Coverage for python/lsst/daf/butler/cli/utils.py: 35%
351 statements
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1# This file is part of daf_butler.
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__ = (
24 "astropyTablesToStr",
25 "printAstropyTables",
26 "textTypeStr",
27 "LogCliRunner",
28 "clickResultMsg",
29 "command_test_env",
30 "addArgumentHelp",
31 "split_commas",
32 "split_kv",
33 "to_upper",
34 "unwrap",
35 "option_section",
36 "MWPath",
37 "MWOption",
38 "MWArgument",
39 "OptionSection",
40 "MWOptionDecorator",
41 "MWArgumentDecorator",
42 "MWCommand",
43 "ButlerCommand",
44 "OptionGroup",
45 "MWCtxObj",
46 "yaml_presets",
47 "sortAstropyTable",
48 "catch_and_exit",
49)
52import itertools
53import logging
54import os
55import re
56import sys
57import textwrap
58import traceback
59import uuid
60import warnings
61from collections import Counter
62from collections.abc import Callable, Iterable, Iterator
63from contextlib import contextmanager
64from functools import partial, wraps
65from typing import TYPE_CHECKING, Any, cast
66from unittest.mock import patch
68import click
69import click.exceptions
70import click.testing
71import yaml
72from lsst.utils.iteration import ensure_iterable
74from ..core.config import Config
75from .cliLog import CliLog
77if TYPE_CHECKING:
78 from astropy.table import Table
79 from lsst.daf.butler import Dimension
81log = logging.getLogger(__name__)
83# This is used as the metavar argument to Options that accept multiple string
84# inputs, which may be comma-separarated. For example:
85# --my-opt foo,bar --my-opt baz.
86# Other arguments to the Option should include multiple=true and
87# callback=split_kv.
88typeStrAcceptsMultiple = "TEXT ..."
89typeStrAcceptsSingle = "TEXT"
91# The standard help string for the --where option when it takes a WHERE clause.
92where_help = (
93 "A string expression similar to a SQL WHERE clause. May involve any column of a "
94 "dimension table or a dimension name as a shortcut for the primary key column of a "
95 "dimension table."
96)
99def astropyTablesToStr(tables: list[Table]) -> str:
100 """Render astropy tables to string as they are displayed in the CLI.
102 Output formatting matches ``printAstropyTables``.
103 """
104 ret = ""
105 for table in tables:
106 ret += "\n"
107 table.pformat_all()
108 ret += "\n"
109 return ret
112def printAstropyTables(tables: list[Table]) -> None:
113 """Print astropy tables to be displayed in the CLI.
115 Output formatting matches ``astropyTablesToStr``.
116 """
117 for table in tables:
118 print("")
119 table.pprint_all()
120 print("")
123def textTypeStr(multiple: bool) -> str:
124 """Get the text type string for CLI help documentation.
126 Parameters
127 ----------
128 multiple : `bool`
129 True if multiple text values are allowed, False if only one value is
130 allowed.
132 Returns
133 -------
134 textTypeStr : `str`
135 The type string to use.
136 """
137 return typeStrAcceptsMultiple if multiple else typeStrAcceptsSingle
140class LogCliRunner(click.testing.CliRunner):
141 """A test runner to use when the logging system will be initialized by code
142 under test, calls CliLog.resetLog(), which undoes any logging setup that
143 was done with the CliLog interface.
145 lsst.log modules can not be set back to an uninitialized state (python
146 logging modules can be set back to NOTSET), instead they are set to
147 `CliLog.defaultLsstLogLevel`.
148 """
150 def invoke(self, *args: Any, **kwargs: Any) -> Any:
151 result = super().invoke(*args, **kwargs)
152 CliLog.resetLog()
153 return result
156def clickResultMsg(result: click.testing.Result) -> str:
157 """Get a standard assert message from a click result.
159 Parameters
160 ----------
161 result : click.testing.Result
162 The result object returned from click.testing.CliRunner.invoke
164 Returns
165 -------
166 msg : `str`
167 The message string.
168 """
169 msg = f"""\noutput: {result.output}\nexception: {result.exception}"""
170 if result.exception:
171 msg += f"""\ntraceback: {"".join(traceback.format_tb(result.exception.__traceback__))}"""
172 return msg
175@contextmanager
176def command_test_env(runner: click.testing.CliRunner, commandModule: str, commandName: str) -> Iterator[None]:
177 """Context manager that creates (and then cleans up) an environment that
178 provides a CLI plugin command with the given name.
