Coverage for python/lsst/daf/butler/tests/utils.py: 36%

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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 software is dual licensed under the GNU General Public License and also 

10# under a 3-clause BSD license. Recipients may choose which of these licenses 

11# to use; please see the files gpl-3.0.txt and/or bsd_license.txt, 

12# respectively. If you choose the GPL option then the following text applies 

13# (but note that there is still no warranty even if you opt for BSD instead): 

14# 

15# This program is free software: you can redistribute it and/or modify 

16# it under the terms of the GNU General Public License as published by 

17# the Free Software Foundation, either version 3 of the License, or 

18# (at your option) any later version. 

19# 

20# This program is distributed in the hope that it will be useful, 

21# but WITHOUT ANY WARRANTY; without even the implied warranty of 

22# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 

23# GNU General Public License for more details. 

24# 

25# You should have received a copy of the GNU General Public License 

26# along with this program. If not, see <http://www.gnu.org/licenses/>. 

27 

28from __future__ import annotations 

29 

30from unittest.mock import patch 

31 

32__all__ = () 

33 

34import os 

35import shutil 

36import tempfile 

37from collections.abc import Callable, Iterator, Sequence 

38from contextlib import contextmanager 

39from typing import TYPE_CHECKING, Any 

40 

41import astropy 

42from astropy.table import Table as AstropyTable 

43 

44from .. import Butler, Config, DatasetRef, StorageClassFactory, Timespan 

45from ..registry import CollectionType 

46from ..tests import MetricsExample, addDatasetType 

47 

48if TYPE_CHECKING: 

49 import unittest 

50 

51 from lsst.daf.butler import DatasetType 

52 

53 class TestCaseMixin(unittest.TestCase): 

54 """Base class for mixin test classes that use TestCase methods.""" 

55 

56 pass 

57 

58else: 

59 

60 class TestCaseMixin: 

61 """Do-nothing definition of mixin base class for regular execution.""" 

62 

63 pass 

64 

65 

66def makeTestTempDir(default_base: str) -> str: 

67 """Create a temporary directory for test usage. 

68 

69 The directory will be created within ``DAF_BUTLER_TEST_TMP`` if that 

70 environment variable is set, falling back to ``default_base`` if it is 

71 not. 

72 

73 Parameters 

74 ---------- 

75 default_base : `str` 

76 Default parent directory. 

77 

78 Returns 

79 ------- 

80 dir : `str` 

81 Name of the new temporary directory. 

82 """ 

83 base = os.environ.get("DAF_BUTLER_TEST_TMP", default_base) 

84 return tempfile.mkdtemp(dir=base) 

85 

86 

87def removeTestTempDir(root: str | None) -> None: 

88 """Attempt to remove a temporary test directory, but do not raise if 

89 unable to. 

90 

91 Unlike `tempfile.TemporaryDirectory`, this passes ``ignore_errors=True`` 

92 to ``shutil.rmtree`` at close, making it safe to use on NFS. 

93 

94 Parameters 

95 ---------- 

96 root : `str`, optional 

97 Name of the directory to be removed. If `None`, nothing will be done. 

98 """ 

99 if root is not None and os.path.exists(root): 

100 shutil.rmtree(root, ignore_errors=True) 

101 

102 

103@contextmanager 

104def safeTestTempDir(default_base: str) -> Iterator[str]: 

105 """Return a context manager that creates a temporary directory and then 

106 attempts to remove it. 

107 

108 Parameters 

109 ---------- 

110 default_base : `str` 

111 Default parent directory, forwarded to `makeTestTempDir`. 

112 

113 Returns 

114 ------- 

115 context : `contextlib.ContextManager` 

116 A context manager that returns the new directory name on ``__enter__`` 

117 and removes the temporary directory (via `removeTestTempDir`) on 

118 ``__exit__``. 

119 """ 

120 root = makeTestTempDir(default_base) 

121 try: 

122 yield root 

123 finally: 

124 removeTestTempDir(root) 

125 

126 

127class ButlerTestHelper: 

128 """Mixin with helpers for unit tests.""" 

