Coverage for python/lsst/obs/base/ingest_tests.py: 29%
204 statements
« prev ^ index » next coverage.py v7.2.7, created at 2023-06-11 09:07 +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#
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/>.
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 def setUp(self):
137 # Want a unique run name per test.
138 self.outputRun = "raw_ingest_" + self.id()
140 @classmethod
141 def tearDownClass(cls):
142 if os.path.exists(cls.root):
143 shutil.rmtree(cls.root, ignore_errors=True)
145 def verifyIngest(self, files=None, cli=False, fullCheck=False):
146 """
147 Test that RawIngestTask ingested the expected files.
149 Parameters
150 ----------
151 files : `list` [`str`], or None
152 List of files to be ingested, or None to use ``self.file``
153 fullCheck : `bool`, optional
154 If `True`, read the full raw dataset and check component
155 consistency. If `False` check that a component can be read
156 but do not read the entire raw exposure.
158 Notes
159 -----
160 Reading all the ingested test data can be expensive. The code paths
161 for reading the second raw are the same as reading the first so
162 we do not gain anything by doing full checks of everything.
163 Only read full pixel data for first dataset from file.
164 Don't even do that if we are requested not to by the caller.
165 This only really affects files that contain multiple datasets.
166 """
167 butler = Butler(self.root, run=self.outputRun)
168 datasets = list(butler.registry.queryDatasets(self.ingestDatasetTypeName, collections=self.outputRun))
169 self.assertEqual(len(datasets), len(self.dataIds))
171 # Get the URI to the first dataset and check it is inside the
172 # datastore.
173 datasetUri = butler.getURI(datasets[0])
174 self.assertIsNotNone(datasetUri.relative_to(butler.datastore.root))
176 # Get the relevant dataset type.
177 datasetType = butler.registry.getDatasetType(self.ingestDatasetTypeName)
179 for dataId in self.dataIds:
180 # For testing we only read the entire dataset the first time
181 # round if this is an Exposure. If it's not an Exposure
182 # we always read it completely but we don't read components
183 # because for an arbitrary dataset type we can't easily tell
184 # what component to test.
186 if not datasetType.storageClass.name.startswith("Exposure"):
187 exposure = butler.get(self.ingestDatasetTypeName, dataId)
188 # Could be anything so nothing to test by default
189 continue
191 # Check that we can read metadata from a raw.
192 metadata = butler.get(f"{self.ingestDatasetTypeName}.metadata", dataId)
193 if not fullCheck:
194 continue
195 fullCheck = False
196 exposure = butler.get(self.ingestDatasetTypeName, dataId)
198 # Comparing headers will not work directly because of header
199 # fix up provenance.
200 metadata_headers = metadata.toDict()
201 exposure_headers = exposure.getMetadata().toDict()
202 metadata_headers.pop("HIERARCH ASTRO METADATA FIX DATE", None)
203 exposure_headers.pop("HIERARCH ASTRO METADATA FIX DATE", None)
204 self.assertEqual(metadata_headers, exposure_headers)
206 # Since components follow a different code path we check that
207 # WCS match and also we check that at least the shape
208 # of the image is the same (rather than doing per-pixel equality)
209 wcs = butler.get(f"{self.ingestDatasetTypeName}.wcs", dataId)
210 self.assertEqual(wcs, exposure.getWcs())
212 rawImage = butler.get(f"{self.ingestDatasetTypeName}.image", dataId)
213 self.assertEqual(rawImage.getBBox(), exposure.getBBox())
215 # Check that the filter label got the correct band.
216 filterLabel = butler.get(f"{self.ingestDatasetTypeName}.filter", dataId)
217 self.assertEqual(filterLabel, self.filterLabel)
219 # Check that the exposure's Detector is the same as the component
220 # we would read (this is tricky for LSST, which modifies its
221 # detector at read time; for most other cameras it should be
222 # trivially satisfied.
223 detector = butler.get(f"{self.ingestDatasetTypeName}.detector", dataId)
224 self.assertDetectorsEqual(detector, exposure.getDetector(), compareTransforms=False)
226 self.checkRepo(files=files)
228 def checkRepo(self, files=None):
229 """Check the state of the repository after ingest.
231 This is an optional hook provided for subclasses; by default it does
232 nothing.
234 Parameters
235 ----------
236 files : `list` [`str`], or None
237 List of files to be ingested, or None to use ``self.file``
238 """
239 pass
241 @classmethod
242 def _createRepo(cls):
243 """Use the Click `testing` module to call the butler command line api
244 to create a repository."""
245 runner = LogCliRunner()
246 args = []
247 if cls.seed_config:
248 args.extend(["--seed-config", cls.seed_config])
249 result = runner.invoke(butlerCli, ["create", cls.root, *args])
250 # Classmethod so assertEqual does not work.
