Coverage for python/lsst/daf/butler/cli/utils.py: 42%
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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/>.
22import copy
23import itertools
24import logging
25import os
26import sys
27import textwrap
28import traceback
29import uuid
30from contextlib import contextmanager
31from functools import partial, wraps
32from unittest.mock import patch
34import click
35import click.exceptions
36import click.testing
37import yaml
38from lsst.utils.iteration import ensure_iterable
40from ..core.config import Config
41from .cliLog import CliLog
43log = logging.getLogger(__name__)
45# This is used as the metavar argument to Options that accept multiple string
46# inputs, which may be comma-separarated. For example:
47# --my-opt foo,bar --my-opt baz.
48# Other arguments to the Option should include multiple=true and
49# callback=split_kv.
50typeStrAcceptsMultiple = "TEXT ..."
51typeStrAcceptsSingle = "TEXT"
53# The standard help string for the --where option when it takes a WHERE clause.
54where_help = (
55 "A string expression similar to a SQL WHERE clause. May involve any column of a "
56 "dimension table or a dimension name as a shortcut for the primary key column of a "
57 "dimension table."
58)
61def astropyTablesToStr(tables):
62 """Render astropy tables to string as they are displayed in the CLI.
64 Output formatting matches ``printAstropyTables``.
65 """
66 ret = ""
67 for table in tables:
68 ret += "\n"
69 table.pformat_all()
70 ret += "\n"
71 return ret
74def printAstropyTables(tables):
75 """Print astropy tables to be displayed in the CLI.
77 Output formatting matches ``astropyTablesToStr``.
78 """
79 for table in tables:
80 print("")
81 table.pprint_all()
82 print("")
85def textTypeStr(multiple):
86 """Get the text type string for CLI help documentation.
88 Parameters
89 ----------
90 multiple : `bool`
91 True if multiple text values are allowed, False if only one value is
92 allowed.
94 Returns
95 -------
96 textTypeStr : `str`
97 The type string to use.
98 """
99 return typeStrAcceptsMultiple if multiple else typeStrAcceptsSingle
102class LogCliRunner(click.testing.CliRunner):
103 """A test runner to use when the logging system will be initialized by code
104 under test, calls CliLog.resetLog(), which undoes any logging setup that
105 was done with the CliLog interface.
107 lsst.log modules can not be set back to an uninitialized state (python
108 logging modules can be set back to NOTSET), instead they are set to
109 `CliLog.defaultLsstLogLevel`."""
111 def invoke(self, *args, **kwargs):
112 result = super().invoke(*args, **kwargs)
113 CliLog.resetLog()
114 return result
117def clickResultMsg(result):
118 """Get a standard assert message from a click result
120 Parameters
121 ----------
122 result : click.Result
123 The result object returned from click.testing.CliRunner.invoke
125 Returns
126 -------
127 msg : `str`
128 The message string.
129 """
130 msg = f"""\noutput: {result.output}\nexception: {result.exception}"""
131 if result.exception:
132 msg += f"""\ntraceback: {"".join(traceback.format_tb(result.exception.__traceback__))}"""
133 return msg
136@contextmanager
137def command_test_env(runner, commandModule, commandName):
138 """A context manager that creates (and then cleans up) an environment that
139 provides a CLI plugin command with the given name.
141 Parameters
142 ----------
143 runner : click.testing.CliRunner
144 The test runner to use to create the isolated filesystem.
145 commandModule : `str`
146 The importable module that the command can be imported from.
147 commandName : `str`
148 The name of the command being published to import.
149 """
150 with runner.isolated_filesystem():
151 with open("resources.yaml", "w") as f:
152 f.write(yaml.dump({"cmd": {"import": commandModule, "commands": [commandName]}}))
153 # Add a colon to the end of the path on the next line, this tests the
154 # case where the lookup in LoaderCLI._getPluginList generates an empty
155 # string in one of the list entries and verifies that the empty string
156 # is properly stripped out.
