Coverage for python/lsst/daf/butler/cli/utils.py: 32%
353 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`."""
149 def invoke(self, *args: Any, **kwargs: Any) -> Any:
150 result = super().invoke(*args, **kwargs)
151 CliLog.resetLog()
152 return result
155def clickResultMsg(result: click.testing.Result) -> str:
156 """Get a standard assert message from a click result
158 Parameters
159 ----------
160 result : click.testing.Result
161 The result object returned from click.testing.CliRunner.invoke
163 Returns
164 -------
165 msg : `str`
166 The message string.
167 """
168 msg = f"""\noutput: {result.output}\nexception: {result.exception}"""
169 if result.exception:
170 msg += f"""\ntraceback: {"".join(traceback.format_tb(result.exception.__traceback__))}"""
171 return msg
174@contextmanager
175def command_test_env(runner: click.testing.CliRunner, commandModule: str, commandName: str) -> Iterator[None]:
176 """A context manager that creates (and then cleans up) an environment that
177 provides a CLI plugin command with the given name.
179 Parameters
180 ----------
181 runner : click.testing.CliRunner
182 The test runner to use to create the isolated filesystem.
183 commandModule : `str`
184 The importable module that the command can be imported from.
185 commandName : `str`
186 The name of the command being published to import.
187 """
188 with runner.isolated_filesystem():
189 with open("resources.yaml", "w") as f:
190 f.write(yaml.dump({"cmd": {"import": commandModule, "commands": [commandName]}}))
191 # Add a colon to the end of the path on the next line, this tests the
192 # case where the lookup in LoaderCLI._getPluginList generates an empty
193 # string in one of the list entries and verifies that the empty string
194 # is properly stripped out.
195 with patch.dict("os.environ", {"DAF_BUTLER_PLUGINS": f"{os.path.realpath(f.name)}:"}):
196 yield
199def addArgumentHelp(doc: str | None, helpText: str) -> str:
200 """Add a Click argument's help message to a function's documentation.
202 This is needed because click presents arguments in the order the argument
203 decorators are applied to a function, top down. But, the evaluation of the
204 decorators happens bottom up, so if arguments just append their help to the
205 function's docstring, the argument descriptions appear in reverse order
206 from the order they are applied in.
208 Parameters
209 ----------
210 doc : `str`
211 The function's docstring.
212 helpText : `str`
213 The argument's help string to be inserted into the function's
214 docstring.
216 Returns
217 -------
218 doc : `str`
219 Updated function documentation.
220 """
221 if doc is None: 221 ↛ 222line 221 didn't jump to line 222, because the condition on line 221 was never true
222 doc = helpText
223 else:
224 # See click documentation for details:
225 # https://click.palletsprojects.com/en/7.x/documentation/#truncating-help-texts
226 # In short, text for the click command help can be truncated by putting
227 # "\f" in the docstring, everything after it should be removed
228 if "\f" in doc: 228 ↛ 229line 228 didn't jump to line 229, because the condition on line 228 was never true
229 doc = doc.split("\f")[0]
231 doclines = doc.splitlines()
232 # The function's docstring may span multiple lines, so combine the
233 # docstring from all the first lines until a blank line is encountered.
234 # (Lines after the first blank line will be argument help.)
235 while len(doclines) > 1 and doclines[1]:
236 doclines[0] = " ".join((doclines[0], doclines.pop(1).strip()))
237 # Add standard indent to help text for proper alignment with command
238 # function documentation:
239 helpText = " " + helpText
240 doclines.insert(1, helpText)
241 doclines.insert(1, "\n")
242 doc = "\n".join(doclines)
243 return doc
246def split_commas(
247 context: click.Context | None, param: click.core.Option | None, values: str | Iterable[str] | None
248) -> tuple[str, ...]:
249 """Process a tuple of values, where each value may contain comma-separated
250 values, and return a single list of all the passed-in values.