251 assert result.exit_code == 0, f"output: {result.output} exception: {result.exception}"
253 def _ingestRaws(self, transfer, file=None):
254 """Use the Click `testing` module to call the butler command line api
255 to ingest raws.
257 Parameters
258 ----------
259 transfer : `str`
260 The external data transfer type.
261 file : `str`
262 Path to a file to ingest instead of the default associated with
263 the object.
264 """
265 if file is None:
266 file = self.file
267 runner = LogCliRunner()
268 result = runner.invoke(
269 butlerCli,
270 [
271 "ingest-raws",
272 self.root,
273 file,
274 "--output-run",
275 self.outputRun,
276 "--transfer",
277 transfer,
278 "--ingest-task",
279 self.rawIngestTask,
280 ],
281 )
282 self.assertEqual(result.exit_code, 0, f"output: {result.output} exception: {result.exception}")
284 @classmethod
285 def _registerInstrument(cls):
286 """Use the Click `testing` module to call the butler command line api
287 to register the instrument."""
288 runner = LogCliRunner()
289 result = runner.invoke(butlerCli, ["register-instrument", cls.root, cls.instrumentClassName])
290 # Classmethod so assertEqual does not work.
291 assert result.exit_code == 0, f"output: {result.output} exception: {result.exception}"
293 def _writeCuratedCalibrations(self):
294 """Use the Click `testing` module to call the butler command line api
295 to write curated calibrations."""
296 runner = LogCliRunner()
297 result = runner.invoke(butlerCli, ["write-curated-calibrations", self.root, self.instrumentName])
298 self.assertEqual(result.exit_code, 0, f"output: {result.output} exception: {result.exception}")
300 def testLink(self):
301 self._ingestRaws(transfer="link")
302 self.verifyIngest()
304 def testSymLink(self):
305 self._ingestRaws(transfer="symlink")
306 self.verifyIngest()
308 def testDirect(self):
309 self._ingestRaws(transfer="direct")
311 # Check that it really did have a URI outside of datastore.
312 srcUri = ResourcePath(self.file, forceAbsolute=True)
313 butler = Butler(self.root, run=self.outputRun)
314 datasets = list(butler.registry.queryDatasets(self.ingestDatasetTypeName, collections=self.outputRun))
315 datastoreUri = butler.getURI(datasets[0])
316 self.assertEqual(datastoreUri, srcUri)
318 def testCopy(self):
319 self._ingestRaws(transfer="copy")
320 # Only test full read of raws for the copy test. No need to do it
321 # in the other tests since the formatter will be the same in all
322 # cases.
323 self.verifyIngest(fullCheck=True)
325 def testHardLink(self):
326 try:
327 self._ingestRaws(transfer="hardlink")
328 # Running ingest through the Click testing infrastructure causes
329 # the original exception indicating that we can't hard-link
330 # on this filesystem to be turned into a nonzero exit code, which
331 # then trips the test assertion.
332 except (AssertionError, PermissionError) as err:
333 raise unittest.SkipTest(
334 "Skipping hard-link test because input data is on a different filesystem."
335 ) from err
336 self.verifyIngest()
338 def testInPlace(self):
339 """Test that files already in the directory can be added to the
340 registry in-place.
341 """
342 butler = Butler(self.root, run=self.outputRun)
344 # If the test uses an index file the index file needs to also
345 # appear in the datastore root along with the file to be ingested.
346 # In that scenario the file name being used for ingest can not
347 # be modified and must have the same name as found in the index
348 # file itself.
349 source_file_uri = ResourcePath(self.file)
350 index_file = source_file_uri.dirname().join("_index.json")
351 pathInStore = source_file_uri.basename()
352 if index_file.exists():
353 os.symlink(index_file.ospath, butler.datastore.root.join("_index.json").ospath)
354 else:
355 # No index file so we are free to pick any name.
356 pathInStore = "prefix-" + pathInStore
358 # Create a symlink to the original file so that it looks like it
359 # is now inside the datastore.
360 newPath = butler.datastore.root.join(pathInStore)
361 os.symlink(os.path.abspath(self.file), newPath.ospath)
363 # If there is a sidecar file it needs to be linked in as well
364 # since ingest code does not follow symlinks.
365 sidecar_uri = ResourcePath(source_file_uri).updatedExtension(".json")
366 if sidecar_uri.exists():
367 newSidecar = ResourcePath(newPath).updatedExtension(".json")
368 os.symlink(sidecar_uri.ospath, newSidecar.ospath)
370 # Run ingest with auto mode since that should automatically determine
371 # that an in-place ingest is happening.
372 self._ingestRaws(transfer="auto", file=newPath.ospath)
373 self.verifyIngest()
375 # Recreate a butler post-ingest (the earlier one won't see the
376 # ingested files).
