Coverage for python/lsst/ctrl/mpexec/cmdLineFwk.py: 11%
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1# This file is part of ctrl_mpexec.
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/>.
22"""Module defining CmdLineFwk class and related methods.
23"""
25__all__ = ['CmdLineFwk']
27# -------------------------------
28# Imports of standard modules --
29# -------------------------------
30import argparse
31import copy
32import datetime
33import fnmatch
34import getpass
35import logging
36import re
37import sys
38from typing import Iterable, Optional, Tuple
39import warnings
41# -----------------------------
42# Imports for other modules --
43# -----------------------------
44from lsst.daf.butler import (
45 Butler,
46 CollectionSearch,
47 CollectionType,
48 Registry,
49)
50from lsst.daf.butler.registry import MissingCollectionError, RegistryDefaults
51import lsst.pex.config as pexConfig
52from lsst.pipe.base import (buildExecutionButler, GraphBuilder, Pipeline,
53 PipelineDatasetTypes, QuantumGraph, TaskDef)
54from lsst.obs.base import Instrument
55from .dotTools import graph2dot, pipeline2dot
56from .executionGraphFixup import ExecutionGraphFixup
57from .mpGraphExecutor import MPGraphExecutor
58from .preExecInit import PreExecInit
59from .singleQuantumExecutor import SingleQuantumExecutor
60from . import util
61from lsst.utils import doImport
63# ----------------------------------
64# Local non-exported definitions --
65# ----------------------------------
67_LOG = logging.getLogger(__name__.partition(".")[2])
70class _OutputChainedCollectionInfo:
71 """A helper class for handling command-line arguments related to an output
72 `~lsst.daf.butler.CollectionType.CHAINED` collection.
74 Parameters
75 ----------
76 registry : `lsst.daf.butler.Registry`
77 Butler registry that collections will be added to and/or queried from.
78 name : `str`
79 Name of the collection given on the command line.
80 """
81 def __init__(self, registry: Registry, name: str):
82 self.name = name
83 try:
84 self.chain = tuple(registry.getCollectionChain(name))
85 self.exists = True
86 except MissingCollectionError:
87 self.chain = ()
88 self.exists = False
90 def __str__(self):
91 return self.name
93 name: str
94 """Name of the collection provided on the command line (`str`).
95 """
97 exists: bool
98 """Whether this collection already exists in the registry (`bool`).
99 """
101 chain: Tuple[str, ...]
102 """The definition of the collection, if it already exists (`tuple`[`str`]).
104 Empty if the collection does not already exist.
105 """
108class _OutputRunCollectionInfo:
109 """A helper class for handling command-line arguments related to an output
110 `~lsst.daf.butler.CollectionType.RUN` collection.
112 Parameters
113 ----------
114 registry : `lsst.daf.butler.Registry`
115 Butler registry that collections will be added to and/or queried from.
116 name : `str`
117 Name of the collection given on the command line.
118 """
119 def __init__(self, registry: Registry, name: str):
120 self.name = name
121 try:
122 actualType = registry.getCollectionType(name)
123 if actualType is not CollectionType.RUN:
124 raise TypeError(f"Collection '{name}' exists but has type {actualType.name}, not RUN.")
125 self.exists = True
126 except MissingCollectionError:
127 self.exists = False
129 name: str
130 """Name of the collection provided on the command line (`str`).
131 """
133 exists: bool
134 """Whether this collection already exists in the registry (`bool`).
135 """
138class _ButlerFactory:
139 """A helper class for processing command-line arguments related to input
140 and output collections.
142 Parameters
143 ----------
144 registry : `lsst.daf.butler.Registry`
145 Butler registry that collections will be added to and/or queried from.
147 args : `types.SimpleNamespace`
148 Parsed command-line arguments. The following attributes are used,
149 either at construction or in later methods.
151 ``output``
152 The name of a `~lsst.daf.butler.CollectionType.CHAINED`
153 input/output collection.
155 ``output_run``
156 The name of a `~lsst.daf.butler.CollectionType.RUN` input/output
157 collection.
159 ``extend_run``
160 A boolean indicating whether ``output_run`` should already exist
161 and be extended.
