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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# (https://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 <https://www.gnu.org/licenses/>. 

21 

22"""Base class for writing Gen3 raw data ingest tests. 

23""" 

24 

25__all__ = ("IngestTestBase",) 

26 

27import abc 

28import tempfile 

29import unittest 

30import os 

31import shutil 

32 

33import lsst.afw.cameraGeom 

34from lsst.daf.butler import Butler, ButlerURI 

35from lsst.daf.butler.cli.butler import cli as butlerCli 

36from lsst.daf.butler.cli.utils import LogCliRunner 

37import lsst.obs.base 

38from lsst.utils import doImport 

39from .utils import getInstrument 

40from . import script 

41 

42 

43class IngestTestBase(metaclass=abc.ABCMeta): 

44 """Base class for tests of gen3 ingest. Subclass from this, then 

45 `unittest.TestCase` to get a working test suite. 

46 """ 

47 

48 ingestDir = "" 

49 """Root path to ingest files into. Typically `obs_package/tests/`; the 

50 actual directory will be a tempdir under this one. 

51 """ 

52 

53 ingestDatasetTypeName = "raw" 

54 """The DatasetType to use for the ingest. 

55 

56 If this is not an Exposure dataset type the tests will be more limited. 

57 """ 

58 

59 dataIds = [] 

60 """list of butler data IDs of files that should have been ingested.""" 

61 

62 file = "" 

63 """Full path to a file to ingest in tests.""" 

64 

65 filterLabel = None 

66 """The lsst.afw.image.FilterLabel that should be returned by the above 

67 file.""" 

68 

69 rawIngestTask = "lsst.obs.base.RawIngestTask" 

70 """The task to use in the Ingest test.""" 

71 

72 curatedCalibrationDatasetTypes = None 

73 """List or tuple of Datasets types that should be present after calling 

74 writeCuratedCalibrations. If `None` writeCuratedCalibrations will 

75 not be called and the test will be skipped.""" 

76 

77 defineVisitsTask = lsst.obs.base.DefineVisitsTask 

78 """The task to use to define visits from groups of exposures. 

79 This is ignored if ``visits`` is `None`. 

80 """ 

81 

82 visits = {} 

83 """A dictionary mapping visit data IDs the lists of exposure data IDs that 

84 are associated with them. 

85 If this is empty (but not `None`), visit definition will be run but no 

86 visits will be expected (e.g. because no exposures are on-sky 

87 observations). 

88 """ 

89 

90 @property 

91 @abc.abstractmethod 

92 def instrumentClassName(self): 

93 """The fully qualified instrument class name. 

94 

95 Returns 

96 ------- 

97 `str` 

98 The fully qualified instrument class name. 

99 """ 

100 pass 

101 

102 @property 

103 def instrumentClass(self): 

104 """The instrument class.""" 

105 return doImport(self.instrumentClassName) 

106 

107 @property 

108 def instrumentName(self): 

109 """The name of the instrument. 

110 

111 Returns 

112 ------- 

113 `str` 

114 The name of the instrument. 

115 """ 

116 return self.instrumentClass.getName() 

117 

118 @classmethod 

119 def setUpClass(cls): 

120 # Use a temporary working directory. 

121 cls.root = tempfile.mkdtemp(dir=cls.ingestDir) 

122 cls._createRepo() 

123 

124 # Register the instrument and its static metadata. 

125 cls._registerInstrument() 

126 

127 def setUp(self): 

128 # Want a unique run name per test. 

129 self.outputRun = "raw_ingest_" + self.id() 

130 

131 @classmethod 

132 def tearDownClass(cls): 

133 if os.path.exists(cls.root): 

134 shutil.rmtree(cls.root, ignore_errors=True) 

135 

136 def verifyIngest(self, files=None, cli=False, fullCheck=False): 

137 """ 

138 Test that RawIngestTask ingested the expected files. 

139 

140 Parameters 

141 ---------- 

142 files : `list` [`str`], or None 

143 List of files to be ingested, or None to use ``self.file`` 

144 fullCheck : `bool`, optional 

145 If `True`, read the full raw dataset and check component 

146 consistency. If `False` check that a component can be read 

147 but do not read the entire raw exposure. 

148 

149 Notes 

150 ----- 

151 Reading all the ingested test data can be expensive. The code paths 

152 for reading the second raw are the same as reading the first so 

153 we do not gain anything by doing full checks of everything. 

