Coverage for python/lsst/pipe/base/_task_metadata.py: 15%
219 statements
« prev ^ index » next coverage.py v6.5.0, created at 2023-02-08 02:43 -0800
1# This file is part of pipe_base.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (https://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 <https://www.gnu.org/licenses/>.
22__all__ = ["TaskMetadata"]
24import itertools
25import numbers
26import warnings
27from collections.abc import Sequence
28from typing import Any, Collection, Dict, Iterator, List, Mapping, Optional, Protocol, Set, Tuple, Union
30from deprecated.sphinx import deprecated
31from pydantic import BaseModel, Field, StrictBool, StrictFloat, StrictInt, StrictStr
33_DEPRECATION_REASON = "Will be removed after v25."
34_DEPRECATION_VERSION = "v24"
36# The types allowed in a Task metadata field are restricted
37# to allow predictable serialization.
38_ALLOWED_PRIMITIVE_TYPES = (str, float, int, bool)
41class PropertySetLike(Protocol):
42 """Protocol that looks like a ``lsst.daf.base.PropertySet``
44 Enough of the API is specified to support conversion of a
45 ``PropertySet`` to a `TaskMetadata`.
46 """
48 def paramNames(self, topLevelOnly: bool = True) -> Collection[str]:
49 ...
51 def getArray(self, name: str) -> Any:
52 ...
55def _isListLike(v: Any) -> bool:
56 return isinstance(v, Sequence) and not isinstance(v, str)
59class TaskMetadata(BaseModel):
60 """Dict-like object for storing task metadata.
62 Metadata can be stored at two levels: single task or task plus subtasks.
63 The later is called full metadata of a task and has a form
65 topLevelTaskName:subtaskName:subsubtaskName.itemName
67 Metadata item key of a task (`itemName` above) must not contain `.`,
68 which serves as a separator in full metadata keys and turns
69 the value into sub-dictionary. Arbitrary hierarchies are supported.
71 Deprecated methods are for compatibility with
72 the predecessor containers.
73 """
75 scalars: Dict[str, Union[StrictFloat, StrictInt, StrictBool, StrictStr]] = Field(default_factory=dict)
76 arrays: Dict[str, Union[List[StrictFloat], List[StrictInt], List[StrictBool], List[StrictStr]]] = Field(
77 default_factory=dict
78 )
79 metadata: Dict[str, "TaskMetadata"] = Field(default_factory=dict)
81 @classmethod
82 def from_dict(cls, d: Mapping[str, Any]) -> "TaskMetadata":
83 """Create a TaskMetadata from a dictionary.
85 Parameters
86 ----------
87 d : `Mapping`
88 Mapping to convert. Can be hierarchical. Any dictionaries
89 in the hierarchy are converted to `TaskMetadata`.
91 Returns
92 -------
93 meta : `TaskMetadata`
94 Newly-constructed metadata.
95 """
96 metadata = cls()
97 for k, v in d.items():
98 metadata[k] = v
99 return metadata
101 @classmethod
102 def from_metadata(cls, ps: PropertySetLike) -> "TaskMetadata":
103 """Create a TaskMetadata from a PropertySet-like object.
105 Parameters
106 ----------
107 ps : `PropertySetLike` or `TaskMetadata`
108 A ``PropertySet``-like object to be transformed to a
109 `TaskMetadata`. A `TaskMetadata` can be copied using this
110 class method.
112 Returns
113 -------
114 tm : `TaskMetadata`
115 Newly-constructed metadata.
117 Notes
118 -----
119 Items stored in single-element arrays in the supplied object
120 will be converted to scalars in the newly-created object.
121 """
122 # Use hierarchical names to assign values from input to output.
123 # This API exists for both PropertySet and TaskMetadata.
124 # from_dict() does not work because PropertySet is not declared
125 # to be a Mapping.
126 # PropertySet.toDict() is not present in TaskMetadata so is best
127 # avoided.
128 metadata = cls()
129 for key in sorted(ps.paramNames(topLevelOnly=False)):
130 value = ps.getArray(key)
131 if len(value) == 1:
132 value = value[0]
133 metadata[key] = value
134 return metadata
136 def to_dict(self) -> Dict[str, Any]:
137 """Convert the class to a simple dictionary.
139 Returns
140 -------
141 d : `dict`
142 Simple dictionary that can contain scalar values, array values
143 or other dictionary values.
145 Notes
146 -----
147 Unlike `dict()`, this method hides the model layout and combines
148 scalars, arrays, and other metadata in the same dictionary. Can be
149 used when a simple dictionary is needed. Use
150 `TaskMetadata.from_dict()` to convert it back.
151 """
152 d: Dict[str, Any] = {}
153 d.update(self.scalars)
154 d.update(self.arrays)
155 for k, v in self.metadata.items():
156 d[k] = v.to_dict()
157 return d
159 def add(self, name: str, value: Any) -> None:
160 """Store a new value, adding to a list if one already exists.
