21 from __future__
import annotations
23 """Module defining GraphBuilder class and related methods.
26 __all__ = [
'GraphBuilder']
32 from collections
import ChainMap
33 from dataclasses
import dataclass
34 from typing
import Dict, Iterable, Iterator, List
40 from .connections
import iterConnections
41 from .pipeline
import PipelineDatasetTypes, TaskDatasetTypes, TaskDef, Pipeline
42 from .graph
import QuantumGraph, QuantumGraphTaskNodes
43 from lsst.daf.butler
import (
49 ExpandedDataCoordinate,
58 _LOG = logging.getLogger(__name__.partition(
".")[2])
61 class _DatasetDict(NamedKeyDict[DatasetType, Dict[DataCoordinate, DatasetRef]]):
62 """A custom dictionary that maps `DatasetType` to a nested dictionary of
63 the known `DatasetRef` instances of that type.
68 Positional arguments are forwarded to the `dict` constructor.
69 universe : `DimensionUniverse`
70 Universe of all possible dimensions.
72 def __init__(self, *args, universe: DimensionGraph):
78 universe: DimensionUniverse) -> _DatasetDict:
79 """Construct a dictionary from a flat iterable of `DatasetType` keys.
83 datasetTypes : `iterable` of `DatasetType`
84 DatasetTypes to use as keys for the dict. Values will be empty
86 universe : `DimensionUniverse`
87 Universe of all possible dimensions.
91 dictionary : `_DatasetDict`
92 A new `_DatasetDict` instance.
94 return cls({datasetType: {}
for datasetType
in datasetTypes}, universe=universe)
97 def fromSubset(cls, datasetTypes: Iterable[DatasetType], first: _DatasetDict, *rest: _DatasetDict
99 """Return a new dictionary by extracting items corresponding to the
100 given keys from one or more existing dictionaries.
104 datasetTypes : `iterable` of `DatasetType`
105 DatasetTypes to use as keys for the dict. Values will be obtained
106 by lookups against ``first`` and ``rest``.
107 first : `_DatasetDict`
108 Another dictionary from which to extract values.
110 Additional dictionaries from which to extract values.
114 dictionary : `_DatasetDict`
115 A new dictionary instance.
117 combined = ChainMap(first, *rest)
118 return cls({datasetType: combined[datasetType]
for datasetType
in datasetTypes},
119 universe=first.universe)
123 """The union of all dimensions used by all dataset types in this
124 dictionary, including implied dependencies (`DimensionGraph`).
129 return base.union(*[datasetType.dimensions
for datasetType
in self.keys()])
132 """Unpack nested single-element `DatasetRef` dicts into a new
133 mapping with `DatasetType` keys and `DatasetRef` values.
135 This method assumes that each nest contains exactly one item, as is the
136 case for all "init" datasets.
140 dictionary : `NamedKeyDict`
141 Dictionary mapping `DatasetType` to `DatasetRef`, with both
142 `DatasetType` instances and string names usable as keys.
144 def getOne(refs: Dict[DataCoordinate, DatasetRef]) -> DatasetRef:
147 return NamedKeyDict({datasetType: getOne(refs)
for datasetType, refs
in self.items()})
150 """Unpack nested multi-element `DatasetRef` dicts into a new
151 mapping with `DatasetType` keys and `set` of `DatasetRef` values.
155 dictionary : `NamedKeyDict`
156 Dictionary mapping `DatasetType` to `DatasetRef`, with both
157 `DatasetType` instances and string names usable as keys.
159 return NamedKeyDict({datasetType:
list(refs.values())
for datasetType, refs
in self.items()})
161 def extract(self, datasetType: DatasetType, dataIds: Iterable[DataCoordinate]
162 ) -> Iterator[DatasetRef]:
163 """Iterate over the contained `DatasetRef` instances that match the
164 given `DatasetType` and data IDs.
168 datasetType : `DatasetType`
169 Dataset type to match.
170 dataIds : `Iterable` [ `DataCoordinate` ]
175 refs : `Iterator` [ `DatasetRef` ]
176 DatasetRef instances for which ``ref.datasetType == datasetType``
177 and ``ref.dataId`` is in ``dataIds``.