180 Parameters
181 ----------
182 runner : click.testing.CliRunner
183 The test runner to use to create the isolated filesystem.
184 commandModule : `str`
185 The importable module that the command can be imported from.
186 commandName : `str`
187 The name of the command being published to import.
188 """
189 with runner.isolated_filesystem():
190 with open("resources.yaml", "w") as f:
191 f.write(yaml.dump({"cmd": {"import": commandModule, "commands": [commandName]}}))
192 # Add a colon to the end of the path on the next line, this tests the
193 # case where the lookup in LoaderCLI._getPluginList generates an empty
194 # string in one of the list entries and verifies that the empty string
195 # is properly stripped out.
196 with patch.dict("os.environ", {"DAF_BUTLER_PLUGINS": f"{os.path.realpath(f.name)}:"}):
197 yield
200def addArgumentHelp(doc: str | None, helpText: str) -> str:
201 """Add a Click argument's help message to a function's documentation.
203 This is needed because click presents arguments in the order the argument
204 decorators are applied to a function, top down. But, the evaluation of the
205 decorators happens bottom up, so if arguments just append their help to the
206 function's docstring, the argument descriptions appear in reverse order
207 from the order they are applied in.
209 Parameters
210 ----------
211 doc : `str`
212 The function's docstring.
213 helpText : `str`
214 The argument's help string to be inserted into the function's
215 docstring.
217 Returns
218 -------
219 doc : `str`
220 Updated function documentation.
221 """
222 if doc is None: 222 ↛ 223line 222 didn't jump to line 223, because the condition on line 222 was never true
223 doc = helpText
224 else:
225 # See click documentation for details:
226 # https://click.palletsprojects.com/en/7.x/documentation/#truncating-help-texts
227 # In short, text for the click command help can be truncated by putting
228 # "\f" in the docstring, everything after it should be removed
229 if "\f" in doc: 229 ↛ 230line 229 didn't jump to line 230, because the condition on line 229 was never true
230 doc = doc.split("\f")[0]
232 doclines = doc.splitlines()
233 # The function's docstring may span multiple lines, so combine the
234 # docstring from all the first lines until a blank line is encountered.
235 # (Lines after the first blank line will be argument help.)
236 while len(doclines) > 1 and doclines[1]:
237 doclines[0] = " ".join((doclines[0], doclines.pop(1).strip()))
238 # Add standard indent to help text for proper alignment with command
239 # function documentation:
240 helpText = " " + helpText
241 doclines.insert(1, helpText)
242 doclines.insert(1, "\n")
243 doc = "\n".join(doclines)
244 return doc
247def split_commas(
248 context: click.Context | None, param: click.core.Option | None, values: str | Iterable[str] | None
249) -> tuple[str, ...]:
250 """Process a tuple of values, where each value may contain comma-separated
251 values, and return a single list of all the passed-in values.
253 This function can be passed to the 'callback' argument of a click.option to
254 allow it to process comma-separated values (e.g. "--my-opt a,b,c"). If
255 the comma is inside ``[]`` there will be no splitting.
257 Parameters
258 ----------
259 context : `click.Context` or `None`
260 The current execution context. Unused, but Click always passes it to
261 callbacks.
262 param : `click.core.Option` or `None`
263 The parameter being handled. Unused, but Click always passes it to
264 callbacks.
265 values : iterable of `str` or `str`
266 All the values passed for this option. Strings may contain commas,
267 which will be treated as delimiters for separate values unless they
268 are within ``[]``.
270 Returns
271 -------
272 results : `tuple` [`str`]
273 The passed in values separated by commas where appropriate and
274 combined into a single tuple.
275 """
276 if values is None:
277 return ()
278 valueList = []
279 for value in ensure_iterable(values):
280 # If we have [, or ,] we do the slow split. If square brackets
281 # are not matching then that is likely a typo that should result
282 # in a warning.
283 opens = "["
284 closes = "]"
285 if re.search(rf"\{opens}.*,|,.*\{closes}", value):
286 in_parens = False
287 current = ""
288 for c in value:
289 if c == opens:
290 if in_parens:
291 warnings.warn(
292 f"Found second opening {opens} without corresponding closing {closes}"
293 f" in {value!r}",
294 stacklevel=2,
295 )
296 in_parens = True
297 elif c == closes:
298 if not in_parens:
299 warnings.warn(
300 f"Found second closing {closes} without corresponding open {opens} in {value!r}",
301 stacklevel=2,
302 )
303 in_parens = False
304 elif c == "," and not in_parens:
305 # Split on this comma.
306 valueList.append(current)
307 current = ""
308 continue
309 current += c
310 if in_parens:
311 warnings.warn(
312 f"Found opening {opens} that was never closed in {value!r}",
313 stacklevel=2,
314 )
315 if current:
316 valueList.append(current)
317 else:
318 # Use efficient split since no parens.
