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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# (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
22import warnings
24__all__ = ("QuantumGraph", "IncompatibleGraphError")
26from collections import defaultdict, deque
28from itertools import chain, count
29import io
30import json
31import networkx as nx
32from networkx.drawing.nx_agraph import write_dot
33import os
34import pickle
35import lzma
36import copy
37import struct
38import time
39from types import MappingProxyType
40from typing import (Any, DefaultDict, Dict, FrozenSet, Iterable, List, Mapping, Set, Generator, Optional,
41 Tuple, Union, TypeVar)
43from ..connections import iterConnections
44from ..pipeline import TaskDef
45from lsst.daf.butler import Quantum, DatasetRef, ButlerURI, DimensionUniverse
47from ._implDetails import _DatasetTracker, DatasetTypeName
48from .quantumNode import QuantumNode, NodeId, BuildId
49from ._loadHelpers import LoadHelper
52_T = TypeVar("_T", bound="QuantumGraph")
54# modify this constant any time the on disk representation of the save file
55# changes, and update the load helpers to behave properly for each version.
56SAVE_VERSION = 2
58# Strings used to describe the format for the preamble bytes in a file save
59# The base is a big endian encoded unsigned short that is used to hold the
60# file format version. This allows reading version bytes and determine which
61# loading code should be used for the rest of the file
62STRUCT_FMT_BASE = '>H'
63#
64# Version 1
65# This marks a big endian encoded format with an unsigned short, an unsigned
66# long long, and an unsigned long long in the byte stream
67# Version 2
68# A big endian encoded format with an unsigned long long byte stream used to
69# indicate the total length of the entire header
70STRUCT_FMT_STRING = {
71 1: '>QQ',
72 2: '>Q'
73}
76# magic bytes that help determine this is a graph save
77MAGIC_BYTES = b"qgraph4\xf6\xe8\xa9"
80class IncompatibleGraphError(Exception):
81 """Exception class to indicate that a lookup by NodeId is impossible due
82 to incompatibilities
83 """
84 pass
87class QuantumGraph:
88 """QuantumGraph is a directed acyclic graph of `QuantumNode` objects
90 This data structure represents a concrete workflow generated from a
91 `Pipeline`.
93 Parameters
94 ----------
95 quanta : Mapping of `TaskDef` to sets of `Quantum`
96 This maps tasks (and their configs) to the sets of data they are to
97 process.
98 metadata : Optional Mapping of `str` to primitives
99 This is an optional parameter of extra data to carry with the graph.
100 Entries in this mapping should be able to be serialized in JSON.
101 """
102 def __init__(self, quanta: Mapping[TaskDef, Set[Quantum]],
103 metadata: Optional[Mapping[str, Any]] = None):
104 self._buildGraphs(quanta, metadata=metadata)
106 def _buildGraphs(self,
107 quanta: Mapping[TaskDef, Set[Quantum]],
108 *,
109 _quantumToNodeId: Optional[Mapping[Quantum, NodeId]] = None,
110 _buildId: Optional[BuildId] = None,
111 metadata: Optional[Mapping[str, Any]] = None):
112 """Builds the graph that is used to store the relation between tasks,
113 and the graph that holds the relations between quanta
114 """
115 self._metadata = metadata
116 self._quanta = quanta
117 self._buildId = _buildId if _buildId is not None else BuildId(f"{time.time()}-{os.getpid()}")
118 # Data structures used to identify relations between components;
119 # DatasetTypeName -> TaskDef for task,
120 # and DatasetRef -> QuantumNode for the quanta
121 self._datasetDict = _DatasetTracker[DatasetTypeName, TaskDef]()
122 self._datasetRefDict = _DatasetTracker[DatasetRef, QuantumNode]()
124 nodeNumberGenerator = count()
125 self._nodeIdMap: Dict[NodeId, QuantumNode] = {}
126 self._taskToQuantumNode: DefaultDict[TaskDef, Set[QuantumNode]] = defaultdict(set)
127 self._count = 0
128 for taskDef, quantumSet in self._quanta.items():
129 connections = taskDef.connections
131 # For each type of connection in the task, add a key to the
132 # `_DatasetTracker` for the connections name, with a value of
133 # the TaskDef in the appropriate field
134 for inpt in iterConnections(connections, ("inputs", "prerequisiteInputs", "initInputs")):
135 self._datasetDict.addInput(DatasetTypeName(inpt.name), taskDef)
137 for output in iterConnections(connections, ("outputs", "initOutputs")):
138 self._datasetDict.addOutput(DatasetTypeName(output.name), taskDef)
140 # For each `Quantum` in the set of all `Quantum` for this task,
141 # add a key to the `_DatasetTracker` that is a `DatasetRef` for one
142 # of the individual datasets inside the `Quantum`, with a value of
143 # a newly created QuantumNode to the appropriate input/output
144 # field.