252 This function can be passed to the 'callback' argument of a click.option to
253 allow it to process comma-separated values (e.g. "--my-opt a,b,c"). If
254 the comma is inside ``[]`` there will be no splitting.
256 Parameters
257 ----------
258 context : `click.Context` or `None`
259 The current execution context. Unused, but Click always passes it to
260 callbacks.
261 param : `click.core.Option` or `None`
262 The parameter being handled. Unused, but Click always passes it to
263 callbacks.
264 values : iterable of `str` or `str`
265 All the values passed for this option. Strings may contain commas,
266 which will be treated as delimiters for separate values unless they
267 are within ``[]``.
269 Returns
270 -------
271 results : `tuple` [`str`]
272 The passed in values separated by commas where appropriate and
273 combined into a single tuple.
274 """
275 if values is None:
276 return tuple()
277 valueList = []
278 for value in ensure_iterable(values):
279 # If we have [, or ,] we do the slow split. If square brackets
280 # are not matching then that is likely a typo that should result
281 # in a warning.
282 opens = "["
283 closes = "]"
284 if re.search(rf"\{opens}.*,|,.*\{closes}", value):
285 in_parens = False
286 current = ""
287 for c in value:
288 if c == opens:
289 if in_parens:
290 warnings.warn(
291 f"Found second opening {opens} without corresponding closing {closes}"
292 f" in {value!r}",
293 stacklevel=2,
294 )
295 in_parens = True
296 elif c == closes:
297 if not in_parens:
298 warnings.warn(
299 f"Found second closing {closes} without corresponding open {opens} in {value!r}",
300 stacklevel=2,
301 )
302 in_parens = False
303 elif c == ",":
304 if 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 )
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(self, value: str, param: click.Parameter | None, ctx: click.Context | None) -> Any:
606 """Called by click.ParamType to "convert values through types".
607 `click.Path` uses this step to verify Path conditions."""
608 if self.mustNotExist and os.path.exists(value):
609 self.fail(f'Path "{value}" should not exist.')
610 return super().convert(value, param, ctx)
613class MWOption(click.Option):
614 """Overrides click.Option with desired behaviors."""
616 def make_metavar(self) -> str:
617 """Overrides `click.Option.make_metavar`. Makes the metavar for the
618 help menu. Adds a space and an elipsis after the metavar name if
619 the option accepts multiple inputs, otherwise defers to the base
620 implementation.
622 By default click does not add an elipsis when multiple is True and
623 nargs is 1. And when nargs does not equal 1 click adds an elipsis
624 without a space between the metavar and the elipsis, but we prefer a
625 space between.
627 Does not get called for some option types (e.g. flag) so metavar
628 transformation that must apply to all types should be applied in
629 get_help_record.
630 """
631 metavar = super().make_metavar()
632 if self.multiple and self.nargs == 1:
633 metavar += " ..."
634 elif self.nargs != 1:
635 metavar = f"{metavar[:-3]} ..."
636 return metavar
639class MWArgument(click.Argument):
640 """Overrides click.Argument with desired behaviors."""
642 def make_metavar(self) -> str:
643 """Overrides `click.Option.make_metavar`. Makes the metavar for the
644 help menu. Always adds a space and an elipsis (' ...') after the
645 metavar name if the option accepts multiple inputs.
647 By default click adds an elipsis without a space between the metavar
648 and the elipsis, but we prefer a space between.
650 Returns
651 -------
652 metavar : `str`
653 The metavar value.
654 """
655 metavar = super().make_metavar()
656 if self.nargs != 1:
657 metavar = f"{metavar[:-3]} ..."
658 return metavar
661class OptionSection(MWOption):
662 """Implements an Option that prints a section label in the help text and
663 does not pass any value to the command function.
665 This class does a bit of hackery to add a section label to a click command
666 help output: first, `expose_value` is set to `False` so that no value is
667 passed to the command function. Second, this class overrides
668 `click.Option.get_help_record` to return the section label string without
669 any prefix so that it stands out as a section label.