157 with patch.dict("os.environ", {"DAF_BUTLER_PLUGINS": f"{os.path.realpath(f.name)}:"}):
158 yield
161def addArgumentHelp(doc, helpText):
162 """Add a Click argument's help message to a function's documentation.
164 This is needed because click presents arguments in the order the argument
165 decorators are applied to a function, top down. But, the evaluation of the
166 decorators happens bottom up, so if arguments just append their help to the
167 function's docstring, the argument descriptions appear in reverse order
168 from the order they are applied in.
170 Parameters
171 ----------
172 doc : `str`
173 The function's docstring.
174 helpText : `str`
175 The argument's help string to be inserted into the function's
176 docstring.
178 Returns
179 -------
180 doc : `str`
181 Updated function documentation.
182 """
183 if doc is None: 183 ↛ 184line 183 didn't jump to line 184, because the condition on line 183 was never true
184 doc = helpText
185 else:
186 # See click documentation for details:
187 # https://click.palletsprojects.com/en/7.x/documentation/#truncating-help-texts
188 # In short, text for the click command help can be truncated by putting
189 # "\f" in the docstring, everything after it should be removed
190 if "\f" in doc: 190 ↛ 191line 190 didn't jump to line 191, because the condition on line 190 was never true
191 doc = doc.split("\f")[0]
193 doclines = doc.splitlines()
194 # The function's docstring may span multiple lines, so combine the
195 # docstring from all the first lines until a blank line is encountered.
196 # (Lines after the first blank line will be argument help.)
197 while len(doclines) > 1 and doclines[1]:
198 doclines[0] = " ".join((doclines[0], doclines.pop(1).strip()))
199 # Add standard indent to help text for proper alignment with command
200 # function documentation:
201 helpText = " " + helpText
202 doclines.insert(1, helpText)
203 doclines.insert(1, "\n")
204 doc = "\n".join(doclines)
205 return doc
208def split_commas(context, param, values):
209 """Process a tuple of values, where each value may contain comma-separated
210 values, and return a single list of all the passed-in values.
212 This function can be passed to the 'callback' argument of a click.option to
213 allow it to process comma-separated values (e.g. "--my-opt a,b,c").
215 Parameters
216 ----------
217 context : `click.Context` or `None`
218 The current execution context. Unused, but Click always passes it to
219 callbacks.
220 param : `click.core.Option` or `None`
221 The parameter being handled. Unused, but Click always passes it to
222 callbacks.
223 values : [`str`]
224 All the values passed for this option. Strings may contain commas,
225 which will be treated as delimiters for separate values.
227 Returns
228 -------
229 list of string
230 The passed in values separated by commas and combined into a single
231 list.
232 """
233 if values is None:
234 return values
235 valueList = []
236 for value in ensure_iterable(values):
237 valueList.extend(value.split(","))
238 return tuple(valueList)
241def split_kv(
242 context,
243 param,
244 values,
245 choice=None,
246 multiple=True,
247 normalize=False,
248 separator="=",
249 unseparated_okay=False,
250 return_type=dict,
251 default_key="",
252 reverse_kv=False,
253 add_to_default=False,
254):
255 """Process a tuple of values that are key-value pairs separated by a given
256 separator. Multiple pairs may be comma separated. Return a dictionary of
257 all the passed-in values.
259 This function can be passed to the 'callback' argument of a click.option to
260 allow it to process comma-separated values (e.g. "--my-opt a=1,b=2").
262 Parameters
263 ----------
264 context : `click.Context` or `None`
265 The current execution context. Unused, but Click always passes it to
266 callbacks.
267 param : `click.core.Option` or `None`
268 The parameter being handled. Unused, but Click always passes it to
269 callbacks.
270 values : [`str`]
271 All the values passed for this option. Strings may contain commas,
272 which will be treated as delimiters for separate values.
273 choice : `click.Choice`, optional
274 If provided, verify each value is a valid choice using the provided
275 `click.Choice` instance. If None, no verification will be done. By
276 default None
277 multiple : `bool`, optional
278 If true, the value may contain multiple comma-separated values. By
279 default True.