145 self._count += len(quantumSet)
146 for quantum in quantumSet:
147 if _quantumToNodeId:
148 nodeId = _quantumToNodeId.get(quantum)
149 if nodeId is None:
150 raise ValueError("If _quantuMToNodeNumber is not None, all quanta must have an "
151 "associated value in the mapping")
152 else:
153 nodeId = NodeId(next(nodeNumberGenerator), self._buildId)
155 inits = quantum.initInputs.values()
156 inputs = quantum.inputs.values()
157 value = QuantumNode(quantum, taskDef, nodeId)
158 self._taskToQuantumNode[taskDef].add(value)
159 self._nodeIdMap[nodeId] = value
161 for dsRef in chain(inits, inputs):
162 # unfortunately, `Quantum` allows inits to be individual
163 # `DatasetRef`s or an Iterable of such, so there must
164 # be an instance check here
165 if isinstance(dsRef, Iterable):
166 for sub in dsRef:
167 self._datasetRefDict.addInput(sub, value)
168 else:
169 self._datasetRefDict.addInput(dsRef, value)
170 for dsRef in chain.from_iterable(quantum.outputs.values()):
171 self._datasetRefDict.addOutput(dsRef, value)
173 # Graph of task relations, used in various methods
174 self._taskGraph = self._datasetDict.makeNetworkXGraph()
176 # Graph of quanta relations
177 self._connectedQuanta = self._datasetRefDict.makeNetworkXGraph()
179 @property
180 def taskGraph(self) -> nx.DiGraph:
181 """Return a graph representing the relations between the tasks inside
182 the quantum graph.
184 Returns
185 -------
186 taskGraph : `networkx.Digraph`
187 Internal datastructure that holds relations of `TaskDef` objects
188 """
189 return self._taskGraph
191 @property
192 def graph(self) -> nx.DiGraph:
193 """Return a graph representing the relations between all the
194 `QuantumNode` objects. Largely it should be preferred to iterate
195 over, and use methods of this class, but sometimes direct access to
196 the networkx object may be helpful
198 Returns
199 -------
200 graph : `networkx.Digraph`
201 Internal datastructure that holds relations of `QuantumNode`
202 objects
203 """
204 return self._connectedQuanta
206 @property
207 def inputQuanta(self) -> Iterable[QuantumNode]:
208 """Make a `list` of all `QuantumNode` objects that are 'input' nodes
209 to the graph, meaning those nodes to not depend on any other nodes in
210 the graph.
212 Returns
213 -------
214 inputNodes : iterable of `QuantumNode`
215 A list of nodes that are inputs to the graph
216 """
217 return (q for q, n in self._connectedQuanta.in_degree if n == 0)
219 @property
220 def outputQuanta(self) -> Iterable[QuantumNode]:
221 """Make a `list` of all `QuantumNode` objects that are 'output' nodes
222 to the graph, meaning those nodes have no nodes that depend them in
223 the graph.
225 Returns
226 -------
227 outputNodes : iterable of `QuantumNode`
228 A list of nodes that are outputs of the graph
229 """
230 return [q for q, n in self._connectedQuanta.out_degree if n == 0]
232 @property
233 def allDatasetTypes(self) -> Tuple[DatasetTypeName, ...]:
234 """Return all the `DatasetTypeName` objects that are contained inside
235 the graph.