163 ``replace_run``
164 A boolean indicating that (if `True`) ``output_run`` should already
165 exist but will be removed from the output chained collection and
166 replaced with a new one.
168 ``prune_replaced``
169 A boolean indicating whether to prune the replaced run (requires
170 ``replace_run``).
172 ``inputs``
173 Input collections of any type; may be any type handled by
174 `lsst.daf.butler.registry.CollectionSearch.fromExpression`.
176 ``butler_config``
177 Path to a data repository root or configuration file.
179 writeable : `bool`
180 If `True`, a `Butler` is being initialized in a context where actual
181 writes should happens, and hence no output run is necessary.
183 Raises
184 ------
185 ValueError
186 Raised if ``writeable is True`` but there are no output collections.
187 """
188 def __init__(self, registry: Registry, args: argparse.Namespace, writeable: bool):
189 if args.output is not None:
190 self.output = _OutputChainedCollectionInfo(registry, args.output)
191 else:
192 self.output = None
193 if args.output_run is not None:
194 self.outputRun = _OutputRunCollectionInfo(registry, args.output_run)
195 elif self.output is not None:
196 if args.extend_run:
197 if not self.output.chain:
198 raise ValueError("Cannot use --extend-run option with non-existing or empty output chain")
199 runName = self.output.chain[0]
200 else:
201 runName = "{}/{}".format(self.output, Instrument.makeCollectionTimestamp())
202 self.outputRun = _OutputRunCollectionInfo(registry, runName)
203 elif not writeable:
204 # If we're not writing yet, ok to have no output run.
205 self.outputRun = None
206 else:
207 raise ValueError("Cannot write without at least one of (--output, --output-run).")
208 # Recursively flatten any input CHAINED collections. We do this up
209 # front so we can tell if the user passes the same inputs on subsequent
210 # calls, even though we also flatten when we define the output CHAINED
211 # collection.
212 self.inputs = tuple(registry.queryCollections(args.input, flattenChains=True)) if args.input else ()
214 def check(self, args: argparse.Namespace):
215 """Check command-line options for consistency with each other and the
216 data repository.
218 Parameters
219 ----------
220 args : `types.SimpleNamespace`
221 Parsed command-line arguments. See class documentation for the
222 construction parameter of the same name.
223 """
224 assert not (args.extend_run and args.replace_run), "In mutually-exclusive group in ArgumentParser."
225 if self.inputs and self.output is not None and self.output.exists:
226 # Passing the same inputs that were used to initialize the output
227 # collection is allowed; this means they must _end_ with the same
228 # collections, because we push new runs to the front of the chain.
229 for c1, c2 in zip(self.inputs[::-1], self.output.chain[::-1]):
230 if c1 != c2:
231 raise ValueError(
232 f"Output CHAINED collection {self.output.name!r} exists, but it ends with "
233 "a different sequence of input collections than those given: "
234 f"{c1!r} != {c2!r} in inputs={self.inputs} vs "
235 f"{self.output.name}={self.output.chain}."
236 )
237 if len(self.inputs) > len(self.output.chain):
238 nNew = len(self.inputs) - len(self.output.chain)
239 raise ValueError(
240 f"Cannot add new input collections {self.inputs[:nNew]} after "
241 "output collection is first created."
242 )
243 if args.extend_run and self.outputRun is None:
244 raise ValueError("Cannot --extend-run when no output collection is given.")
245 if args.extend_run and not self.outputRun.exists:
246 raise ValueError(f"Cannot --extend-run; output collection "
247 f"'{self.outputRun.name}' does not exist.")
248 if not args.extend_run and self.outputRun is not None and self.outputRun.exists:
249 raise ValueError(f"Output run '{self.outputRun.name}' already exists, but "
250 f"--extend-run was not given.")
251 if args.prune_replaced and not args.replace_run:
252 raise ValueError("--prune-replaced requires --replace-run.")
253 if args.replace_run and (self.output is None or not self.output.exists):
254 raise ValueError("--output must point to an existing CHAINED collection for --replace-run.")
