Coverage for python/lsst/pipe/base/pipelineIR.py: 18%
Shortcuts on this page
r m x p toggle line displays
j k next/prev highlighted chunk
0 (zero) top of page
1 (one) first highlighted chunk
Shortcuts on this page
r m x p toggle line displays
j k next/prev highlighted chunk
0 (zero) top of page
1 (one) first highlighted chunk
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
23__all__ = ("ConfigIR", "ContractError", "ContractIR", "ImportIR", "PipelineIR", "TaskIR", "LabeledSubset")
25from collections import Counter
26from collections.abc import Iterable as abcIterable
27from dataclasses import dataclass, field
28from deprecated.sphinx import deprecated
29from typing import Any, List, Set, Union, Generator, MutableMapping, Optional, Dict, Type
31import copy
32import re
33import os
34import yaml
35import warnings
37from lsst.daf.butler import ButlerURI
40class KeepInstrument:
41 pass
44class PipelineYamlLoader(yaml.SafeLoader):
45 """This is a specialized version of yaml's SafeLoader. It checks and raises
46 an exception if it finds that there are multiple instances of the same key
47 found inside a pipeline file at a given scope.
48 """
49 def construct_mapping(self, node, deep=False):
50 # do the call to super first so that it can do all the other forms of
51 # checking on this node. If you check the uniqueness of keys first
52 # it would save the work that super does in the case of a failure, but
53 # it might fail in the case that the node was the incorrect node due
54 # to a parsing error, and the resulting exception would be difficult to
55 # understand.
56 mapping = super().construct_mapping(node, deep)
57 # Check if there are any duplicate keys
58 all_keys = Counter(key_node.value for key_node, _ in node.value)
59 duplicates = {k for k, i in all_keys.items() if i != 1}
60 if duplicates:
61 raise KeyError("Pipeline files must not have duplicated keys, "
62 f"{duplicates} appeared multiple times")
63 return mapping
66class ContractError(Exception):
67 """An exception that is raised when a pipeline contract is not satisfied
68 """
69 pass
72@dataclass
73class ContractIR:
74 """Intermediate representation of contracts read from a pipeline yaml file.
75 """
76 contract: str
77 """A string of python code representing one or more conditions on configs
78 in a pipeline. This code-as-string should, once evaluated, should be True
79 if the configs are fine, and False otherwise.
80 """
81 msg: Union[str, None] = None
82 """An optional message to be shown to the user if a contract fails
83 """
85 def to_primitives(self) -> Dict[str, str]:
86 """Convert to a representation used in yaml serialization
87 """
88 accumulate = {"contract": self.contract}
89 if self.msg is not None:
90 accumulate['msg'] = self.msg
91 return accumulate
93 def __eq__(self, other: object):
94 if not isinstance(other, ContractIR):
95 return False
96 elif self.contract == other.contract and self.msg == other.msg:
97 return True
98 else:
99 return False
102@dataclass
103class LabeledSubset:
104 """Intermediate representation of named subset of task labels read from
105 a pipeline yaml file.
106 """
107 label: str
108 """The label used to identify the subset of task labels.
109 """
110 subset: Set[str]
111 """A set of task labels contained in this subset.
112 """
113 description: Optional[str]
114 """A description of what this subset of tasks is intended to do
115 """
117 @staticmethod
118 def from_primitives(label: str, value: Union[List[str], dict]) -> LabeledSubset:
119 """Generate `LabeledSubset` objects given a properly formatted object
120 that as been created by a yaml loader.
122 Parameters
123 ----------
124 label : `str`
125 The label that will be used to identify this labeled subset.
126 value : `list` of `str` or `dict`
127 Object returned from loading a labeled subset section from a yaml
128 document.