129 

130 assertEqual: Callable 

131 assertIsInstance: Callable 

132 maxDiff: int | None 

133 

134 def assertAstropyTablesEqual( 

135 self, 

136 tables: AstropyTable | Sequence[AstropyTable], 

137 expectedTables: AstropyTable | Sequence[AstropyTable], 

138 filterColumns: bool = False, 

139 unorderedRows: bool = False, 

140 ) -> None: 

141 """Verify that a list of astropy tables matches a list of expected 

142 astropy tables. 

143 

144 Parameters 

145 ---------- 

146 tables : `astropy.table.Table` or iterable [`astropy.table.Table`] 

147 The table or tables that should match the expected tables. 

148 expectedTables : `astropy.table.Table` 

149 or iterable [`astropy.table.Table`] 

150 The tables with expected values to which the tables under test will 

151 be compared. 

152 filterColumns : `bool` 

153 If `True` then only compare columns that exist in 

154 ``expectedTables``. 

155 unorderedRows : `bool`, optional 

156 If `True` (`False` is default), don't require tables to have their 

157 rows in the same order. 

158 """ 

159 # If a single table is passed in for tables or expectedTables, put it 

160 # in a list. 

161 if isinstance(tables, AstropyTable): 

162 tables = [tables] 

163 if isinstance(expectedTables, AstropyTable): 

164 expectedTables = [expectedTables] 

165 self.assertEqual(len(tables), len(expectedTables)) 

166 for table, expected in zip(tables, expectedTables, strict=True): 

167 # Assert that we are testing what we think we are testing: 

168 self.assertIsInstance(table, AstropyTable) 

169 self.assertIsInstance(expected, AstropyTable) 

170 if filterColumns: 

171 table = table.copy() 

172 table.keep_columns(expected.colnames) 

173 if unorderedRows: 

174 table = table.copy() 

175 table.sort(table.colnames) 

176 expected = expected.copy() 

177 expected.sort(expected.colnames) 

178 # Assert that they match. 

179 # Recommendation from Astropy Slack is to format the table into 

180 # lines for comparison. We do not compare column data types. 

181 table1 = table.pformat_all() 

182 expected1 = expected.pformat_all() 

183 original_max = self.maxDiff 

184 self.maxDiff = None # This is required to get the full diff. 

185 try: 

186 self.assertEqual(table1, expected1) 

187 finally: 

188 self.maxDiff = original_max 

189 

190 

191def readTable(textTable: str) -> AstropyTable: 

192 """Read an astropy table from formatted text. 

193 

194 Contains formatting that causes the astropy table to print an empty string 

195 instead of "--" for missing/unpopulated values in the text table. 

196 

197 Parameters 

198 ---------- 

199 textTable : `str` 

200 The text version of the table to read. 

201 

202 Returns 

203 ------- 

204 table : `astropy.table.Table` 

205 The table as an astropy table. 

206 """ 

207 return AstropyTable.read( 

208 textTable, 

209 format="ascii", 

210 data_start=2, # skip the header row and the header row underlines. 

211 fill_values=[("", 0, "")], 

212 ) 

213 

214 

215class MetricTestRepo: 

216 """Creates and manage a test repository on disk with datasets that 

217 may be queried and modified for unit tests. 

218 

219 Parameters 

220 ---------- 

221 root : `str` 

222 The location of the repository, to pass to ``Butler.makeRepo``. 

223 configFile : `str` 

224 The path to the config file, to pass to ``Butler.makeRepo``. 

225 forceConfigRoot : `bool`, optional 

226 If `False`, any values present in the supplied ``config`` that 

227 would normally be reset are not overridden and will appear 

228 directly in the output config. Passed to ``Butler.makeRepo``. 

229 """ 

230 

231 METRICS_EXAMPLE_SUMMARY = {"AM1": 5.2, "AM2": 30.6} 

232 """The summary data included in ``MetricsExample`` objects stored in the 

233 test repo 

234 """ 

235 

236 @staticmethod 

237 def _makeExampleMetrics() -> MetricsExample: 

238 """Make an object to put into the repository.""" 