179 refs = self[datasetType]
180 return (refs[dataId]
for dataId
in dataIds)
184 """Helper class aggregating information about a `Quantum`, used when
185 constructing a `QuantumGraph`.
187 See `_PipelineScaffolding` for a top-down description of the full
188 scaffolding data structure.
192 task : _TaskScaffolding
193 Back-reference to the helper object for the `PipelineTask` this quantum
194 represents an execution of.
195 dataId : `DataCoordinate`
196 Data ID for this quantum.
198 def __init__(self, task: _TaskScaffolding, dataId: DataCoordinate):
201 self.
inputs = _DatasetDict.fromDatasetTypes(task.inputs.keys(), universe=dataId.universe)
202 self.
outputs = _DatasetDict.fromDatasetTypes(task.outputs.keys(), universe=dataId.universe)
203 self.
prerequisites = _DatasetDict.fromDatasetTypes(task.prerequisites.keys(),
204 universe=dataId.universe)
206 __slots__ = (
"task",
"dataId",
"inputs",
"outputs",
"prerequisites")
209 return f
"_QuantumScaffolding(taskDef={self.taskDef}, dataId={self.dataId}, ...)"
211 task: _TaskScaffolding
212 """Back-reference to the helper object for the `PipelineTask` this quantum
213 represents an execution of.
216 dataId: DataCoordinate
217 """Data ID for this quantum.
221 """Nested dictionary containing `DatasetRef` inputs to this quantum.
223 This is initialized to map each `DatasetType` to an empty dictionary at
224 construction. Those nested dictionaries are populated (with data IDs as
225 keys) with unresolved `DatasetRef` instances in
226 `_PipelineScaffolding.connectDataIds`.
229 outputs: _DatasetDict
230 """Nested dictionary containing `DatasetRef` outputs this quantum.
233 prerequisites: _DatasetDict
234 """Nested dictionary containing `DatasetRef` prerequisite inputs to this
239 """Transform the scaffolding object into a true `Quantum` instance.
244 An actual `Quantum` instance.
246 allInputs = self.
inputs.unpackMultiRefs()
250 config = self.
task.taskDef.config
251 connections = config.connections.ConnectionsClass(config=config)
254 allInputs = connections.adjustQuantum(allInputs)
256 taskName=self.
task.taskDef.taskName,
257 taskClass=self.
task.taskDef.taskClass,
259 initInputs=self.
task.initInputs.unpackSingleRefs(),
260 predictedInputs=allInputs,
261 outputs=self.
outputs.unpackMultiRefs(),
267 """Helper class aggregating information about a `PipelineTask`, used when
268 constructing a `QuantumGraph`.
270 See `_PipelineScaffolding` for a top-down description of the full
271 scaffolding data structure.
276 Data structure that identifies the task class and its config.
277 parent : `_PipelineScaffolding`
278 The parent data structure that will hold the instance being
280 datasetTypes : `TaskDatasetTypes`
281 Data structure that categorizes the dataset types used by this task.
283 def __init__(self, taskDef: TaskDef, parent: _PipelineScaffolding, datasetTypes: TaskDatasetTypes):
284 universe = parent.dimensions.universe
286 self.
dimensions = DimensionGraph(universe, names=taskDef.connections.dimensions)
287 assert self.
dimensions.issubset(parent.dimensions)
290 self.
initInputs = _DatasetDict.fromSubset(datasetTypes.initInputs, parent.initInputs,
291 parent.initIntermediates)
292 self.
initOutputs = _DatasetDict.fromSubset(datasetTypes.initOutputs, parent.initIntermediates,
294 self.
inputs = _DatasetDict.fromSubset(datasetTypes.inputs, parent.inputs, parent.intermediates)
295 self.
outputs = _DatasetDict.fromSubset(datasetTypes.outputs, parent.intermediates, parent.outputs)
296 self.
prerequisites = _DatasetDict.fromSubset(datasetTypes.prerequisites, parent.prerequisites)
303 return f
"_TaskScaffolding(taskDef={self.taskDef}, ...)"
306 """Data structure that identifies the task class and its config
310 dimensions: DimensionGraph
311 """The dimensions of a single `Quantum` of this task (`DimensionGraph`).
314 initInputs: _DatasetDict
315 """Dictionary containing information about datasets used to construct this
316 task (`_DatasetDict`).