280 normalize : `bool`, optional
281 If True and `choice.case_sensitive == False`, normalize the string the
282 user provided to match the choice's case. By default False.
283 separator : str, optional
284 The character that separates key-value pairs. May not be a comma or an
285 empty space (for space separators use Click's default implementation
286 for tuples; `type=(str, str)`). By default "=".
287 unseparated_okay : `bool`, optional
288 If True, allow values that do not have a separator. They will be
289 returned in the values dict as a tuple of values in the key '', that
290 is: `values[''] = (unseparated_values, )`. By default False.
291 return_type : `type`, must be `dict` or `tuple`
292 The type of the value that should be returned.
293 If `dict` then the returned object will be a dict, for each item in
294 values, the value to the left of the separator will be the key and the
295 value to the right of the separator will be the value.
296 If `tuple` then the returned object will be a tuple. Each item in the
297 tuple will be 2-item tuple, the first item will be the value to the
298 left of the separator and the second item will be the value to the
299 right. By default `dict`.
300 default_key : `Any`
301 The key to use if a value is passed that is not a key-value pair.
302 (Passing values that are not key-value pairs requires
303 ``unseparated_okay`` to be `True`.)
304 reverse_kv : bool
305 If true then for each item in values, the value to the left of the
306 separator is treated as the value and the value to the right of the
307 separator is treated as the key. By default False.
308 add_to_default : `bool`, optional
309 If True, then passed-in values will not overwrite the default value
310 unless the ``return_type`` is `dict` and passed-in value(s) have the
311 same key(s) as the default value.
313 Returns
314 -------
315 values : `dict` [`str`, `str`]
316 The passed-in values in dict form.
318 Raises
319 ------
320 `click.ClickException`
321 Raised if the separator is not found in an entry, or if duplicate keys
322 are encountered.
323 """
325 def norm(val):
326 """If `normalize` is True and `choice` is not `None`, find the value
327 in the available choices and return the value as spelled in the
328 choices.
330 Assumes that val exists in choices; `split_kv` uses the `choice`
331 instance to verify val is a valid choice.
332 """
333 if normalize and choice is not None:
334 v = val.casefold()
335 for opt in choice.choices:
336 if opt.casefold() == v:
337 return opt
338 return val
340 class RetDict:
341 def __init__(self):
342 self.ret = {}
344 def add(self, key, val):
345 if reverse_kv:
346 key, val = val, key
347 self.ret[key] = val
349 def get(self):
350 return self.ret
352 class RetTuple:
353 def __init__(self):
354 self.ret = []
356 def add(self, key, val):
357 if reverse_kv:
358 key, val = val, key
359 self.ret.append((key, val))
361 def get(self):
362 return tuple(self.ret)
364 if separator in (",", " "):
365 raise RuntimeError(f"'{separator}' is not a supported separator for key-value pairs.")
366 vals = values # preserve the original argument for error reporting below.
368 if add_to_default:
369 default = param.get_default(context)
370 if default:
371 vals = itertools.chain(default, vals)
373 if return_type is dict:
374 ret = RetDict()
375 elif return_type is tuple:
376 ret = RetTuple()
377 else:
378 raise click.ClickException(
379 message=f"Internal error: invalid return type '{return_type}' for split_kv."
380 )
381 if multiple:
382 vals = split_commas(context, param, vals)
383 for val in ensure_iterable(vals):
384 if unseparated_okay and separator not in val:
385 if choice is not None:
386 choice(val) # will raise if val is an invalid choice
387 ret.add(default_key, norm(val))
388 else:
389 try:
390 k, v = val.split(separator)
391 if choice is not None:
392 choice(v) # will raise if val is an invalid choice
393 except ValueError:
394 raise click.ClickException(
395 message=f"Could not parse key-value pair '{val}' using separator '{separator}', "
396 f"with multiple values {'allowed' if multiple else 'not allowed'}."
