Coverage for python/lsst/obs/base/ingest_tests.py: 33%
208 statements
« prev ^ index » next coverage.py v7.3.0, created at 2023-08-25 09:47 +0000
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#
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20# along with this program. If not, see <https://www.gnu.org/licenses/>.
22"""Base class for writing Gen3 raw data ingest tests.
23"""
25__all__ = ("IngestTestBase",)
27import abc
28import os
29import shutil
30import tempfile
31import unittest
33import lsst.afw.cameraGeom
34import lsst.afw.cameraGeom.testUtils # For assertDetectorsEqual
35import lsst.obs.base
36from lsst.daf.butler import Butler, Registry
37from lsst.daf.butler.cli.butler import cli as butlerCli
38from lsst.daf.butler.cli.utils import LogCliRunner
39from lsst.pipe.base import Instrument
40from lsst.resources import ResourcePath
41from lsst.utils import doImportType
43from . import script
46class IngestTestBase(metaclass=abc.ABCMeta):
47 """Base class for tests of gen3 ingest. Subclass from this, then
48 `unittest.TestCase` to get a working test suite.
49 """
51 ingestDir = ""
52 """Root path to ingest files into. Typically `obs_package/tests/`; the
53 actual directory will be a tempdir under this one.
54 """
56 ingestDatasetTypeName = "raw"
57 """The DatasetType to use for the ingest.
59 If this is not an Exposure dataset type the tests will be more limited.
60 """
62 dataIds = []
63 """list of butler data IDs of files that should have been ingested."""
65 file = ""
66 """Full path to a file to ingest in tests."""
68 filterLabel = None
69 """The lsst.afw.image.FilterLabel that should be returned by the above
70 file."""
72 rawIngestTask = "lsst.obs.base.RawIngestTask"
73 """The task to use in the Ingest test."""
75 curatedCalibrationDatasetTypes = None
76 """List or tuple of Datasets types that should be present after calling
77 writeCuratedCalibrations. If `None` writeCuratedCalibrations will
78 not be called and the test will be skipped."""
80 defineVisitsTask = lsst.obs.base.DefineVisitsTask
81 """The task to use to define visits from groups of exposures.
82 This is ignored if ``visits`` is `None`.
83 """
85 visits = {}
86 """A dictionary mapping visit data IDs the lists of exposure data IDs that
87 are associated with them.
88 If this is empty (but not `None`), visit definition will be run but no
89 visits will be expected (e.g. because no exposures are on-sky
90 observations).
91 """
93 seed_config = None
94 """Location of a seed configuration file to pass to butler create.
96 Useful if additional formatters or storage classes need to be defined.
97 """
99 @property
100 @abc.abstractmethod
101 def instrumentClassName(self):
102 """The fully qualified instrument class name.
104 Returns
105 -------
106 `str`
107 The fully qualified instrument class name.
108 """
109 pass
111 @property
112 def instrumentClass(self):
113 """The instrument class."""
114 return doImportType(self.instrumentClassName)
116 @property
117 def instrumentName(self):
118 """The name of the instrument.
120 Returns
121 -------
122 `str`
123 The name of the instrument.
124 """
125 return self.instrumentClass.getName()
127 @classmethod
128 def setUpClass(cls):
129 # Use a temporary working directory.
130 cls.root = tempfile.mkdtemp(dir=cls.ingestDir)
131 cls._createRepo()
133 # Register the instrument and its static metadata.
134 cls._registerInstrument()
136 # Determine the relevant datastore root to use for testing.
137 butler = Butler(cls.root)
138 roots = butler.get_datastore_roots()
139 assert len(roots) == 1 # Only one datastore.
140 cls.datastore_root = list(roots.values())[0]
142 def setUp(self):
143 # Want a unique run name per test.
144 self.outputRun = "raw_ingest_" + self.id()
146 @classmethod
147 def tearDownClass(cls):
148 if os.path.exists(cls.root):
149 shutil.rmtree(cls.root, ignore_errors=True)
151 def verifyIngest(self, files=None, cli=False, fullCheck=False):
152 """
153 Test that RawIngestTask ingested the expected files.
155 Parameters
156 ----------
157 files : `list` [`str`], or None
158 List of files to be ingested, or None to use ``self.file``
159 fullCheck : `bool`, optional
160 If `True`, read the full raw dataset and check component
161 consistency. If `False` check that a component can be read
162 but do not read the entire raw exposure.
