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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 # Comparing headers will not work directly because of header 

190 # fix up provenance. 

191 metadata_headers = metadata.toDict() 

192 exposure_headers = exposure.getMetadata().toDict() 

193 metadata_headers.pop("HIERARCH ASTRO METADATA FIX DATE", None) 

194 exposure_headers.pop("HIERARCH ASTRO METADATA FIX DATE", None) 

195 self.assertEqual(metadata_headers, exposure_headers) 

196 

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

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

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

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

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

202 

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

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

205 

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

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

208 self.assertEqual(filterLabel, self.filterLabel) 

209 

210 self.checkRepo(files=files) 

211 

212 def checkRepo(self, files=None): 

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

214 

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

216 nothing. 

217 

218 Parameters 

219 ---------- 

220 files : `list` [`str`], or None 

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

222 """ 

223 pass 

224 

225 @classmethod 

226 def _createRepo(cls): 

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

228 to create a repository.""" 

229 runner = LogCliRunner() 

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

231 # Classmethod so assertEqual does not work. 

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

233 

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

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

236 to ingest raws. 

237 

238 Parameters 

239 ---------- 

240 transfer : `str` 

241 The external data transfer type. 

242 file : `str` 

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

244 the object. 

245 """ 

246 if file is None: 

247 file = self.file 

248 runner = LogCliRunner() 

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

250 "--output-run", self.outputRun, 

251 "--transfer", transfer, 

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

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

254 

255 @classmethod 

256 def _registerInstrument(cls): 

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

258 to register the instrument.""" 

259 runner = LogCliRunner() 

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

261 # Classmethod so assertEqual does not work. 

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

263 

264 def _writeCuratedCalibrations(self): 

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

266 to write curated calibrations.""" 

267 runner = LogCliRunner() 

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

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

270 

271 def testLink(self): 

272 self._ingestRaws(transfer="link") 

273 self.verifyIngest() 

274 

275 def testSymLink(self): 

276 self._ingestRaws(transfer="symlink") 

277 self.verifyIngest() 

278 

279 def testDirect(self): 

280 self._ingestRaws(transfer="direct") 

281 

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

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

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

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

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

287 self.assertEqual(datastoreUri, srcUri) 

288 

289 def testCopy(self): 

290 self._ingestRaws(transfer="copy") 

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

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

293 # cases. 

294 self.verifyIngest(fullCheck=True) 

295 

296 def testHardLink(self): 

297 try: 

298 self._ingestRaws(transfer="hardlink") 

299 # Running ingest through the Click testing infrastructure causes 

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

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

302 # then trips the test assertion. 

303 except (AssertionError, PermissionError) as err: 

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

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

306 self.verifyIngest() 

307 

308 def testInPlace(self): 

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

310 registry in-place. 

311 """ 

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

313 

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

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

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

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

318 # file itself. 

319 source_file_uri = ButlerURI(self.file) 

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

321 pathInStore = source_file_uri.basename() 

322 if index_file.exists(): 

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

324 else: 

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

326 pathInStore = "prefix-" + pathInStore 

327 

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

329 # is now inside the datastore. 

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

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

332 

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

334 # since ingest code does not follow symlinks. 

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

336 if sidecar_uri.exists(): 

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

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

339 

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

341 # that an in-place ingest is happening. 

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

343 self.verifyIngest() 

344 

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

346 # ingested files). 

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

348 

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

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

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

352 

353 def testFailOnConflict(self): 

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

355 """ 

356 self._ingestRaws(transfer="symlink") 

357 with self.assertRaises(Exception): 

358 self._ingestRaws(transfer="symlink") 

359 

360 def testWriteCuratedCalibrations(self): 

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

362 with `loadCamera` both before and after. 

363 """ 

364 if self.curatedCalibrationDatasetTypes is None: 

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

366 

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

368 collection = self.instrumentClass.makeCalibrationCollectionName() 

369 

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

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

372 with self.assertRaises(LookupError): 

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

374 

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

376 self._ingestRaws(transfer="auto") 

377 

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

379 # nothing in the repo. 

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

381 self.assertFalse(isVersioned) 

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

383 

384 self._writeCuratedCalibrations() 

385 

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

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

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

389 # trying to test the CLI interface anyway. 

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

391 

392 for datasetTypeName in self.curatedCalibrationDatasetTypes: 

393 with self.subTest(dtype=datasetTypeName): 

394 found = list( 

395 butler.registry.queryDatasetAssociations( 

396 datasetTypeName, 

397 collections=collection, 

398 ) 

399 ) 

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

401 

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

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

404 self.assertTrue(isVersioned) 

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

406 

407 def testDefineVisits(self): 

408 if self.visits is None: 

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

410 self._ingestRaws(transfer="link") 

411 

412 # Calling defineVisits tests the implementation of the butler command 

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

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

415 # as public api. 

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

417 instrument=self.instrumentName) 

418 

419 # Test that we got the visits we expected. 

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

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

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

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

424 camera = instr.getCamera() 

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

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

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

428 ).expanded().toSet() 

429 self.assertCountEqual(foundExposures, expectedExposures) 

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

431 # detector+visit regions. 

432 self.assertIsNotNone(foundVisit.region) 

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

434 ).expanded().toSet() 

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

436 for dataId in detectorVisitDataIds: 

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