397 )
398 ret.add(k, norm(v))
399 return ret.get()
402def to_upper(context, param, value):
403 """Convert a value to upper case.
405 Parameters
406 ----------
407 context : click.Context
409 values : string
410 The value to be converted.
412 Returns
413 -------
414 string
415 A copy of the passed-in value, converted to upper case.
416 """
417 return value.upper()
420def unwrap(val):
421 """Remove newlines and leading whitespace from a multi-line string with
422 a consistent indentation level.
424 The first line of the string may be only a newline or may contain text
425 followed by a newline, either is ok. After the first line, each line must
426 begin with a consistant amount of whitespace. So, content of a
427 triple-quoted string may begin immediately after the quotes, or the string
428 may start with a newline. Each line after that must be the same amount of
429 indentation/whitespace followed by text and a newline. The last line may
430 end with a new line but is not required to do so.
432 Parameters
433 ----------
434 val : `str`
435 The string to change.
437 Returns
438 -------
439 strippedString : `str`
440 The string with newlines, indentation, and leading and trailing
441 whitespace removed.
442 """
444 def splitSection(val):
445 if not val.startswith("\n"): 445 ↛ 449line 445 didn't jump to line 449, because the condition on line 445 was never false
446 firstLine, _, val = val.partition("\n")
447 firstLine += " "
448 else:
449 firstLine = ""
450 return (firstLine + textwrap.dedent(val).replace("\n", " ")).strip()
452 return "\n\n".join([splitSection(s) for s in val.split("\n\n")])
455class option_section: # noqa: N801
456 """Decorator to add a section label between options in the help text of a
457 command.
459 Parameters
460 ----------
461 sectionText : `str`
462 The text to print in the section identifier.
463 """
465 def __init__(self, sectionText):
466 self.sectionText = "\n" + sectionText
468 def __call__(self, f):
469 # Generate a parameter declaration that will be unique for this
470 # section.
471 return click.option(
472 f"--option-section-{str(uuid.uuid4())}", sectionText=self.sectionText, cls=OptionSection
473 )(f)
476class MWPath(click.Path):
477 """Overrides click.Path to implement file-does-not-exist checking.
479 Changes the definition of ``exists` so that `True` indicates the location
480 (file or directory) must exist, `False` indicates the location must *not*
481 exist, and `None` indicates that the file may exist or not. The standard
482 definition for the `click.Path` ``exists`` parameter is that for `True` a
483 location must exist, but `False` means it is not required to exist (not
484 that it is required to not exist).
486 Parameters
487 ----------
488 exists : `True`, `False`, or `None`
489 If `True`, the location (file or directory) indicated by the caller
490 must exist. If `False` the location must not exist. If `None`, the
491 location may exist or not.
493 For other parameters see `click.Path`.
494 """
496 def __init__(
497 self,
498 exists=None,
499 file_okay=True,
500 dir_okay=True,
501 writable=False,
502 readable=True,
503 resolve_path=False,
504 allow_dash=False,
505 path_type=None,
506 ):
507 self.mustNotExist = exists is False
508 if exists is None: 508 ↛ 510line 508 didn't jump to line 510, because the condition on line 508 was never false
509 exists = False
510 super().__init__(
511 exists=exists,
512 file_okay=file_okay,
513 dir_okay=dir_okay,
514 writable=writable,
515 readable=readable,
516 resolve_path=resolve_path,
517 allow_dash=allow_dash,
518 path_type=path_type,
519 )
521 def convert(self, value, param, ctx):
522 """Called by click.ParamType to "convert values through types".
523 `click.Path` uses this step to verify Path conditions."""
524 if self.mustNotExist and os.path.exists(value):
525 self.fail(f'Path "{value}" should not exist.')
526 return super().convert(value, param, ctx)
529class MWOption(click.Option):
530 """Overrides click.Option with desired behaviors."""