237 Returns
238 -------
239 tuple of `DatasetTypeName`
240 All the data set type names that are present in the graph
241 """
242 return tuple(self._datasetDict.keys())
244 @property
245 def isConnected(self) -> bool:
246 """Return True if all of the nodes in the graph are connected, ignores
247 directionality of connections.
248 """
249 return nx.is_weakly_connected(self._connectedQuanta)
251 def getQuantumNodeByNodeId(self, nodeId: NodeId) -> QuantumNode:
252 """Lookup a `QuantumNode` from an id associated with the node.
254 Parameters
255 ----------
256 nodeId : `NodeId`
257 The number associated with a node
259 Returns
260 -------
261 node : `QuantumNode`
262 The node corresponding with input number
264 Raises
265 ------
266 IndexError
267 Raised if the requested nodeId is not in the graph.
268 IncompatibleGraphError
269 Raised if the nodeId was built with a different graph than is not
270 this instance (or a graph instance that produced this instance
271 through and operation such as subset)
272 """
273 if nodeId.buildId != self._buildId:
274 raise IncompatibleGraphError("This node was built from a different, incompatible, graph instance")
275 return self._nodeIdMap[nodeId]
277 def getQuantaForTask(self, taskDef: TaskDef) -> FrozenSet[Quantum]:
278 """Return all the `Quantum` associated with a `TaskDef`.
280 Parameters
281 ----------
282 taskDef : `TaskDef`
283 The `TaskDef` for which `Quantum` are to be queried
285 Returns
286 -------
287 frozenset of `Quantum`
288 The `set` of `Quantum` that is associated with the specified
289 `TaskDef`.
290 """
291 return frozenset(self._quanta[taskDef])
293 def getNodesForTask(self, taskDef: TaskDef) -> FrozenSet[QuantumNode]:
294 """Return all the `QuantumNodes` associated with a `TaskDef`.
296 Parameters
297 ----------
298 taskDef : `TaskDef`
299 The `TaskDef` for which `Quantum` are to be queried
301 Returns
302 -------
303 frozenset of `QuantumNodes`
304 The `frozenset` of `QuantumNodes` that is associated with the
305 specified `TaskDef`.
306 """
307 return frozenset(self._taskToQuantumNode[taskDef])
309 def findTasksWithInput(self, datasetTypeName: DatasetTypeName) -> Iterable[TaskDef]:
310 """Find all tasks that have the specified dataset type name as an
311 input.
313 Parameters
314 ----------
315 datasetTypeName : `str`
316 A string representing the name of a dataset type to be queried,
317 can also accept a `DatasetTypeName` which is a `NewType` of str for
318 type safety in static type checking.
320 Returns
321 -------
322 tasks : iterable of `TaskDef`
323 `TaskDef` objects that have the specified `DatasetTypeName` as an
324 input, list will be empty if no tasks use specified
325 `DatasetTypeName` as an input.
327 Raises
328 ------
329 KeyError
330 Raised if the `DatasetTypeName` is not part of the `QuantumGraph`
331 """
332 return (c for c in self._datasetDict.getInputs(datasetTypeName))
334 def findTaskWithOutput(self, datasetTypeName: DatasetTypeName) -> Optional[TaskDef]:
335 """Find all tasks that have the specified dataset type name as an
336 output.
338 Parameters
339 ----------
340 datasetTypeName : `str`
341 A string representing the name of a dataset type to be queried,
342 can also accept a `DatasetTypeName` which is a `NewType` of str for
343 type safety in static type checking.
345 Returns
346 -------
347 `TaskDef` or `None`
348 `TaskDef` that outputs `DatasetTypeName` as an output or None if
349 none of the tasks produce this `DatasetTypeName`.
351 Raises
352 ------
353 KeyError
354 Raised if the `DatasetTypeName` is not part of the `QuantumGraph`
355 """
356 return self._datasetDict.getOutput(datasetTypeName)
358 def tasksWithDSType(self, datasetTypeName: DatasetTypeName) -> Iterable[TaskDef]:
359 """Find all tasks that are associated with the specified dataset type
360 name.