239 return MetricsExample( 

240 MetricTestRepo.METRICS_EXAMPLE_SUMMARY, 

241 {"a": [1, 2, 3], "b": {"blue": 5, "red": "green"}}, 

242 [563, 234, 456.7, 752, 8, 9, 27], 

243 ) 

244 

245 def __init__(self, root: str, configFile: str, forceConfigRoot: bool = True) -> None: 

246 self.root = root 

247 Butler.makeRepo(self.root, config=Config(configFile), forceConfigRoot=forceConfigRoot) 

248 butlerConfigFile = os.path.join(self.root, "butler.yaml") 

249 self.storageClassFactory = StorageClassFactory() 

250 self.storageClassFactory.addFromConfig(butlerConfigFile) 

251 

252 # New datasets will be added to run and tag, but we will only look in 

253 # tag when looking up datasets. 

254 run = "ingest/run" 

255 tag = "ingest" 

256 self.butler = Butler.from_config(butlerConfigFile, run=run, collections=[tag]) 

257 self.butler.registry.registerCollection(tag, CollectionType.TAGGED) 

258 

259 # Create and register a DatasetType 

260 self.datasetType = addDatasetType( 

261 self.butler, "test_metric_comp", {"instrument", "visit"}, "StructuredCompositeReadComp" 

262 ) 

263 

264 # Add needed Dimensions 

265 self.butler.registry.insertDimensionData("instrument", {"name": "DummyCamComp"}) 

266 self.butler.registry.insertDimensionData( 

267 "physical_filter", {"instrument": "DummyCamComp", "name": "d-r", "band": "R"} 

268 ) 

269 self.butler.registry.insertDimensionData( 

270 "visit_system", {"instrument": "DummyCamComp", "id": 1, "name": "default"} 

271 ) 

272 visitStart = astropy.time.Time("2020-01-01 08:00:00.123456789", scale="tai") 

273 visitEnd = astropy.time.Time("2020-01-01 08:00:36.66", scale="tai") 

274 self.butler.registry.insertDimensionData( 

275 "visit", 

276 dict( 

277 instrument="DummyCamComp", 

278 id=423, 

279 name="fourtwentythree", 

280 physical_filter="d-r", 

281 timespan=Timespan(visitStart, visitEnd), 

282 ), 

283 ) 

284 self.butler.registry.insertDimensionData( 

285 "visit", 

286 dict( 

287 instrument="DummyCamComp", 

288 id=424, 

289 name="fourtwentyfour", 

290 physical_filter="d-r", 

291 ), 

292 ) 

293 

294 self.addDataset({"instrument": "DummyCamComp", "visit": 423}) 

295 self.addDataset({"instrument": "DummyCamComp", "visit": 424}) 

296 

297 def addDataset( 

298 self, dataId: dict[str, Any], run: str | None = None, datasetType: DatasetType | None = None 

299 ) -> DatasetRef: 

300 """Create a new example metric and add it to the named run with the 

301 given dataId. 

302 

303 Overwrites tags, so this does not try to associate the new dataset with 

304 existing tags. (If/when tags are needed this can be added to the 

305 arguments of this function.) 

306 

307 Parameters 

308 ---------- 

309 dataId : `dict` 

310 The dataId for the new metric. 

311 run : `str`, optional 

312 The name of the run to create and add a dataset to. If `None`, the 

313 dataset will be added to the root butler. 

314 datasetType : ``DatasetType``, optional 

315 The dataset type of the added dataset. If `None`, will use the 

316 default dataset type. 

317 

318 Returns 

319 ------- 

320 datasetRef : `DatasetRef` 

321 A reference to the added dataset. 

322 """ 

323 if run: 

324 self.butler.registry.registerCollection(run, type=CollectionType.RUN) 

325 metric = self._makeExampleMetrics() 

326 return self.butler.put( 

327 metric, self.datasetType if datasetType is None else datasetType, dataId, run=run 

328 ) 

329 

330 

331@contextmanager 

332def mock_env(new_environment: dict[str, str]) -> Iterator[None]: 

333 """Context manager to clear the process environment variables, replace them 

334 with new values, and restore them at the end of the test. 

335 

336 Parameters 

337 ---------- 

338 new_environment : `dict`[`str`, `str`] 

339 New environment variable values. 

340 """ 

341 with patch.dict(os.environ, new_environment, clear=True): 

342 yield