164 Notes
165 -----
166 Reading all the ingested test data can be expensive. The code paths
167 for reading the second raw are the same as reading the first so
168 we do not gain anything by doing full checks of everything.
169 Only read full pixel data for first dataset from file.
170 Don't even do that if we are requested not to by the caller.
171 This only really affects files that contain multiple datasets.
172 """
173 butler = Butler(self.root, run=self.outputRun)
174 datasets = list(butler.registry.queryDatasets(self.ingestDatasetTypeName, collections=self.outputRun))
175 self.assertEqual(len(datasets), len(self.dataIds))
177 # Get the URI to the first dataset and check it is inside the
178 # datastore.
179 datasetUri = butler.getURI(datasets[0])
180 self.assertIsNotNone(datasetUri.relative_to(self.datastore_root))
182 # Get the relevant dataset type.
183 datasetType = butler.registry.getDatasetType(self.ingestDatasetTypeName)
185 for dataId in self.dataIds:
186 # For testing we only read the entire dataset the first time
187 # round if this is an Exposure. If it's not an Exposure
188 # we always read it completely but we don't read components
189 # because for an arbitrary dataset type we can't easily tell
190 # what component to test.
192 if not datasetType.storageClass.name.startswith("Exposure"):
193 exposure = butler.get(self.ingestDatasetTypeName, dataId)
194 # Could be anything so nothing to test by default
195 continue
197 # Check that we can read metadata from a raw.
198 metadata = butler.get(f"{self.ingestDatasetTypeName}.metadata", dataId)
199 if not fullCheck:
200 continue
201 fullCheck = False
202 exposure = butler.get(self.ingestDatasetTypeName, dataId)
204 # Comparing headers will not work directly because of header
205 # fix up provenance.
206 metadata_headers = metadata.toDict()
207 exposure_headers = exposure.getMetadata().toDict()
208 metadata_headers.pop("HIERARCH ASTRO METADATA FIX DATE", None)
209 exposure_headers.pop("HIERARCH ASTRO METADATA FIX DATE", None)
210 self.assertEqual(metadata_headers, exposure_headers)
212 # Since components follow a different code path we check that
213 # WCS match and also we check that at least the shape
214 # of the image is the same (rather than doing per-pixel equality)
215 wcs = butler.get(f"{self.ingestDatasetTypeName}.wcs", dataId)
216 self.assertEqual(wcs, exposure.getWcs())
218 rawImage = butler.get(f"{self.ingestDatasetTypeName}.image", dataId)
219 self.assertEqual(rawImage.getBBox(), exposure.getBBox())
221 # Check that the filter label got the correct band.
222 filterLabel = butler.get(f"{self.ingestDatasetTypeName}.filter", dataId)
223 self.assertEqual(filterLabel, self.filterLabel)
225 # Check that the exposure's Detector is the same as the component
226 # we would read (this is tricky for LSST, which modifies its
227 # detector at read time; for most other cameras it should be
228 # trivially satisfied.
229 detector = butler.get(f"{self.ingestDatasetTypeName}.detector", dataId)
230 self.assertDetectorsEqual(detector, exposure.getDetector(), compareTransforms=False)
232 self.checkRepo(files=files)
234 def checkRepo(self, files=None):
235 """Check the state of the repository after ingest.
237 This is an optional hook provided for subclasses; by default it does
238 nothing.
240 Parameters
241 ----------
242 files : `list` [`str`], or None
243 List of files to be ingested, or None to use ``self.file``
244 """
245 return
247 @classmethod
248 def _createRepo(cls):
249 """Use the Click `testing` module to call the butler command line api
250 to create a repository.
251 """
252 runner = LogCliRunner()
253 args = []
254 if cls.seed_config:
255 args.extend(["--seed-config", cls.seed_config])
256 result = runner.invoke(butlerCli, ["create", cls.root, *args])
257 # Classmethod so assertEqual does not work.
258 assert result.exit_code == 0, f"output: {result.output} exception: {result.exception}"
260 def _ingestRaws(self, transfer, file=None):
261 """Use the Click `testing` module to call the butler command line api
262 to ingest raws.
264 Parameters
265 ----------
266 transfer : `str`
267 The external data transfer type.
268 file : `str`
269 Path to a file to ingest instead of the default associated with
270 the object.
