Coverage for python/lsst/daf/butler/script/queryDatasets.py: 26%
72 statements
« prev ^ index » next coverage.py v7.2.5, created at 2023-05-06 09:33 +0000
« prev ^ index » next coverage.py v7.2.5, created at 2023-05-06 09:33 +0000
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
23import dataclasses
24import uuid
25from collections import defaultdict
26from collections.abc import Iterable
27from typing import TYPE_CHECKING
29import numpy as np
30from astropy.table import Table as AstropyTable
31from lsst.utils.ellipsis import Ellipsis, EllipsisType
33from .._butler import Butler
34from ..cli.utils import sortAstropyTable
36if TYPE_CHECKING:
37 from lsst.daf.butler import DatasetRef
38 from lsst.daf.butler.registry.queries import DatasetQueryResults
39 from lsst.resources import ResourcePath
42@dataclasses.dataclass(frozen=True)
43class _RefInfo:
44 datasetRef: DatasetRef
45 uri: str | None
48class _Table:
49 """Aggregates rows for a single dataset type, and creates an astropy table
50 with the aggregated data. Eliminates duplicate rows.
51 """
53 datasetRefs: set[_RefInfo]
55 def __init__(self) -> None:
56 self.datasetRefs = set()
58 def add(self, datasetRef: DatasetRef, uri: ResourcePath | None = None) -> None:
59 """Add a row of information to the table.
61 ``uri`` is optional but must be the consistent; provided or not, for
62 every call to a ``_Table`` instance.
64 Parameters
65 ----------
66 datasetRef : `DatasetRef`
67 A dataset ref that will be added as a row in the table.
68 uri : `lsst.resources.ResourcePath`, optional
69 The URI to show as a file location in the table, by default None
70 """
71 uri_str = str(uri) if uri else None
72 self.datasetRefs.add(_RefInfo(datasetRef, uri_str))
74 def getAstropyTable(self, datasetTypeName: str) -> AstropyTable:
75 """Get the table as an astropy table.
77 Parameters
78 ----------
79 datasetTypeName : `str`
80 The dataset type name to show in the ``type`` column of the table.
82 Returns
83 -------
84 table : `astropy.table._Table`
85 The table with the provided column names and rows.
86 """
88 def _id_type(datasetRef: DatasetRef) -> type[str] | type[np.int64]:
89 if isinstance(datasetRef.id, uuid.UUID):
90 return str
91 else:
92 return np.int64
94 # Should never happen; adding a dataset should be the action that
95 # causes a _Table to be created.
96 if not self.datasetRefs:
97 raise RuntimeError(f"No DatasetRefs were provided for dataset type {datasetTypeName}")
99 refInfo = next(iter(self.datasetRefs))
100 dimensions = list(refInfo.datasetRef.dataId.full.keys())
101 columnNames = ["type", "run", "id", *[str(item) for item in dimensions]]
103 # Need to hint the column types for numbers since the per-row
104 # constructor of Table does not work this out on its own and sorting
105 # will not work properly without.
106 typeMap = {float: np.float64, int: np.int64}
107 idType = _id_type(refInfo.datasetRef)
108 columnTypes = [
109 None,
110 None,
111 idType,
112 *[typeMap.get(type(value)) for value in refInfo.datasetRef.dataId.full.values()],
113 ]
114 if refInfo.uri:
115 columnNames.append("URI")
116 columnTypes.append(None)
118 rows = []
119 for refInfo in self.datasetRefs:
120 row = [
121 datasetTypeName,
122 refInfo.datasetRef.run,
123 str(refInfo.datasetRef.id) if idType is str else refInfo.datasetRef.id,
124 *[value for value in refInfo.datasetRef.dataId.full.values()],
125 ]
126 if refInfo.uri:
127 row.append(refInfo.uri)
128 rows.append(row)
130 dataset_table = AstropyTable(np.array(rows), names=columnNames, dtype=columnTypes)
131 return sortAstropyTable(dataset_table, dimensions, ["type", "run"])
134class QueryDatasets:
135 """Get dataset refs from a repository.
137 Parameters
138 ----------
139 glob : iterable [`str`]
140 A list of glob-style search string that fully or partially identify
141 the dataset type names to search for.
142 collections : iterable [`str`]
143 A list of glob-style search string that fully or partially identify
144 the collections to search for.
145 where : `str`
146 A string expression similar to a SQL WHERE clause. May involve any
147 column of a dimension table or (as a shortcut for the primary key
148 column of a dimension table) dimension name.
149 find_first : `bool`
150 For each result data ID, only yield one DatasetRef of each DatasetType,
151 from the first collection in which a dataset of that dataset type
152 appears (according to the order of `collections` passed in). If used,
153 `collections` must specify at least one expression and must not contain
154 wildcards.
155 show_uri : `bool`
156 If True, include the dataset URI in the output.
157 repo : `str` or `None`
158 URI to the location of the repo or URI to a config file describing the
159 repo and its location. One of `repo` and `butler` must be `None` and
160 the other must not be `None`.
161 butler : `lsst.daf.butler.Butler` or `None`
162 The butler to use to query. One of `repo` and `butler` must be `None`
163 and the other must not be `None`.
165 """
167 def __init__(
168 self,
169 glob: Iterable[str],
170 collections: Iterable[str],
171 where: str,
172 find_first: bool,
173 show_uri: bool,
174 repo: str | None = None,
175 butler: Butler | None = None,
176 ):
177 if (repo and butler) or (not repo and not butler):
178 raise RuntimeError("One of repo and butler must be provided and the other must be None.")
179 self.butler = butler or Butler(repo)
180 self._getDatasets(glob, collections, where, find_first)
181 self.showUri = show_uri
183 def _getDatasets(
184 self, glob: Iterable[str], collections: Iterable[str], where: str, find_first: bool
185 ) -> None:
186 datasetTypes = glob if glob else ...
187 query_collections: Iterable[str] | EllipsisType = collections if collections else Ellipsis
189 self.datasets = self.butler.registry.queryDatasets(
190 datasetType=datasetTypes, collections=query_collections, where=where, findFirst=find_first
191 ).expanded()
193 def getTables(self) -> list[AstropyTable]:
194 """Get the datasets as a list of astropy tables.
196 Returns
197 -------
198 datasetTables : `list` [``astropy.table._Table``]
199 A list of astropy tables, one for each dataset type.
200 """
201 tables: dict[str, _Table] = defaultdict(_Table)
202 if not self.showUri:
203 for dataset_ref in self.datasets:
204 tables[dataset_ref.datasetType.name].add(dataset_ref)
205 else:
206 d = list(self.datasets)
207 ref_uris = self.butler.datastore.getManyURIs(d, predict=True)
208 for ref, uris in ref_uris.items():
209 if uris.primaryURI:
210 tables[ref.datasetType.name].add(ref, uris.primaryURI)
211 for name, uri in uris.componentURIs.items():
212 tables[ref.datasetType.componentTypeName(name)].add(ref, uri)
214 return [table.getAstropyTable(datasetTypeName) for datasetTypeName, table in tables.items()]
216 def getDatasets(self) -> DatasetQueryResults:
217 """Get the datasets as a list of ``DatasetQueryResults``.
219 Returns
220 -------
221 refs : `lsst.daf.butler.registry.queries.DatasetQueryResults`
222 Dataset references matching the given query criteria.
223 """
224 return self.datasets