671 This class overrides the hidden attribute because our documentation build
672 tool, sphinx-click, implements its own `get_help_record` function which
673 builds the record from other option values (e.g. `name`, `opts`), which
674 breaks the hack we use to make `get_help_record` only return the
675 `sectionText`. Fortunately, Click gets the value of `hidden` inside the
676 `Option`'s `get_help_record`, and `sphinx-click` calls `opt.hidden` before
677 entering its `_get_help_record` function. So, making the hidden property
678 return True hides this option from sphinx-click, while allowing the section
679 text to be returned by our `get_help_record` method when using Click.
681 The intention for this implementation is to do minimally invasive overrides
682 of the click classes so as to be robust and easy to fix if the click
683 internals change.
685 Parameters
686 ----------
687 sectionName : `str`
688 The parameter declaration for this option. It is not shown to the user,
689 it must be unique within the command. If using the `section` decorator
690 to add a section to a command's options, the section name is
691 auto-generated.
692 sectionText : `str`
693 The text to print in the section identifier.
694 """
696 @property
697 def hidden(self) -> bool:
698 return True
700 @hidden.setter
701 def hidden(self, val: Any) -> None:
702 pass
704 def __init__(self, sectionName: str, sectionText: str) -> None:
705 super().__init__(sectionName, expose_value=False)
706 self.sectionText = sectionText
708 def get_help_record(self, ctx: click.Context | None) -> tuple[str, str]:
709 return (self.sectionText, "")
712class MWOptionDecorator:
713 """Wraps the click.option decorator to enable shared options to be declared
714 and allows inspection of the shared option.
715 """
717 def __init__(self, *param_decls: Any, **kwargs: Any) -> None:
718 self.partialOpt = partial(click.option, *param_decls, cls=partial(MWOption), **kwargs)
719 opt = click.Option(param_decls, **kwargs)
720 self._name = opt.name
721 self._opts = opt.opts
723 def name(self) -> str:
724 """Get the name that will be passed to the command function for this
725 option."""
726 return cast(str, self._name)
728 def opts(self) -> list[str]:
729 """Get the flags that will be used for this option on the command
730 line."""
731 return self._opts
733 @property
734 def help(self) -> str:
735 """Get the help text for this option. Returns an empty string if no
736 help was defined."""
737 return self.partialOpt.keywords.get("help", "")
739 def __call__(self, *args: Any, **kwargs: Any) -> Any:
740 return self.partialOpt(*args, **kwargs)
743class MWArgumentDecorator:
744 """Wraps the click.argument decorator to enable shared arguments to be
745 declared."""
747 def __init__(self, *param_decls: Any, **kwargs: Any) -> None:
748 self._helpText = kwargs.pop("help", None)
749 self.partialArg = partial(click.argument, *param_decls, cls=MWArgument, **kwargs)
751 def __call__(self, *args: Any, help: str | None = None, **kwargs: Any) -> Callable:
752 def decorator(f: Any) -> Any:
753 if help is not None:
754 self._helpText = help
755 if self._helpText:
756 f.__doc__ = addArgumentHelp(f.__doc__, self._helpText)
757 return self.partialArg(*args, **kwargs)(f)
759 return decorator
762class MWCommand(click.Command):
763 """Command subclass that stores a copy of the args list for use by the
764 command."""
766 extra_epilog: str | None = None
768 def __init__(self, *args: Any, **kwargs: Any) -> None:
769 # wrap callback method with catch_and_exit decorator
770 callback = kwargs.get("callback")
771 if callback is not None: 771 ↛ 774line 771 didn't jump to line 774, because the condition on line 771 was never false
772 kwargs = kwargs.copy()
773 kwargs["callback"] = catch_and_exit(callback)
774 super().__init__(*args, **kwargs)
776 def _capture_args(self, ctx: click.Context, args: list[str]) -> None:
777 """Capture the command line options and arguments.
