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 software is dual licensed under the GNU General Public License and also
10# under a 3-clause BSD license. Recipients may choose which of these licenses
11# to use; please see the files gpl-3.0.txt and/or bsd_license.txt,
12# respectively. If you choose the GPL option then the following text applies
13# (but note that there is still no warranty even if you opt for BSD instead):
14#
15# This program is free software: you can redistribute it and/or modify
16# it under the terms of the GNU General Public License as published by
17# the Free Software Foundation, either version 3 of the License, or
18# (at your option) any later version.
19#
20# This program is distributed in the hope that it will be useful,
21# but WITHOUT ANY WARRANTY; without even the implied warranty of
22# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23# GNU General Public License for more details.
24#
25# You should have received a copy of the GNU General Public License
26# along with this program. If not, see <http://www.gnu.org/licenses/>.
27from __future__ import annotations
29__all__ = (
30 "astropyTablesToStr",
31 "printAstropyTables",
32 "textTypeStr",
33 "LogCliRunner",
34 "clickResultMsg",
35 "command_test_env",
36 "addArgumentHelp",
37 "split_commas",
38 "split_kv",
39 "to_upper",
40 "unwrap",
41 "option_section",
42 "MWPath",
43 "MWOption",
44 "MWArgument",
45 "OptionSection",
46 "MWOptionDecorator",
47 "MWArgumentDecorator",
48 "MWCommand",
49 "ButlerCommand",
50 "OptionGroup",
51 "MWCtxObj",
52 "yaml_presets",
53 "sortAstropyTable",
54 "catch_and_exit",
55)
58import itertools
59import logging
60import os
61import re
62import sys
63import textwrap
64import traceback
65import uuid
66import warnings
67from collections import Counter
68from collections.abc import Callable, Iterable, Iterator
69from contextlib import contextmanager
70from functools import partial, wraps
71from typing import TYPE_CHECKING, Any, cast
72from unittest.mock import patch
74import click
75import click.exceptions
76import click.testing
77import yaml
78from lsst.utils.iteration import ensure_iterable
80from .._config import Config
81from .cliLog import CliLog
83if TYPE_CHECKING:
84 from astropy.table import Table
85 from lsst.daf.butler import Dimension
87log = logging.getLogger(__name__)
89# This is used as the metavar argument to Options that accept multiple string
90# inputs, which may be comma-separarated. For example:
91# --my-opt foo,bar --my-opt baz.
92# Other arguments to the Option should include multiple=true and
93# callback=split_kv.
94typeStrAcceptsMultiple = "TEXT ..."
95typeStrAcceptsSingle = "TEXT"
97# The standard help string for the --where option when it takes a WHERE clause.
98where_help = (
99 "A string expression similar to a SQL WHERE clause. May involve any column of a "
100 "dimension table or a dimension name as a shortcut for the primary key column of a "
101 "dimension table."
102)
105def astropyTablesToStr(tables: list[Table]) -> str:
106 """Render astropy tables to string as they are displayed in the CLI.
108 Output formatting matches ``printAstropyTables``.
110 Parameters
111 ----------
112 tables : `list` of `astropy.table.Table`
113 The tables to format.
115 Returns
116 -------
117 formatted : `str`
118 Tables formatted into a string.
119 """
120 ret = ""
121 for table in tables:
122 ret += "\n"
123 table.pformat_all()
124 ret += "\n"
125 return ret
128def printAstropyTables(tables: list[Table]) -> None:
129 """Print astropy tables to be displayed in the CLI.
131 Output formatting matches ``astropyTablesToStr``.
133 Parameters
134 ----------
135 tables : `list` of `astropy.table.Table`
136 The tables to print.
137 """
138 for table in tables:
139 print("")
140 table.pprint_all()
141 print("")
144def textTypeStr(multiple: bool) -> str:
145 """Get the text type string for CLI help documentation.
147 Parameters
148 ----------
149 multiple : `bool`
150 True if multiple text values are allowed, False if only one value is
151 allowed.
153 Returns
154 -------
155 textTypeStr : `str`
156 The type string to use.
157 """
158 return typeStrAcceptsMultiple if multiple else typeStrAcceptsSingle
161class LogCliRunner(click.testing.CliRunner):
162 """A test runner to use when the logging system will be initialized by code
163 under test, calls CliLog.resetLog(), which undoes any logging setup that
164 was done with the CliLog interface.
166 lsst.log modules can not be set back to an uninitialized state (python
167 logging modules can be set back to NOTSET), instead they are set to
168 `CliLog.defaultLsstLogLevel`.
169 """
171 def invoke(self, *args: Any, **kwargs: Any) -> click.testing.Result:
172 result = super().invoke(*args, **kwargs)
173 CliLog.resetLog()
174 return result
177def clickResultMsg(result: click.testing.Result) -> str:
178 """Get a standard assert message from a click result.