271 """
272 if file is None:
273 file = self.file
274 runner = LogCliRunner()
275 result = runner.invoke(
276 butlerCli,
277 [
278 "ingest-raws",
279 self.root,
280 file,
281 "--output-run",
282 self.outputRun,
283 "--transfer",
284 transfer,
285 "--ingest-task",
286 self.rawIngestTask,
287 ],
288 )
289 self.assertEqual(result.exit_code, 0, f"output: {result.output} exception: {result.exception}")
291 @classmethod
292 def _registerInstrument(cls):
293 """Use the Click `testing` module to call the butler command line api
294 to register the instrument.
295 """
296 runner = LogCliRunner()
297 result = runner.invoke(butlerCli, ["register-instrument", cls.root, cls.instrumentClassName])
298 # Classmethod so assertEqual does not work.
299 assert result.exit_code == 0, f"output: {result.output} exception: {result.exception}"
301 def _writeCuratedCalibrations(self):
302 """Use the Click `testing` module to call the butler command line api
303 to write curated calibrations.
304 """
305 runner = LogCliRunner()
306 result = runner.invoke(butlerCli, ["write-curated-calibrations", self.root, self.instrumentName])
307 self.assertEqual(result.exit_code, 0, f"output: {result.output} exception: {result.exception}")
309 def testLink(self):
310 self._ingestRaws(transfer="link")
311 self.verifyIngest()
313 def testSymLink(self):
314 self._ingestRaws(transfer="symlink")
315 self.verifyIngest()
317 def testDirect(self):
318 self._ingestRaws(transfer="direct")
320 # Check that it really did have a URI outside of datastore.
321 srcUri = ResourcePath(self.file, forceAbsolute=True)
322 butler = Butler(self.root, run=self.outputRun)
323 datasets = list(butler.registry.queryDatasets(self.ingestDatasetTypeName, collections=self.outputRun))
324 datastoreUri = butler.getURI(datasets[0])
325 self.assertEqual(datastoreUri, srcUri)
327 def testCopy(self):
328 self._ingestRaws(transfer="copy")
329 # Only test full read of raws for the copy test. No need to do it
330 # in the other tests since the formatter will be the same in all
331 # cases.
332 self.verifyIngest(fullCheck=True)
334 def testHardLink(self):
335 try:
336 self._ingestRaws(transfer="hardlink")
337 # Running ingest through the Click testing infrastructure causes
338 # the original exception indicating that we can't hard-link
339 # on this filesystem to be turned into a nonzero exit code, which
340 # then trips the test assertion.
341 except (AssertionError, PermissionError) as err:
342 raise unittest.SkipTest(
343 "Skipping hard-link test because input data is on a different filesystem."
344 ) from err
345 self.verifyIngest()
347 def testInPlace(self):
348 """Test that files already in the directory can be added to the
349 registry in-place.
350 """
351 butler = Butler(self.root, run=self.outputRun)
353 # If the test uses an index file the index file needs to also
354 # appear in the datastore root along with the file to be ingested.
355 # In that scenario the file name being used for ingest can not
356 # be modified and must have the same name as found in the index
357 # file itself.
358 source_file_uri = ResourcePath(self.file)
359 index_file = source_file_uri.dirname().join("_index.json")
360 pathInStore = source_file_uri.basename()
361 if index_file.exists():
362 os.symlink(index_file.ospath, self.datastore_root.join("_index.json").ospath)
363 else:
364 # No index file so we are free to pick any name.
365 pathInStore = "prefix-" + pathInStore
367 # Create a symlink to the original file so that it looks like it
368 # is now inside the datastore.
369 newPath = self.datastore_root.join(pathInStore)
370 os.symlink(os.path.abspath(self.file), newPath.ospath)
372 # If there is a sidecar file it needs to be linked in as well
373 # since ingest code does not follow symlinks.
374 sidecar_uri = ResourcePath(source_file_uri).updatedExtension(".json")
375 if sidecar_uri.exists():
376 newSidecar = ResourcePath(newPath).updatedExtension(".json")
377 os.symlink(sidecar_uri.ospath, newSidecar.ospath)
379 # Run ingest with auto mode since that should automatically determine
380 # that an in-place ingest is happening.
381 self._ingestRaws(transfer="auto", file=newPath.ospath)
382 self.verifyIngest()
384 # Recreate a butler post-ingest (the earlier one won't see the
385 # ingested files).
386 butler = Butler(self.root, run=self.outputRun)
388 # Check that the URI associated with this path is the right one.
389 uri = butler.getURI(self.ingestDatasetTypeName, self.dataIds[0])
390 self.assertEqual(uri.relative_to(self.datastore_root), pathInStore)
392 def testFailOnConflict(self):
393 """Re-ingesting the same data into the repository should fail."""
