord) -> None:
528 """Add single record to cache."""
529 self._records[record.key] = record
531 def _removeCachedRecord(self, record: CollectionRecord) -> None:
532 """Remove single record from cache."""
533 del self._records[record.key]
535 @abstractmethod
536 def _getByName(self, name: str) -> CollectionRecord | None:
537 """Find collection record given collection name."""
538 raise NotImplementedError()