319 valueList.extend(value.split(","))
320 return tuple(valueList)
323def split_kv(
324 context: click.Context,
325 param: click.core.Option,
326 values: list[str],
327 *,
328 choice: click.Choice | None = None,
329 multiple: bool = True,
330 normalize: bool = False,
331 separator: str = "=",
332 unseparated_okay: bool = False,
333 return_type: type[dict] | type[tuple] = dict,
334 default_key: str = "",
335 reverse_kv: bool = False,
336 add_to_default: bool = False,
337) -> dict[str, str] | tuple[tuple[str, str], ...]:
338 """Process a tuple of values that are key-value pairs separated by a given
339 separator. Multiple pairs may be comma separated. Return a dictionary of
340 all the passed-in values.
342 This function can be passed to the 'callback' argument of a click.option to
343 allow it to process comma-separated values (e.g. "--my-opt a=1,b=2").
345 Parameters
346 ----------
347 context : `click.Context` or `None`
348 The current execution context. Unused, but Click always passes it to
349 callbacks.
350 param : `click.core.Option` or `None`
351 The parameter being handled. Unused, but Click always passes it to
352 callbacks.
353 values : [`str`]
354 All the values passed for this option. Strings may contain commas,
355 which will be treated as delimiters for separate values.
356 choice : `click.Choice`, optional
357 If provided, verify each value is a valid choice using the provided
358 `click.Choice` instance. If None, no verification will be done. By
359 default None
360 multiple : `bool`, optional
361 If true, the value may contain multiple comma-separated values. By
362 default True.
363 normalize : `bool`, optional
364 If True and `choice.case_sensitive == False`, normalize the string the
365 user provided to match the choice's case. By default False.
366 separator : str, optional
367 The character that separates key-value pairs. May not be a comma or an
368 empty space (for space separators use Click's default implementation
369 for tuples; `type=(str, str)`). By default "=".
370 unseparated_okay : `bool`, optional
371 If True, allow values that do not have a separator. They will be
372 returned in the values dict as a tuple of values in the key '', that
373 is: `values[''] = (unseparated_values, )`. By default False.
374 return_type : `type`, must be `dict` or `tuple`
375 The type of the value that should be returned.
376 If `dict` then the returned object will be a dict, for each item in
377 values, the value to the left of the separator will be the key and the
378 value to the right of the separator will be the value.
379 If `tuple` then the returned object will be a tuple. Each item in the
380 tuple will be 2-item tuple, the first item will be the value to the
381 left of the separator and the second item will be the value to the
382 right. By default `dict`.
383 default_key : `Any`
384 The key to use if a value is passed that is not a key-value pair.
385 (Passing values that are not key-value pairs requires
386 ``unseparated_okay`` to be `True`.)
387 reverse_kv : bool
388 If true then for each item in values, the value to the left of the
389 separator is treated as the value and the value to the right of the
390 separator is treated as the key. By default False.
391 add_to_default : `bool`, optional
392 If True, then passed-in values will not overwrite the default value
393 unless the ``return_type`` is `dict` and passed-in value(s) have the
394 same key(s) as the default value.
396 Returns
397 -------
398 values : `dict` [`str`, `str`] or `tuple`[`tuple`[`str`, `str`], ...]
399 The passed-in values in dict form or tuple form.
401 Raises
402 ------
403 `click.ClickException`
404 Raised if the separator is not found in an entry, or if duplicate keys
405 are encountered.
406 """
408 def norm(val: str) -> str:
409 """If `normalize` is True and `choice` is not `None`, find the value
410 in the available choices and return the value as spelled in the
411 choices.
413 Assumes that val exists in choices; `split_kv` uses the `choice`
414 instance to verify val is a valid choice.
415 """
416 if normalize and choice is not None:
417 v = val.casefold()
418 for opt in choice.choices:
419 if opt.casefold() == v:
420 return opt
421 return val
423 class RetDict:
424 def __init__(self) -> None:
425 self.ret: dict[str, str] = {}
427 def add(self, key: str, val: str) -> None:
428 if reverse_kv:
429 key, val = val, key
430 self.ret[key] = val
432 def get(self) -> dict[str, str]:
433 return self.ret
435 class RetTuple:
436 def __init__(self) -> None:
437 self.ret: list[tuple[str, str]] = []
439 def add(self, key: str, val: str) -> None:
440 if reverse_kv:
441 key, val = val, key
442 self.ret.append((key, val))
444 def get(self) -> tuple[tuple[str, str], ...]:
445 return tuple(self.ret)
447 if separator in (",", " "):
448 raise RuntimeError(f"'{separator}' is not a supported separator for key-value pairs.")