180 Parameters
181 ----------
182 result : click.testing.Result
183 The result object returned from `click.testing.CliRunner.invoke`.
185 Returns
186 -------
187 msg : `str`
188 The message string.
189 """
190 msg = f"""\noutput: {result.output}\nexception: {result.exception}"""
191 if result.exception:
192 msg += f"""\ntraceback: {"".join(traceback.format_tb(result.exception.__traceback__))}"""
193 return msg
196@contextmanager
197def command_test_env(runner: click.testing.CliRunner, commandModule: str, commandName: str) -> Iterator[None]:
198 """Context manager that creates (and then cleans up) an environment that
199 provides a CLI plugin command with the given name.
201 Parameters
202 ----------
203 runner : click.testing.CliRunner
204 The test runner to use to create the isolated filesystem.
205 commandModule : `str`
206 The importable module that the command can be imported from.
207 commandName : `str`
208 The name of the command being published to import.
209 """
210 with runner.isolated_filesystem():
211 with open("resources.yaml", "w") as f:
212 f.write(yaml.dump({"cmd": {"import": commandModule, "commands": [commandName]}}))
213 # Add a colon to the end of the path on the next line, this tests the
214 # case where the lookup in LoaderCLI._getPluginList generates an empty
215 # string in one of the list entries and verifies that the empty string
216 # is properly stripped out.
217 with patch.dict("os.environ", {"DAF_BUTLER_PLUGINS": f"{os.path.realpath(f.name)}:"}):
218 yield
221def addArgumentHelp(doc: str | None, helpText: str) -> str:
222 """Add a Click argument's help message to a function's documentation.
224 This is needed because click presents arguments in the order the argument
225 decorators are applied to a function, top down. But, the evaluation of the
226 decorators happens bottom up, so if arguments just append their help to the
227 function's docstring, the argument descriptions appear in reverse order
228 from the order they are applied in.
230 Parameters
231 ----------
232 doc : `str`
233 The function's docstring.
234 helpText : `str`
235 The argument's help string to be inserted into the function's
236 docstring.
238 Returns
239 -------
240 doc : `str`
241 Updated function documentation.
242 """
243 if doc is None: 243 ↛ 244line 243 didn't jump to line 244, because the condition on line 243 was never true
244 doc = helpText
245 else:
246 # See click documentation for details:
247 # https://click.palletsprojects.com/en/7.x/documentation/#truncating-help-texts
248 # In short, text for the click command help can be truncated by putting
249 # "\f" in the docstring, everything after it should be removed
250 if "\f" in doc: 250 ↛ 251line 250 didn't jump to line 251, because the condition on line 250 was never true
251 doc = doc.split("\f")[0]
253 doclines = doc.splitlines()
254 # The function's docstring may span multiple lines, so combine the
255 # docstring from all the first lines until a blank line is encountered.
256 # (Lines after the first blank line will be argument help.)
257 while len(doclines) > 1 and doclines[1]:
258 doclines[0] = " ".join((doclines[0], doclines.pop(1).strip()))
259 # Add standard indent to help text for proper alignment with command
260 # function documentation:
261 helpText = " " + helpText
262 doclines.insert(1, helpText)
263 doclines.insert(1, "\n")
264 doc = "\n".join(doclines)
265 return doc
268def split_commas(
269 context: click.Context | None, param: click.core.Option | None, values: str | Iterable[str] | None
270) -> tuple[str, ...]:
271 """Process a tuple of values, where each value may contain comma-separated
272 values, and return a single list of all the passed-in values.
274 This function can be passed to the 'callback' argument of a click.option to
275 allow it to process comma-separated values (e.g. "--my-opt a,b,c"). If
276 the comma is inside ``[]`` there will be no splitting.
278 Parameters
279 ----------
280 context : `click.Context` or `None`
281 The current execution context. Unused, but Click always passes it to
282 callbacks.
283 param : `click.core.Option` or `None`
284 The parameter being handled. Unused, but Click always passes it to
285 callbacks.
286 values : iterable of `str` or `str`
287 All the values passed for this option. Strings may contain commas,
288 which will be treated as delimiters for separate values unless they
289 are within ``[]``.
291 Returns
292 -------
293 results : `tuple` [`str`]
294 The passed in values separated by commas where appropriate and
295 combined into a single tuple.
296 """
297 if values is None:
298 return ()
299 valueList = []
300 for value in ensure_iterable(values):
301 # If we have [, or ,] we do the slow split. If square brackets
302 # are not matching then that is likely a typo that should result
303 # in a warning.
304 opens = "["
305 closes = "]"
306 if re.search(rf"\{opens}.*,|,.*\{closes}", value):
307 in_parens = False
308 current = ""
309 for c in value:
310 if c == opens:
311 if in_parens:
312 warnings.warn(
313 f"Found second opening {opens} without corresponding closing {closes}"
314 f" in {value!r}",
315 stacklevel=2,
316 )
317 in_parens = True
318 elif c == closes:
319 if not in_parens:
320 warnings.warn(
321 f"Found second closing {closes} without corresponding open {opens} in {value!r}",
322 stacklevel=2,
323 )
324 in_parens = False
325 elif c == "," and not in_parens:
326 # Split on this comma.