130 Returns
131 -------
132 labeledSubset : `LabeledSubset`
133 A `LabeledSubset` object build from the inputs.
135 Raises
136 ------
137 ValueError
138 Raised if the value input is not properly formatted for parsing
139 """
140 if isinstance(value, MutableMapping):
141 subset = value.pop("subset", None)
142 if subset is None:
143 raise ValueError("If a labeled subset is specified as a mapping, it must contain the key "
144 "'subset'")
145 description = value.pop("description", None)
146 elif isinstance(value, abcIterable):
147 subset = value
148 description = None
149 else:
150 raise ValueError(f"There was a problem parsing the labeled subset {label}, make sure the "
151 "definition is either a valid yaml list, or a mapping with keys "
152 "(subset, description) where subset points to a yaml list, and description is "
153 "associated with a string")
154 return LabeledSubset(label, set(subset), description)
156 def to_primitives(self) -> Dict[str, Union[List[str], str]]:
157 """Convert to a representation used in yaml serialization
158 """
159 accumulate: Dict[str, Union[List[str], str]] = {"subset": list(self.subset)}
160 if self.description is not None:
161 accumulate["description"] = self.description
162 return accumulate
165@dataclass
166class ParametersIR:
167 """Intermediate representation of parameters that are global to a pipeline
169 These parameters are specified under a top level key named `parameters`
170 and are declared as a yaml mapping. These entries can then be used inside
171 task configuration blocks to specify configuration values. They may not be
172 used in the special ``file`` or ``python`` blocks.
174 Example:
175 paramters:
176 shared_value: 14
177 tasks:
178 taskA:
179 class: modA
180 config:
181 field1: parameters.shared_value
182 taskB:
183 class: modB
184 config:
185 field2: parameters.shared_value
186 """
187 mapping: MutableMapping[str, str]
188 """A mutable mapping of identifiers as keys, and shared configuration
189 as values.
190 """
191 def update(self, other: Optional[ParametersIR]):
192 if other is not None:
193 self.mapping.update(other.mapping)
195 def to_primitives(self) -> MutableMapping[str, str]:
196 """Convert to a representation used in yaml serialization
197 """
198 return self.mapping
200 def __contains__(self, value: str) -> bool:
201 return value in self.mapping
203 def __getitem__(self, item: str) -> Any:
204 return self.mapping[item]
206 def __bool__(self) -> bool:
207 return bool(self.mapping)
210@dataclass
211class ConfigIR:
212 """Intermediate representation of configurations read from a pipeline yaml
213 file.
214 """
215 python: Union[str, None] = None
216 """A string of python code that is used to modify a configuration. This can
217 also be None if there are no modifications to do.
218 """
219 dataId: Union[dict, None] = None
220 """A dataId that is used to constrain these config overrides to only quanta
221 with matching dataIds. This field can be None if there is no constraint.
222 This is currently an unimplemented feature, and is placed here for future
223 use.
224 """
225 file: List[str] = field(default_factory=list)
226 """A list of paths which points to a file containing config overrides to be
227 applied. This value may be an empty list if there are no overrides to
228 apply.
229 """
230 rest: dict = field(default_factory=dict)
231 """This is a dictionary of key value pairs, where the keys are strings
232 corresponding to qualified fields on a config to override, and the values
233 are strings representing the values to apply.
234 """
236 def to_primitives(self) -> Dict[str, Union[str, dict, List[str]]]:
237 """Convert to a representation used in yaml serialization
238 """
239 accumulate = {}
240 for name in ("python", "dataId", "file"):
241 # if this attribute is thruthy add it to the accumulation
242 # dictionary
243 if getattr(self, name):
244 accumulate[name] = getattr(self, name)
245 # Add the dictionary containing the rest of the config keys to the
246 # # accumulated dictionary
247 accumulate.update(self.rest)
248 return accumulate
250 def formatted(self, parameters: ParametersIR) -> ConfigIR:
251 """Returns a new ConfigIR object that is formatted according to the
252 specified parameters
254 Parameters
255 ----------
256 parameters : ParametersIR
257 Object that contains variable mappings used in substitution.
259 Returns
260 -------
261 config : ConfigIR
262 A new ConfigIR object formatted with the input parameters
263 """
264 new_config = copy.deepcopy(self)
265 for key, value in new_config.rest.items():
266 if not isinstance(value, str):
267 continue
268 match = re.match("parameters[.](.*)", value)
269 if match and match.group(1) in parameters:
270 new_config.rest[key] = parameters[match.group(1)]
271 if match and match.group(1) not in parameters:
272 warnings.warn(f"config {key} contains value {match.group(0)} which is formatted like a "
273 "Pipeline parameter but was not found within the Pipeline, if this was not "
274 "intentional, check for a typo")
275 return new_config
277 def maybe_merge(self, other_config: "ConfigIR") -> Generator["ConfigIR", None, None]:
278 """Merges another instance of a `ConfigIR` into this instance if
279 possible. This function returns a generator that is either self
280 if the configs were merged, or self, and other_config if that could
281 not be merged.
283 Parameters
284 ----------
285 other_config : `ConfigIR`
286 An instance of `ConfigIR` to merge into this instance.
288 Returns
289 -------
290 Generator : `ConfigIR`
291 A generator containing either self, or self and other_config if
292 the configs could be merged or not respectively.
293 """
294 # Verify that the config blocks can be merged
295 if self.dataId != other_config.dataId or self.python or other_config.python or\
296 self.file or other_config.file:
297 yield from (self, other_config)
298 return
300 # create a set of all keys, and verify two keys do not have different
301 # values
302 key_union = self.rest.keys() & other_config.rest.keys()
303 for key in key_union:
304 if self.rest[key] != other_config.rest[key]:
305 yield from (self, other_config)
306 return
307 self.rest.update(other_config.rest)
309 # Combine the lists of override files to load
310 self_file_set = set(self.file)
311 other_file_set = set(other_config.file)
312 self.file = list(self_file_set.union(other_file_set))
314 yield self
316 def __eq__(self, other: object):
317 if not isinstance(other, ConfigIR):
318 return False
319 elif all(getattr(self, attr) == getattr(other, attr) for attr in
320 ("python", "dataId", "file", "rest")):
321 return True
322 else:
323 return False
326@dataclass
327class TaskIR:
328 """Intermediate representation of tasks read from a pipeline yaml file.
329 """
330 label: str
331 """An identifier used to refer to a task.
332 """
333 klass: str
334 """A string containing a fully qualified python class to be run in a
335 pipeline.
336 """
337 config: Union[List[ConfigIR], None] = None
338 """List of all configs overrides associated with this task, and may be
339 `None` if there are no config overrides.
340 """
342 def to_primitives(self) -> Dict[str, Union[str, List[dict]]]:
343 """Convert to a representation used in yaml serialization
344 """
345 accumulate: Dict[str, Union[str, List[dict]]] = {'class': self.klass}
346 if self.config:
347 accumulate['config'] = [c.to_primitives() for c in self.config]
348 return accumulate
350 def add_or_update_config(self, other_config: ConfigIR):
351 """Adds a `ConfigIR` to this task if one is not present. Merges configs
352 if there is a `ConfigIR` present and the dataId keys of both configs
353 match, otherwise adds a new entry to the config list. The exception to
354 the above is that if either the last config or other_config has a
355 python block, then other_config is always added, as python blocks can
356 modify configs in ways that cannot be predicted.
358 Parameters
359 ----------
360 other_config : `ConfigIR`
361 A `ConfigIR` instance to add or merge into the config attribute of
362 this task.
363 """
364 if not self.config:
365 self.config = [other_config]
366 return
367 self.config.extend(self.config.pop().maybe_merge(other_config))
369 def __eq__(self, other: object):
370 if not isinstance(other, TaskIR):
371 return False
372 elif all(getattr(self, attr) == getattr(other, attr) for attr in
373 ("label", "klass", "config")):
374 return True
375 else:
376 return False
379@dataclass
380class ImportIR:
381 """An intermediate representation of imported pipelines
382 """
383 location: str
384 """This is the location of the pipeline to inherit. The path should be
385 specified as an absolute path. Environment variables may be used in the
386 path and should be specified as a python string template, with the name of
387 the environment variable inside braces.