256 @classmethod
257 def _makeReadParts(cls, args: argparse.Namespace):
258 """Common implementation for `makeReadButler` and
259 `makeRegistryAndCollections`.
261 Parameters
262 ----------
263 args : `types.SimpleNamespace`
264 Parsed command-line arguments. See class documentation for the
265 construction parameter of the same name.
267 Returns
268 -------
269 butler : `lsst.daf.butler.Butler`
270 A read-only butler constructed from the repo at
271 ``args.butler_config``, but with no default collections.
272 inputs : `lsst.daf.butler.registry.CollectionSearch`
273 A collection search path constructed according to ``args``.
274 self : `_ButlerFactory`
275 A new `_ButlerFactory` instance representing the processed version
276 of ``args``.
277 """
278 butler = Butler(args.butler_config, writeable=False)
279 self = cls(butler.registry, args, writeable=False)
280 self.check(args)
281 if self.output and self.output.exists:
282 if args.replace_run:
283 replaced = self.output.chain[0]
284 inputs = self.output.chain[1:]
285 _LOG.debug("Simulating collection search in '%s' after removing '%s'.",
286 self.output.name, replaced)
287 else:
288 inputs = [self.output.name]
289 else:
290 inputs = list(self.inputs)
291 if args.extend_run:
292 inputs.insert(0, self.outputRun.name)
293 inputs = CollectionSearch.fromExpression(inputs)
294 return butler, inputs, self
296 @classmethod
297 def makeReadButler(cls, args: argparse.Namespace) -> Butler:
298 """Construct a read-only butler according to the given command-line
299 arguments.
301 Parameters
302 ----------
303 args : `types.SimpleNamespace`
304 Parsed command-line arguments. See class documentation for the
305 construction parameter of the same name.
307 Returns
308 -------
309 butler : `lsst.daf.butler.Butler`
310 A read-only butler initialized with the collections specified by
311 ``args``.
312 """
313 butler, inputs, _ = cls._makeReadParts(args)
314 _LOG.debug("Preparing butler to read from %s.", inputs)
315 return Butler(butler=butler, collections=inputs)
317 @classmethod
318 def makeRegistryAndCollections(cls, args: argparse.Namespace) -> \
319 Tuple[Registry, CollectionSearch, Optional[str]]:
320 """Return a read-only registry, a collection search path, and the name
321 of the run to be used for future writes.
323 Parameters
324 ----------
325 args : `types.SimpleNamespace`
326 Parsed command-line arguments. See class documentation for the
327 construction parameter of the same name.
329 Returns
330 -------
331 registry : `lsst.daf.butler.Registry`
332 Butler registry that collections will be added to and/or queried
333 from.
334 inputs : `lsst.daf.butler.registry.CollectionSearch`
335 Collections to search for datasets.
336 run : `str` or `None`
337 Name of the output `~lsst.daf.butler.CollectionType.RUN` collection
338 if it already exists, or `None` if it does not.
339 """
340 butler, inputs, self = cls._makeReadParts(args)
341 run = self.outputRun.name if args.extend_run else None
342 _LOG.debug("Preparing registry to read from %s and expect future writes to '%s'.", inputs, run)
343 return butler.registry, inputs, run
345 @classmethod
346 def makeWriteButler(cls, args: argparse.Namespace,
347 taskDefs: Optional[Iterable[TaskDef]] = None) -> Butler:
348 """Return a read-write butler initialized to write to and read from
349 the collections specified by the given command-line arguments.
351 Parameters
352 ----------
353 args : `types.SimpleNamespace`
354 Parsed command-line arguments. See class documentation for the
355 construction parameter of the same name.
356 taskDefs : iterable of `TaskDef`, optional
357 Definitions for tasks in a pipeline. This argument is only needed
358 if ``args.replace_run`` is `True` and ``args.prune_replaced`` is
359 "unstore".