162 Parameters
163 ----------
164 name : `str`
165 Name of the metadata property.
166 value
167 Metadata property value.
168 """
169 keys = self._getKeys(name)
170 key0 = keys.pop(0)
171 if len(keys) == 0:
172 # If add() is being used, always store the value in the arrays
173 # property as a list. It's likely there will be another call.
174 slot_type, value = self._validate_value(value)
175 if slot_type == "array":
176 pass
177 elif slot_type == "scalar":
178 value = [value]
179 else:
180 raise ValueError("add() can only be used for primitive types or sequences of those types.")
182 if key0 in self.metadata:
183 raise ValueError(f"Can not add() to key '{name}' since that is a TaskMetadata")
185 if key0 in self.scalars:
186 # Convert scalar to array.
187 # MyPy should be able to figure out that List[Union[T1, T2]] is
188 # compatible with Union[List[T1], List[T2]] if the list has
189 # only one element, but it can't.
190 self.arrays[key0] = [self.scalars.pop(key0)] # type: ignore
192 if key0 in self.arrays:
193 # Check that the type is not changing.
194 if (curtype := type(self.arrays[key0][0])) is not (newtype := type(value[0])):
195 raise ValueError(f"Type mismatch in add() -- currently {curtype} but adding {newtype}")
196 self.arrays[key0].extend(value)
197 else:
198 self.arrays[key0] = value
200 return
202 self.metadata[key0].add(".".join(keys), value)
204 @deprecated(
205 reason="Cast the return value to float explicitly. " + _DEPRECATION_REASON,
206 version=_DEPRECATION_VERSION,
207 category=FutureWarning,
208 )
209 def getAsDouble(self, key: str) -> float:
210 """Return the value cast to a `float`.
212 Parameters
213 ----------
214 key : `str`
215 Item to return. Can be dot-separated hierarchical.
217 Returns
218 -------
219 value : `float`
220 The value cast to a `float`.
222 Raises
223 ------
224 KeyError
225 Raised if the item is not found.
226 """
227 return float(self.__getitem__(key))
229 def getScalar(self, key: str) -> Union[str, int, float, bool]:
230 """Retrieve a scalar item even if the item is a list.
232 Parameters
233 ----------
234 key : `str`
235 Item to retrieve.
237 Returns
238 -------
239 value : `str`, `int`, `float`, or `bool`
240 Either the value associated with the key or, if the key
241 corresponds to a list, the last item in the list.
243 Raises
244 ------
245 KeyError
246 Raised if the item is not found.
247 """
248 # Used in pipe_tasks.
249 # getScalar() is the default behavior for __getitem__.
250 return self[key]
252 def getArray(self, key: str) -> List[Any]:
253 """Retrieve an item as a list even if it is a scalar.
255 Parameters
256 ----------
257 key : `str`
258 Item to retrieve.
260 Returns
261 -------
262 values : `list` of any
263 A list containing the value or values associated with this item.
265 Raises
266 ------
267 KeyError
268 Raised if the item is not found.
269 """
270 keys = self._getKeys(key)
271 key0 = keys.pop(0)
272 if len(keys) == 0:
273 if key0 in self.arrays:
274 return self.arrays[key0]
275 elif key0 in self.scalars:
276 return [self.scalars[key0]]
277 elif key0 in self.metadata:
278 return [self.metadata[key0]]
279 raise KeyError(f"'{key}' not found")
281 try:
282 return self.metadata[key0].getArray(".".join(keys))
283 except KeyError:
284 # Report the correct key.
285 raise KeyError(f"'{key}' not found") from None
287 def names(self, topLevelOnly: bool = True) -> Set[str]:
288 """Return the hierarchical keys from the metadata.
290 Parameters
291 ----------
292 topLevelOnly : `bool`
293 If true, return top-level keys, otherwise full metadata item keys.
295 Returns
296 -------
297 names : `collection.abc.Set`
298 A set of top-level keys or full metadata item keys, including
299 the top-level keys.
301 Notes
302 -----
303 Should never be called in new code with ``topLevelOnly`` set to `True`
304 -- this is equivalent to asking for the keys and is the default
305 when iterating through the task metadata. In this case a deprecation
306 message will be issued and the ability will raise an exception
307 in a future release.
309 When ``topLevelOnly`` is `False` all keys, including those from the
310 hierarchy and the top-level hierarchy, are returned.
311 """
312 if topLevelOnly:
313 warnings.warn("Use keys() instead. " + _DEPRECATION_REASON, FutureWarning)
314 return set(self.keys())
315 else:
316 names = set()
317 for k, v in self.items():
318 names.add(k) # Always include the current level
319 if isinstance(v, TaskMetadata):
320 names.update({k + "." + item for item in v.names(topLevelOnly=topLevelOnly)})
321 return names
323 def paramNames(self, topLevelOnly: bool) -> Set[str]:
324 """Return hierarchical names.