388 """
389 include: Union[List[str], None] = None
390 """List of tasks that should be included when inheriting this pipeline.
391 Either the include or exclude attributes may be specified, but not both.
392 """
393 exclude: Union[List[str], None] = None
394 """List of tasks that should be excluded when inheriting this pipeline.
395 Either the include or exclude attributes may be specified, but not both.
396 """
397 importContracts: bool = True
398 """Boolean attribute to dictate if contracts should be inherited with the
399 pipeline or not.
400 """
401 instrument: Union[Type[KeepInstrument], str, None] = KeepInstrument
402 """Instrument to assign to the Pipeline at import. The default value of
403 KEEP_INSTRUMENT indicates that whatever instrument the pipeline is declared
404 with will not be modified. Setting this value to None will drop any
405 declared instrument prior to import.
406 """
408 def toPipelineIR(self) -> "PipelineIR":
409 """Load in the Pipeline specified by this object, and turn it into a
410 PipelineIR instance.
412 Returns
413 -------
414 pipeline : `PipelineIR`
415 A pipeline generated from the imported pipeline file
416 """
417 if self.include and self.exclude:
418 raise ValueError("Both an include and an exclude list cant be specified"
419 " when declaring a pipeline import")
420 tmp_pipeline = PipelineIR.from_uri(os.path.expandvars(self.location))
421 if self.instrument is not KeepInstrument:
422 tmp_pipeline.instrument = self.instrument
424 included_labels = set()
425 for label in tmp_pipeline.tasks:
426 if (self.include and label in self.include) or (self.exclude and label not in self.exclude)\
427 or (self.include is None and self.exclude is None):
428 included_labels.add(label)
430 # Handle labeled subsets being specified in the include or exclude
431 # list, adding or removing labels.
432 if self.include is not None:
433 subsets_in_include = tmp_pipeline.labeled_subsets.keys() & self.include
434 for label in subsets_in_include:
435 included_labels.update(tmp_pipeline.labeled_subsets[label].subset)
437 elif self.exclude is not None:
438 subsets_in_exclude = tmp_pipeline.labeled_subsets.keys() & self.exclude
439 for label in subsets_in_exclude:
440 included_labels.difference_update(tmp_pipeline.labeled_subsets[label].subset)
442 tmp_pipeline = tmp_pipeline.subset_from_labels(included_labels)
444 if not self.importContracts:
445 tmp_pipeline.contracts = []
447 return tmp_pipeline
449 def __eq__(self, other: object):
450 if not isinstance(other, ImportIR):
451 return False
452 elif all(getattr(self, attr) == getattr(other, attr) for attr in
453 ("location", "include", "exclude", "importContracts")):
454 return True
455 else:
456 return False
459class PipelineIR:
460 """Intermediate representation of a pipeline definition
462 Parameters
463 ----------
464 loaded_yaml : `dict`
465 A dictionary which matches the structure that would be produced by a
466 yaml reader which parses a pipeline definition document
468 Raises
469 ------
470 ValueError :
471 - If a pipeline is declared without a description
472 - If no tasks are declared in a pipeline, and no pipelines are to be
473 inherited
474 - If more than one instrument is specified
475 - If more than one inherited pipeline share a label
476 """
477 def __init__(self, loaded_yaml):
478 # Check required fields are present
479 if "description" not in loaded_yaml:
480 raise ValueError("A pipeline must be declared with a description")
481 if "tasks" not in loaded_yaml and len({"imports", "inherits"} - loaded_yaml.keys()) == 2:
482 raise ValueError("A pipeline must be declared with one or more tasks")
484 # These steps below must happen in this call order
486 # Process pipeline description
487 self.description = loaded_yaml.pop("description")
489 # Process tasks
490 self._read_tasks(loaded_yaml)
492 # Process instrument keys
493 inst = loaded_yaml.pop("instrument", None)
494 if isinstance(inst, list):
495 raise ValueError("Only one top level instrument can be defined in a pipeline")
496 self.instrument = inst
498 # Process any contracts
499 self._read_contracts(loaded_yaml)
501 # Process any defined parameters
502 self._read_parameters(loaded_yaml)
504 # Process any named label subsets
505 self._read_labeled_subsets(loaded_yaml)
507 # Process any inherited pipelines
508 self._read_imports(loaded_yaml)
510 # verify named subsets, must be done after inheriting
511 self._verify_labeled_subsets()
513 def _read_contracts(self, loaded_yaml):
514 """Process the contracts portion of the loaded yaml document