779 See details about what is captured and the order in which it is stored
780 in the documentation of `MWCtxObj`.
782 Parameters
783 ----------
784 ctx : `click.Context`
785 The current Context.
786 args : `list` [`str`]
787 The list of arguments from the command line, split at spaces but
788 not at separators (like "=").
789 """
790 parser = self.make_parser(ctx)
791 opts, _, param_order = parser.parse_args(args=list(args))
792 # `param_order` is a list of click.Option and click.Argument, there is
793 # one item for each time the Option or Argument was used on the
794 # command line. Options will precede Arguments, within each sublist
795 # they are in the order they were used on the command line. Note that
796 # click.Option and click.Argument do not contain the value from the
797 # command line; values are in `opts`.
798 #
799 # `opts` is a dict where the key is the argument name to the
800 # click.Command function, this name matches the `click.Option.name` or
801 # `click.Argument.name`. For Options, an item will only be present if
802 # the Option was used on the command line. For Arguments, an item will
803 # always be present and if no value was provided on the command line
804 # the value will be `None`. If the option accepts multiple values, the
805 # value in `opts` is a tuple, otherwise it is a single item.
806 next_idx: Counter = Counter()
807 captured_args = []
808 for param in param_order:
809 if isinstance(param, click.Option):
810 param_name = cast(str, param.name)
811 if param.multiple:
812 val = opts[param_name][next_idx[param_name]]
813 next_idx[param_name] += 1
814 else:
815 val = opts[param_name]
816 if param.is_flag:
817 # Bool options store their True flags in opts and their
818 # False flags in secondary_opts.
819 if val:
820 flag = max(param.opts, key=len)
821 else:
822 flag = max(param.secondary_opts, key=len)
823 captured_args.append(flag)
824 else:
825 captured_args.append(max(param.opts, key=len))
826 captured_args.append(val)
827 elif isinstance(param, click.Argument):
828 param_name = cast(str, param.name)
829 if (opt := opts[param_name]) is not None:
830 captured_args.append(opt)
831 else:
832 assert False # All parameters should be an Option or an Argument.
833 MWCtxObj.getFrom(ctx).args = captured_args
835 def parse_args(self, ctx: click.Context, args: Any) -> list[str]:
836 """Given a context and a list of arguments this creates the parser and
837 parses the arguments, then modifies the context as necessary. This is
838 automatically invoked by make_context().
840 This function overrides `click.Command.parse_args`.
842 The call to `_capture_args` in this override stores the arguments
843 (option names, option value, and argument values) that were used by the
844 caller on the command line in the context object. These stored
845 arugments can be used by the command function, e.g. to process options
846 in the order they appeared on the command line (pipetask uses this
847 feature to create pipeline actions in an order from different options).
849 Parameters
850 ----------
851 ctx : `click.core.Context`
852 The current Context.ß
853 args : `list` [`str`]
854 The list of arguments from the command line, split at spaces but
855 not at separators (like "=").
856 """
857 self._capture_args(ctx, args)
858 return super().parse_args(ctx, args)
860 @property
861 def epilog(self) -> str | None:
862 """Override the epilog attribute to add extra_epilog (if defined by a
863 subclass) to the end of any epilog provided by a subcommand.
864 """
865 ret = self._epilog if self._epilog else ""
866 if self.extra_epilog:
867 if ret:
868 ret += "\n\n"
869 ret += self.extra_epilog
870 return ret
872 @epilog.setter
873 def epilog(self, val: str) -> None:
874 self._epilog = val
877class ButlerCommand(MWCommand):
878 """Command subclass with butler-command specific overrides."""
880 extra_epilog = "See 'butler --help' for more options."
883class OptionGroup:
884 """Base class for an option group decorator. Requires the option group
885 subclass to have a property called `decorator`."""