326 Parameters
327 ----------
328 topLevelOnly : `bool`
329 Control whether only top-level items are returned or items
330 from the hierarchy.
332 Returns
333 -------
334 paramNames : `set` of `str`
335 If ``topLevelOnly`` is `True`, returns any keys that are not
336 part of a hierarchy. If `False` also returns fully-qualified
337 names from the hierarchy. Keys associated with the top
338 of a hierarchy are never returned.
339 """
340 # Currently used by the verify package.
341 paramNames = set()
342 for k, v in self.items():
343 if isinstance(v, TaskMetadata):
344 if not topLevelOnly:
345 paramNames.update({k + "." + item for item in v.paramNames(topLevelOnly=topLevelOnly)})
346 else:
347 paramNames.add(k)
348 return paramNames
350 @deprecated(
351 reason="Use standard assignment syntax. " + _DEPRECATION_REASON,
352 version=_DEPRECATION_VERSION,
353 category=FutureWarning,
354 )
355 def set(self, key: str, item: Any) -> None:
356 """Set the value of the supplied key."""
357 self.__setitem__(key, item)
359 @deprecated(
360 reason="Use standard del dict syntax. " + _DEPRECATION_REASON,
361 version=_DEPRECATION_VERSION,
362 category=FutureWarning,
363 )
364 def remove(self, key: str) -> None:
365 """Remove the item without raising if absent."""
366 try:
367 self.__delitem__(key)
368 except KeyError:
369 # The PropertySet.remove() should always work.
370 pass
372 @staticmethod
373 def _getKeys(key: str) -> List[str]:
374 """Return the key hierarchy.
376 Parameters
377 ----------
378 key : `str`
379 The key to analyze. Can be dot-separated.
381 Returns
382 -------
383 keys : `list` of `str`
384 The key hierarchy that has been split on ``.``.
386 Raises
387 ------
388 KeyError
389 Raised if the key is not a string.
390 """
391 try:
392 keys = key.split(".")
393 except Exception:
394 raise KeyError(f"Invalid key '{key}': only string keys are allowed") from None
395 return keys
397 def keys(self) -> Tuple[str, ...]:
398 """Return the top-level keys."""
399 return tuple(k for k in self)
401 def items(self) -> Iterator[Tuple[str, Any]]:
402 """Yield the top-level keys and values."""
403 for k, v in itertools.chain(self.scalars.items(), self.arrays.items(), self.metadata.items()):
404 yield (k, v)
406 def __len__(self) -> int:
407 """Return the number of items."""
408 return len(self.scalars) + len(self.arrays) + len(self.metadata)
410 # This is actually a Liskov substitution violation, because
411 # pydantic.BaseModel says __iter__ should return something else. But the
412 # pydantic docs say to do exactly this to in order to make a mapping-like
413 # BaseModel, so that's what we do.
414 def __iter__(self) -> Iterator[str]: # type: ignore
415 """Return an iterator over each key."""
416 # The order of keys is not preserved since items can move
417 # from scalar to array.
418 return itertools.chain(iter(self.scalars), iter(self.arrays), iter(self.metadata))
420 def __getitem__(self, key: str) -> Any:
421 """Retrieve the item associated with the key.
423 Parameters
424 ----------
425 key : `str`
426 The key to retrieve. Can be dot-separated hierarchical.
428 Returns
429 -------
430 value : `TaskMetadata`, `float`, `int`, `bool`, `str`
431 A scalar value. For compatibility with ``PropertySet``, if the key
432 refers to an array, the final element is returned and not the
433 array itself.
435 Raises
436 ------
437 KeyError
438 Raised if the item is not found.
439 """
440 keys = self._getKeys(key)
441 key0 = keys.pop(0)
442 if len(keys) == 0:
443 if key0 in self.scalars:
444 return self.scalars[key0]
445 if key0 in self.metadata:
446 return self.metadata[key0]
447 if key0 in self.arrays:
448 return self.arrays[key0][-1]
449 raise KeyError(f"'{key}' not found")
450 # Hierarchical lookup so the top key can only be in the metadata
451 # property. Trap KeyError and reraise so that the correct key
452 # in the hierarchy is reported.
453 try:
454 # And forward request to that metadata.
455 return self.metadata[key0][".".join(keys)]
456 except KeyError:
457 raise KeyError(f"'{key}' not found") from None
459 def get(self, key: str, default: Any = None) -> Any:
460 """Retrieve the item associated with the key or a default.