516 Parameters
517 ---------
518 loaded_yaml : `dict`
519 A dictionary which matches the structure that would be produced by
520 a yaml reader which parses a pipeline definition document
521 """
522 loaded_contracts = loaded_yaml.pop("contracts", [])
523 if isinstance(loaded_contracts, str):
524 loaded_contracts = [loaded_contracts]
525 self.contracts = []
526 for contract in loaded_contracts:
527 if isinstance(contract, dict):
528 self.contracts.append(ContractIR(**contract))
529 if isinstance(contract, str):
530 self.contracts.append(ContractIR(contract=contract))
532 def _read_parameters(self, loaded_yaml):
533 """Process the parameters portion of the loaded yaml document
535 Parameters
536 ---------
537 loaded_yaml : `dict`
538 A dictionary which matches the structure that would be produced by
539 a yaml reader which parses a pipeline definition document
540 """
541 loaded_parameters = loaded_yaml.pop("parameters", {})
542 if not isinstance(loaded_parameters, dict):
543 raise ValueError("The parameters section must be a yaml mapping")
544 self.parameters = ParametersIR(loaded_parameters)
546 def _read_labeled_subsets(self, loaded_yaml: dict):
547 """Process the subsets portion of the loaded yaml document
549 Parameters
550 ----------
551 loaded_yaml: `MutableMapping`
552 A dictionary which matches the structure that would be produced
553 by a yaml reader which parses a pipeline definition document
554 """
555 loaded_subsets = loaded_yaml.pop("subsets", {})
556 self.labeled_subsets = {}
557 if not loaded_subsets and "subset" in loaded_yaml:
558 raise ValueError("Top level key should be subsets and not subset, add an s")
559 for key, value in loaded_subsets.items():
560 self.labeled_subsets[key] = LabeledSubset.from_primitives(key, value)
562 def _verify_labeled_subsets(self):
563 """Verifies that all the labels in each named subset exist within the
564 pipeline.
565 """
566 # Verify that all labels defined in a labeled subset are in the
567 # Pipeline
568 for labeled_subset in self.labeled_subsets.values():
569 if not labeled_subset.subset.issubset(self.tasks.keys()):
570 raise ValueError(f"Labels {labeled_subset.subset - self.tasks.keys()} were not found in the "
571 "declared pipeline")
572 # Verify subset labels are not already task labels
573 label_intersection = self.labeled_subsets.keys() & self.tasks.keys()
574 if label_intersection:
575 raise ValueError(f"Labeled subsets can not use the same label as a task: {label_intersection}")
577 def _read_imports(self, loaded_yaml):
578 """Process the inherits portion of the loaded yaml document
580 Parameters
581 ---------
582 loaded_yaml : `dict`
583 A dictionary which matches the structure that would be produced by
584 a yaml reader which parses a pipeline definition document
585 """
586 def process_args(argument: Union[str, dict]) -> dict:
587 if isinstance(argument, str):
588 return {"location": argument}
589 elif isinstance(argument, dict):
590 if "exclude" in argument and isinstance(argument["exclude"], str):
591 argument["exclude"] = [argument["exclude"]]
592 if "include" in argument and isinstance(argument["include"], str):
593 argument["include"] = [argument["include"]]
594 if "instrument" in argument and argument["instrument"] == "None":
595 argument["instrument"] = None
596 return argument
597 if not {"inherits", "imports"} - loaded_yaml.keys():
598 raise ValueError("Cannot define both inherits and imports sections, use imports")
599 tmp_import = loaded_yaml.pop("inherits", None)
600 if tmp_import is None:
601 tmp_import = loaded_yaml.pop("imports", None)
602 else:
603 warnings.warn("The 'inherits' key is deprecated, and will be "
604 "removed around June 2021. Please use the key "
605 "'imports' instead")
606 if tmp_import is None:
607 self.imports = []
608 elif isinstance(tmp_import, list):
609 self.imports = [ImportIR(**process_args(args)) for args in tmp_import]
610 else:
611 self.imports = [ImportIR(**process_args(tmp_import))]
613 # integrate any imported pipelines
614 accumulate_tasks = {}
615 accumulate_labeled_subsets = {}
616 accumulated_parameters = ParametersIR({})
617 for other_pipeline in self.imports:
618 tmp_IR = other_pipeline.toPipelineIR()
619 if self.instrument is None:
620 self.instrument = tmp_IR.instrument
621 elif self.instrument != tmp_IR.instrument and tmp_IR.instrument is not None:
622 msg = ("Only one instrument can be declared in a pipeline or its imports. "
623 f"Top level pipeline defines {self.instrument} but {other_pipeline.location} "
624 f"defines {tmp_IR.instrument}.")