362 Parameters
363 ----------
364 datasetTypeName : `str`
365 A string representing the name of a dataset type to be queried,
366 can also accept a `DatasetTypeName` which is a `NewType` of str for
367 type safety in static type checking.
369 Returns
370 -------
371 result : iterable of `TaskDef`
372 `TaskDef` objects that are associated with the specified
373 `DatasetTypeName`
375 Raises
376 ------
377 KeyError
378 Raised if the `DatasetTypeName` is not part of the `QuantumGraph`
379 """
380 results = self.findTasksWithInput(datasetTypeName)
381 output = self.findTaskWithOutput(datasetTypeName)
382 if output is not None:
383 results = chain(results, (output,))
384 return results
386 def findTaskDefByName(self, taskName: str) -> List[TaskDef]:
387 """Determine which `TaskDef` objects in this graph are associated
388 with a `str` representing a task name (looks at the taskName property
389 of `TaskDef` objects).
391 Returns a list of `TaskDef` objects as a `PipelineTask` may appear
392 multiple times in a graph with different labels.
394 Parameters
395 ----------
396 taskName : str
397 Name of a task to search for
399 Returns
400 -------
401 result : list of `TaskDef`
402 List of the `TaskDef` objects that have the name specified.
403 Multiple values are returned in the case that a task is used
404 multiple times with different labels.
405 """
406 results = []
407 for task in self._quanta.keys():
408 split = task.taskName.split('.')
409 if split[-1] == taskName:
410 results.append(task)
411 return results
413 def findTaskDefByLabel(self, label: str) -> Optional[TaskDef]:
414 """Determine which `TaskDef` objects in this graph are associated
415 with a `str` representing a tasks label.
417 Parameters
418 ----------
419 taskName : str
420 Name of a task to search for
422 Returns
423 -------
424 result : `TaskDef`
425 `TaskDef` objects that has the specified label.
426 """
427 for task in self._quanta.keys():
428 if label == task.label:
429 return task
430 return None
432 def findQuantaWithDSType(self, datasetTypeName: DatasetTypeName) -> Set[Quantum]:
433 """Return all the `Quantum` that contain a specified `DatasetTypeName`.
435 Parameters
436 ----------
437 datasetTypeName : `str`
438 The name of the dataset type to search for as a string,
439 can also accept a `DatasetTypeName` which is a `NewType` of str for
440 type safety in static type checking.
442 Returns
443 -------
444 result : `set` of `QuantumNode` objects
445 A `set` of `QuantumNode`s that contain specified `DatasetTypeName`
447 Raises
448 ------
449 KeyError
450 Raised if the `DatasetTypeName` is not part of the `QuantumGraph`
452 """
453 tasks = self._datasetDict.getAll(datasetTypeName)
454 result: Set[Quantum] = set()
455 result = result.union(*(self._quanta[task] for task in tasks))
456 return result
458 def checkQuantumInGraph(self, quantum: Quantum) -> bool:
459 """Check if specified quantum appears in the graph as part of a node.
461 Parameters
462 ----------
463 quantum : `Quantum`
464 The quantum to search for
466 Returns
467 -------
468 `bool`
469 The result of searching for the quantum
470 """
471 for qset in self._quanta.values():
472 if quantum in qset:
473 return True
474 return False
476 def writeDotGraph(self, output: Union[str, io.BufferedIOBase]):
477 """Write out the graph as a dot graph.
479 Parameters
480 ----------
481 output : str or `io.BufferedIOBase`
482 Either a filesystem path to write to, or a file handle object
483 """
484 write_dot(self._connectedQuanta, output)
486 def subset(self: _T, nodes: Union[QuantumNode, Iterable[QuantumNode]]) -> _T:
487 """Create a new graph object that contains the subset of the nodes
488 specified as input. Node number is preserved.
