Coverage for python/lsst/obs/base/ingest_tests.py: 30%
191 statements
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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/>.
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.obs.base
35from lsst.daf.butler import Butler
36from lsst.daf.butler.cli.butler import cli as butlerCli
37from lsst.daf.butler.cli.utils import LogCliRunner
38from lsst.pipe.base import Instrument
39from lsst.resources import ResourcePath
40from lsst.utils import doImportType
42from . import script
45class IngestTestBase(metaclass=abc.ABCMeta):
46 """Base class for tests of gen3 ingest. Subclass from this, then
47 `unittest.TestCase` to get a working test suite.
48 """
50 ingestDir = ""
51 """Root path to ingest files into. Typically `obs_package/tests/`; the
52 actual directory will be a tempdir under this one.
53 """
55 ingestDatasetTypeName = "raw"
56 """The DatasetType to use for the ingest.
58 If this is not an Exposure dataset type the tests will be more limited.
59 """
61 dataIds = []
62 """list of butler data IDs of files that should have been ingested."""
64 file = ""
65 """Full path to a file to ingest in tests."""
67 filterLabel = None
68 """The lsst.afw.image.FilterLabel that should be returned by the above
69 file."""
71 rawIngestTask = "lsst.obs.base.RawIngestTask"
72 """The task to use in the Ingest test."""
74 curatedCalibrationDatasetTypes = None
75 """List or tuple of Datasets types that should be present after calling
76 writeCuratedCalibrations. If `None` writeCuratedCalibrations will
77 not be called and the test will be skipped."""
79 defineVisitsTask = lsst.obs.base.DefineVisitsTask
80 """The task to use to define visits from groups of exposures.
81 This is ignored if ``visits`` is `None`.
82 """
84 visits = {}
85 """A dictionary mapping visit data IDs the lists of exposure data IDs that
86 are associated with them.
87 If this is empty (but not `None`), visit definition will be run but no
88 visits will be expected (e.g. because no exposures are on-sky
89 observations).
90 """
92 @property
93 @abc.abstractmethod
94 def instrumentClassName(self):
95 """The fully qualified instrument class name.
97 Returns
98 -------
99 `str`
100 The fully qualified instrument class name.
101 """
102 pass
104 @property
105 def instrumentClass(self):
106 """The instrument class."""
107 return doImportType(self.instrumentClassName)
109 @property
110 def instrumentName(self):
111 """The name of the instrument.
113 Returns
114 -------
115 `str`
116 The name of the instrument.
117 """
118 return self.instrumentClass.getName()
120 @classmethod
121 def setUpClass(cls):
122 # Use a temporary working directory.
123 cls.root = tempfile.mkdtemp(dir=cls.ingestDir)
124 cls._createRepo()
126 # Register the instrument and its static metadata.
127 cls._registerInstrument()
129 def setUp(self):
130 # Want a unique run name per test.
131 self.outputRun = "raw_ingest_" + self.id()
133 @classmethod
134 def tearDownClass(cls):
135 if os.path.exists(cls.root):
136 shutil.rmtree(cls.root, ignore_errors=True)
138 def verifyIngest(self, files=None, cli=False, fullCheck=False):
139 """
140 Test that RawIngestTask ingested the expected files.
142 Parameters
143 ----------
144 files : `list` [`str`], or None
145 List of files to be ingested, or None to use ``self.file``
146 fullCheck : `bool`, optional
147 If `True`, read the full raw dataset and check component
148 consistency. If `False` check that a component can be read
149 but do not read the entire raw exposure.
151 Notes
152 -----
153 Reading all the ingested test data can be expensive. The code paths
154 for reading the second raw are the same as reading the first so
155 we do not gain anything by doing full checks of everything.
156 Only read full pixel data for first dataset from file.
157 Don't even do that if we are requested not to by the caller.
158 This only really affects files that contain multiple datasets.
159 """
160 butler = Butler(self.root, run=self.outputRun)
161 datasets = list(butler.registry.queryDatasets(self.ingestDatasetTypeName, collections=self.outputRun))
162 self.assertEqual(len(datasets), len(self.dataIds))
164 # Get the URI to the first dataset and check it is inside the
165 # datastore.
166 datasetUri = butler.getURI(datasets[0])
167 self.assertIsNotNone(datasetUri.relative_to(butler.datastore.root))
169 # Get the relevant dataset type.