327 valueList.append(current)
328 current = ""
329 continue
330 current += c
331 if in_parens:
332 warnings.warn(
333 f"Found opening {opens} that was never closed in {value!r}",
334 stacklevel=2,
335 )
336 if current:
337 valueList.append(current)
338 else:
339 # Use efficient split since no parens.
340 valueList.extend(value.split(","))
341 return tuple(valueList)
344def split_kv(
345 context: click.Context,
346 param: click.core.Option,
347 values: list[str],
348 *,
349 choice: click.Choice | None = None,
350 multiple: bool = True,
351 normalize: bool = False,
352 separator: str = "=",
353 unseparated_okay: bool = False,
354 return_type: type[dict] | type[tuple] = dict,
355 default_key: str = "",
356 reverse_kv: bool = False,
357 add_to_default: bool = False,
358) -> dict[str, str] | tuple[tuple[str, str], ...]:
359 """Process a tuple of values that are key-value pairs separated by a given
360 separator. Multiple pairs may be comma separated. Return a dictionary of
361 all the passed-in values.
363 This function can be passed to the 'callback' argument of a click.option to
364 allow it to process comma-separated values (e.g. "--my-opt a=1,b=2").
366 Parameters
367 ----------
368 context : `click.Context` or `None`
369 The current execution context. Unused, but Click always passes it to
370 callbacks.
371 param : `click.core.Option` or `None`
372 The parameter being handled. Unused, but Click always passes it to
373 callbacks.
374 values : [`str`]
375 All the values passed for this option. Strings may contain commas,
376 which will be treated as delimiters for separate values.
377 choice : `click.Choice`, optional
378 If provided, verify each value is a valid choice using the provided
379 `click.Choice` instance. If None, no verification will be done. By
380 default `None`.
381 multiple : `bool`, optional
382 If true, the value may contain multiple comma-separated values. By
383 default True.
384 normalize : `bool`, optional
385 If True and `choice.case_sensitive == False`, normalize the string the
386 user provided to match the choice's case. By default `False`.
387 separator : str, optional
388 The character that separates key-value pairs. May not be a comma or an
389 empty space (for space separators use Click's default implementation
390 for tuples; `type=(str, str)`). By default "=".
391 unseparated_okay : `bool`, optional
392 If True, allow values that do not have a separator. They will be
393 returned in the values dict as a tuple of values in the key '', that
394 is: `values[''] = (unseparated_values, )`. By default False.
395 return_type : `type`, must be `dict` or `tuple`
396 The type of the value that should be returned.
397 If `dict` then the returned object will be a dict, for each item in
398 values, the value to the left of the separator will be the key and the
399 value to the right of the separator will be the value.
400 If `tuple` then the returned object will be a tuple. Each item in the
401 tuple will be 2-item tuple, the first item will be the value to the
402 left of the separator and the second item will be the value to the
403 right. By default `dict`.
404 default_key : `Any`
405 The key to use if a value is passed that is not a key-value pair.
406 (Passing values that are not key-value pairs requires
407 ``unseparated_okay`` to be `True`).
408 reverse_kv : bool
409 If true then for each item in values, the value to the left of the
410 separator is treated as the value and the value to the right of the
411 separator is treated as the key. By default `False`.
412 add_to_default : `bool`, optional
413 If True, then passed-in values will not overwrite the default value
414 unless the ``return_type`` is `dict` and passed-in value(s) have the
415 same key(s) as the default value.
417 Returns
418 -------
419 values : `dict` [`str`, `str`] or `tuple`[`tuple`[`str`, `str`], ...]
420 The passed-in values in dict form or tuple form.
422 Raises
423 ------
424 `click.ClickException`
425 Raised if the separator is not found in an entry, or if duplicate keys
426 are encountered.
427 """
429 def norm(val: str) -> str:
430 """If `normalize` is `True` and `choice` is not `None`, find the value
431 in the available choices and return the value as spelled in the
432 choices.
434 Assumes that val exists in choices; `split_kv` uses the `choice`
435 instance to verify val is a valid choice.
437 Parameters
438 ----------
439 val : `str`
440 Value to be found.
442 Returns
443 -------
444 val : `str`
445 The value that was found or the value that was given.
446 """
447 if normalize and choice is not None:
448 v = val.casefold()
449 for opt in choice.choices:
450 if opt.casefold() == v:
451 return opt
452 return val
454 class RetDict:
455 def __init__(self) -> None:
456 self.ret: dict[str, str] = {}
458 def add(self, key: str, val: str) -> None:
459 if reverse_kv:
460 key, val = val, key
461 self.ret[key] = val
463 def get(self) -> dict[str, str]:
464 return self.ret
466 class RetTuple:
467 def __init__(self) -> None:
468 self.ret: list[tuple[str, str]] = []
470 def add(self, key: str, val: str) -> None:
471 if reverse_kv:
472 key, val = val, key
473 self.ret.append((key, val))
475 def get(self) -> tuple[tuple[str, str], ...]:
476 return tuple(self.ret)
478 if separator in (",", " "):
479 raise RuntimeError(f"'{separator}' is not a supported separator for key-value pairs.")