361 Returns
362 -------
363 butler : `lsst.daf.butler.Butler`
364 A read-write butler initialized according to the given arguments.
365 """
366 butler = Butler(args.butler_config, writeable=True)
367 self = cls(butler.registry, args, writeable=True)
368 self.check(args)
369 if self.output is not None:
370 chainDefinition = list(self.output.chain if self.output.exists else self.inputs)
371 if args.replace_run:
372 replaced = chainDefinition.pop(0)
373 if args.prune_replaced == "unstore":
374 # Remove datasets from datastore
375 with butler.transaction():
376 refs = butler.registry.queryDatasets(..., collections=replaced)
377 # we want to remove regular outputs but keep
378 # initOutputs, configs, and versions.
379 if taskDefs is not None:
380 initDatasetNames = set(PipelineDatasetTypes.initOutputNames(taskDefs))
381 refs = [ref for ref in refs if ref.datasetType.name not in initDatasetNames]
382 butler.pruneDatasets(refs, unstore=True, run=replaced, disassociate=False)
383 elif args.prune_replaced == "purge":
384 # Erase entire collection and all datasets, need to remove
385 # collection from its chain collection first.
386 with butler.transaction():
387 butler.registry.setCollectionChain(self.output.name, chainDefinition, flatten=True)
388 butler.pruneCollection(replaced, purge=True, unstore=True)
389 elif args.prune_replaced is not None:
390 raise NotImplementedError(
391 f"Unsupported --prune-replaced option '{args.prune_replaced}'."
392 )
393 if not self.output.exists:
394 butler.registry.registerCollection(self.output.name, CollectionType.CHAINED)
395 if not args.extend_run:
396 butler.registry.registerCollection(self.outputRun.name, CollectionType.RUN)
397 chainDefinition.insert(0, self.outputRun.name)
398 butler.registry.setCollectionChain(self.output.name, chainDefinition, flatten=True)
399 _LOG.debug("Preparing butler to write to '%s' and read from '%s'=%s",
400 self.outputRun.name, self.output.name, chainDefinition)
401 butler.registry.defaults = RegistryDefaults(run=self.outputRun.name, collections=self.output.name)
402 else:
403 inputs = CollectionSearch.fromExpression((self.outputRun.name,) + self.inputs)
404 _LOG.debug("Preparing butler to write to '%s' and read from %s.", self.outputRun.name, inputs)
405 butler.registry.defaults = RegistryDefaults(run=self.outputRun.name, collections=inputs)
406 return butler
408 output: Optional[_OutputChainedCollectionInfo]
409 """Information about the output chained collection, if there is or will be
410 one (`_OutputChainedCollectionInfo` or `None`).
411 """
413 outputRun: Optional[_OutputRunCollectionInfo]
414 """Information about the output run collection, if there is or will be
415 one (`_OutputRunCollectionInfo` or `None`).
416 """
418 inputs: Tuple[str, ...]
419 """Input collections provided directly by the user (`tuple` [ `str` ]).
420 """
423class _FilteredStream:
424 """A file-like object that filters some config fields.
426 Note
427 ----
428 This class depends on implementation details of ``Config.saveToStream``
429 methods, in particular that that method uses single call to write()
430 method to save information about single config field, and that call
431 combines comments string(s) for a field and field path and value.
432 This class will not work reliably on the "import" strings, so imports
433 should be disabled by passing ``skipImports=True`` to ``saveToStream()``.
434 """
435 def __init__(self, pattern):
436 # obey case if pattern isn't lowercase or requests NOIGNORECASE
437 mat = re.search(r"(.*):NOIGNORECASE$", pattern)
439 if mat:
440 pattern = mat.group(1)
441 self._pattern = re.compile(fnmatch.translate(pattern))
442 else:
443 if pattern != pattern.lower():
444 print(f"Matching \"{pattern}\" without regard to case "
445 "(append :NOIGNORECASE to prevent this)", file=sys.stdout)
446 self._pattern = re.compile(fnmatch.translate(pattern), re.IGNORECASE)
448 def write(self, showStr):
449 # Strip off doc string line(s) and cut off at "=" for string matching
450 matchStr = showStr.rstrip().split("\n")[-1].split("=")[0]
451 if self._pattern.search(matchStr):
452 sys.stdout.write(showStr)
454# ------------------------
455# Exported definitions --
456# ------------------------
459class CmdLineFwk:
460 """PipelineTask framework which executes tasks from command line.