319 initOutputs: _DatasetDict
320 """Dictionary containing information about datasets produced as a
321 side-effect of constructing this task (`_DatasetDict`).
325 """Dictionary containing information about datasets used as regular,
326 graph-constraining inputs to this task (`_DatasetDict`).
329 outputs: _DatasetDict
330 """Dictionary containing information about datasets produced by this task
334 prerequisites: _DatasetDict
335 """Dictionary containing information about input datasets that must be
336 present in the repository before any Pipeline containing this task is run
340 quanta: Dict[DataCoordinate, _QuantumScaffolding]
341 """Dictionary mapping data ID to a scaffolding object for the Quantum of
342 this task with that data ID.
346 """Create a `QuantumGraphTaskNodes` instance from the information in
351 nodes : `QuantumGraphTaskNodes`
352 The `QuantumGraph` elements corresponding to this task.
356 quanta=[q.makeQuantum()
for q
in self.
quanta.values()],
357 initInputs=self.
initInputs.unpackSingleRefs(),
364 """A helper data structure that organizes the information involved in
365 constructing a `QuantumGraph` for a `Pipeline`.
369 pipeline : `Pipeline`
370 Sequence of tasks from which a graph is to be constructed. Must
371 have nested task classes already imported.
372 universe : `DimensionUniverse`
373 Universe of all possible dimensions.
377 The scaffolding data structure contains nested data structures for both
378 tasks (`_TaskScaffolding`) and datasets (`_DatasetDict`). The dataset
379 data structures are shared between the pipeline-level structure (which
380 aggregates all datasets and categorizes them from the perspective of the
381 complete pipeline) and the individual tasks that use them as inputs and
384 `QuantumGraph` construction proceeds in four steps, with each corresponding
385 to a different `_PipelineScaffolding` method:
387 1. When `_PipelineScaffolding` is constructed, we extract and categorize
388 the DatasetTypes used by the pipeline (delegating to
389 `PipelineDatasetTypes.fromPipeline`), then use these to construct the
390 nested `_TaskScaffolding` and `_DatasetDict` objects.
392 2. In `connectDataIds`, we construct and run the "Big Join Query", which
393 returns related tuples of all dimensions used to identify any regular
394 input, output, and intermediate datasets (not prerequisites). We then
395 iterate over these tuples of related dimensions, identifying the subsets
396 that correspond to distinct data IDs for each task and dataset type,
397 and then create `_QuantumScaffolding` objects.
399 3. In `resolveDatasetRefs`, we run follow-up queries against all of the
400 dataset data IDs previously identified, transforming unresolved
401 DatasetRefs into resolved DatasetRefs where appropriate. We then look
402 up prerequisite datasets for all quanta.
404 4. In `makeQuantumGraph`, we construct a `QuantumGraph` from the lists of
405 per-task `_QuantumScaffolding` objects.
408 _LOG.debug(
"Initializing data structures for QuantumGraph generation.")
411 datasetTypes = PipelineDatasetTypes.fromPipeline(pipeline, registry=registry)
414 for attr
in (
"initInputs",
"initIntermediates",
"initOutputs",
415 "inputs",
"intermediates",
"outputs",
"prerequisites"):
416 setattr(self, attr, _DatasetDict.fromDatasetTypes(getattr(datasetTypes, attr),
417 universe=registry.dimensions))
420 self.
dimensions = self.inputs.dimensions.union(self.intermediates.dimensions,
421 self.outputs.dimensions)
426 if isinstance(pipeline, Pipeline):
427 pipeline = pipeline.toExpandedPipeline()
429 for taskDef, taskDatasetTypes
in zip(pipeline,
430 datasetTypes.byTask.values())]
435 return f
"_PipelineScaffolding(tasks={self.tasks}, ...)"
437 tasks: List[_TaskScaffolding]
438 """Scaffolding data structures for each task in the pipeline
439 (`list` of `_TaskScaffolding`).
442 initInputs: _DatasetDict
443 """Datasets consumed but not produced when constructing the tasks in this
444 pipeline (`_DatasetDict`).
447 initIntermediates: _DatasetDict
448 """Datasets that are both consumed and produced when constructing the tasks
449 in this pipeline (`_DatasetDict`).