625 raise ValueError(msg)
626 if duplicate_labels := accumulate_tasks.keys() & tmp_IR.tasks.keys():
627 msg = ("Task labels in the imported pipelines must be unique. "
628 f"These labels appear multiple times: {duplicate_labels}")
629 raise ValueError(msg)
630 accumulate_tasks.update(tmp_IR.tasks)
631 self.contracts.extend(tmp_IR.contracts)
632 # verify that tmp_IR has unique labels for named subset among
633 # existing labeled subsets, and with existing task labels.
634 overlapping_subsets = accumulate_labeled_subsets.keys() & tmp_IR.labeled_subsets.keys()
635 task_subset_overlap = ((accumulate_labeled_subsets.keys() | tmp_IR.labeled_subsets.keys())
636 & accumulate_tasks.keys())
637 if overlapping_subsets or task_subset_overlap:
638 raise ValueError("Labeled subset names must be unique amongst imports in both labels and "
639 f" named Subsets. Duplicate: {overlapping_subsets | task_subset_overlap}")
640 accumulate_labeled_subsets.update(tmp_IR.labeled_subsets)
641 accumulated_parameters.update(tmp_IR.parameters)
643 # verify that any accumulated labeled subsets dont clash with a label
644 # from this pipeline
645 if accumulate_labeled_subsets.keys() & self.tasks.keys():
646 raise ValueError("Labeled subset names must be unique amongst imports in both labels and "
647 " named Subsets")
648 # merge in the named subsets for self so this document can override any
649 # that have been delcared
650 accumulate_labeled_subsets.update(self.labeled_subsets)
651 self.labeled_subsets = accumulate_labeled_subsets
653 # merge the dict of label:TaskIR objects, preserving any configs in the
654 # imported pipeline if the labels point to the same class
655 for label, task in self.tasks.items():
656 if label not in accumulate_tasks:
657 accumulate_tasks[label] = task
658 elif accumulate_tasks[label].klass == task.klass:
659 if task.config is not None:
660 for config in task.config:
661 accumulate_tasks[label].add_or_update_config(config)
662 else:
663 accumulate_tasks[label] = task
664 self.tasks = accumulate_tasks
665 accumulated_parameters.update(self.parameters)
666 self.parameters = accumulated_parameters
668 def _read_tasks(self, loaded_yaml):
669 """Process the tasks portion of the loaded yaml document
671 Parameters
672 ---------
673 loaded_yaml : `dict`
674 A dictionary which matches the structure that would be produced by
675 a yaml reader which parses a pipeline definition document
676 """
677 self.tasks = {}
678 tmp_tasks = loaded_yaml.pop("tasks", None)
679 if tmp_tasks is None:
680 tmp_tasks = {}
682 if "parameters" in tmp_tasks:
683 raise ValueError("parameters is a reserved word and cannot be used as a task label")
685 for label, definition in tmp_tasks.items():
686 if isinstance(definition, str):
687 definition = {"class": definition}
688 config = definition.get('config', None)
689 if config is None:
690 task_config_ir = None
691 else:
692 if isinstance(config, dict):
693 config = [config]
694 task_config_ir = []
695 for c in config:
696 file = c.pop("file", None)
697 if file is None:
698 file = []
699 elif not isinstance(file, list):
700 file = [file]
701 task_config_ir.append(ConfigIR(python=c.pop("python", None),
702 dataId=c.pop("dataId", None),
703 file=file,
704 rest=c))
705 self.tasks[label] = TaskIR(label, definition["class"], task_config_ir)
707 def _remove_contracts(self, label: str):
708 """Remove any contracts that contain the given label
710 String comparison used in this way is not the most elegant and may
711 have issues, but it is the only feasible way when users can specify
712 contracts with generic strings.