462 In addition to executing tasks this activator provides additional methods
463 for task management like dumping configuration or execution chain.
464 """
466 MP_TIMEOUT = 9999 # Default timeout (sec) for multiprocessing
468 def __init__(self):
469 pass
471 def makePipeline(self, args):
472 """Build a pipeline from command line arguments.
474 Parameters
475 ----------
476 args : `types.SimpleNamespace`
477 Parsed command line
479 Returns
480 -------
481 pipeline : `~lsst.pipe.base.Pipeline`
482 """
483 if args.pipeline:
484 pipeline = Pipeline.from_uri(args.pipeline)
485 else:
486 pipeline = Pipeline("anonymous")
488 # loop over all pipeline actions and apply them in order
489 for action in args.pipeline_actions:
490 if action.action == "add_instrument":
492 pipeline.addInstrument(action.value)
494 elif action.action == "new_task":
496 pipeline.addTask(action.value, action.label)
498 elif action.action == "delete_task":
500 pipeline.removeTask(action.label)
502 elif action.action == "config":
504 # action value string is "field=value", split it at '='
505 field, _, value = action.value.partition("=")
506 pipeline.addConfigOverride(action.label, field, value)
508 elif action.action == "configfile":
510 pipeline.addConfigFile(action.label, action.value)
512 else:
514 raise ValueError(f"Unexpected pipeline action: {action.action}")
516 if args.save_pipeline:
517 pipeline.write_to_uri(args.save_pipeline)
519 if args.pipeline_dot:
520 pipeline2dot(pipeline, args.pipeline_dot)
522 return pipeline
524 def makeGraph(self, pipeline, args):
525 """Build a graph from command line arguments.
527 Parameters
528 ----------
529 pipeline : `~lsst.pipe.base.Pipeline`
530 Pipeline, can be empty or ``None`` if graph is read from a file.
531 args : `types.SimpleNamespace`
532 Parsed command line
534 Returns
535 -------
536 graph : `~lsst.pipe.base.QuantumGraph` or `None`
537 If resulting graph is empty then `None` is returned.
538 """
540 # make sure that --extend-run always enables --skip-existing
541 if args.extend_run:
542 args.skip_existing = True
544 registry, collections, run = _ButlerFactory.makeRegistryAndCollections(args)
546 if args.skip_existing and run:
547 args.skip_existing_in += (run,)
549 if args.qgraph:
550 # click passes empty tuple as default value for qgraph_node_id
551 nodes = args.qgraph_node_id or None
552 qgraph = QuantumGraph.loadUri(args.qgraph, registry.dimensions,
553 nodes=nodes, graphID=args.qgraph_id)
555 # pipeline can not be provided in this case
556 if pipeline:
557 raise ValueError("Pipeline must not be given when quantum graph is read from file.")
559 else:
561 # make execution plan (a.k.a. DAG) for pipeline
562 graphBuilder = GraphBuilder(registry,
563 skipExistingIn=args.skip_existing_in,
564 clobberOutputs=args.clobber_outputs)
565 # accumulate metadata
566 metadata = {"input": args.input, "output": args.output, "butler_argument": args.butler_config,
567 "output_run": args.output_run, "extend_run": args.extend_run,
568 "skip_existing_in": args.skip_existing_in, "skip_existing": args.skip_existing,
569 "data_query": args.data_query, "user": getpass.getuser(),
570 "time": f"{datetime.datetime.now()}"}
571 qgraph = graphBuilder.makeGraph(pipeline, collections, run, args.data_query, metadata=metadata)
573 # Count quanta in graph and give a warning if it's empty and return
574 # None.