449 vals = tuple(ensure_iterable(values)) # preserve the original argument for error reporting below.
451 if add_to_default:
452 default = param.get_default(context)
453 if default:
454 vals = tuple(v for v in itertools.chain(default, vals)) # Convert to tuple for mypy
456 ret: RetDict | RetTuple
457 if return_type is dict:
458 ret = RetDict()
459 elif return_type is tuple:
460 ret = RetTuple()
461 else:
462 raise click.ClickException(
463 message=f"Internal error: invalid return type '{return_type}' for split_kv."
464 )
465 if multiple:
466 vals = split_commas(context, param, vals)
467 for val in ensure_iterable(vals):
468 if unseparated_okay and separator not in val:
469 if choice is not None:
470 choice(val) # will raise if val is an invalid choice
471 ret.add(default_key, norm(val))
472 else:
473 try:
474 k, v = val.split(separator)
475 if choice is not None:
476 choice(v) # will raise if val is an invalid choice
477 except ValueError as e:
478 raise click.ClickException(
479 message=f"Could not parse key-value pair '{val}' using separator '{separator}', "
480 f"with multiple values {'allowed' if multiple else 'not allowed'}: {e}"
481 ) from None
482 ret.add(k, norm(v))
483 return ret.get()
486def to_upper(context: click.Context, param: click.core.Option, value: str) -> str:
487 """Convert a value to upper case.
489 Parameters
490 ----------
491 context : click.Context
493 values : string
494 The value to be converted.
496 Returns
497 -------
498 string
499 A copy of the passed-in value, converted to upper case.
500 """
501 return value.upper()
504def unwrap(val: str) -> str:
505 """Remove newlines and leading whitespace from a multi-line string with
506 a consistent indentation level.
508 The first line of the string may be only a newline or may contain text
509 followed by a newline, either is ok. After the first line, each line must
510 begin with a consistant amount of whitespace. So, content of a
511 triple-quoted string may begin immediately after the quotes, or the string
512 may start with a newline. Each line after that must be the same amount of
513 indentation/whitespace followed by text and a newline. The last line may
514 end with a new line but is not required to do so.
516 Parameters
517 ----------
518 val : `str`
519 The string to change.
521 Returns
522 -------
523 strippedString : `str`
524 The string with newlines, indentation, and leading and trailing
525 whitespace removed.
526 """
528 def splitSection(val: str) -> str:
529 if not val.startswith("\n"): 529 ↛ 533line 529 didn't jump to line 533, because the condition on line 529 was never false
530 firstLine, _, val = val.partition("\n")
531 firstLine += " "
532 else:
533 firstLine = ""
534 return (firstLine + textwrap.dedent(val).replace("\n", " ")).strip()
536 return "\n\n".join([splitSection(s) for s in val.split("\n\n")])
539class option_section: # noqa: N801
540 """Decorator to add a section label between options in the help text of a
541 command.
543 Parameters
544 ----------
545 sectionText : `str`
546 The text to print in the section identifier.
547 """
549 def __init__(self, sectionText: str) -> None:
550 self.sectionText = "\n" + sectionText
552 def __call__(self, f: Any) -> click.Option:
553 # Generate a parameter declaration that will be unique for this
554 # section.
555 return click.option(
556 f"--option-section-{str(uuid.uuid4())}", sectionText=self.sectionText, cls=OptionSection
557 )(f)
560class MWPath(click.Path):
561 """Overrides click.Path to implement file-does-not-exist checking.
563 Changes the definition of ``exists` so that `True` indicates the location
564 (file or directory) must exist, `False` indicates the location must *not*
565 exist, and `None` indicates that the file may exist or not. The standard
566 definition for the `click.Path` ``exists`` parameter is that for `True` a
567 location must exist, but `False` means it is not required to exist (not
568 that it is required to not exist).
570 Parameters
571 ----------
572 exists : `True`, `False`, or `None`
573 If `True`, the location (file or directory) indicated by the caller
574 must exist. If `False` the location must not exist. If `None`, the
575 location may exist or not.