480 vals = tuple(ensure_iterable(values)) # preserve the original argument for error reporting below.
482 if add_to_default:
483 default = param.get_default(context)
484 if default:
485 vals = tuple(v for v in itertools.chain(default, vals)) # Convert to tuple for mypy
487 ret: RetDict | RetTuple
488 if return_type is dict:
489 ret = RetDict()
490 elif return_type is tuple:
491 ret = RetTuple()
492 else:
493 raise click.ClickException(
494 message=f"Internal error: invalid return type '{return_type}' for split_kv."
495 )
496 if multiple:
497 vals = split_commas(context, param, vals)
498 for val in ensure_iterable(vals):
499 if unseparated_okay and separator not in val:
500 if choice is not None:
501 choice(val) # will raise if val is an invalid choice
502 ret.add(default_key, norm(val))
503 else:
504 try:
505 k, v = val.split(separator)
506 if choice is not None:
507 choice(v) # will raise if val is an invalid choice
508 except ValueError as e:
509 raise click.ClickException(
510 message=f"Could not parse key-value pair '{val}' using separator '{separator}', "
511 f"with multiple values {'allowed' if multiple else 'not allowed'}: {e}"
512 ) from None
513 ret.add(k, norm(v))
514 return ret.get()
517def to_upper(context: click.Context, param: click.core.Option, value: str) -> str:
518 """Convert a value to upper case.
520 Parameters
521 ----------
522 context : `click.Context`
523 Context given by Click.
524 param : `click.core.Option`
525 Provided by Click. Ignored.
526 value : `str`
527 The value to be converted.
529 Returns
530 -------
531 string
532 A copy of the passed-in value, converted to upper case.
533 """
534 return value.upper()
537def unwrap(val: str) -> str:
538 """Remove newlines and leading whitespace from a multi-line string with
539 a consistent indentation level.
541 The first line of the string may be only a newline or may contain text
542 followed by a newline, either is ok. After the first line, each line must
543 begin with a consistant amount of whitespace. So, content of a
544 triple-quoted string may begin immediately after the quotes, or the string
545 may start with a newline. Each line after that must be the same amount of
546 indentation/whitespace followed by text and a newline. The last line may
547 end with a new line but is not required to do so.
549 Parameters
550 ----------
551 val : `str`
552 The string to change.
554 Returns
555 -------
556 strippedString : `str`
557 The string with newlines, indentation, and leading and trailing
558 whitespace removed.
559 """
561 def splitSection(val: str) -> str:
562 if not val.startswith("\n"): 562 ↛ 566line 562 didn't jump to line 566, because the condition on line 562 was always true
563 firstLine, _, val = val.partition("\n")
564 firstLine += " "
565 else:
566 firstLine = ""
567 return (firstLine + textwrap.dedent(val).replace("\n", " ")).strip()
569 return "\n\n".join([splitSection(s) for s in val.split("\n\n")])
572class option_section: # noqa: N801
573 """Decorator to add a section label between options in the help text of a
574 command.
576 Parameters
577 ----------
578 sectionText : `str`
579 The text to print in the section identifier.
580 """
582 def __init__(self, sectionText: str) -> None:
583 self.sectionText = "\n" + sectionText
585 def __call__(self, f: Any) -> click.Option:
586 # Generate a parameter declaration that will be unique for this
587 # section.
588 return click.option(
589 f"--option-section-{str(uuid.uuid4())}", sectionText=self.sectionText, cls=OptionSection
590 )(f)
593class MWPath(click.Path):
594 """Overrides click.Path to implement file-does-not-exist checking.
596 Changes the definition of ``exists`` so that `True` indicates the location
597 (file or directory) must exist, `False` indicates the location must *not*
598 exist, and `None` indicates that the file may exist or not. The standard
599 definition for the `click.Path` ``exists`` parameter is that for `True` a
600 location must exist, but `False` means it is not required to exist (not
601 that it is required to not exist).
603 Parameters
604 ----------
605 exists : `bool` or `None`, optional
606 If `True`, the location (file or directory) indicated by the caller
607 must exist. If `False` the location must not exist. If `None`, the
608 location may exist or not.