575 nQuanta = len(qgraph)
576 if nQuanta == 0:
577 warnings.warn("QuantumGraph is empty", stacklevel=2)
578 return None
579 else:
580 _LOG.info("QuantumGraph contains %d quanta for %d tasks, graph ID: %r",
581 nQuanta, len(qgraph.taskGraph), qgraph.graphID)
583 if args.save_qgraph:
584 qgraph.saveUri(args.save_qgraph)
586 if args.save_single_quanta:
587 for quantumNode in qgraph:
588 sqgraph = qgraph.subset(quantumNode)
589 uri = args.save_single_quanta.format(quantumNode.nodeId.number)
590 sqgraph.saveUri(uri)
592 if args.qgraph_dot:
593 graph2dot(qgraph, args.qgraph_dot)
595 if args.execution_butler_location:
596 butler = Butler(args.butler_config)
597 newArgs = copy.deepcopy(args)
599 def builderShim(butler):
600 newArgs.butler_config = butler._config
601 # Calling makeWriteButler is done for the side effects of
602 # calling that method, maining parsing all the args into
603 # collection names, creating collections, etc.
604 newButler = _ButlerFactory.makeWriteButler(newArgs)
605 return newButler
607 # Include output collection in collections for input
608 # files if it exists in the repo.
609 all_inputs = args.input
610 if args.output is not None:
611 try:
612 all_inputs += (next(iter(butler.registry.queryCollections(args.output))), )
613 except MissingCollectionError:
614 pass
616 _LOG.debug("Calling buildExecutionButler with collections=%s", all_inputs)
617 buildExecutionButler(butler, qgraph, args.execution_butler_location, run,
618 butlerModifier=builderShim, collections=all_inputs,
619 clobber=args.clobber_execution_butler)
621 return qgraph
623 def runPipeline(self, graph, taskFactory, args, butler=None):
624 """Execute complete QuantumGraph.
626 Parameters
627 ----------
628 graph : `QuantumGraph`
629 Execution graph.
630 taskFactory : `~lsst.pipe.base.TaskFactory`
631 Task factory
632 args : `types.SimpleNamespace`
633 Parsed command line
634 butler : `~lsst.daf.butler.Butler`, optional
635 Data Butler instance, if not defined then new instance is made
636 using command line options.
637 """
638 # make sure that --extend-run always enables --skip-existing
639 if args.extend_run:
640 args.skip_existing = True
642 # make butler instance
643 if butler is None:
644 butler = _ButlerFactory.makeWriteButler(args, graph.iterTaskGraph())
646 if args.skip_existing:
647 args.skip_existing_in += (butler.run, )
649 # Enable lsstDebug debugging. Note that this is done once in the
650 # main process before PreExecInit and it is also repeated before
651 # running each task in SingleQuantumExecutor (which may not be
652 # needed if `multipocessing` always uses fork start method).
653 if args.enableLsstDebug:
654 try:
655 _LOG.debug("Will try to import debug.py")
656 import debug # noqa:F401
657 except ImportError:
658 _LOG.warn("No 'debug' module found.")
660 # Save all InitOutputs, configs, etc.
661 preExecInit = PreExecInit(butler, taskFactory, extendRun=args.extend_run)
662 preExecInit.initialize(graph,
663 saveInitOutputs=not args.skip_init_writes,
664 registerDatasetTypes=args.register_dataset_types,
665 saveVersions=not args.no_versions)
667 if not args.init_only:
668 graphFixup = self._importGraphFixup(args)
669 quantumExecutor = SingleQuantumExecutor(taskFactory,
670 skipExistingIn=args.skip_existing_in,
671 clobberOutputs=args.clobber_outputs,
672 enableLsstDebug=args.enableLsstDebug,
673 exitOnKnownError=args.fail_fast)
674 timeout = self.MP_TIMEOUT if args.timeout is None else args.timeout
675 executor = MPGraphExecutor(numProc=args.processes, timeout=timeout,
676 startMethod=args.start_method,
677 quantumExecutor=quantumExecutor,
678 failFast=args.fail_fast,
679 executionGraphFixup=graphFixup)
680 with util.profile(args.profile, _LOG):
681 executor.execute(graph, butler)
683 def showInfo(self, args, pipeline, graph=None):
684 """Display useful info about pipeline and environment.