532 def make_metavar(self):
533 """Overrides `click.Option.make_metavar`. Makes the metavar for the
534 help menu. Adds a space and an elipsis after the metavar name if
535 the option accepts multiple inputs, otherwise defers to the base
536 implementation.
538 By default click does not add an elipsis when multiple is True and
539 nargs is 1. And when nargs does not equal 1 click adds an elipsis
540 without a space between the metavar and the elipsis, but we prefer a
541 space between.
543 Does not get called for some option types (e.g. flag) so metavar
544 transformation that must apply to all types should be applied in
545 get_help_record.
546 """
547 metavar = super().make_metavar()
548 if self.multiple and self.nargs == 1:
549 metavar += " ..."
550 elif self.nargs != 1:
551 metavar = f"{metavar[:-3]} ..."
552 return metavar
555class MWArgument(click.Argument):
556 """Overrides click.Argument with desired behaviors."""
558 def make_metavar(self):
559 """Overrides `click.Option.make_metavar`. Makes the metavar for the
560 help menu. Always adds a space and an elipsis (' ...') after the
561 metavar name if the option accepts multiple inputs.
563 By default click adds an elipsis without a space between the metavar
564 and the elipsis, but we prefer a space between.
566 Returns
567 -------
568 metavar : `str`
569 The metavar value.
570 """
571 metavar = super().make_metavar()
572 if self.nargs != 1:
573 metavar = f"{metavar[:-3]} ..."
574 return metavar
577class OptionSection(MWOption):
578 """Implements an Option that prints a section label in the help text and
579 does not pass any value to the command function.
581 This class does a bit of hackery to add a section label to a click command
582 help output: first, `expose_value` is set to `False` so that no value is
583 passed to the command function. Second, this class overrides
584 `click.Option.get_help_record` to return the section label string without
585 any prefix so that it stands out as a section label.
587 This class overrides the hidden attribute because our documentation build
588 tool, sphinx-click, implements its own `get_help_record` function which
589 builds the record from other option values (e.g. `name`, `opts`), which
590 breaks the hack we use to make `get_help_record` only return the
591 `sectionText`. Fortunately, Click gets the value of `hidden` inside the
592 `Option`'s `get_help_record`, and `sphinx-click` calls `opt.hidden` before
593 entering its `_get_help_record` function. So, making the hidden property
594 return True hides this option from sphinx-click, while allowing the section
595 text to be returned by our `get_help_record` method when using Click.
597 The intention for this implementation is to do minimally invasive overrides
598 of the click classes so as to be robust and easy to fix if the click
599 internals change.
601 Parameters
602 ----------
603 sectionName : `str`
604 The parameter declaration for this option. It is not shown to the user,
605 it must be unique within the command. If using the `section` decorator
606 to add a section to a command's options, the section name is
607 auto-generated.
608 sectionText : `str`
609 The text to print in the section identifier.
610 """
612 @property
613 def hidden(self):
614 return True
616 @hidden.setter
617 def hidden(self, val):
618 pass
620 def __init__(self, sectionName, sectionText):
621 super().__init__(sectionName, expose_value=False)
622 self.sectionText = sectionText
624 def get_help_record(self, ctx):
625 return (self.sectionText, "")
628class MWOptionDecorator:
629 """Wraps the click.option decorator to enable shared options to be declared
630 and allows inspection of the shared option.
631 """
633 def __init__(self, *param_decls, **kwargs):
634 self.partialOpt = partial(click.option, *param_decls, cls=partial(MWOption), **kwargs)
635 opt = click.Option(param_decls, **kwargs)
636 self._name = opt.name
637 self._opts = opt.opts
639 def name(self):
640 """Get the name that will be passed to the command function for this
641 option."""
642 return self._name
644 def opts(self):
645 """Get the flags that will be used for this option on the command
646 line."""
647 return self._opts
649 @property
650 def help(self):
651 """Get the help text for this option. Returns an empty string if no
652 help was defined."""