377 butler = Butler(self.root, run=self.outputRun)
379 # Check that the URI associated with this path is the right one.
380 uri = butler.getURI(self.ingestDatasetTypeName, self.dataIds[0])
381 self.assertEqual(uri.relative_to(butler.datastore.root), pathInStore)
383 def testFailOnConflict(self):
384 """Re-ingesting the same data into the repository should fail."""
385 self._ingestRaws(transfer="symlink")
386 with self.assertRaises(Exception):
387 self._ingestRaws(transfer="symlink")
389 def testWriteCuratedCalibrations(self):
390 """Test that we can ingest the curated calibrations, and read them
391 with `loadCamera` both before and after.
392 """
393 if self.curatedCalibrationDatasetTypes is None:
394 raise unittest.SkipTest("Class requests disabling of writeCuratedCalibrations test")
396 butler = Butler(self.root, writeable=False)
397 collection = self.instrumentClass().makeCalibrationCollectionName()
399 # Trying to load a camera with a data ID not known to the registry
400 # is an error, because we can't get any temporal information.
401 with self.assertRaises(LookupError):
402 lsst.obs.base.loadCamera(butler, {"exposure": 0}, collections=collection)
404 # Ingest raws in order to get some exposure records.
405 self._ingestRaws(transfer="auto")
407 # Load camera should returned an unversioned camera because there's
408 # nothing in the repo.
409 camera, isVersioned = lsst.obs.base.loadCamera(butler, self.dataIds[0], collections=collection)
410 self.assertFalse(isVersioned)
411 self.assertIsInstance(camera, lsst.afw.cameraGeom.Camera)
413 self._writeCuratedCalibrations()
415 # Make a new butler instance to make sure we don't have any stale
416 # caches (e.g. of DatasetTypes). Note that we didn't give
417 # _writeCuratedCalibrations the butler instance we had, because it's
418 # trying to test the CLI interface anyway.
419 butler = Butler(self.root, writeable=False)
421 instrumentClass = self.instrumentClass()
422 calibration_names = instrumentClass.getCuratedCalibrationNames()
424 for datasetTypeName in self.curatedCalibrationDatasetTypes:
425 with self.subTest(dtype=datasetTypeName):
426 found = list(
427 butler.registry.queryDatasetAssociations(
428 datasetTypeName,
429 collections=collection,
430 )
431 )
432 self.assertGreater(len(found), 0, f"Checking {datasetTypeName}")
433 self.assertIn(datasetTypeName, calibration_names)
435 # Load camera should returned the versioned camera from the repo.
436 camera, isVersioned = lsst.obs.base.loadCamera(butler, self.dataIds[0], collections=collection)
437 self.assertTrue(isVersioned)
438 self.assertIsInstance(camera, lsst.afw.cameraGeom.Camera)
440 def testDefineVisits(self):
441 if self.visits is None:
442 self.skipTest("Expected visits were not defined.")
443 self._ingestRaws(transfer="link")
445 # Check that obscore table (if configured) has correct contents.
446 butler = Butler(self.root, run=self.outputRun)
447 self._check_obscore(butler.registry, has_visits=False)
449 # Calling defineVisits tests the implementation of the butler command
450 # line interface "define-visits" subcommand. Functions in the script
451 # folder are generally considered protected and should not be used
452 # as public api.
453 script.defineVisits(
454 self.root,
455 config_file=None,
456 collections=self.outputRun,
457 instrument=self.instrumentName,
458 raw_name=self.ingestDatasetTypeName,
459 )
461 # Test that we got the visits we expected.
462 visits = butler.registry.queryDataIds(["visit"]).expanded().toSet()
463 self.assertCountEqual(visits, self.visits.keys())
464 instr = Instrument.from_string(self.instrumentName, butler.registry)
465 camera = instr.getCamera()
466 for foundVisit, (expectedVisit, expectedExposures) in zip(visits, self.visits.items()):
467 # Test that this visit is associated with the expected exposures.
468 foundExposures = (
469 butler.registry.queryDataIds(["exposure"], dataId=expectedVisit).expanded().toSet()
470 )
471 self.assertCountEqual(foundExposures, expectedExposures)
472 # Test that we have a visit region, and that it contains all of the
473 # detector+visit regions.
474 self.assertIsNotNone(foundVisit.region)
475 detectorVisitDataIds = (
476 butler.registry.queryDataIds(["visit", "detector"], dataId=expectedVisit).expanded().toSet()
477 )
478 self.assertEqual(len(detectorVisitDataIds), len(camera))
479 for dataId in detectorVisitDataIds:
480 self.assertTrue(foundVisit.region.contains(dataId.region))
482 # Check obscore table again.
483 self._check_obscore(butler.registry, has_visits=True)
485 def _check_obscore(self, registry: Registry, has_visits: bool) -> None:
486 """Verify contents of obscore table."""
487 return