154 Only read full pixel data for first dataset from file. 

155 Don't even do that if we are requested not to by the caller. 

156 This only really affects files that contain multiple datasets. 

157 """ 

158 butler = Butler(self.root, run=self.outputRun) 

159 datasets = list(butler.registry.queryDatasets(self.ingestDatasetTypeName, collections=self.outputRun)) 

160 self.assertEqual(len(datasets), len(self.dataIds)) 

161 

162 # Get the URI to the first dataset and check it is inside the 

163 # datastore. 

164 datasetUri = butler.getURI(datasets[0]) 

165 self.assertIsNotNone(datasetUri.relative_to(butler.datastore.root)) 

166 

167 # Get the relevant dataset type. 

168 datasetType = butler.registry.getDatasetType(self.ingestDatasetTypeName) 

169 

170 for dataId in self.dataIds: 

171 # For testing we only read the entire dataset the first time 

172 # round if this is an Exposure. If it's not an Exposure 

173 # we always read it completely but we don't read components 

174 # because for an arbitrary dataset type we can't easily tell 

175 # what component to test. 

176 

177 if not datasetType.storageClass.name.startswith("Exposure"): 

178 exposure = butler.get(self.ingestDatasetTypeName, dataId) 

179 # Could be anything so nothing to test by default 

180 continue 

181 

182 # Check that we can read metadata from a raw. 

183 metadata = butler.get(f"{self.ingestDatasetTypeName}.metadata", dataId) 

184 if not fullCheck: 

185 continue 

186 fullCheck = False 

187 exposure = butler.get(self.ingestDatasetTypeName, dataId) 

188 

189 self.assertEqual(metadata.toDict(), exposure.getMetadata().toDict()) 

190 

191 # Since components follow a different code path we check that 

192 # WCS match and also we check that at least the shape 

193 # of the image is the same (rather than doing per-pixel equality) 

194 wcs = butler.get(f"{self.ingestDatasetTypeName}.wcs", dataId) 

195 self.assertEqual(wcs, exposure.getWcs()) 

196 

197 rawImage = butler.get(f"{self.ingestDatasetTypeName}.image", dataId) 

198 self.assertEqual(rawImage.getBBox(), exposure.getBBox()) 

199 

200 # Check that the filter label got the correct band. 

201 filterLabel = butler.get(f"{self.ingestDatasetTypeName}.filterLabel", dataId) 

202 self.assertEqual(filterLabel, self.filterLabel) 

203 

204 self.checkRepo(files=files) 

205 

206 def checkRepo(self, files=None): 

207 """Check the state of the repository after ingest. 

208 

209 This is an optional hook provided for subclasses; by default it does 

210 nothing. 

211 

212 Parameters 

213 ---------- 

214 files : `list` [`str`], or None 

215 List of files to be ingested, or None to use ``self.file`` 

216 """ 

217 pass 

218 

219 @classmethod 

220 def _createRepo(cls): 

221 """Use the Click `testing` module to call the butler command line api 

222 to create a repository.""" 

223 runner = LogCliRunner() 

224 result = runner.invoke(butlerCli, ["create", cls.root]) 

225 # Classmethod so assertEqual does not work. 

226 assert result.exit_code == 0, f"output: {result.output} exception: {result.exception}" 

227 

228 def _ingestRaws(self, transfer, file=None): 

229 """Use the Click `testing` module to call the butler command line api 

230 to ingest raws. 

231 

232 Parameters 

233 ---------- 

234 transfer : `str` 

235 The external data transfer type. 

236 file : `str` 

237 Path to a file to ingest instead of the default associated with 

238 the object. 

239 """ 

240 if file is None: 

241 file = self.file 

242 runner = LogCliRunner() 

243 result = runner.invoke(butlerCli, ["ingest-raws", self.root, file, 

244 "--output-run", self.outputRun, 

245 "--transfer", transfer, 

246 "--ingest-task", self.rawIngestTask]) 

247 self.assertEqual(result.exit_code, 0, f"output: {result.output} exception: {result.exception}") 

248 

249 @classmethod 

250 def _registerInstrument(cls): 

251 """Use the Click `testing` module to call the butler command line api 

252 to register the instrument.""" 