577 For other parameters see `click.Path`.
578 """
580 def __init__(
581 self,
582 exists: bool | None = None,
583 file_okay: bool = True,
584 dir_okay: bool = True,
585 writable: bool = False,
586 readable: bool = True,
587 resolve_path: bool = False,
588 allow_dash: bool = False,
589 path_type: type | None = None,
590 ):
591 self.mustNotExist = exists is False
592 if exists is None: 592 ↛ 594line 592 didn't jump to line 594, because the condition on line 592 was never false
593 exists = False
594 super().__init__(
595 exists=exists,
596 file_okay=file_okay,
597 dir_okay=dir_okay,
598 writable=writable,
599 readable=readable,
600 resolve_path=resolve_path,
601 allow_dash=allow_dash,
602 path_type=path_type,
603 )
605 def convert(
606 self, value: str | os.PathLike[str], param: click.Parameter | None, ctx: click.Context | None
607 ) -> Any:
608 """Convert values through types.
610 Called by `click.ParamType` to "convert values through types".
611 `click.Path` uses this step to verify Path conditions.
612 """
613 if self.mustNotExist and os.path.exists(value):
614 self.fail(f'Path "{value}" should not exist.')
615 return super().convert(value, param, ctx)
618class MWOption(click.Option):
619 """Overrides click.Option with desired behaviors."""
621 def make_metavar(self) -> str:
622 """Make the metavar for the help menu.
624 Overrides `click.Option.make_metavar`.
625 Adds a space and an ellipsis after the metavar name if
626 the option accepts multiple inputs, otherwise defers to the base
627 implementation.
629 By default click does not add an ellipsis when multiple is True and
630 nargs is 1. And when nargs does not equal 1 click adds an ellipsis
631 without a space between the metavar and the ellipsis, but we prefer a
632 space between.
634 Does not get called for some option types (e.g. flag) so metavar
635 transformation that must apply to all types should be applied in
636 get_help_record.
637 """
638 metavar = super().make_metavar()
639 if self.multiple and self.nargs == 1:
640 metavar += " ..."
641 elif self.nargs != 1:
642 metavar = f"{metavar[:-3]} ..."
643 return metavar
646class MWArgument(click.Argument):
647 """Overrides click.Argument with desired behaviors."""
649 def make_metavar(self) -> str:
650 """Make the metavar for the help menu.
652 Overrides `click.Option.make_metavar`.
653 Always adds a space and an ellipsis (' ...') after the
654 metavar name if the option accepts multiple inputs.
656 By default click adds an ellipsis without a space between the metavar
657 and the ellipsis, but we prefer a space between.
659 Returns
660 -------
661 metavar : `str`
662 The metavar value.
663 """
664 metavar = super().make_metavar()
665 if self.nargs != 1:
666 metavar = f"{metavar[:-3]} ..."
667 return metavar
670class OptionSection(MWOption):
671 """Implements an Option that prints a section label in the help text and
672 does not pass any value to the command function.
674 This class does a bit of hackery to add a section label to a click command
675 help output: first, `expose_value` is set to `False` so that no value is
676 passed to the command function. Second, this class overrides
677 `click.Option.get_help_record` to return the section label string without
678 any prefix so that it stands out as a section label.
680 This class overrides the hidden attribute because our documentation build
681 tool, sphinx-click, implements its own `get_help_record` function which
682 builds the record from other option values (e.g. `name`, `opts`), which
683 breaks the hack we use to make `get_help_record` only return the
684 `sectionText`. Fortunately, Click gets the value of `hidden` inside the
685 `Option`'s `get_help_record`, and `sphinx-click` calls `opt.hidden` before
686 entering its `_get_help_record` function. So, making the hidden property
687 return True hides this option from sphinx-click, while allowing the section
688 text to be returned by our `get_help_record` method when using Click.
690 The intention for this implementation is to do minimally invasive overrides
691 of the click classes so as to be robust and easy to fix if the click
692 internals change.
694 Parameters
695 ----------
696 sectionName : `str`
697 The parameter declaration for this option. It is not shown to the user,
698 it must be unique within the command. If using the `section` decorator
699 to add a section to a command's options, the section name is
700 auto-generated.
701 sectionText : `str`
702 The text to print in the section identifier.
703 """
705 @property
706 def hidden(self) -> bool:
707 return True
709 @hidden.setter
710 def hidden(self, val: Any) -> None:
711 pass
713 def __init__(self, sectionName: str, sectionText: str) -> None:
714 super().__init__(sectionName, expose_value=False)
715 self.sectionText = sectionText
717 def get_help_record(self, ctx: click.Context | None) -> tuple[str, str]:
718 return (self.sectionText, "")
721class MWOptionDecorator:
722 """Wraps the click.option decorator to enable shared options to be declared
723 and allows inspection of the shared option.
724 """
726 def __init__(self, *param_decls: Any, **kwargs: Any) -> None:
727 self.partialOpt = partial(click.option, *param_decls, cls=partial(MWOption), **kwargs)
728 opt = click.Option(param_decls, **kwargs)
729 self._name = opt.name
730 self._opts = opt.opts
732 def name(self) -> str:
733 """Get the name that will be passed to the command function for this
734 option.