609 file_okay : `bool`, optional
610 Allow a file as a value.
611 dir_okay : `bool`, optional
612 Allow a directory as a value.
613 writable : `bool`, optional
614 If `True`, a writable check is performed.
615 readable : `bool, optional
616 If `True`, a readable check is performed.
617 resolve_path : `bool`, optional
618 Resolve the path.
619 allow_dash : `bool`, optional
620 Allow single dash as value to mean a standard stream.
621 path_type : `type` or `None`, optional
622 Convert the incoming value to this type.
624 Notes
625 -----
626 All parameters other than ``exists`` come directly from `click.Path`.
627 """
629 def __init__(
630 self,
631 exists: bool | None = None,
632 file_okay: bool = True,
633 dir_okay: bool = True,
634 writable: bool = False,
635 readable: bool = True,
636 resolve_path: bool = False,
637 allow_dash: bool = False,
638 path_type: type | None = None,
639 ):
640 self.mustNotExist = exists is False
641 if exists is None: 641 ↛ 643line 641 didn't jump to line 643, because the condition on line 641 was always true
642 exists = False
643 super().__init__(
644 exists=exists,
645 file_okay=file_okay,
646 dir_okay=dir_okay,
647 writable=writable,
648 readable=readable,
649 resolve_path=resolve_path,
650 allow_dash=allow_dash,
651 path_type=path_type,
652 )
654 def convert(
655 self, value: str | os.PathLike[str], param: click.Parameter | None, ctx: click.Context | None
656 ) -> Any:
657 """Convert values through types.
659 Called by `click.ParamType` to "convert values through types".
660 `click.Path` uses this step to verify Path conditions.
662 Parameters
663 ----------
664 value : `str` or `os.PathLike`
665 File path.
666 param : `click.Parameter`
667 Parameters provided by Click.
668 ctx : `click.Context`
669 Context provided by Click.
670 """
671 if self.mustNotExist and os.path.exists(value):
672 self.fail(f'Path "{value}" should not exist.')
673 return super().convert(value, param, ctx)
676class MWOption(click.Option):
677 """Overrides click.Option with desired behaviors."""
679 def make_metavar(self) -> str:
680 """Make the metavar for the help menu.
682 Overrides `click.Option.make_metavar`.
683 Adds a space and an ellipsis after the metavar name if
684 the option accepts multiple inputs, otherwise defers to the base
685 implementation.
687 By default click does not add an ellipsis when multiple is True and
688 nargs is 1. And when nargs does not equal 1 click adds an ellipsis
689 without a space between the metavar and the ellipsis, but we prefer a
690 space between.
692 Does not get called for some option types (e.g. flag) so metavar
693 transformation that must apply to all types should be applied in
694 get_help_record.
695 """
696 metavar = super().make_metavar()
697 if self.multiple and self.nargs == 1:
698 metavar += " ..."
699 elif self.nargs != 1:
700 metavar = f"{metavar[:-3]} ..."
701 return metavar
704class MWArgument(click.Argument):
705 """Overrides click.Argument with desired behaviors."""
707 def make_metavar(self) -> str:
708 """Make the metavar for the help menu.
710 Overrides `click.Option.make_metavar`.
711 Always adds a space and an ellipsis (' ...') after the
712 metavar name if the option accepts multiple inputs.
714 By default click adds an ellipsis without a space between the metavar
715 and the ellipsis, but we prefer a space between.
717 Returns
718 -------
719 metavar : `str`
720 The metavar value.
721 """
722 metavar = super().make_metavar()
723 if self.nargs != 1:
724 metavar = f"{metavar[:-3]} ..."
725 return metavar
728class OptionSection(MWOption):
729 """Implements an Option that prints a section label in the help text and
730 does not pass any value to the command function.
732 This class does a bit of hackery to add a section label to a click command
733 help output: first, `expose_value` is set to `False` so that no value is
734 passed to the command function. Second, this class overrides
735 `click.Option.get_help_record` to return the section label string without
736 any prefix so that it stands out as a section label.
738 This class overrides the hidden attribute because our documentation build
739 tool, sphinx-click, implements its own `get_help_record` function which
740 builds the record from other option values (e.g. `name`, `opts`), which
741 breaks the hack we use to make `get_help_record` only return the
742 `sectionText`. Fortunately, Click gets the value of `hidden` inside the
743 `Option`'s `get_help_record`, and `sphinx-click` calls `opt.hidden` before
744 entering its `_get_help_record` function. So, making the hidden property
745 return True hides this option from sphinx-click, while allowing the section
746 text to be returned by our `get_help_record` method when using Click.
748 The intention for this implementation is to do minimally invasive overrides
749 of the click classes so as to be robust and easy to fix if the click
750 internals change.
752 Parameters
753 ----------
754 sectionName : `str`
755 The parameter declaration for this option. It is not shown to the user,
756 it must be unique within the command. If using the `section` decorator
757 to add a section to a command's options, the section name is
758 auto-generated.
759 sectionText : `str`
760 The text to print in the section identifier.
761 """
763 @property
764 def hidden(self) -> bool:
765 return True
767 @hidden.setter
768 def hidden(self, val: Any) -> None:
769 pass
771 def __init__(self, sectionName: str, sectionText: str) -> None:
772 super().__init__(sectionName, expose_value=False)
773 self.sectionText = sectionText
775 def get_help_record(self, ctx: click.Context | None) -> tuple[str, str]:
776 return (self.sectionText, "")
779class MWOptionDecorator:
780 """Wraps the click.option decorator to enable shared options to be declared
781 and allows inspection of the shared option.