452 initOutputs: _DatasetDict
453 """Datasets produced but not consumed when constructing the tasks in this
454 pipeline (`_DatasetDict`).
458 """Datasets that are consumed but not produced when running this pipeline
462 intermediates: _DatasetDict
463 """Datasets that are both produced and consumed when running this pipeline
467 outputs: _DatasetDict
468 """Datasets produced but not consumed when when running this pipeline
472 prerequisites: _DatasetDict
473 """Datasets that are consumed when running this pipeline and looked up
474 per-Quantum when generating the graph (`_DatasetDict`).
477 dimensions: DimensionGraph
478 """All dimensions used by any regular input, intermediate, or output
479 (not prerequisite) dataset; the set of dimension used in the "Big Join
480 Query" (`DimensionGraph`).
482 This is required to be a superset of all task quantum dimensions.
486 """Query for the data IDs that connect nodes in the `QuantumGraph`.
488 This method populates `_TaskScaffolding.dataIds` and
489 `_DatasetScaffolding.dataIds` (except for those in `prerequisites`).
493 registry : `lsst.daf.butler.Registry`
494 Registry for the data repository; used for all data ID queries.
495 collections : `lsst.daf.butler.CollectionSearch`
496 Object representing the collections to search for input datasets.
497 userQuery : `str`, optional
498 User-provided expression to limit the data IDs processed.
500 _LOG.debug(
"Building query for data IDs.")
502 emptyDataId = ExpandedDataCoordinate(registry.dimensions.empty, (), records={})
503 for datasetType, refs
in itertools.chain(self.initInputs.
items(),
504 self.initIntermediates.
items(),
505 self.initOutputs.
items()):
506 refs[emptyDataId] = DatasetRef(datasetType, emptyDataId)
511 _LOG.debug(
"Submitting data ID query and processing results.")
512 resultIter = registry.queryDimensions(
514 datasets=
list(self.inputs),
515 collections=collections,
520 for n, commonDataId
in enumerate(resultIter):
526 for datasetType, refs
in itertools.chain(self.inputs.
items(), self.intermediates.
items(),
527 self.outputs.
items()):
528 datasetDataId = commonDataId.subset(datasetType.dimensions)
529 ref = refs.get(datasetDataId)
531 ref = DatasetRef(datasetType, datasetDataId)
532 refs[datasetDataId] = ref
533 refsForRow[datasetType.name] = ref
536 for task
in self.
tasks:
537 quantumDataId = commonDataId.subset(task.dimensions)
538 quantum = task.quanta.get(quantumDataId)
541 task.quanta[quantumDataId] = quantum
550 for datasetType
in task.inputs:
551 ref = refsForRow[datasetType.name]
552 quantum.inputs[datasetType.name][ref.dataId] = ref
553 for datasetType
in task.outputs:
554 ref = refsForRow[datasetType.name]
555 quantum.outputs[datasetType.name][ref.dataId] = ref
556 _LOG.debug(
"Finished processing %d rows from data ID query.", n)
559 """Perform follow up queries for each dataset data ID produced in
562 This method populates `_DatasetScaffolding.refs` (except for those in
567 registry : `lsst.daf.butler.Registry`
568 Registry for the data repository; used for all data ID queries.
569 collections : `lsst.daf.butler.CollectionSearch`
570 Object representing the collections to search for input datasets.
571 run : `str`, optional
572 Name of the `~lsst.daf.butler.CollectionType.RUN` collection for
573 output datasets, if it already exists.
574 skipExisting : `bool`, optional
575 If `True` (default), a Quantum is not created if all its outputs
576 already exist in ``run``. Ignored if ``run`` is `None`.
581 Raised if an output dataset already exists in the output run
582 and ``skipExisting`` is `False`. The case where some but not all
583 of a quantum's outputs are present and ``skipExisting`` is `True`
584 cannot be identified at this stage, and is handled by `fillQuanta`
590 for datasetType, refs
in itertools.chain(self.initIntermediates.
items(),
591 self.initOutputs.
items(),
592 self.intermediates.
items(),
593 self.outputs.
items()):
594 _LOG.debug(
"Resolving %d datasets for intermediate and/or output dataset %s.",
595 len(refs), datasetType.name)
596 for dataId, unresolvedRef
in refs.items():
601 ref = registry.findDataset(datasetType=datasetType, dataId=dataId, collections=run)
607 f
"output RUN collection '{run}' with data ID {dataId}.")