490 Parameters
491 ----------
492 nodes : `QuantumNode` or iterable of `QuantumNode`
494 Returns
495 -------
496 graph : instance of graph type
497 An instance of the type from which the subset was created
498 """
499 if not isinstance(nodes, Iterable):
500 nodes = (nodes, )
501 quantumSubgraph = self._connectedQuanta.subgraph(nodes).nodes
502 quantumMap = defaultdict(set)
504 node: QuantumNode
505 for node in quantumSubgraph:
506 quantumMap[node.taskDef].add(node.quantum)
507 # Create an empty graph, and then populate it with custom mapping
508 newInst = type(self)({})
509 newInst._buildGraphs(quantumMap, _quantumToNodeId={n.quantum: n.nodeId for n in nodes},
510 _buildId=self._buildId)
511 return newInst
513 def subsetToConnected(self: _T) -> Tuple[_T, ...]:
514 """Generate a list of subgraphs where each is connected.
516 Returns
517 -------
518 result : list of `QuantumGraph`
519 A list of graphs that are each connected
520 """
521 return tuple(self.subset(connectedSet)
522 for connectedSet in nx.weakly_connected_components(self._connectedQuanta))
524 def determineInputsToQuantumNode(self, node: QuantumNode) -> Set[QuantumNode]:
525 """Return a set of `QuantumNode` that are direct inputs to a specified
526 node.
528 Parameters
529 ----------
530 node : `QuantumNode`
531 The node of the graph for which inputs are to be determined
533 Returns
534 -------
535 set of `QuantumNode`
536 All the nodes that are direct inputs to specified node
537 """
538 return set(pred for pred in self._connectedQuanta.predecessors(node))
540 def determineOutputsOfQuantumNode(self, node: QuantumNode) -> Set[QuantumNode]:
541 """Return a set of `QuantumNode` that are direct outputs of a specified
542 node.
544 Parameters
545 ----------
546 node : `QuantumNode`
547 The node of the graph for which outputs are to be determined
549 Returns
550 -------
551 set of `QuantumNode`
552 All the nodes that are direct outputs to specified node
553 """
554 return set(succ for succ in self._connectedQuanta.successors(node))
556 def determineConnectionsOfQuantumNode(self: _T, node: QuantumNode) -> _T:
557 """Return a graph of `QuantumNode` that are direct inputs and outputs
558 of a specified node.
560 Parameters
561 ----------
562 node : `QuantumNode`
563 The node of the graph for which connected nodes are to be
564 determined.
566 Returns
567 -------
568 graph : graph of `QuantumNode`
569 All the nodes that are directly connected to specified node
570 """
571 nodes = self.determineInputsToQuantumNode(node).union(self.determineOutputsOfQuantumNode(node))
572 nodes.add(node)
573 return self.subset(nodes)
575 def determineAncestorsOfQuantumNode(self: _T, node: QuantumNode) -> _T:
576 """Return a graph of the specified node and all the ancestor nodes
577 directly reachable by walking edges.
579 Parameters
580 ----------
581 node : `QuantumNode`
582 The node for which all ansestors are to be determined
584 Returns
585 -------
586 graph of `QuantumNode`
587 Graph of node and all of its ansestors
588 """
589 predecessorNodes = nx.ancestors(self._connectedQuanta, node)
590 predecessorNodes.add(node)
591 return self.subset(predecessorNodes)
593 def findCycle(self) -> List[Tuple[QuantumNode, QuantumNode]]:
594 """Check a graph for the presense of cycles and returns the edges of
595 any cycles found, or an empty list if there is no cycle.
597 Returns
598 -------
599 result : list of tuple of `QuantumNode`, `QuantumNode`
600 A list of any graph edges that form a cycle, or an empty list if
601 there is no cycle. Empty list to so support if graph.find_cycle()
602 syntax as an empty list is falsy.
603 """
604 try:
605 return nx.find_cycle(self._connectedQuanta)
606 except nx.NetworkXNoCycle:
607 return []
609 def saveUri(self, uri):
610 """Save `QuantumGraph` to the specified URI.