253 runner = LogCliRunner() 

254 result = runner.invoke(butlerCli, ["register-instrument", cls.root, cls.instrumentClassName]) 

255 # Classmethod so assertEqual does not work. 

256 assert result.exit_code == 0, f"output: {result.output} exception: {result.exception}" 

257 

258 def _writeCuratedCalibrations(self): 

259 """Use the Click `testing` module to call the butler command line api 

260 to write curated calibrations.""" 

261 runner = LogCliRunner() 

262 result = runner.invoke(butlerCli, ["write-curated-calibrations", self.root, self.instrumentName]) 

263 self.assertEqual(result.exit_code, 0, f"output: {result.output} exception: {result.exception}") 

264 

265 def testLink(self): 

266 self._ingestRaws(transfer="link") 

267 self.verifyIngest() 

268 

269 def testSymLink(self): 

270 self._ingestRaws(transfer="symlink") 

271 self.verifyIngest() 

272 

273 def testDirect(self): 

274 self._ingestRaws(transfer="direct") 

275 

276 # Check that it really did have a URI outside of datastore. 

277 srcUri = ButlerURI(self.file, forceAbsolute=True) 

278 butler = Butler(self.root, run=self.outputRun) 

279 datasets = list(butler.registry.queryDatasets(self.ingestDatasetTypeName, collections=self.outputRun)) 

280 datastoreUri = butler.getURI(datasets[0]) 

281 self.assertEqual(datastoreUri, srcUri) 

282 

283 def testCopy(self): 

284 self._ingestRaws(transfer="copy") 

285 # Only test full read of raws for the copy test. No need to do it 

286 # in the other tests since the formatter will be the same in all 

287 # cases. 

288 self.verifyIngest(fullCheck=True) 

289 

290 def testHardLink(self): 

291 try: 

292 self._ingestRaws(transfer="hardlink") 

293 # Running ingest through the Click testing infrastructure causes 

294 # the original exception indicating that we can't hard-link 

295 # on this filesystem to be turned into a nonzero exit code, which 

296 # then trips the test assertion. 

297 except (AssertionError, PermissionError) as err: 

298 raise unittest.SkipTest("Skipping hard-link test because input data" 

299 " is on a different filesystem.") from err 

300 self.verifyIngest() 

301 

302 def testInPlace(self): 

303 """Test that files already in the directory can be added to the 

304 registry in-place. 

305 """ 

306 butler = Butler(self.root, run=self.outputRun) 

307 

308 # If the test uses an index file the index file needs to also 

309 # appear in the datastore root along with the file to be ingested. 

310 # In that scenario the file name being used for ingest can not 

311 # be modified and must have the same name as found in the index 

312 # file itself. 

313 source_file_uri = ButlerURI(self.file) 

314 index_file = source_file_uri.dirname().join("_index.json") 

315 pathInStore = source_file_uri.basename() 

316 if index_file.exists(): 

317 os.symlink(index_file.ospath, butler.datastore.root.join("_index.json").ospath) 

318 else: 

319 # No index file so we are free to pick any name. 

320 pathInStore = "prefix-" + pathInStore 

321 

322 # Create a symlink to the original file so that it looks like it 

323 # is now inside the datastore. 

324 newPath = butler.datastore.root.join(pathInStore) 

325 os.symlink(os.path.abspath(self.file), newPath.ospath) 

326 

327 # If there is a sidecar file it needs to be linked in as well 

328 # since ingest code does not follow symlinks. 

329 sidecar_uri = ButlerURI(source_file_uri).updatedExtension(".json") 

330 if sidecar_uri.exists(): 

331 newSidecar = ButlerURI(newPath).updatedExtension(".json") 

332 os.symlink(sidecar_uri.ospath, newSidecar.ospath) 

333 

334 # Run ingest with auto mode since that should automatically determine 

335 # that an in-place ingest is happening. 

336 self._ingestRaws(transfer="auto", file=newPath.ospath) 

337 self.verifyIngest() 

338 

339 # Recreate a butler post-ingest (the earlier one won't see the 

340 # ingested files). 

341 butler = Butler(self.root, run=self.outputRun) 

342 

343 # Check that the URI associated with this path is the right one. 

