Coverage for python/lsst/daf/butler/script/ingest_files.py: 21%
56 statements
« prev ^ index » next coverage.py v7.2.3, created at 2023-04-22 02:18 -0700
« prev ^ index » next coverage.py v7.2.3, created at 2023-04-22 02:18 -0700
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__ = ("ingest_files",)
25import logging
26import warnings
27from collections import defaultdict
28from typing import TYPE_CHECKING, Any
30from astropy.table import Table
31from lsst.resources import ResourcePath
32from lsst.utils import doImport
34from .._butler import Butler
35from ..core import DatasetIdGenEnum, DatasetRef, FileDataset, UnresolvedRefWarning
37if TYPE_CHECKING:
38 from ..core import DatasetType, DimensionUniverse
40log = logging.getLogger(__name__)
43def ingest_files(
44 repo: str,
45 dataset_type: str,
46 run: str,
47 table_file: str,
48 data_id: tuple[str, ...] = (),
49 formatter: str | None = None,
50 id_generation_mode: str = "UNIQUE",
51 prefix: str | None = None,
52 transfer: str = "auto",
53) -> None:
54 """Ingest files from a table.
56 Parameters
57 ----------
58 repo : `str`
59 URI string of the Butler repo to use.
60 dataset_type : `str`
61 The name of the dataset type for the files to be ingested. This
62 dataset type must exist.
63 run : `str`
64 The run in which the files should be ingested.
65 table_file : `str`
66 Path to a table file to read. This file can be in any format that
67 can be read by Astropy so long as Astropy can determine the format
68 itself.
69 data_id : `tuple` of `str`
70 Tuple of strings of the form ``keyword=value`` that can be used
71 to define dataId elements that are fixed for all ingested files
72 found in the table file. This allows those columns to be missing
73 from the table file. Dimensions given here override table columns.
74 formatter : `str`, optional
75 Fully-qualified python class name for the `Formatter` to use
76 to read the ingested files. If `None` the formatter is read from
77 datastore configuration based on the dataset type.
78 id_generation_mode : `str`, optional
79 Mode to use for generating IDs. Should map to `DatasetGenIdEnum`.
80 prefix : `str`, optional
81 Prefix to use when resolving relative paths in table files. The default
82 is to use the current working directory.
83 transfer : `str`, optional
84 Transfer mode to use for ingest.
85 """
87 # Check that the formatter can be imported -- validate this as soon
88 # as possible before we read a potentially large table file.
89 if formatter:
90 doImport(formatter)
91 else:
92 formatter = None
94 # Force empty string prefix (from click) to None for API compatibility.
95 if not prefix:
96 prefix = None
98 # Convert the dataset ID gen mode string to enum.
99 id_gen_mode = DatasetIdGenEnum.__members__[id_generation_mode]
101 # Create the butler with the relevant run attached.
102 butler = Butler(repo, run=run)
104 datasetType = butler.registry.getDatasetType(dataset_type)
106 # Convert the k=v strings into a dataId dict.
107 universe = butler.registry.dimensions
108 common_data_id = parse_data_id_tuple(data_id, universe)
110 # Read the table assuming that Astropy can work out the format.
111 uri = ResourcePath(table_file, forceAbsolute=False)
112 with uri.as_local() as local_file:
113 table = Table.read(local_file.ospath)
115 datasets = extract_datasets_from_table(table, common_data_id, datasetType, formatter, prefix)
117 butler.ingest(*datasets, transfer=transfer, run=run, idGenerationMode=id_gen_mode)
120def extract_datasets_from_table(
121 table: Table,
122 common_data_id: dict,
123 datasetType: DatasetType,
124 formatter: str | None = None,
125 prefix: str | None = None,
126) -> list[FileDataset]:
127 """Extract datasets from the supplied table.
129 Parameters
130 ----------
131 table : `astropy.table.Table`
132 Table containing the datasets. The first column is assumed to be
133 the file URI and the remaining columns are dimensions.
134 common_data_id : `dict`
135 Data ID values that are common to every row in the table. These
136 take priority if a dimension in this dataId is also present as
137 a column in the table.
138 datasetType : `DatasetType`
139 The dataset type to be associated with the ingested data.
140 formatter : `str`, optional
141 Fully-qualified python class name for the `Formatter` to use
142 to read the ingested files. If `None` the formatter is read from
143 datastore configuration based on the dataset type.
144 prefix : `str`
145 Prefix to be used for relative paths. Can be `None` for current
146 working directory.
148 Returns
149 -------
150 datasets : `list` of `FileDataset`
151 The `FileDataset` objects corresponding to the rows in the table.
152 The number of elements in this list can be smaller than the number
153 of rows in the file because one file can appear in multiple rows
154 with different dataIds.
155 """
156 # The file is the first column and everything else is assumed to
157 # be dimensions so we need to know the name of that column.
158 file_column = table.colnames[0]
160 # Handle multiple dataIds per file by grouping by file.
161 refs_by_file = defaultdict(list)
162 n_dataset_refs = 0
163 for row in table:
164 # Convert the row to a dataId, remembering to extract the
165 # path column.
166 dataId = dict(row)
167 path = dataId.pop(file_column)
169 # The command line can override a column.
170 dataId.update(common_data_id)
172 # Create the dataset ref that is to be ingested.
173 with warnings.catch_warnings():
174 warnings.simplefilter("ignore", category=UnresolvedRefWarning)
175 # Could create a resolved ref here but first need to consider
176 # the broader problem of Butler.ingest() taking a run parameter
177 # that is no longer guaranteed to match the run in the
178 # ref attached to the FileDataset.
179 ref = DatasetRef(datasetType, dataId) # type: ignore
181 # Convert path to absolute (because otherwise system will
182 # assume relative to datastore root and that is almost certainly
183 # never the right default here).
184 path_uri = ResourcePath(path, root=prefix, forceAbsolute=True)
186 refs_by_file[path_uri].append(ref)
187 n_dataset_refs += 1
189 datasets = [
190 FileDataset(
191 path=file_uri,
192 refs=refs,
193 formatter=formatter,
194 )
195 for file_uri, refs in refs_by_file.items()
196 ]
198 log.info("Ingesting %d dataset ref(s) from %d file(s)", n_dataset_refs, len(datasets))
200 return datasets
203def parse_data_id_tuple(data_ids: tuple[str, ...], universe: DimensionUniverse) -> dict[str, Any]:
204 # Convert any additional k=v strings in the dataId tuple to dict
205 # form.
206 data_id: dict[str, Any] = {}
207 for id_str in data_ids:
208 dimension_str, value = id_str.split("=")
210 try:
211 dimension = universe.getStaticDimensions()[dimension_str]
212 except KeyError:
213 raise ValueError(f"DataID dimension '{dimension_str}' is not known to this universe.") from None
215 # Cast the value to the right python type (since they will be
216 # strings at this point).
217 value = dimension.primaryKey.getPythonType()(value)
219 data_id[dimension_str] = value
220 return data_id