609 for datasetType, refs
in itertools.chain(self.initInputs.
items(), self.inputs.
items()):
610 _LOG.debug(
"Resolving %d datasets for input dataset %s.", len(refs), datasetType.name)
612 refs[dataId] = registry.findDataset(datasetType, dataId=dataId, collections=collections)
613 if any(ref
is None for ref
in refs.values()):
615 f
"One or more dataset of type '{datasetType.name}' was "
616 f
"present in a previous query, but could not be found now."
617 f
"This is either a logic bug in QuantumGraph generation, "
618 f
"or the input collections have been modified since "
619 f
"QuantumGraph generation began."
623 for task
in self.
tasks:
625 "Applying resolutions and finding prerequisites for %d quanta of task with label '%s'.",
630 c.name: c.lookupFunction
631 for c
in iterConnections(task.taskDef.connections,
"prerequisiteInputs")
632 if c.lookupFunction
is not None
635 for quantum
in task.quanta.values():
642 if run
is not None and skipExisting:
645 for datasetType, originalRefs
in quantum.outputs.items():
646 for ref
in task.outputs.extract(datasetType, originalRefs.keys()):
647 if ref.id
is not None:
648 resolvedRefs.append(ref)
650 unresolvedRefs.append(ref)
654 f
"Quantum {quantum.dataId} of task with label "
655 f
"'{quantum.taskDef.label}' has some outputs that exist ({resolvedRefs}) "
656 f
"and others that don't ({unresolvedRefs})."
661 dataIdsToSkip.append(quantum.dataId)
665 for datasetType, refs
in quantum.inputs.items():
666 for ref
in task.inputs.extract(datasetType, refs.keys()):
667 refs[ref.dataId] = ref
676 for datasetType
in task.prerequisites:
677 lookupFunction = lookupFunctions.get(datasetType.name)
678 if lookupFunction
is not None:
680 lookupFunction(datasetType, registry, quantum.dataId, collections)
684 registry.queryDatasets(
686 collections=collections,
687 dataId=quantum.dataId,
692 quantum.prerequisites[datasetType].update({ref.dataId: ref
for ref
in refs})
695 _LOG.debug(
"Pruning %d quanta for task with label '%s' because all of their outputs exist.",
696 len(dataIdsToSkip), task.taskDef.label)
697 for dataId
in dataIdsToSkip:
698 del task.quanta[dataId]
701 """Create a `QuantumGraph` from the quanta already present in
702 the scaffolding data structure.
706 graph : `QuantumGraph`
707 The full `QuantumGraph`.
710 graph.initInputs = self.initInputs.unpackSingleRefs()
711 graph.initOutputs = self.initOutputs.unpackSingleRefs()
712 graph.initIntermediates = self.initIntermediates.unpackSingleRefs()
722 """Base class for exceptions generated by graph builder.
727 class OutputExistsError(GraphBuilderError):
728 """Exception generated when output datasets already exist.
734 """Exception generated when a prerequisite dataset does not exist.
740 """GraphBuilder class is responsible for building task execution graph from
745 registry : `~lsst.daf.butler.Registry`
746 Data butler instance.
747 skipExisting : `bool`, optional
748 If `True` (default), a Quantum is not created if all its outputs
757 def makeGraph(self, pipeline, collections, run, userQuery):
758 """Create execution graph for a pipeline.
762 pipeline : `Pipeline`
763 Pipeline definition, task names/classes and their configs.
764 collections : `lsst.daf.butler.CollectionSearch`
765 Object representing the collections to search for input datasets.
766 run : `str`, optional
767 Name of the `~lsst.daf.butler.CollectionType.RUN` collection for
768 output datasets, if it already exists.
770 String which defunes user-defined selection for registry, should be
771 empty or `None` if there is no restrictions on data selection.
775 graph : `QuantumGraph`
780 Raised when user expression cannot be parsed.
782 Raised when output datasets already exist.
784 Other exceptions types may be raised by underlying registry
788 scaffolding.connectDataIds(self.
registry, collections, userQuery)
790 return scaffolding.makeQuantumGraph()