653 return self.partialOpt.keywords.get("help", "")
655 def __call__(self, *args, **kwargs):
656 return self.partialOpt(*args, **kwargs)
659class MWArgumentDecorator:
660 """Wraps the click.argument decorator to enable shared arguments to be
661 declared."""
663 def __init__(self, *param_decls, **kwargs):
664 self._helpText = kwargs.pop("help", None)
665 self.partialArg = partial(click.argument, *param_decls, cls=MWArgument, **kwargs)
667 def __call__(self, *args, help=None, **kwargs):
668 def decorator(f):
669 if help is not None:
670 self._helpText = help
671 if self._helpText:
672 f.__doc__ = addArgumentHelp(f.__doc__, self._helpText)
673 return self.partialArg(*args, **kwargs)(f)
675 return decorator
678class MWCommand(click.Command):
679 """Command subclass that stores a copy of the args list for use by the
680 command."""
682 extra_epilog = None
684 def __init__(self, *args, **kwargs):
685 # wrap callback method with catch_and_exit decorator
686 callback = kwargs.get("callback")
687 if callback is not None: 687 ↛ 690line 687 didn't jump to line 690, because the condition on line 687 was never false
688 kwargs = kwargs.copy()
689 kwargs["callback"] = catch_and_exit(callback)
690 super().__init__(*args, **kwargs)
692 def parse_args(self, ctx, args):
693 MWCtxObj.getFrom(ctx).args = copy.copy(args)
694 super().parse_args(ctx, args)
696 @property
697 def epilog(self):
698 """Override the epilog attribute to add extra_epilog (if defined by a
699 subclass) to the end of any epilog provided by a subcommand.
700 """
701 ret = self._epilog if self._epilog else ""
702 if self.extra_epilog:
703 if ret:
704 ret += "\n\n"
705 ret += self.extra_epilog
706 return ret
708 @epilog.setter
709 def epilog(self, val):
710 self._epilog = val
713class ButlerCommand(MWCommand):
714 """Command subclass with butler-command specific overrides."""
716 extra_epilog = "See 'butler --help' for more options."
719class OptionGroup:
720 """Base class for an option group decorator. Requires the option group
721 subclass to have a property called `decorator`."""
723 def __call__(self, f):
724 for decorator in reversed(self.decorators):
725 f = decorator(f)
726 return f
729class MWCtxObj:
730 """Helper object for managing the `click.Context.obj` parameter, allows
731 obj data to be managed in a consistent way.
733 `Context.obj` defaults to None. `MWCtxObj.getFrom(ctx)` can be used to
734 initialize the obj if needed and return a new or existing MWCtxObj.
736 Attributes
737 ----------
738 args : `list` [`str`]
739 The list of arguments (argument values, option flags, and option
740 values), split using whitespace, that were passed in on the command
741 line for the subcommand represented by the parent context object.
742 """
744 def __init__(self):
746 self.args = None
748 @staticmethod
749 def getFrom(ctx):
750 """If needed, initialize `ctx.obj` with a new MWCtxObj, and return the
751 new or already existing MWCtxObj."""
752 if ctx.obj is not None:
753 return ctx.obj
754 ctx.obj = MWCtxObj()
755 return ctx.obj
758def yaml_presets(ctx, param, value):
759 """Click callback that reads additional values from the supplied
760 YAML file.
762 Parameters
763 ----------
764 ctx : `click.context`
765 The context for the click operation. Used to extract the subcommand
766 name and translate option & argument names.
767 param : `str`
768 The parameter name.
769 value : `object`
770 The value of the parameter.
771 """
773 def _name_for_option(ctx: click.Context, option: str) -> str:
774 """Use a CLI option name to find the name of the argument to the
775 command function.
777 Parameters
778 ----------
779 ctx : `click.Context`
780 The context for the click operation.
781 option : `str`
782 The option/argument name from the yaml file.
784 Returns
785 -------
786 name : str
787 The name of the argument to use when calling the click.command
788 function, as it should appear in the `ctx.default_map`.