713 """
714 new_contracts = []
715 for contract in self.contracts:
716 # match a label that is not preceded by an ASCII identifier, or
717 # is the start of a line and is followed by a dot
718 if re.match(f".*([^A-Za-z0-9_]|^){label}[.]", contract.contract):
719 continue
720 new_contracts.append(contract)
721 self.contracts = new_contracts
723 def subset_from_labels(self, labelSpecifier: Set[str]) -> PipelineIR:
724 """Subset a pipelineIR to contain only labels specified in
725 labelSpecifier.
727 Parameters
728 ----------
729 labelSpecifier : `set` of `str`
730 Set containing labels that describes how to subset a pipeline.
732 Returns
733 -------
734 pipeline : `PipelineIR`
735 A new pipelineIR object that is a subset of the old pipelineIR
737 Raises
738 ------
739 ValueError
740 Raised if there is an issue with specified labels
742 Notes
743 -----
744 This method attempts to prune any contracts that contain labels which
745 are not in the declared subset of labels. This pruning is done using a
746 string based matching due to the nature of contracts and may prune more
747 than it should. Any labeled subsets defined that no longer have all
748 members of the subset present in the pipeline will be removed from the
749 resulting pipeline.
750 """
752 pipeline = copy.deepcopy(self)
754 # update the label specifier to expand any named subsets
755 toRemove = set()
756 toAdd = set()
757 for label in labelSpecifier:
758 if label in pipeline.labeled_subsets:
759 toRemove.add(label)
760 toAdd.update(pipeline.labeled_subsets[label].subset)
761 labelSpecifier.difference_update(toRemove)
762 labelSpecifier.update(toAdd)
763 # verify all the labels are in the pipeline
764 if not labelSpecifier.issubset(pipeline.tasks.keys()
765 | pipeline.labeled_subsets):
766 difference = labelSpecifier.difference(pipeline.tasks.keys())
767 raise ValueError("Not all supplied labels (specified or named subsets) are in the pipeline "
768 f"definition, extra labels: {difference}")
769 # copy needed so as to not modify while iterating
770 pipeline_labels = set(pipeline.tasks.keys())
771 # Remove the labels from the pipelineIR, and any contracts that contain
772 # those labels (see docstring on _remove_contracts for why this may
773 # cause issues)
774 for label in pipeline_labels:
775 if label not in labelSpecifier:
776 pipeline.tasks.pop(label)
777 pipeline._remove_contracts(label)
779 # create a copy of the object to iterate over
780 labeled_subsets = copy.copy(pipeline.labeled_subsets)
781 # remove any labeled subsets that no longer have a complete set
782 for label, labeled_subset in labeled_subsets.items():
783 if labeled_subset.subset - pipeline.tasks.keys():
784 pipeline.labeled_subsets.pop(label)
786 return pipeline
788 @classmethod
789 def from_string(cls, pipeline_string: str):
790 """Create a `PipelineIR` object from a string formatted like a pipeline
791 document
793 Parameters
794 ----------
795 pipeline_string : `str`
796 A string that is formatted according like a pipeline document
797 """
798 loaded_yaml = yaml.load(pipeline_string, Loader=PipelineYamlLoader)
799 return cls(loaded_yaml)
801 @classmethod
802 @deprecated(reason="This has been replaced with `from_uri`. will be removed after v23",
803 version="v21.0,", category=FutureWarning) # type: ignore
804 def from_file(cls, filename: str) -> PipelineIR:
805 """Create a `PipelineIR` object from the document specified by the
806 input path.