783 Parameters
784 ----------
785 *param_decls : `typing.Any`
786 Parameters to be stored in the option.
787 **kwargs : `typing.Any`
788 Keyword arguments for the option.
789 """
791 def __init__(self, *param_decls: Any, **kwargs: Any) -> None:
792 self.partialOpt = partial(click.option, *param_decls, cls=partial(MWOption), **kwargs)
793 opt = click.Option(param_decls, **kwargs)
794 self._name = opt.name
795 self._opts = opt.opts
797 def name(self) -> str:
798 """Get the name that will be passed to the command function for this
799 option.
800 """
801 return cast(str, self._name)
803 def opts(self) -> list[str]:
804 """Get the flags that will be used for this option on the command
805 line.
806 """
807 return self._opts
809 @property
810 def help(self) -> str:
811 """Get the help text for this option. Returns an empty string if no
812 help was defined.
813 """
814 return self.partialOpt.keywords.get("help", "")
816 def __call__(self, *args: Any, **kwargs: Any) -> Any:
817 return self.partialOpt(*args, **kwargs)
820class MWArgumentDecorator:
821 """Wraps the click.argument decorator to enable shared arguments to be
822 declared.
824 Parameters
825 ----------
826 *param_decls : `typing.Any`
827 Parameters to be stored in the argument.
828 **kwargs : `typing.Any`
829 Keyword arguments for the argument.
830 """
832 def __init__(self, *param_decls: Any, **kwargs: Any) -> None:
833 self._helpText = kwargs.pop("help", None)
834 self.partialArg = partial(click.argument, *param_decls, cls=MWArgument, **kwargs)
836 def __call__(self, *args: Any, help: str | None = None, **kwargs: Any) -> Callable:
837 def decorator(f: Any) -> Any:
838 if help is not None:
839 self._helpText = help
840 if self._helpText:
841 f.__doc__ = addArgumentHelp(f.__doc__, self._helpText)
842 return self.partialArg(*args, **kwargs)(f)
844 return decorator
847class MWCommand(click.Command):
848 """Command subclass that stores a copy of the args list for use by the
849 command.
851 Parameters
852 ----------
853 *args : `typing.Any`
854 Arguments for `click.Command`.
855 **kwargs : `typing.Any`
856 Keyword arguments for `click.Command`.
857 """
859 extra_epilog: str | None = None
861 def __init__(self, *args: Any, **kwargs: Any) -> None:
862 # wrap callback method with catch_and_exit decorator
863 callback = kwargs.get("callback")
864 if callback is not None: 864 ↛ 867line 864 didn't jump to line 867, because the condition on line 864 was always true
865 kwargs = kwargs.copy()
866 kwargs["callback"] = catch_and_exit(callback)
867 super().__init__(*args, **kwargs)
869 def _capture_args(self, ctx: click.Context, args: list[str]) -> None:
870 """Capture the command line options and arguments.
872 See details about what is captured and the order in which it is stored
873 in the documentation of `MWCtxObj`.
875 Parameters
876 ----------
877 ctx : `click.Context`
878 The current Context.
879 args : `list` [`str`]
880 The list of arguments from the command line, split at spaces but
881 not at separators (like "=").
882 """
883 parser = self.make_parser(ctx)
884 opts, _, param_order = parser.parse_args(args=list(args))
885 # `param_order` is a list of click.Option and click.Argument, there is
886 # one item for each time the Option or Argument was used on the
887 # command line. Options will precede Arguments, within each sublist
888 # they are in the order they were used on the command line. Note that
889 # click.Option and click.Argument do not contain the value from the
890 # command line; values are in `opts`.
891 #
892 # `opts` is a dict where the key is the argument name to the
893 # click.Command function, this name matches the `click.Option.name` or
894 # `click.Argument.name`. For Options, an item will only be present if
895 # the Option was used on the command line. For Arguments, an item will
896 # always be present and if no value was provided on the command line
897 # the value will be `None`. If the option accepts multiple values, the
898 # value in `opts` is a tuple, otherwise it is a single item.
899 next_idx: Counter = Counter()
900 captured_args = []
901 for param in param_order:
902 if isinstance(param, click.Option):
903 param_name = cast(str, param.name)
904 if param.multiple:
905 val = opts[param_name][next_idx[param_name]]
906 next_idx[param_name] += 1
907 else:
908 val = opts[param_name]
909 if param.is_flag:
910 # Bool options store their True flags in opts and their
911 # False flags in secondary_opts.
912 if val:
913 flag = max(param.opts, key=len)
914 else:
915 flag = max(param.secondary_opts, key=len)
916 captured_args.append(flag)
917 else:
918 captured_args.append(max(param.opts, key=len))
919 captured_args.append(val)
920 elif isinstance(param, click.Argument):
921 param_name = cast(str, param.name)
922 if (opt := opts[param_name]) is not None:
923 captured_args.append(opt)
924 else:
925 raise AssertionError("All parameters should be an Option or an Argument")
926 MWCtxObj.getFrom(ctx).args = captured_args
928 def parse_args(self, ctx: click.Context, args: Any) -> list[str]:
929 """Given a context and a list of arguments this creates the parser and
930 parses the arguments, then modifies the context as necessary. This is
931 automatically invoked by make_context().