686 Parameters
687 ----------
688 args : `types.SimpleNamespace`
689 Parsed command line
690 pipeline : `Pipeline`
691 Pipeline definition
692 graph : `QuantumGraph`, optional
693 Execution graph
694 """
695 showOpts = args.show
696 for what in showOpts:
697 showCommand, _, showArgs = what.partition("=")
699 if showCommand in ["pipeline", "config", "history", "tasks"]:
700 if not pipeline:
701 _LOG.warning("Pipeline is required for --show=%s", showCommand)
702 continue
704 if showCommand in ["graph", "workflow", "uri"]:
705 if not graph:
706 _LOG.warning("QuantumGraph is required for --show=%s", showCommand)
707 continue
709 if showCommand == "pipeline":
710 print(pipeline)
711 elif showCommand == "config":
712 self._showConfig(pipeline, showArgs, False)
713 elif showCommand == "dump-config":
714 self._showConfig(pipeline, showArgs, True)
715 elif showCommand == "history":
716 self._showConfigHistory(pipeline, showArgs)
717 elif showCommand == "tasks":
718 self._showTaskHierarchy(pipeline)
719 elif showCommand == "graph":
720 if graph:
721 self._showGraph(graph)
722 elif showCommand == "uri":
723 if graph:
724 self._showUri(graph, args)
725 elif showCommand == "workflow":
726 if graph:
727 self._showWorkflow(graph, args)
728 else:
729 print("Unknown value for show: %s (choose from '%s')" %
730 (what, "', '".join("pipeline config[=XXX] history=XXX tasks graph".split())),
731 file=sys.stderr)
732 sys.exit(1)
734 def _showConfig(self, pipeline, showArgs, dumpFullConfig):
735 """Show task configuration
737 Parameters
738 ----------
739 pipeline : `Pipeline`
740 Pipeline definition
741 showArgs : `str`
742 Defines what to show
743 dumpFullConfig : `bool`
744 If true then dump complete task configuration with all imports.
745 """
746 stream = sys.stdout
747 if dumpFullConfig:
748 # Task label can be given with this option
749 taskName = showArgs
750 else:
751 # The argument can have form [TaskLabel::][pattern:NOIGNORECASE]
752 matConfig = re.search(r"^(?:(\w+)::)?(?:config.)?(.+)?", showArgs)
753 taskName = matConfig.group(1)
754 pattern = matConfig.group(2)
755 if pattern:
756 stream = _FilteredStream(pattern)
758 tasks = util.filterTasks(pipeline, taskName)
759 if not tasks:
760 print("Pipeline has no tasks named {}".format(taskName), file=sys.stderr)
761 sys.exit(1)
763 for taskDef in tasks:
764 print("### Configuration for task `{}'".format(taskDef.label))
765 taskDef.config.saveToStream(stream, root="config", skipImports=not dumpFullConfig)
767 def _showConfigHistory(self, pipeline, showArgs):
768 """Show history for task configuration
770 Parameters
771 ----------
772 pipeline : `Pipeline`
773 Pipeline definition
774 showArgs : `str`
775 Defines what to show
776 """
778 taskName = None
779 pattern = None
780 matHistory = re.search(r"^(?:(\w+)::)?(?:config[.])?(.+)", showArgs)
781 if matHistory:
782 taskName = matHistory.group(1)
783 pattern = matHistory.group(2)
784 if not pattern:
785 print("Please provide a value with --show history (e.g. history=Task::param)", file=sys.stderr)
786 sys.exit(1)
788 tasks = util.filterTasks(pipeline, taskName)
789 if not tasks:
790 print(f"Pipeline has no tasks named {taskName}", file=sys.stderr)
791 sys.exit(1)
793 found = False
794 for taskDef in tasks:
796 config = taskDef.config
798 # Look for any matches in the config hierarchy for this name
799 for nmatch, thisName in enumerate(fnmatch.filter(config.names(), pattern)):
800 if nmatch > 0:
801 print("")
803 cpath, _, cname = thisName.rpartition(".")