462 Parameters
463 ----------
464 key : `str`
465 The key to retrieve. Can be dot-separated hierarchical.
466 default
467 The value to return if the key doesnot exist.
469 Returns
470 -------
471 value : `TaskMetadata`, `float`, `int`, `bool`, `str`
472 A scalar value. If the key refers to an array, the final element
473 is returned and not the array itself; this is consistent with
474 `__getitem__` and `PropertySet.get`, but not ``to_dict().get``.
475 """
476 try:
477 return self[key]
478 except KeyError:
479 return default
481 def __setitem__(self, key: str, item: Any) -> None:
482 """Store the given item."""
483 keys = self._getKeys(key)
484 key0 = keys.pop(0)
485 if len(keys) == 0:
486 slots: Dict[str, Dict[str, Any]] = {
487 "array": self.arrays,
488 "scalar": self.scalars,
489 "metadata": self.metadata,
490 }
491 primary: Optional[Dict[str, Any]] = None
492 slot_type, item = self._validate_value(item)
493 primary = slots.pop(slot_type, None)
494 if primary is None:
495 raise AssertionError(f"Unknown slot type returned from validator: {slot_type}")
497 # Assign the value to the right place.
498 primary[key0] = item
499 for property in slots.values():
500 # Remove any other entries.
501 property.pop(key0, None)
502 return
504 # This must be hierarchical so forward to the child TaskMetadata.
505 if key0 not in self.metadata:
506 self.metadata[key0] = TaskMetadata()
507 self.metadata[key0][".".join(keys)] = item
509 # Ensure we have cleared out anything with the same name elsewhere.
510 self.scalars.pop(key0, None)
511 self.arrays.pop(key0, None)
513 def __contains__(self, key: str) -> bool:
514 """Determine if the key exists."""
515 keys = self._getKeys(key)
516 key0 = keys.pop(0)
517 if len(keys) == 0:
518 return key0 in self.scalars or key0 in self.arrays or key0 in self.metadata
520 if key0 in self.metadata:
521 return ".".join(keys) in self.metadata[key0]
522 return False
524 def __delitem__(self, key: str) -> None:
525 """Remove the specified item.
527 Raises
528 ------
529 KeyError
530 Raised if the item is not present.
531 """
532 keys = self._getKeys(key)
533 key0 = keys.pop(0)
534 if len(keys) == 0:
535 # MyPy can't figure out that this way to combine the types in the
536 # tuple is the one that matters, and annotating a local variable
537 # helps it out.
538 properties: Tuple[Dict[str, Any], ...] = (self.scalars, self.arrays, self.metadata)
539 for property in properties:
540 if key0 in property:
541 del property[key0]
542 return
543 raise KeyError(f"'{key}' not found'")
545 try:
546 del self.metadata[key0][".".join(keys)]
547 except KeyError:
548 # Report the correct key.
549 raise KeyError(f"'{key}' not found'") from None
551 def _validate_value(self, value: Any) -> Tuple[str, Any]:
552 """Validate the given value.
554 Parameters
555 ----------
556 value : Any
557 Value to check.
559 Returns
560 -------
561 slot_type : `str`
562 The type of value given. Options are "scalar", "array", "metadata".
563 item : Any
564 The item that was given but possibly modified to conform to
565 the slot type.
567 Raises
568 ------
569 ValueError
570 Raised if the value is not a recognized type.
571 """
572 # Test the simplest option first.
573 value_type = type(value)
574 if value_type in _ALLOWED_PRIMITIVE_TYPES:
575 return "scalar", value
577 if isinstance(value, TaskMetadata):
578 return "metadata", value
579 if isinstance(value, Mapping):
580 return "metadata", self.from_dict(value)
582 if _isListLike(value):
583 # For model consistency, need to check that every item in the
584 # list has the same type.
585 value = list(value)
587 type0 = type(value[0])
588 for i in value:
589 if type(i) != type0:
590 raise ValueError(
591 "Type mismatch in supplied list. TaskMetadata requires all"
592 f" elements have same type but see {type(i)} and {type0}."
593 )
595 if type0 not in _ALLOWED_PRIMITIVE_TYPES:
596 # Must check to see if we got numpy floats or something.
597 type_cast: type
598 if isinstance(value[0], numbers.Integral):
599 type_cast = int
600 elif isinstance(value[0], numbers.Real):
601 type_cast = float
602 else:
603 raise ValueError(
604 f"Supplied list has element of type '{type0}'. "
605 "TaskMetadata can only accept primitive types in lists."
606 )
608 value = [type_cast(v) for v in value]
610 return "array", value
612 # Sometimes a numpy number is given.
613 if isinstance(value, numbers.Integral):
614 value = int(value)
615 return "scalar", value
616 if isinstance(value, numbers.Real):
617 value = float(value)
618 return "scalar", value
620 raise ValueError(f"TaskMetadata does not support values of type {value!r}.")
623# Needed because a TaskMetadata can contain a TaskMetadata.
624TaskMetadata.update_forward_refs()