394 self._ingestRaws(transfer="symlink")
395 with self.assertRaises(AssertionError):
396 self._ingestRaws(transfer="symlink")
398 def testWriteCuratedCalibrations(self):
399 """Test that we can ingest the curated calibrations, and read them
400 with `loadCamera` both before and after.
401 """
402 if self.curatedCalibrationDatasetTypes is None:
403 raise unittest.SkipTest("Class requests disabling of writeCuratedCalibrations test")
405 butler = Butler(self.root, writeable=False)
406 collection = self.instrumentClass().makeCalibrationCollectionName()
408 # Trying to load a camera with a data ID not known to the registry
409 # is an error, because we can't get any temporal information.
410 with self.assertRaises(LookupError):
411 lsst.obs.base.loadCamera(butler, {"exposure": 0}, collections=collection)
413 # Ingest raws in order to get some exposure records.
414 self._ingestRaws(transfer="auto")
416 # Load camera should returned an unversioned camera because there's
417 # nothing in the repo.
418 camera, isVersioned = lsst.obs.base.loadCamera(butler, self.dataIds[0], collections=collection)
419 self.assertFalse(isVersioned)
420 self.assertIsInstance(camera, lsst.afw.cameraGeom.Camera)
422 self._writeCuratedCalibrations()
424 # Make a new butler instance to make sure we don't have any stale
425 # caches (e.g. of DatasetTypes). Note that we didn't give
426 # _writeCuratedCalibrations the butler instance we had, because it's
427 # trying to test the CLI interface anyway.
428 butler = Butler(self.root, writeable=False)
430 instrumentClass = self.instrumentClass()
431 calibration_names = instrumentClass.getCuratedCalibrationNames()
433 for datasetTypeName in self.curatedCalibrationDatasetTypes:
434 with self.subTest(dtype=datasetTypeName):
435 found = list(
436 butler.registry.queryDatasetAssociations(
437 datasetTypeName,
438 collections=collection,
439 )
440 )
441 self.assertGreater(len(found), 0, f"Checking {datasetTypeName}")
442 self.assertIn(datasetTypeName, calibration_names)
444 # Load camera should returned the versioned camera from the repo.
445 camera, isVersioned = lsst.obs.base.loadCamera(butler, self.dataIds[0], collections=collection)
446 self.assertTrue(isVersioned)
447 self.assertIsInstance(camera, lsst.afw.cameraGeom.Camera)
449 def testDefineVisits(self):
450 if self.visits is None:
451 self.skipTest("Expected visits were not defined.")
452 self._ingestRaws(transfer="link")
454 # Check that obscore table (if configured) has correct contents.
455 butler = Butler(self.root, run=self.outputRun)
456 self._check_obscore(butler.registry, has_visits=False)
458 # Calling defineVisits tests the implementation of the butler command
459 # line interface "define-visits" subcommand. Functions in the script
460 # folder are generally considered protected and should not be used
461 # as public api.
462 script.defineVisits(
463 self.root,
464 config_file=None,
465 collections=self.outputRun,
466 instrument=self.instrumentName,
467 raw_name=self.ingestDatasetTypeName,
468 )
470 # Test that we got the visits we expected.
471 visits = butler.registry.queryDataIds(["visit"]).expanded().toSet()
472 self.assertCountEqual(visits, self.visits.keys())
473 instr = Instrument.from_string(self.instrumentName, butler.registry)
474 camera = instr.getCamera()
475 for foundVisit, (expectedVisit, expectedExposures) in zip(visits, self.visits.items(), strict=True):
476 # Test that this visit is associated with the expected exposures.
477 foundExposures = (
478 butler.registry.queryDataIds(["exposure"], dataId=expectedVisit).expanded().toSet()
479 )
480 self.assertCountEqual(foundExposures, expectedExposures)
481 # Test that we have a visit region, and that it contains all of the
482 # detector+visit regions.
483 self.assertIsNotNone(foundVisit.region)
484 detectorVisitDataIds = (
485 butler.registry.queryDataIds(["visit", "detector"], dataId=expectedVisit).expanded().toSet()
486 )
487 self.assertEqual(len(detectorVisitDataIds), len(camera))
488 for dataId in detectorVisitDataIds:
489 self.assertTrue(foundVisit.region.contains(dataId.region))
491 # Check obscore table again.
492 self._check_obscore(butler.registry, has_visits=True)
494 def _check_obscore(self, registry: Registry, has_visits: bool) -> None:
495 """Verify contents of obscore table."""
496 return