735 """
736 return cast(str, self._name)
738 def opts(self) -> list[str]:
739 """Get the flags that will be used for this option on the command
740 line.
741 """
742 return self._opts
744 @property
745 def help(self) -> str:
746 """Get the help text for this option. Returns an empty string if no
747 help was defined.
748 """
749 return self.partialOpt.keywords.get("help", "")
751 def __call__(self, *args: Any, **kwargs: Any) -> Any:
752 return self.partialOpt(*args, **kwargs)
755class MWArgumentDecorator:
756 """Wraps the click.argument decorator to enable shared arguments to be
757 declared.
758 """
760 def __init__(self, *param_decls: Any, **kwargs: Any) -> None:
761 self._helpText = kwargs.pop("help", None)
762 self.partialArg = partial(click.argument, *param_decls, cls=MWArgument, **kwargs)
764 def __call__(self, *args: Any, help: str | None = None, **kwargs: Any) -> Callable:
765 def decorator(f: Any) -> Any:
766 if help is not None:
767 self._helpText = help
768 if self._helpText:
769 f.__doc__ = addArgumentHelp(f.__doc__, self._helpText)
770 return self.partialArg(*args, **kwargs)(f)
772 return decorator
775class MWCommand(click.Command):
776 """Command subclass that stores a copy of the args list for use by the
777 command.
778 """
780 extra_epilog: str | None = None
782 def __init__(self, *args: Any, **kwargs: Any) -> None:
783 # wrap callback method with catch_and_exit decorator
784 callback = kwargs.get("callback")
785 if callback is not None: 785 ↛ 788line 785 didn't jump to line 788, because the condition on line 785 was never false
786 kwargs = kwargs.copy()
787 kwargs["callback"] = catch_and_exit(callback)
788 super().__init__(*args, **kwargs)
790 def _capture_args(self, ctx: click.Context, args: list[str]) -> None:
791 """Capture the command line options and arguments.
793 See details about what is captured and the order in which it is stored
794 in the documentation of `MWCtxObj`.
796 Parameters
797 ----------
798 ctx : `click.Context`
799 The current Context.
800 args : `list` [`str`]
801 The list of arguments from the command line, split at spaces but
802 not at separators (like "=").
803 """
804 parser = self.make_parser(ctx)
805 opts, _, param_order = parser.parse_args(args=list(args))
806 # `param_order` is a list of click.Option and click.Argument, there is
807 # one item for each time the Option or Argument was used on the
808 # command line. Options will precede Arguments, within each sublist
809 # they are in the order they were used on the command line. Note that
810 # click.Option and click.Argument do not contain the value from the
811 # command line; values are in `opts`.
812 #
813 # `opts` is a dict where the key is the argument name to the
814 # click.Command function, this name matches the `click.Option.name` or
815 # `click.Argument.name`. For Options, an item will only be present if
816 # the Option was used on the command line. For Arguments, an item will
817 # always be present and if no value was provided on the command line
818 # the value will be `None`. If the option accepts multiple values, the
819 # value in `opts` is a tuple, otherwise it is a single item.
820 next_idx: Counter = Counter()
821 captured_args = []
822 for param in param_order:
823 if isinstance(param, click.Option):
824 param_name = cast(str, param.name)
825 if param.multiple:
826 val = opts[param_name][next_idx[param_name]]
827 next_idx[param_name] += 1
828 else:
829 val = opts[param_name]
830 if param.is_flag:
831 # Bool options store their True flags in opts and their
832 # False flags in secondary_opts.
833 if val:
834 flag = max(param.opts, key=len)
835 else:
836 flag = max(param.secondary_opts, key=len)
837 captured_args.append(flag)
838 else:
839 captured_args.append(max(param.opts, key=len))
840 captured_args.append(val)
841 elif isinstance(param, click.Argument):
842 param_name = cast(str, param.name)
843 if (opt := opts[param_name]) is not None:
844 captured_args.append(opt)
845 else:
846 raise AssertionError("All parameters should be an Option or an Argument")
847 MWCtxObj.getFrom(ctx).args = captured_args
849 def parse_args(self, ctx: click.Context, args: Any) -> list[str]:
850 """Given a context and a list of arguments this creates the parser and
851 parses the arguments, then modifies the context as necessary. This is
852 automatically invoked by make_context().