808 Parameters
809 ----------
810 filename : `str`
811 Location of document to use in creating a `PipelineIR` object.
813 Returns
814 -------
815 pipelineIR : `PipelineIR`
816 The loaded pipeline
818 Note
819 ----
820 This method is deprecated, please use from_uri
821 """
822 return cls.from_uri(filename)
824 @classmethod
825 def from_uri(cls, uri: Union[str, ButlerURI]) -> PipelineIR:
826 """Create a `PipelineIR` object from the document specified by the
827 input uri.
829 Parameters
830 ----------
831 uri: `str` or `ButlerURI`
832 Location of document to use in creating a `PipelineIR` object.
834 Returns
835 -------
836 pipelineIR : `PipelineIR`
837 The loaded pipeline
838 """
839 loaded_uri = ButlerURI(uri)
840 # With ButlerURI we have the choice of always using a local file or
841 # reading in the bytes directly. Reading in bytes can be more
842 # efficient for reasonably-sized files when the resource is remote.
843 # For now use the local file variant. For a local file as_local() does
844 # nothing.
845 with loaded_uri.as_local() as local:
846 # explicitly read here, there was some issue with yaml trying
847 # to read the ButlerURI itself (I think because it only
848 # pretends to be conformant to the io api)
849 loaded_yaml = yaml.load(local.read(), Loader=PipelineYamlLoader)
850 return cls(loaded_yaml)
852 @deprecated(reason="This has been replaced with `write_to_uri`. will be removed after v23",
853 version="v21.0,", category=FutureWarning) # type: ignore
854 def to_file(self, filename: str):
855 """Serialize this `PipelineIR` object into a yaml formatted string and
856 write the output to a file at the specified path.
858 Parameters
859 ----------
860 filename : `str`
861 Location of document to write a `PipelineIR` object.
862 """
863 self.write_to_uri(filename)
865 def write_to_uri(self, uri: Union[ButlerURI, str]):
866 """Serialize this `PipelineIR` object into a yaml formatted string and
867 write the output to a file at the specified uri.
869 Parameters
870 ----------
871 uri: `str` or `ButlerURI`
872 Location of document to write a `PipelineIR` object.
873 """
874 butlerUri = ButlerURI(uri)
875 butlerUri.write(yaml.dump(self.to_primitives(), sort_keys=False).encode())
877 def to_primitives(self) -> Dict[str, Any]:
878 """Convert to a representation used in yaml serialization
879 """
880 accumulate = {"description": self.description}
881 if self.instrument is not None:
882 accumulate['instrument'] = self.instrument
883 if self.parameters:
884 accumulate['parameters'] = self.parameters.to_primitives()
885 accumulate['tasks'] = {m: t.to_primitives() for m, t in self.tasks.items()}
886 if len(self.contracts) > 0:
887 accumulate['contracts'] = [c.to_primitives() for c in self.contracts]
888 if self.labeled_subsets:
889 accumulate['subsets'] = {k: v.to_primitives() for k, v in self.labeled_subsets.items()}
890 return accumulate
892 def __str__(self) -> str:
893 """Instance formatting as how it would look in yaml representation
894 """
895 return yaml.dump(self.to_primitives(), sort_keys=False)
897 def __repr__(self) -> str:
898 """Instance formatting as how it would look in yaml representation
899 """
900 return str(self)
902 def __eq__(self, other: object):
903 if not isinstance(other, PipelineIR):
904 return False
905 elif all(getattr(self, attr) == getattr(other, attr) for attr in
906 ("contracts", "tasks", "instrument")):
907 return True
908 else:
909 return False