887 decorators: list[Any]
889 def __call__(self, f: Any) -> Any:
890 for decorator in reversed(self.decorators):
891 f = decorator(f)
892 return f
895class MWCtxObj:
896 """Helper object for managing the `click.Context.obj` parameter, allows
897 obj data to be managed in a consistent way.
899 `Context.obj` defaults to None. `MWCtxObj.getFrom(ctx)` can be used to
900 initialize the obj if needed and return a new or existing `MWCtxObj`.
902 The `args` attribute contains a list of options, option values, and
903 argument values that is similar to the list of arguments and options that
904 were passed in on the command line, with differences noted below:
906 * Option namess and option values are first in the list, and argument
907 values come last. The order of options and option values is preserved
908 within the options. The order of argument values is preserved.
910 * The longest option name is used for the option in the `args` list, e.g.
911 if an option accepts both short and long names "-o / --option" and the
912 short option name "-o" was used on the command line, the longer name will
913 be the one that appears in `args`.
915 * A long option name (which begins with two dashes "--") and its value may
916 be separated by an equal sign; the name and value are split at the equal
917 sign and it is removed. In `args`, the option is in one list item, and
918 the option value (without the equal sign) is in the next list item. e.g.
919 "--option=foo" and "--option foo" both become `["--opt", "foo"]` in
920 `args`.
922 * A short option name, (which begins with one dash "-") and its value are
923 split immediately after the short option name, and if there is
924 whitespace between the short option name and its value it is removed.
925 Everything after the short option name (excluding whitespace) is included
926 in the value. If the `Option` has a long name, the long name will be used
927 in `args` e.g. for the option "-o / --option": "-ofoo" and "-o foo"
928 become `["--option", "foo"]`, and (note!) "-o=foo" will become
929 `["--option", "=foo"]` (because everything after the short option name,
930 except whitespace, is used for the value (as is standard with unix
931 command line tools).
933 Attributes
934 ----------
935 args : `list` [`str`]
936 A list of options, option values, and arguments simialr to those that
937 were passed in on the command line. See comments about captured options
938 & arguments above.
939 """
941 def __init__(self) -> None:
942 self.args = None
944 @staticmethod
945 def getFrom(ctx: click.Context) -> Any:
946 """If needed, initialize `ctx.obj` with a new `MWCtxObj`, and return
947 the new or already existing `MWCtxObj`."""
948 if ctx.obj is not None:
949 return ctx.obj
950 ctx.obj = MWCtxObj()
951 return ctx.obj
954def yaml_presets(ctx: click.Context, param: str, value: Any) -> None:
955 """Click callback that reads additional values from the supplied
956 YAML file.
958 Parameters
959 ----------
960 ctx : `click.context`
961 The context for the click operation. Used to extract the subcommand
962 name and translate option & argument names.
963 param : `str`
964 The parameter name.
965 value : `object`
966 The value of the parameter.
967 """
969 def _name_for_option(ctx: click.Context, option: str) -> str:
970 """Use a CLI option name to find the name of the argument to the
971 command function.
973 Parameters
974 ----------
975 ctx : `click.Context`
976 The context for the click operation.
977 option : `str`
978 The option/argument name from the yaml file.
980 Returns
981 -------
982 name : str
983 The name of the argument to use when calling the click.command
984 function, as it should appear in the `ctx.default_map`.
986 Raises
987 ------
988 RuntimeError
989 Raised if the option name from the yaml file does not exist in the
990 command parameters. This catches misspellings and incorrect useage
991 in the yaml file.
992 """
993 for param in ctx.command.params:
994 # Remove leading dashes: they are not used for option names in the
995 # yaml file.
