Coverage for python / lsst / obs / base / cli / cmd / commands.py: 90%
73 statements
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1# This file is part of obs_base.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (http://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <http://www.gnu.org/licenses/>.
22from collections.abc import Sequence
23from typing import Any
25import click
27from lsst.daf.butler import Butler
28from lsst.daf.butler.cli.opt import (
29 collections_argument,
30 config_file_option,
31 config_option,
32 locations_argument,
33 options_file_option,
34 processes_option,
35 regex_option,
36 repo_argument,
37 run_option,
38 transfer_option,
39 where_option,
40)
41from lsst.daf.butler.cli.utils import ButlerCommand, split_commas, typeStrAcceptsMultiple
42from lsst.pipe.base.cli.opt import instrument_argument
44from ... import script
45from ..opt import failfast_option, labels_argument
47# regular expression that can be used to find supported fits file extensions.
48fits_re = r"\.fit[s]?\b"
51@click.command(short_help="Define visits from exposures.", cls=ButlerCommand)
52@repo_argument(required=True)
53@instrument_argument(required=True)
54@config_file_option(
55 help="Path to a pex_config override to be included after the Instrument config overrides are applied."
56)
57@click.option(
58 "--collections",
59 help="The collections to be searched (in order) for camera geometry.",
60 multiple=True,
61 callback=split_commas,
62 metavar=typeStrAcceptsMultiple,
63)
64@where_option()
65@click.option(
66 "--update-records/--no-update-records",
67 default=False,
68 help="Use this option to force updates to the visit definition record. "
69 "Should only be used if you know that there has been a change to the "
70 "exposure records, such as a change to the metadata translator.",
71)
72@click.option(
73 "--incremental/--no-incremental",
74 default=False,
75 help="Use this option to force updates to the visit definition record "
76 "when multi-snap visits are being ingested incrementally and so you "
77 "might encounter partial visits. Implies --update-records.",
78)
79@click.option(
80 "--skip-conflicting/--no-skip-conflicting",
81 default=False,
82 help="Use this option to skip over any visits that are currently defined "
83 "with a different value and you are not sure whether to accept the new "
84 "value. Ignored if incremental or update mode is enabled.",
85)
86@options_file_option()
87def define_visits(*args: Any, **kwargs: Any) -> None:
88 """Define visits from exposures in the butler registry.
90 The calibration collection containing the camera geometry can not
91 be specified.
92 """
93 script.defineVisits(*args, **kwargs)
96@click.command(short_help="Ingest raw frames.", cls=ButlerCommand)
97@repo_argument(required=True)
98@locations_argument(
99 help="LOCATIONS specifies files to ingest and/or locations to search for files.", required=True
100)
101@regex_option(
102 default=fits_re,
103 help="Regex string used to find files in directories listed in LOCATIONS. "
104 "Searches for fits files by default.",
105)
106@config_option(metavar="TEXT=TEXT", multiple=True)
107@config_file_option(type=click.Path(exists=True, writable=False, file_okay=True, dir_okay=False))
108@run_option(required=False)
109@transfer_option()
110@processes_option(help="Number of workers to use.")
111@click.option(
112 "--ingest-task",
113 default="lsst.obs.base.RawIngestTask",
114 help="The fully qualified class name of the ingest task to use.",
115)
116@click.option(
117 "--track-file-attrs/--no-track-file-attrs",
118 default=True,
119 help="Indicate to the datastore whether file attributes such as file size"
120 " or checksum should be tracked or not. Whether this parameter is honored"
121 " depends on the specific datastore implentation.",
122)
123@failfast_option()
124@click.option(
125 "--update-records/--no-update-records",
126 default=False,
127 help="Use this option to force updates to the exposure records. "
128 "Should only be used if you know that there has been a change to the "
129 "exposure records, such as a change to the metadata translator.",
130)
131@click.option(
132 "--skip-existing/--no-skip-existing",
133 default=True,
134 help="Use this option to control whether a raw file already existing "
135 "in the Butler repository is an error or not.",
136)
137@click.option(
138 "--search-indexes/--no-search-indexes",
139 default=True,
140 help="By default ingest searches for index files in each directory being "
141 "searched. Turning this off can improve performance if you know for a fact "
142 "you have no indexes and you are using an object store.",
143)
144@options_file_option()
145def ingest_raws(*args: Any, **kwargs: Any) -> None:
146 """Ingest raw frames into from a directory into the butler registry."""
147 script.ingestRaws(*args, **kwargs)
150@click.command(short_help="Add an instrument's curated calibrations.", cls=ButlerCommand)
151@repo_argument(required=True)
152@instrument_argument(required=True)
153@labels_argument()
154@click.option(
155 "--collection",
156 required=False,
157 help="Name of the calibration collection that associates datasets with validity ranges.",
158)
159@click.option(
160 "--label",
161 "labels",
162 multiple=True,
163 help=(
164 "Extra strings to include (with automatic delimiters) in all RUN collection names, "
165 "as well as the calibration collection name if it is not provided via --collection. "
166 "May be provided as a positional argument instead of or in addition to this option, "
167 "as long as at least one label is provided. Positional-argument labels appear before "
168 "those provided by this option."
169 ),
170)
171@click.option(
172 "--prefix",
173 required=False,
174 help=(
175 "Prefix for the collection name. Default is the instrument name. "
176 "This is ignored if --collection is passed."
177 ),
178)
179@options_file_option()
180def write_curated_calibrations(
181 *,
182 repo: str,
183 instrument: str,
184 collection: str,
185 labels: list[str],
186 labels_arg: list[str],
187 prefix: str,
188) -> None:
189 """Add an instrument's curated calibrations to the data repository."""
190 script.writeCuratedCalibrations(
191 repo=repo, instrument=instrument, collection=collection, labels=labels_arg + labels, prefix=prefix
192 )
195@click.command()
196@repo_argument(required=True)
197@instrument_argument(required=True, help="Name of the instrument to use for updates.")
198@collections_argument(help="Collections to search for visit geometry datasets.")
199@click.option("--dataset-type", default="visit_geometry", help="Name of the visit geometry dataset type.")
200@click.option("--batch-size", default=11, help="Number of visits to process in each transaction.")
201@where_option()
202def update_dimension_regions(
203 *,
204 repo: str,
205 instrument: str,
206 collections: Sequence[str],
207 dataset_type: str,
208 batch_size: int,
209 where: str,
210) -> None:
211 """Update dimension record regions from visit geometry datasets."""
212 from ...visit_geometry import VisitGeometry
214 with Butler.from_config(repo, writeable=True, collections=collections) as butler:
215 VisitGeometry.update_dimension_records(
216 butler, instrument, where, dataset_type=dataset_type, batch_size=batch_size
217 )
220@click.command
221@repo_argument(required=True)
222@instrument_argument(required=True, help="Instrument to use for finding raw datasets.")
223@collections_argument(help="List of collections to search for raws instead of the default.")
224@where_option(
225 help="A string expression to use to query the butler to find raw datasets to use for record updates."
226)
227@failfast_option()
228@config_option(metavar="TEXT=TEXT", multiple=True)
229@config_file_option(type=click.Path(exists=True, writable=False, file_okay=True, dir_okay=False))
230@processes_option()
231@options_file_option()
232def update_exposures_from_raws(*args: Any, **kwargs: Any) -> None:
233 """Update exposure records associated with specific raw datasets."""
234 script.updateExposures(*args, **kwargs)