790 Raises
791 ------
792 RuntimeError
793 Raised if the option name from the yaml file does not exist in the
794 command parameters. This catches misspellings and incorrect useage
795 in the yaml file.
796 """
797 for param in ctx.command.params:
798 # Remove leading dashes: they are not used for option names in the
799 # yaml file.
800 if option in [opt.lstrip("-") for opt in param.opts]:
801 return param.name
802 raise RuntimeError(f"'{option}' is not a valid option for {ctx.info_name}")
804 ctx.default_map = ctx.default_map or {}
805 cmd_name = ctx.info_name
806 if value:
807 try:
808 overrides = _read_yaml_presets(value, cmd_name)
809 options = list(overrides.keys())
810 for option in options:
811 name = _name_for_option(ctx, option)
812 if name == option:
813 continue
814 overrides[name] = overrides.pop(option)
815 except Exception as e:
816 raise click.BadOptionUsage(
817 option_name=param.name,
818 message=f"Error reading overrides file: {e}",
819 ctx=ctx,
820 )
821 # Override the defaults for this subcommand
822 ctx.default_map.update(overrides)
823 return
826def _read_yaml_presets(file_uri, cmd_name):
827 """Read file command line overrides from YAML config file.
829 Parameters
830 ----------
831 file_uri : `str`
832 URI of override YAML file containing the command line overrides.
833 They should be grouped by command name.
834 cmd_name : `str`
835 The subcommand name that is being modified.
837 Returns
838 -------
839 overrides : `dict` of [`str`, Any]
840 The relevant command line options read from the override file.
841 """
842 log.debug("Reading command line overrides for subcommand %s from URI %s", cmd_name, file_uri)
843 config = Config(file_uri)
844 return config[cmd_name]
847def sortAstropyTable(table, dimensions, sort_first=None):
848 """Sort an astropy table, with prioritization given to columns in this
849 order:
850 1. the provided named columns
851 2. spatial and temporal columns
852 3. the rest of the columns
854 The table is sorted in-place, and is also returned for convenience.
856 Parameters
857 ----------
858 table : `astropy.table.Table`
859 The table to sort
860 dimensions : `list` [``Dimension``]
861 The dimensions of the dataIds in the table (the dimensions should be
862 the same for all the dataIds). Used to determine if the column is
863 spatial, temporal, or neither.
864 sort_first : `list` [`str`]
865 The names of columns that should be sorted first, before spatial and
866 temporal columns.
868 Returns
869 -------
870 `astropy.table.Table`
871 For convenience, the table that has been sorted.
872 """
873 # For sorting we want to ignore the id
874 # We also want to move temporal or spatial dimensions earlier
875 sort_first = sort_first or []
876 sort_early = []
877 sort_late = []
878 for dim in dimensions:
879 if dim.spatial or dim.temporal:
880 sort_early.extend(dim.required.names)
881 else:
882 sort_late.append(str(dim))
883 sort_keys = sort_first + sort_early + sort_late
884 # The required names above means that we have the possibility of
885 # repeats of sort keys. Now have to remove them
886 # (order is retained by dict creation).
887 sort_keys = list(dict.fromkeys(sort_keys).keys())
889 table.sort(sort_keys)
890 return table
893def catch_and_exit(func):
894 """Decorator which catches all exceptions, prints an exception traceback
895 and signals click to exit.
896 """
898 @wraps(func)
899 def inner(*args, **kwargs):
900 try:
901 func(*args, **kwargs)
902 except (click.exceptions.ClickException, click.exceptions.Exit, click.exceptions.Abort):
903 # this is handled by click itself
904 raise
905 except Exception:
906 exc_type, exc_value, exc_tb = sys.exc_info()
907 if exc_tb.tb_next:
908 # do not show this decorator in traceback
909 exc_tb = exc_tb.tb_next
910 log.exception(
911 "Caught an exception, details are in traceback:", exc_info=(exc_type, exc_value, exc_tb)
912 )
913 # tell click to stop, this never returns.
914 click.get_current_context().exit(1)
916 return inner