170 datasetType = butler.registry.getDatasetType(self.ingestDatasetTypeName)
172 for dataId in self.dataIds:
173 # For testing we only read the entire dataset the first time
174 # round if this is an Exposure. If it's not an Exposure
175 # we always read it completely but we don't read components
176 # because for an arbitrary dataset type we can't easily tell
177 # what component to test.
179 if not datasetType.storageClass.name.startswith("Exposure"):
180 exposure = butler.get(self.ingestDatasetTypeName, dataId)
181 # Could be anything so nothing to test by default
182 continue
184 # Check that we can read metadata from a raw.
185 metadata = butler.get(f"{self.ingestDatasetTypeName}.metadata", dataId)
186 if not fullCheck:
187 continue
188 fullCheck = False
189 exposure = butler.get(self.ingestDatasetTypeName, dataId)
191 # Comparing headers will not work directly because of header
192 # fix up provenance.
193 metadata_headers = metadata.toDict()
194 exposure_headers = exposure.getMetadata().toDict()
195 metadata_headers.pop("HIERARCH ASTRO METADATA FIX DATE", None)
196 exposure_headers.pop("HIERARCH ASTRO METADATA FIX DATE", None)
197 self.assertEqual(metadata_headers, exposure_headers)
199 # Since components follow a different code path we check that
200 # WCS match and also we check that at least the shape
201 # of the image is the same (rather than doing per-pixel equality)
202 wcs = butler.get(f"{self.ingestDatasetTypeName}.wcs", dataId)
203 self.assertEqual(wcs, exposure.getWcs())
205 rawImage = butler.get(f"{self.ingestDatasetTypeName}.image", dataId)
206 self.assertEqual(rawImage.getBBox(), exposure.getBBox())
208 # Check that the filter label got the correct band.
209 filterLabel = butler.get(f"{self.ingestDatasetTypeName}.filterLabel", dataId)
210 self.assertEqual(filterLabel, self.filterLabel)
212 # Check that the exposure's Detector is the same as the component
213 # we would read (this is tricky for LSST, which modifies its
214 # detector at read time; for most other cameras it should be
215 # trivially satisfied.
216 detector = butler.get(f"{self.ingestDatasetTypeName}.detector", dataId)
217 self.assertDetectorsEqual(detector, exposure.getDetector(), compareTransforms=False)
219 self.checkRepo(files=files)
221 def checkRepo(self, files=None):
222 """Check the state of the repository after ingest.
224 This is an optional hook provided for subclasses; by default it does
225 nothing.
227 Parameters
228 ----------
229 files : `list` [`str`], or None
230 List of files to be ingested, or None to use ``self.file``
231 """
232 pass
234 @classmethod
235 def _createRepo(cls):
236 """Use the Click `testing` module to call the butler command line api
237 to create a repository."""
238 runner = LogCliRunner()
239 result = runner.invoke(butlerCli, ["create", cls.root])
240 # Classmethod so assertEqual does not work.
241 assert result.exit_code == 0, f"output: {result.output} exception: {result.exception}"
243 def _ingestRaws(self, transfer, file=None):
244 """Use the Click `testing` module to call the butler command line api
245 to ingest raws.
247 Parameters
248 ----------
249 transfer : `str`
250 The external data transfer type.
251 file : `str`
252 Path to a file to ingest instead of the default associated with
253 the object.
254 """
255 if file is None:
256 file = self.file
257 runner = LogCliRunner()
258 result = runner.invoke(
259 butlerCli,
260 [
261 "ingest-raws",
262 self.root,
263 file,
264 "--output-run",
265 self.outputRun,
266 "--transfer",
267 transfer,
268 "--ingest-task",
269 self.rawIngestTask,
270 ],
271 )
272 self.assertEqual(result.exit_code, 0, f"output: {result.output} exception: {result.exception}")
274 @classmethod
275 def _registerInstrument(cls):
276 """Use the Click `testing` module to call the butler command line api
277 to register the instrument."""
278 runner = LogCliRunner()
279 result = runner.invoke(butlerCli, ["register-instrument", cls.root, cls.instrumentClassName])
280 # Classmethod so assertEqual does not work.
281 assert result.exit_code == 0, f"output: {result.output} exception: {result.exception}"
283 def _writeCuratedCalibrations(self):
284 """Use the Click `testing` module to call the butler command line api
285 to write curated calibrations."""