344 uri = butler.getURI(self.ingestDatasetTypeName, self.dataIds[0]) 

345 self.assertEqual(uri.relative_to(butler.datastore.root), pathInStore) 

346 

347 def testFailOnConflict(self): 

348 """Re-ingesting the same data into the repository should fail. 

349 """ 

350 self._ingestRaws(transfer="symlink") 

351 with self.assertRaises(Exception): 

352 self._ingestRaws(transfer="symlink") 

353 

354 def testWriteCuratedCalibrations(self): 

355 """Test that we can ingest the curated calibrations, and read them 

356 with `loadCamera` both before and after. 

357 """ 

358 if self.curatedCalibrationDatasetTypes is None: 

359 raise unittest.SkipTest("Class requests disabling of writeCuratedCalibrations test") 

360 

361 butler = Butler(self.root, writeable=False) 

362 collection = self.instrumentClass.makeCalibrationCollectionName() 

363 

364 # Trying to load a camera with a data ID not known to the registry 

365 # is an error, because we can't get any temporal information. 

366 with self.assertRaises(LookupError): 

367 lsst.obs.base.loadCamera(butler, {"exposure": 0}, collections=collection) 

368 

369 # Ingest raws in order to get some exposure records. 

370 self._ingestRaws(transfer="auto") 

371 

372 # Load camera should returned an unversioned camera because there's 

373 # nothing in the repo. 

374 camera, isVersioned = lsst.obs.base.loadCamera(butler, self.dataIds[0], collections=collection) 

375 self.assertFalse(isVersioned) 

376 self.assertIsInstance(camera, lsst.afw.cameraGeom.Camera) 

377 

378 self._writeCuratedCalibrations() 

379 

380 # Make a new butler instance to make sure we don't have any stale 

381 # caches (e.g. of DatasetTypes). Note that we didn't give 

382 # _writeCuratedCalibrations the butler instance we had, because it's 

383 # trying to test the CLI interface anyway. 

384 butler = Butler(self.root, writeable=False) 

385 

386 for datasetTypeName in self.curatedCalibrationDatasetTypes: 

387 with self.subTest(dtype=datasetTypeName): 

388 found = list( 

389 butler.registry.queryDatasetAssociations( 

390 datasetTypeName, 

391 collections=collection, 

392 ) 

393 ) 

394 self.assertGreater(len(found), 0, f"Checking {datasetTypeName}") 

395 

396 # Load camera should returned the versioned camera from the repo. 

397 camera, isVersioned = lsst.obs.base.loadCamera(butler, self.dataIds[0], collections=collection) 

398 self.assertTrue(isVersioned) 

399 self.assertIsInstance(camera, lsst.afw.cameraGeom.Camera) 

400 

401 def testDefineVisits(self): 

402 if self.visits is None: 

403 self.skipTest("Expected visits were not defined.") 

404 self._ingestRaws(transfer="link") 

405 

406 # Calling defineVisits tests the implementation of the butler command 

407 # line interface "define-visits" subcommand. Functions in the script 

408 # folder are generally considered protected and should not be used 

409 # as public api. 

410 script.defineVisits(self.root, config_file=None, collections=self.outputRun, 

411 instrument=self.instrumentName) 

412 

413 # Test that we got the visits we expected. 

414 butler = Butler(self.root, run=self.outputRun) 

415 visits = butler.registry.queryDataIds(["visit"]).expanded().toSet() 

416 self.assertCountEqual(visits, self.visits.keys()) 

417 instr = getInstrument(self.instrumentName, butler.registry) 

418 camera = instr.getCamera() 

419 for foundVisit, (expectedVisit, expectedExposures) in zip(visits, self.visits.items()): 

420 # Test that this visit is associated with the expected exposures. 

421 foundExposures = butler.registry.queryDataIds(["exposure"], dataId=expectedVisit 

422 ).expanded().toSet() 

423 self.assertCountEqual(foundExposures, expectedExposures) 

424 # Test that we have a visit region, and that it contains all of the 

425 # detector+visit regions. 

426 self.assertIsNotNone(foundVisit.region) 

427 detectorVisitDataIds = butler.registry.queryDataIds(["visit", "detector"], dataId=expectedVisit 

428 ).expanded().toSet() 

429 self.assertEqual(len(detectorVisitDataIds), len(camera)) 

430 for dataId in detectorVisitDataIds: 

431 self.assertTrue(foundVisit.region.contains(dataId.region))