854 This function overrides `click.Command.parse_args`.
856 The call to `_capture_args` in this override stores the arguments
857 (option names, option value, and argument values) that were used by the
858 caller on the command line in the context object. These stored
859 arugments can be used by the command function, e.g. to process options
860 in the order they appeared on the command line (pipetask uses this
861 feature to create pipeline actions in an order from different options).
863 Parameters
864 ----------
865 ctx : `click.core.Context`
866 The current Context.ß
867 args : `list` [`str`]
868 The list of arguments from the command line, split at spaces but
869 not at separators (like "=").
870 """
871 self._capture_args(ctx, args)
872 return super().parse_args(ctx, args)
874 @property
875 def epilog(self) -> str | None:
876 """Override the epilog attribute to add extra_epilog (if defined by a
877 subclass) to the end of any epilog provided by a subcommand.
878 """
879 ret = self._epilog if self._epilog else ""
880 if self.extra_epilog:
881 if ret:
882 ret += "\n\n"
883 ret += self.extra_epilog
884 return ret
886 @epilog.setter
887 def epilog(self, val: str) -> None:
888 self._epilog = val
891class ButlerCommand(MWCommand):
892 """Command subclass with butler-command specific overrides."""
894 extra_epilog = "See 'butler --help' for more options."
897class OptionGroup:
898 """Base class for an option group decorator. Requires the option group
899 subclass to have a property called `decorator`.
900 """
902 decorators: list[Any]
904 def __call__(self, f: Any) -> Any:
905 for decorator in reversed(self.decorators):
906 f = decorator(f)
907 return f
910class MWCtxObj:
911 """Helper object for managing the `click.Context.obj` parameter, allows
912 obj data to be managed in a consistent way.
914 `Context.obj` defaults to None. `MWCtxObj.getFrom(ctx)` can be used to
915 initialize the obj if needed and return a new or existing `MWCtxObj`.
917 The `args` attribute contains a list of options, option values, and
918 argument values that is similar to the list of arguments and options that
919 were passed in on the command line, with differences noted below:
921 * Option namess and option values are first in the list, and argument
922 values come last. The order of options and option values is preserved
923 within the options. The order of argument values is preserved.
925 * The longest option name is used for the option in the `args` list, e.g.
926 if an option accepts both short and long names "-o / --option" and the
927 short option name "-o" was used on the command line, the longer name will
928 be the one that appears in `args`.
930 * A long option name (which begins with two dashes "--") and its value may
931 be separated by an equal sign; the name and value are split at the equal
932 sign and it is removed. In `args`, the option is in one list item, and
933 the option value (without the equal sign) is in the next list item. e.g.
934 "--option=foo" and "--option foo" both become `["--opt", "foo"]` in
935 `args`.
937 * A short option name, (which begins with one dash "-") and its value are
938 split immediately after the short option name, and if there is
939 whitespace between the short option name and its value it is removed.
940 Everything after the short option name (excluding whitespace) is included
941 in the value. If the `Option` has a long name, the long name will be used
942 in `args` e.g. for the option "-o / --option": "-ofoo" and "-o foo"
943 become `["--option", "foo"]`, and (note!) "-o=foo" will become
944 `["--option", "=foo"]` (because everything after the short option name,
945 except whitespace, is used for the value (as is standard with unix
946 command line tools).
948 Attributes
949 ----------
950 args : `list` [`str`]
951 A list of options, option values, and arguments simialr to those that
952 were passed in on the command line. See comments about captured options
953 & arguments above.
954 """
956 def __init__(self) -> None:
957 self.args = None
959 @staticmethod
960 def getFrom(ctx: click.Context) -> Any:
961 """If needed, initialize `ctx.obj` with a new `MWCtxObj`, and return
962 the new or already existing `MWCtxObj`.
963 """
964 if ctx.obj is not None:
965 return ctx.obj
966 ctx.obj = MWCtxObj()
967 return ctx.obj
970def yaml_presets(ctx: click.Context, param: str, value: Any) -> None:
971 """Read additional values from the supplied YAML file.
973 Parameters
974 ----------
975 ctx : `click.context`
976 The context for the click operation. Used to extract the subcommand
977 name and translate option & argument names.
978 param : `str`
979 The parameter name.
980 value : `object`
981 The value of the parameter.
982 """
984 def _name_for_option(ctx: click.Context, option: str) -> str:
985 """Use a CLI option name to find the name of the argument to the
986 command function.
988 Parameters
989 ----------
990 ctx : `click.Context`
991 The context for the click operation.
992 option : `str`
993 The option/argument name from the yaml file.
995 Returns
996 -------
997 name : str
998 The name of the argument to use when calling the click.command
999 function, as it should appear in the `ctx.default_map`.