612 Parameters
613 ----------
614 uri : `ButlerURI` or `str`
615 URI to where the graph should be saved.
616 """
617 buffer = self._buildSaveObject()
618 butlerUri = ButlerURI(uri)
619 if butlerUri.getExtension() not in (".qgraph"):
620 raise TypeError(f"Can currently only save a graph in qgraph format not {uri}")
621 butlerUri.write(buffer) # type: ignore # Ignore because bytearray is safe to use in place of bytes
623 @property
624 def metadata(self) -> Optional[MappingProxyType[str, Any]]:
625 """
626 """
627 if self._metadata is None:
628 return None
629 return MappingProxyType(self._metadata)
631 @classmethod
632 def loadUri(cls, uri: Union[ButlerURI, str], universe: DimensionUniverse,
633 nodes: Optional[Iterable[int]] = None,
634 graphID: Optional[BuildId] = None
635 ) -> QuantumGraph:
636 """Read `QuantumGraph` from a URI.
638 Parameters
639 ----------
640 uri : `ButlerURI` or `str`
641 URI from where to load the graph.
642 universe: `~lsst.daf.butler.DimensionUniverse`
643 DimensionUniverse instance, not used by the method itself but
644 needed to ensure that registry data structures are initialized.
645 nodes: iterable of `int` or None
646 Numbers that correspond to nodes in the graph. If specified, only
647 these nodes will be loaded. Defaults to None, in which case all
648 nodes will be loaded.
649 graphID : `str` or `None`
650 If specified this ID is verified against the loaded graph prior to
651 loading any Nodes. This defaults to None in which case no
652 validation is done.
654 Returns
655 -------
656 graph : `QuantumGraph`
657 Resulting QuantumGraph instance.
659 Raises
660 ------
661 TypeError
662 Raised if pickle contains instance of a type other than
663 QuantumGraph.
664 ValueError
665 Raised if one or more of the nodes requested is not in the
666 `QuantumGraph` or if graphID parameter does not match the graph
667 being loaded or if the supplied uri does not point at a valid
668 `QuantumGraph` save file.
671 Notes
672 -----
673 Reading Quanta from pickle requires existence of singleton
674 DimensionUniverse which is usually instantiated during Registry
675 initialization. To make sure that DimensionUniverse exists this method
676 accepts dummy DimensionUniverse argument.
677 """
678 uri = ButlerURI(uri)
679 # With ButlerURI we have the choice of always using a local file
680 # or reading in the bytes directly. Reading in bytes can be more
681 # efficient for reasonably-sized pickle files when the resource
682 # is remote. For now use the local file variant. For a local file
683 # as_local() does nothing.
685 if uri.getExtension() in (".pickle", ".pkl"):
686 with uri.as_local() as local, open(local.ospath, "rb") as fd:
687 warnings.warn("Pickle graphs are deprecated, please re-save your graph with the save method")
688 qgraph = pickle.load(fd)
689 elif uri.getExtension() in ('.qgraph'):
690 with LoadHelper(uri) as loader:
691 qgraph = loader.load(nodes, graphID)
692 else:
693 raise ValueError("Only know how to handle files saved as `pickle`, `pkl`, or `qgraph`")
694 if not isinstance(qgraph, QuantumGraph):
695 raise TypeError(f"QuantumGraph save file contains unexpected object type: {type(qgraph)}")
696 return qgraph
698 def save(self, file: io.IO[bytes]):
699 """Save QuantumGraph to a file.
701 Presently we store QuantumGraph in pickle format, this could
702 potentially change in the future if better format is found.
704 Parameters
705 ----------
706 file : `io.BufferedIOBase`
707 File to write pickle data open in binary mode.
708 """
709 buffer = self._buildSaveObject()
710 file.write(buffer) # type: ignore # Ignore because bytearray is safe to use in place of bytes
712 def _buildSaveObject(self) -> bytearray:
713 # make some containers
714 pickleData = deque()
715 # node map is a list because json does not accept mapping keys that
716 # are not strings, so we store a list of key, value pairs that will
717 # be converted to a mapping on load
718 nodeMap = []
719 taskDefMap = {}
720 headerData = {}
721 protocol = 3
723 # Store the QauntumGraph BuildId, this will allow validating BuildIds
724 # at load time, prior to loading any QuantumNodes. Name chosen for
725 # unlikely conflicts.
