Coverage for python/lsst/daf/butler/script/queryDatasets.py : 19%

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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/>.
21from __future__ import annotations
23from astropy.table import Table as AstropyTable
24from collections import defaultdict, namedtuple
25from typing import Any, Dict
26import numpy as np
27import uuid
29from .. import Butler
30from ..core.utils import globToRegex
31from ..cli.utils import sortAstropyTable
34_RefInfo = namedtuple("_RefInfo", ["datasetRef", "uri"])
37class _Table:
38 """Aggregates rows for a single dataset type, and creates an astropy table
39 with the aggregated data. Eliminates duplicate rows.
40 """
42 def __init__(self):
43 self.datasetRefs = set()
45 def add(self, datasetRef, uri=None):
46 """Add a row of information to the table.
48 ``uri`` is optional but must be the consistent; provided or not, for
49 every call to a ``_Table`` instance.
51 Parameters
52 ----------
53 datasetRef : ``DatasetRef``
54 A dataset ref that will be added as a row in the table.
55 uri : ``ButlerURI``, optional
56 The URI to show as a file location in the table, by default None
57 """
58 if uri:
59 uri = str(uri)
60 self.datasetRefs.add(_RefInfo(datasetRef, uri))
62 def getAstropyTable(self, datasetTypeName):
63 """Get the table as an astropy table.
65 Parameters
66 ----------
67 datasetTypeName : `str`
68 The dataset type name to show in the ``type`` column of the table.
70 Returns
71 -------
72 table : `astropy.table._Table`
73 The table with the provided column names and rows.
74 """
75 def _id_type(datasetRef):
76 if isinstance(datasetRef.id, uuid.UUID):
77 return str
78 else:
79 return np.int64
81 # Should never happen; adding a dataset should be the action that
82 # causes a _Table to be created.
83 if not self.datasetRefs:
84 raise RuntimeError(f"No DatasetRefs were provided for dataset type {datasetTypeName}")
86 refInfo = next(iter(self.datasetRefs))
87 dimensions = list(refInfo.datasetRef.dataId.full.keys())
88 columnNames = ["type", "run", "id",
89 *[str(item) for item in dimensions]]
91 # Need to hint the column types for numbers since the per-row
92 # constructor of Table does not work this out on its own and sorting
93 # will not work properly without.
94 typeMap = {float: np.float64, int: np.int64}
95 idType = _id_type(refInfo.datasetRef)
96 columnTypes = [None, None, idType,
97 *[typeMap.get(type(value)) for value in refInfo.datasetRef.dataId.full.values()]]
98 if refInfo.uri:
99 columnNames.append("URI")
100 columnTypes.append(None)
102 rows = []
103 for refInfo in self.datasetRefs:
104 row = [datasetTypeName,
105 refInfo.datasetRef.run,
106 str(refInfo.datasetRef.id) if idType is str else refInfo.datasetRef.id,
107 *[value for value in refInfo.datasetRef.dataId.full.values()]]
108 if refInfo.uri:
109 row.append(refInfo.uri)
110 rows.append(row)
112 dataset_table = AstropyTable(np.array(rows), names=columnNames, dtype=columnTypes)
113 return sortAstropyTable(dataset_table, dimensions, ["type", "run"])
116class QueryDatasets:
117 """Get dataset refs from a repository.
119 Parameters
120 ----------
121 repo : `str` or `None`
122 URI to the location of the repo or URI to a config file describing the
123 repo and its location. One of `repo` and `butler` must be `None` and
124 the other must not be `None`.
125 butler : ``lsst.daf.butler.Butler`` or `None`
126 The butler to use to query. One of `repo` and `butler` must be `None`
127 and the other must not be `None`.
128 glob : iterable [`str`]
129 A list of glob-style search string that fully or partially identify
130 the dataset type names to search for.
131 collections : iterable [`str`]
132 A list of glob-style search string that fully or partially identify
133 the collections to search for.
134 where : `str`
135 A string expression similar to a SQL WHERE clause. May involve any
136 column of a dimension table or (as a shortcut for the primary key
137 column of a dimension table) dimension name.
138 find_first : `bool`
139 For each result data ID, only yield one DatasetRef of each DatasetType,
140 from the first collection in which a dataset of that dataset type
141 appears (according to the order of `collections` passed in). If used,
142 `collections` must specify at least one expression and must not contain
143 wildcards.
144 show_uri : `bool`
145 If True, include the dataset URI in the output.
146 """
148 def __init__(self, glob, collections, where, find_first, show_uri, repo=None, butler=None):
149 if (repo and butler) or (not repo and not butler):
150 raise RuntimeError("One of repo and butler must be provided and the other must be None.")
151 self.butler = butler or Butler(repo)
152 self._getDatasets(glob, collections, where, find_first)
153 self.showUri = show_uri
155 def _getDatasets(self, glob, collections, where, find_first):
156 dataset: Any = globToRegex(glob)
157 if not dataset:
158 dataset = ...
160 if not find_first:
161 collections = globToRegex(collections)
163 self.datasets = self.butler.registry.queryDatasets(datasetType=dataset,
164 collections=collections,
165 where=where,
166 findFirst=find_first)
168 def getTables(self):
169 """Get the datasets as a list of astropy tables.
171 Returns
172 -------
173 datasetTables : `list` [``astropy.table._Table``]
174 A list of astropy tables, one for each dataset type.
175 """
176 tables: Dict[str, _Table] = defaultdict(_Table)
177 for datasetRef in self.datasets:
178 if not self.showUri:
179 tables[datasetRef.datasetType.name].add(datasetRef)
180 else:
181 primaryURI, componentURIs = self.butler.getURIs(datasetRef, collections=datasetRef.run)
182 if primaryURI:
183 tables[datasetRef.datasetType.name].add(datasetRef, primaryURI)
184 for name, uri in componentURIs.items():
185 tables[datasetRef.datasetType.componentTypeName(name)].add(datasetRef, uri)
187 return [table.getAstropyTable(datasetTypeName) for datasetTypeName, table in tables.items()]
189 def getDatasets(self):
190 """Get the datasets as a list of ``DatasetQueryResults``.
192 Returns
193 -------
194 refs : ``queries.DatasetQueryResults``
195 Dataset references matching the given query criteria.
196 """
197 return self.datasets