1001 Raises
1002 ------
1003 RuntimeError
1004 Raised if the option name from the yaml file does not exist in the
1005 command parameters. This catches misspellings and incorrect useage
1006 in the yaml file.
1007 """
1008 for param in ctx.command.params:
1009 # Remove leading dashes: they are not used for option names in the
1010 # yaml file.
1011 if option in [opt.lstrip("-") for opt in param.opts]:
1012 return cast(str, param.name)
1013 raise RuntimeError(f"'{option}' is not a valid option for {ctx.info_name}")
1015 ctx.default_map = ctx.default_map or {}
1016 cmd_name = ctx.info_name
1017 assert cmd_name is not None, "command name cannot be None"
1018 if value:
1019 try:
1020 overrides = _read_yaml_presets(value, cmd_name)
1021 options = list(overrides.keys())
1022 for option in options:
1023 name = _name_for_option(ctx, option)
1024 if name == option:
1025 continue
1026 overrides[name] = overrides.pop(option)
1027 except Exception as e:
1028 raise click.BadOptionUsage(
1029 option_name=param,
1030 message=f"Error reading overrides file: {e}",
1031 ctx=ctx,
1032 ) from None
1033 # Override the defaults for this subcommand
1034 ctx.default_map.update(overrides)
1035 return
1038def _read_yaml_presets(file_uri: str, cmd_name: str) -> dict[str, Any]:
1039 """Read file command line overrides from YAML config file.
1041 Parameters
1042 ----------
1043 file_uri : `str`
1044 URI of override YAML file containing the command line overrides.
1045 They should be grouped by command name.
1046 cmd_name : `str`
1047 The subcommand name that is being modified.
1049 Returns
1050 -------
1051 overrides : `dict` of [`str`, Any]
1052 The relevant command line options read from the override file.
1053 """
1054 log.debug("Reading command line overrides for subcommand %s from URI %s", cmd_name, file_uri)
1055 config = Config(file_uri)
1056 return config[cmd_name]
1059def sortAstropyTable(table: Table, dimensions: list[Dimension], sort_first: list[str] | None = None) -> Table:
1060 """Sort an astropy table, with prioritization given to columns in this
1061 order:
1062 1. the provided named columns
1063 2. spatial and temporal columns
1064 3. the rest of the columns.
1066 The table is sorted in-place, and is also returned for convenience.
1068 Parameters
1069 ----------
1070 table : `astropy.table.Table`
1071 The table to sort
1072 dimensions : `list` [``Dimension``]
1073 The dimensions of the dataIds in the table (the dimensions should be
1074 the same for all the dataIds). Used to determine if the column is
1075 spatial, temporal, or neither.
1076 sort_first : `list` [`str`]
1077 The names of columns that should be sorted first, before spatial and
1078 temporal columns.
1080 Returns
1081 -------
1082 `astropy.table.Table`
1083 For convenience, the table that has been sorted.
1084 """
1085 # For sorting we want to ignore the id
1086 # We also want to move temporal or spatial dimensions earlier
1087 sort_first = sort_first or []
1088 sort_early: list[str] = []
1089 sort_late: list[str] = []
1090 for dim in dimensions:
1091 if dim.spatial or dim.temporal:
1092 sort_early.extend(dim.required.names)
1093 else:
1094 sort_late.append(str(dim))
1095 sort_keys = sort_first + sort_early + sort_late
1096 # The required names above means that we have the possibility of
1097 # repeats of sort keys. Now have to remove them
1098 # (order is retained by dict creation).
1099 sort_keys = list(dict.fromkeys(sort_keys).keys())
1101 table.sort(sort_keys)
1102 return table
1105def catch_and_exit(func: Callable) -> Callable:
1106 """Catch all exceptions, prints an exception traceback
1107 and signals click to exit.
1109 Use as decorator.
1110 """
1112 @wraps(func)
1113 def inner(*args: Any, **kwargs: Any) -> None:
1114 try:
1115 func(*args, **kwargs)
1116 except (click.exceptions.ClickException, click.exceptions.Exit, click.exceptions.Abort):
1117 # this is handled by click itself
1118 raise
1119 except Exception:
1120 exc_type, exc_value, exc_tb = sys.exc_info()
1121 assert exc_type is not None
1122 assert exc_value is not None
1123 assert exc_tb is not None
1124 if exc_tb.tb_next:
1125 # do not show this decorator in traceback
1126 exc_tb = exc_tb.tb_next
1127 log.exception(
1128 "Caught an exception, details are in traceback:", exc_info=(exc_type, exc_value, exc_tb)
1129 )
1130 # tell click to stop, this never returns.
1131 click.get_current_context().exit(1)
1133 return inner