804 try:
805 if not cpath:
806 # looking for top-level field
807 hconfig = taskDef.config
808 else:
809 hconfig = eval("config." + cpath, {}, {"config": config})
810 except AttributeError:
811 print(f"Error: Unable to extract attribute {cpath} from task {taskDef.label}",
812 file=sys.stderr)
813 hconfig = None
815 # Sometimes we end up with a non-Config so skip those
816 if isinstance(hconfig, (pexConfig.Config, pexConfig.ConfigurableInstance)) and \
817 hasattr(hconfig, cname):
818 print(f"### Configuration field for task `{taskDef.label}'")
819 print(pexConfig.history.format(hconfig, cname))
820 found = True
822 if not found:
823 print(f"None of the tasks has field matching {pattern}", file=sys.stderr)
824 sys.exit(1)
826 def _showTaskHierarchy(self, pipeline):
827 """Print task hierarchy to stdout
829 Parameters
830 ----------
831 pipeline: `Pipeline`
832 """
833 for taskDef in pipeline.toExpandedPipeline():
834 print("### Subtasks for task `{}'".format(taskDef.taskName))
836 for configName, taskName in util.subTaskIter(taskDef.config):
837 print("{}: {}".format(configName, taskName))
839 def _showGraph(self, graph):
840 """Print quanta information to stdout
842 Parameters
843 ----------
844 graph : `QuantumGraph`
845 Execution graph.
846 """
847 for taskNode in graph.taskGraph:
848 print(taskNode)
850 for iq, quantum in enumerate(graph.getQuantaForTask(taskNode)):
851 print(" Quantum {}:".format(iq))
852 print(" inputs:")
853 for key, refs in quantum.inputs.items():
854 dataIds = ["DataId({})".format(ref.dataId) for ref in refs]
855 print(" {}: [{}]".format(key, ", ".join(dataIds)))
856 print(" outputs:")
857 for key, refs in quantum.outputs.items():
858 dataIds = ["DataId({})".format(ref.dataId) for ref in refs]
859 print(" {}: [{}]".format(key, ", ".join(dataIds)))
861 def _showWorkflow(self, graph, args):
862 """Print quanta information and dependency to stdout
864 Parameters
865 ----------
866 graph : `QuantumGraph`
867 Execution graph.
868 args : `types.SimpleNamespace`
869 Parsed command line
870 """
871 for node in graph:
872 print(f"Quantum {node.nodeId.number}: {node.taskDef.taskName}")
873 for parent in graph.determineInputsToQuantumNode(node):
874 print(f"Parent Quantum {parent.nodeId.number} - Child Quantum {node.nodeId.number}")
876 def _showUri(self, graph, args):
877 """Print input and predicted output URIs to stdout
879 Parameters
880 ----------
881 graph : `QuantumGraph`
882 Execution graph
883 args : `types.SimpleNamespace`
884 Parsed command line
885 """
886 def dumpURIs(thisRef):
887 primary, components = butler.getURIs(thisRef, predict=True, run="TBD")
888 if primary:
889 print(f" {primary}")
890 else:
891 print(" (disassembled artifact)")
892 for compName, compUri in components.items():
893 print(f" {compName}: {compUri}")
895 butler = _ButlerFactory.makeReadButler(args)
896 for node in graph:
897 print(f"Quantum {node.nodeId.number}: {node.taskDef.taskName}")
898 print(" inputs:")
899 for key, refs in node.quantum.inputs.items():
900 for ref in refs:
901 dumpURIs(ref)
902 print(" outputs:")
903 for key, refs in node.quantum.outputs.items():
904 for ref in refs:
905 dumpURIs(ref)
907 def _importGraphFixup(self, args):
908 """Import/instantiate graph fixup object.
910 Parameters
911 ----------
912 args : `types.SimpleNamespace`
913 Parsed command line.
915 Returns
916 -------
917 fixup : `ExecutionGraphFixup` or `None`
919 Raises
920 ------
921 ValueError
922 Raised if import fails, method call raises exception, or returned
923 instance has unexpected type.
924 """
925 if args.graph_fixup:
926 try:
927 factory = doImport(args.graph_fixup)
928 except Exception as exc:
929 raise ValueError("Failed to import graph fixup class/method") from exc
930 try:
931 fixup = factory()
932 except Exception as exc:
933 raise ValueError("Failed to make instance of graph fixup") from exc
934 if not isinstance(fixup, ExecutionGraphFixup):
935 raise ValueError("Graph fixup is not an instance of ExecutionGraphFixup class")
936 return fixup