726 headerData['GraphBuildID'] = self.graphID
727 headerData['Metadata'] = self._metadata
729 # counter for the number of bytes processed thus far
730 count = 0
731 # serialize out the task Defs recording the start and end bytes of each
732 # taskDef
733 for taskDef in self.taskGraph:
734 # compressing has very little impact on saving or load time, but
735 # a large impact on on disk size, so it is worth doing
736 dump = lzma.compress(pickle.dumps(taskDef, protocol=protocol))
737 taskDefMap[taskDef.label] = {"bytes": (count, count+len(dump))}
738 count += len(dump)
739 pickleData.append(dump)
741 headerData['TaskDefs'] = taskDefMap
743 # serialize the nodes, recording the start and end bytes of each node
744 for node in self:
745 node = copy.copy(node)
746 taskDef = node.taskDef
747 # Explicitly overload the "frozen-ness" of nodes to normalized out
748 # the taskDef, this saves a lot of space and load time. The label
749 # will be used to retrive the taskDef from the taskDefMap upon load
750 #
751 # This strategy was chosen instead of creating a new class that
752 # looked just like a QuantumNode but containing a label in place of
753 # a TaskDef because it would be needlessly slow to construct a
754 # bunch of new object to immediately serialize them and destroy the
755 # object. This seems like an acceptable use of Python's dynamic
756 # nature in a controlled way for optimization and simplicity.
757 object.__setattr__(node, 'taskDef', taskDef.label)
758 # compressing has very little impact on saving or load time, but
759 # a large impact on on disk size, so it is worth doing
760 dump = lzma.compress(pickle.dumps(node, protocol=protocol))
761 pickleData.append(dump)
762 nodeMap.append((int(node.nodeId.number), {"bytes": (count, count+len(dump))}))
763 count += len(dump)
765 # need to serialize this as a series of key,value tuples because of
766 # a limitation on how json cant do anyting but strings as keys
767 headerData['Nodes'] = nodeMap
769 # dump the headerData to json
770 header_encode = lzma.compress(json.dumps(headerData).encode())
772 # record the sizes as 2 unsigned long long numbers for a total of 16
773 # bytes
774 save_bytes = struct.pack(STRUCT_FMT_BASE, SAVE_VERSION)
776 fmt_string = STRUCT_FMT_STRING[SAVE_VERSION]
777 map_lengths = struct.pack(fmt_string, len(header_encode))
779 # write each component of the save out in a deterministic order
780 # buffer = io.BytesIO()
781 # buffer.write(map_lengths)
782 # buffer.write(taskDef_pickle)
783 # buffer.write(map_pickle)
784 buffer = bytearray()
785 buffer.extend(MAGIC_BYTES)
786 buffer.extend(save_bytes)
787 buffer.extend(map_lengths)
788 buffer.extend(header_encode)
789 # Iterate over the length of pickleData, and for each element pop the
790 # leftmost element off the deque and write it out. This is to save
791 # memory, as the memory is added to the buffer object, it is removed
792 # from from the container.
793 #
794 # Only this section needs to worry about memory pressue because
795 # everything else written to the buffer prior to this pickle data is
796 # only on the order of kilobytes to low numbers of megabytes.
797 while pickleData:
798 buffer.extend(pickleData.popleft())
799 return buffer
801 @classmethod
802 def load(cls, file: io.IO[bytes], universe: DimensionUniverse,
803 nodes: Optional[Iterable[int]] = None,
804 graphID: Optional[BuildId] = None
805 ) -> QuantumGraph:
806 """Read QuantumGraph from a file that was made by `save`.
808 Parameters
809 ----------
810 file : `io.IO` of bytes
811 File with pickle data open in binary mode.
812 universe: `~lsst.daf.butler.DimensionUniverse`
813 DimensionUniverse instance, not used by the method itself but
814 needed to ensure that registry data structures are initialized.