933 This function overrides `click.Command.parse_args`.
935 The call to `_capture_args` in this override stores the arguments
936 (option names, option value, and argument values) that were used by the
937 caller on the command line in the context object. These stored
938 arugments can be used by the command function, e.g. to process options
939 in the order they appeared on the command line (pipetask uses this
940 feature to create pipeline actions in an order from different options).
942 Parameters
943 ----------
944 ctx : `click.core.Context`
945 The current Context.
946 args : `list` [`str`]
947 The list of arguments from the command line, split at spaces but
948 not at separators (like "=").
949 """
950 self._capture_args(ctx, args)
951 return super().parse_args(ctx, args)
953 @property
954 def epilog(self) -> str | None:
955 """Override the epilog attribute to add extra_epilog (if defined by a
956 subclass) to the end of any epilog provided by a subcommand.
957 """
958 ret = self._epilog if self._epilog else ""
959 if self.extra_epilog:
960 if ret:
961 ret += "\n\n"
962 ret += self.extra_epilog
963 return ret
965 @epilog.setter
966 def epilog(self, val: str) -> None:
967 self._epilog = val
970class ButlerCommand(MWCommand):
971 """Command subclass with butler-command specific overrides."""
973 extra_epilog = "See 'butler --help' for more options."
976class OptionGroup:
977 """Base class for an option group decorator. Requires the option group
978 subclass to have a property called `decorator`.
979 """
981 decorators: list[Any]
983 def __call__(self, f: Any) -> Any:
984 for decorator in reversed(self.decorators):
985 f = decorator(f)
986 return f
989class MWCtxObj:
990 """Helper object for managing the `click.Context.obj` parameter, allows
991 obj data to be managed in a consistent way.
993 `Context.obj` defaults to None. `MWCtxObj.getFrom(ctx)` can be used to
994 initialize the obj if needed and return a new or existing `MWCtxObj`.
996 The `args` attribute contains a list of options, option values, and
997 argument values that is similar to the list of arguments and options that
998 were passed in on the command line, with differences noted below:
1000 * Option namess and option values are first in the list, and argument
1001 values come last. The order of options and option values is preserved
1002 within the options. The order of argument values is preserved.
1004 * The longest option name is used for the option in the `args` list, e.g.
1005 if an option accepts both short and long names "-o / --option" and the
1006 short option name "-o" was used on the command line, the longer name will
1007 be the one that appears in `args`.
1009 * A long option name (which begins with two dashes "--") and its value may
1010 be separated by an equal sign; the name and value are split at the equal
1011 sign and it is removed. In `args`, the option is in one list item, and
1012 the option value (without the equal sign) is in the next list item. e.g.
1013 "--option=foo" and "--option foo" both become `["--opt", "foo"]` in
1014 `args`.
1016 * A short option name, (which begins with one dash "-") and its value are
1017 split immediately after the short option name, and if there is
1018 whitespace between the short option name and its value it is removed.
1019 Everything after the short option name (excluding whitespace) is included
1020 in the value. If the `Option` has a long name, the long name will be used
1021 in `args` e.g. for the option "-o / --option": "-ofoo" and "-o foo"
1022 become `["--option", "foo"]`, and (note!) "-o=foo" will become
1023 `["--option", "=foo"]` (because everything after the short option name,
1024 except whitespace, is used for the value (as is standard with unix
1025 command line tools).
1027 Attributes
1028 ----------
1029 args : `list` [`str`]
1030 A list of options, option values, and arguments simialr to those that
1031 were passed in on the command line. See comments about captured options
1032 & arguments above.
1033 """
1035 def __init__(self) -> None:
1036 self.args = None
1038 @staticmethod
1039 def getFrom(ctx: click.Context) -> Any:
1040 """If needed, initialize `ctx.obj` with a new `MWCtxObj`, and return
1041 the new or already existing `MWCtxObj`.
1043 Parameters
1044 ----------
1045 ctx : `click.Context`
1046 Context provided by Click.
1047 """
1048 if ctx.obj is not None:
1049 return ctx.obj
1050 ctx.obj = MWCtxObj()
1051 return ctx.obj
1054def yaml_presets(ctx: click.Context, param: str, value: Any) -> None:
1055 """Read additional values from the supplied YAML file.
1057 Parameters
1058 ----------
1059 ctx : `click.context`
1060 The context for the click operation. Used to extract the subcommand
1061 name and translate option & argument names.
1062 param : `str`
1063 The parameter name.
1064 value : `object`
1065 The value of the parameter.
1066 """
1068 def _name_for_option(ctx: click.Context, option: str) -> str:
1069 """Use a CLI option name to find the name of the argument to the
1070 command function.
1072 Parameters
1073 ----------
1074 ctx : `click.Context`
1075 The context for the click operation.
1076 option : `str`
1077 The option/argument name from the yaml file.
1079 Returns
1080 -------
1081 name : str
1082 The name of the argument to use when calling the click.command
1083 function, as it should appear in the `ctx.default_map`.