996 if option in [opt.lstrip("-") for opt in param.opts]:
997 return cast(str, param.name)
998 raise RuntimeError(f"'{option}' is not a valid option for {ctx.info_name}")
1000 ctx.default_map = ctx.default_map or {}
1001 cmd_name = ctx.info_name
1002 assert cmd_name is not None, "command name cannot be None"
1003 if value:
1004 try:
1005 overrides = _read_yaml_presets(value, cmd_name)
1006 options = list(overrides.keys())
1007 for option in options:
1008 name = _name_for_option(ctx, option)
1009 if name == option:
1010 continue
1011 overrides[name] = overrides.pop(option)
1012 except Exception as e:
1013 raise click.BadOptionUsage(
1014 option_name=param,
1015 message=f"Error reading overrides file: {e}",
1016 ctx=ctx,
1017 )
1018 # Override the defaults for this subcommand
1019 ctx.default_map.update(overrides)
1020 return
1023def _read_yaml_presets(file_uri: str, cmd_name: str) -> dict[str, Any]:
1024 """Read file command line overrides from YAML config file.
1026 Parameters
1027 ----------
1028 file_uri : `str`
1029 URI of override YAML file containing the command line overrides.
1030 They should be grouped by command name.
1031 cmd_name : `str`
1032 The subcommand name that is being modified.
1034 Returns
1035 -------
1036 overrides : `dict` of [`str`, Any]
1037 The relevant command line options read from the override file.
1038 """
1039 log.debug("Reading command line overrides for subcommand %s from URI %s", cmd_name, file_uri)
1040 config = Config(file_uri)
1041 return config[cmd_name]
1044def sortAstropyTable(table: Table, dimensions: list[Dimension], sort_first: list[str] | None = None) -> Table:
1045 """Sort an astropy table, with prioritization given to columns in this
1046 order:
1047 1. the provided named columns
1048 2. spatial and temporal columns
1049 3. the rest of the columns
1051 The table is sorted in-place, and is also returned for convenience.
1053 Parameters
1054 ----------
1055 table : `astropy.table.Table`
1056 The table to sort
1057 dimensions : `list` [``Dimension``]
1058 The dimensions of the dataIds in the table (the dimensions should be
1059 the same for all the dataIds). Used to determine if the column is
1060 spatial, temporal, or neither.
1061 sort_first : `list` [`str`]
1062 The names of columns that should be sorted first, before spatial and
1063 temporal columns.
1065 Returns
1066 -------
1067 `astropy.table.Table`
1068 For convenience, the table that has been sorted.
1069 """
1070 # For sorting we want to ignore the id
1071 # We also want to move temporal or spatial dimensions earlier
1072 sort_first = sort_first or []
1073 sort_early: list[str] = []
1074 sort_late: list[str] = []
1075 for dim in dimensions:
1076 if dim.spatial or dim.temporal:
1077 sort_early.extend(dim.required.names)
1078 else:
1079 sort_late.append(str(dim))
1080 sort_keys = sort_first + sort_early + sort_late
1081 # The required names above means that we have the possibility of
1082 # repeats of sort keys. Now have to remove them
1083 # (order is retained by dict creation).
1084 sort_keys = list(dict.fromkeys(sort_keys).keys())
1086 table.sort(sort_keys)
1087 return table
1090def catch_and_exit(func: Callable) -> Callable:
1091 """Decorator which catches all exceptions, prints an exception traceback
1092 and signals click to exit.
1093 """
1095 @wraps(func)
1096 def inner(*args: Any, **kwargs: Any) -> None:
1097 try:
1098 func(*args, **kwargs)
1099 except (click.exceptions.ClickException, click.exceptions.Exit, click.exceptions.Abort):
1100 # this is handled by click itself
1101 raise
1102 except Exception:
1103 exc_type, exc_value, exc_tb = sys.exc_info()
1104 assert exc_type is not None
1105 assert exc_value is not None
1106 assert exc_tb is not None
1107 if exc_tb.tb_next:
1108 # do not show this decorator in traceback
1109 exc_tb = exc_tb.tb_next
1110 log.exception(
1111 "Caught an exception, details are in traceback:", exc_info=(exc_type, exc_value, exc_tb)
1112 )
1113 # tell click to stop, this never returns.
1114 click.get_current_context().exit(1)
1116 return inner