815 nodes: iterable of `int` or None
816 Numbers that correspond to nodes in the graph. If specified, only
817 these nodes will be loaded. Defaults to None, in which case all
818 nodes will be loaded.
819 graphID : `str` or `None`
820 If specified this ID is verified against the loaded graph prior to
821 loading any Nodes. This defaults to None in which case no
822 validation is done.
824 Returns
825 -------
826 graph : `QuantumGraph`
827 Resulting QuantumGraph instance.
829 Raises
830 ------
831 TypeError
832 Raised if pickle contains instance of a type other than
833 QuantumGraph.
834 ValueError
835 Raised if one or more of the nodes requested is not in the
836 `QuantumGraph` or if graphID parameter does not match the graph
837 being loaded or if the supplied uri does not point at a valid
838 `QuantumGraph` save file.
840 Notes
841 -----
842 Reading Quanta from pickle requires existence of singleton
843 DimensionUniverse which is usually instantiated during Registry
844 initialization. To make sure that DimensionUniverse exists this method
845 accepts dummy DimensionUniverse argument.
846 """
847 # Try to see if the file handle contains pickle data, this will be
848 # removed in the future
849 try:
850 qgraph = pickle.load(file)
851 warnings.warn("Pickle graphs are deprecated, please re-save your graph with the save method")
852 except pickle.UnpicklingError:
853 with LoadHelper(file) as loader: # type: ignore # needed because we don't have Protocols yet
854 qgraph = loader.load(nodes, graphID)
855 if not isinstance(qgraph, QuantumGraph):
856 raise TypeError(f"QuantumGraph pickle file has contains unexpected object type: {type(qgraph)}")
857 return qgraph
859 def iterTaskGraph(self) -> Generator[TaskDef, None, None]:
860 """Iterate over the `taskGraph` attribute in topological order
862 Yields
863 ------
864 taskDef : `TaskDef`
865 `TaskDef` objects in topological order
866 """
867 yield from nx.topological_sort(self.taskGraph)
869 @property
870 def graphID(self):
871 """Returns the ID generated by the graph at construction time
872 """
873 return self._buildId
875 def __iter__(self) -> Generator[QuantumNode, None, None]:
876 yield from nx.topological_sort(self._connectedQuanta)
878 def __len__(self) -> int:
879 return self._count
881 def __contains__(self, node: QuantumNode) -> bool:
882 return self._connectedQuanta.has_node(node)
884 def __getstate__(self) -> dict:
885 """Stores a compact form of the graph as a list of graph nodes, and a
886 tuple of task labels and task configs. The full graph can be
887 reconstructed with this information, and it preseves the ordering of
888 the graph ndoes.
889 """
890 return {"nodesList": list(self)}
892 def __setstate__(self, state: dict):
893 """Reconstructs the state of the graph from the information persisted
894 in getstate.
895 """
896 quanta: DefaultDict[TaskDef, Set[Quantum]] = defaultdict(set)
897 quantumToNodeId: Dict[Quantum, NodeId] = {}
898 quantumNode: QuantumNode
899 for quantumNode in state['nodesList']:
900 quanta[quantumNode.taskDef].add(quantumNode.quantum)
901 quantumToNodeId[quantumNode.quantum] = quantumNode.nodeId
902 _buildId = quantumNode.nodeId.buildId if state['nodesList'] else None # type: ignore
903 self._buildGraphs(quanta, _quantumToNodeId=quantumToNodeId, _buildId=_buildId)
905 def __eq__(self, other: object) -> bool:
906 if not isinstance(other, QuantumGraph):
907 return False
908 if len(self) != len(other):
909 return False
910 for node in self:
911 if node not in other:
912 return False
913 if self.determineInputsToQuantumNode(node) != other.determineInputsToQuantumNode(node):
914 return False
915 if self.determineOutputsOfQuantumNode(node) != other.determineOutputsOfQuantumNode(node):
916 return False
917 return list(self.taskGraph) == list(other.taskGraph)