1085 Raises
1086 ------
1087 RuntimeError
1088 Raised if the option name from the yaml file does not exist in the
1089 command parameters. This catches misspellings and incorrect useage
1090 in the yaml file.
1091 """
1092 for param in ctx.command.params:
1093 # Remove leading dashes: they are not used for option names in the
1094 # yaml file.
1095 if option in [opt.lstrip("-") for opt in param.opts]:
1096 return cast(str, param.name)
1097 raise RuntimeError(f"'{option}' is not a valid option for {ctx.info_name}")
1099 ctx.default_map = ctx.default_map or {}
1100 cmd_name = ctx.info_name
1101 assert cmd_name is not None, "command name cannot be None"
1102 if value:
1103 try:
1104 overrides = _read_yaml_presets(value, cmd_name)
1105 options = list(overrides.keys())
1106 for option in options:
1107 name = _name_for_option(ctx, option)
1108 if name == option:
1109 continue
1110 overrides[name] = overrides.pop(option)
1111 except Exception as e:
1112 raise click.BadOptionUsage(
1113 option_name=param,
1114 message=f"Error reading overrides file: {e}",
1115 ctx=ctx,
1116 ) from None
1117 # Override the defaults for this subcommand
1118 ctx.default_map.update(overrides)
1119 return
1122def _read_yaml_presets(file_uri: str, cmd_name: str) -> dict[str, Any]:
1123 """Read file command line overrides from YAML config file.
1125 Parameters
1126 ----------
1127 file_uri : `str`
1128 URI of override YAML file containing the command line overrides.
1129 They should be grouped by command name.
1130 cmd_name : `str`
1131 The subcommand name that is being modified.
1133 Returns
1134 -------
1135 overrides : `dict` of [`str`, Any]
1136 The relevant command line options read from the override file.
1137 """
1138 log.debug("Reading command line overrides for subcommand %s from URI %s", cmd_name, file_uri)
1139 config = Config(file_uri)
1140 return config[cmd_name]
1143def sortAstropyTable(table: Table, dimensions: list[Dimension], sort_first: list[str] | None = None) -> Table:
1144 """Sort an astropy table.
1146 Prioritization is given to columns in this order:
1148 1. the provided named columns
1149 2. spatial and temporal columns
1150 3. the rest of the columns.
1152 The table is sorted in-place, and is also returned for convenience.
1154 Parameters
1155 ----------
1156 table : `astropy.table.Table`
1157 The table to sort.
1158 dimensions : `list` [``Dimension``]
1159 The dimensions of the dataIds in the table (the dimensions should be
1160 the same for all the dataIds). Used to determine if the column is
1161 spatial, temporal, or neither.
1162 sort_first : `list` [`str`]
1163 The names of columns that should be sorted first, before spatial and
1164 temporal columns.
1166 Returns
1167 -------
1168 `astropy.table.Table`
1169 For convenience, the table that has been sorted.
1170 """
1171 # For sorting we want to ignore the id
1172 # We also want to move temporal or spatial dimensions earlier
1173 sort_first = sort_first or []
1174 sort_early: list[str] = []
1175 sort_late: list[str] = []
1176 for dim in dimensions:
1177 if dim.spatial or dim.temporal:
1178 sort_early.extend(dim.required.names)
1179 else:
1180 sort_late.append(str(dim))
1181 sort_keys = sort_first + sort_early + sort_late
1182 # The required names above means that we have the possibility of
1183 # repeats of sort keys. Now have to remove them
1184 # (order is retained by dict creation).
1185 sort_keys = list(dict.fromkeys(sort_keys).keys())
1187 table.sort(sort_keys)
1188 return table
1191def catch_and_exit(func: Callable) -> Callable:
1192 """Catch all exceptions, prints an exception traceback
1193 and signals click to exit.
1195 Use as decorator.
1197 Parameters
1198 ----------
1199 func : `collections.abc.Callable`
1200 The function to be decorated.
1202 Returns
1203 -------
1204 `collections.abc.Callable`
1205 The decorated function.
1206 """
1208 @wraps(func)
1209 def inner(*args: Any, **kwargs: Any) -> None:
1210 try:
1211 func(*args, **kwargs)
1212 except (click.exceptions.ClickException, click.exceptions.Exit, click.exceptions.Abort):
1213 # this is handled by click itself
1214 raise
1215 except Exception:
1216 exc_type, exc_value, exc_tb = sys.exc_info()
1217 assert exc_type is not None
1218 assert exc_value is not None
1219 assert exc_tb is not None
1220 if exc_tb.tb_next:
1221 # do not show this decorator in traceback
1222 exc_tb = exc_tb.tb_next
1223 log.exception(
1224 "Caught an exception, details are in traceback:", exc_info=(exc_type, exc_value, exc_tb)
1225 )
1226 # tell click to stop, this never returns.
1227 click.get_current_context().exit(1)
1229 return inner