286 runner = LogCliRunner()
287 result = runner.invoke(butlerCli, ["write-curated-calibrations", self.root, self.instrumentName])
288 self.assertEqual(result.exit_code, 0, f"output: {result.output} exception: {result.exception}")
290 def testLink(self):
291 self._ingestRaws(transfer="link")
292 self.verifyIngest()
294 def testSymLink(self):
295 self._ingestRaws(transfer="symlink")
296 self.verifyIngest()
298 def testDirect(self):
299 self._ingestRaws(transfer="direct")
301 # Check that it really did have a URI outside of datastore.
302 srcUri = ResourcePath(self.file, forceAbsolute=True)
303 butler = Butler(self.root, run=self.outputRun)
304 datasets = list(butler.registry.queryDatasets(self.ingestDatasetTypeName, collections=self.outputRun))
305 datastoreUri = butler.getURI(datasets[0])
306 self.assertEqual(datastoreUri, srcUri)
308 def testCopy(self):
309 self._ingestRaws(transfer="copy")
310 # Only test full read of raws for the copy test. No need to do it
311 # in the other tests since the formatter will be the same in all
312 # cases.
313 self.verifyIngest(fullCheck=True)
315 def testHardLink(self):
316 try:
317 self._ingestRaws(transfer="hardlink")
318 # Running ingest through the Click testing infrastructure causes
319 # the original exception indicating that we can't hard-link
320 # on this filesystem to be turned into a nonzero exit code, which
321 # then trips the test assertion.
322 except (AssertionError, PermissionError) as err:
323 raise unittest.SkipTest(
324 "Skipping hard-link test because input data is on a different filesystem."
325 ) from err
326 self.verifyIngest()
328 def testInPlace(self):
329 """Test that files already in the directory can be added to the
330 registry in-place.
331 """
332 butler = Butler(self.root, run=self.outputRun)
334 # If the test uses an index file the index file needs to also
335 # appear in the datastore root along with the file to be ingested.
336 # In that scenario the file name being used for ingest can not
337 # be modified and must have the same name as found in the index
338 # file itself.
339 source_file_uri = ResourcePath(self.file)
340 index_file = source_file_uri.dirname().join("_index.json")
341 pathInStore = source_file_uri.basename()
342 if index_file.exists():
343 os.symlink(index_file.ospath, butler.datastore.root.join("_index.json").ospath)
344 else:
345 # No index file so we are free to pick any name.
346 pathInStore = "prefix-" + pathInStore
348 # Create a symlink to the original file so that it looks like it
349 # is now inside the datastore.
350 newPath = butler.datastore.root.join(pathInStore)
351 os.symlink(os.path.abspath(self.file), newPath.ospath)
353 # If there is a sidecar file it needs to be linked in as well
354 # since ingest code does not follow symlinks.
355 sidecar_uri = ResourcePath(source_file_uri).updatedExtension(".json")
356 if sidecar_uri.exists():
357 newSidecar = ResourcePath(newPath).updatedExtension(".json")
358 os.symlink(sidecar_uri.ospath, newSidecar.ospath)
360 # Run ingest with auto mode since that should automatically determine
361 # that an in-place ingest is happening.
362 self._ingestRaws(transfer="auto", file=newPath.ospath)
363 self.verifyIngest()
365 # Recreate a butler post-ingest (the earlier one won't see the
366 # ingested files).
367 butler = Butler(self.root, run=self.outputRun)
369 # Check that the URI associated with this path is the right one.
370 uri = butler.getURI(self.ingestDatasetTypeName, self.dataIds[0])
371 self.assertEqual(uri.relative_to(butler.datastore.root), pathInStore)
373 def testFailOnConflict(self):
374 """Re-ingesting the same data into the repository should fail."""
375 self._ingestRaws(transfer="symlink")
376 with self.assertRaises(Exception):
377 self._ingestRaws(transfer="symlink")
379 def testWriteCuratedCalibrations(self):
380 """Test that we can ingest the curated calibrations, and read them
381 with `loadCamera` both before and after.
382 """
383 if self.curatedCalibrationDatasetTypes is None:
384 raise unittest.SkipTest("Class requests disabling of writeCuratedCalibrations test")
386 butler = Butler(self.root, writeable=False)
387 collection = self.instrumentClass().makeCalibrationCollectionName()
389 # Trying to load a camera with a data ID not known to the registry
390 # is an error, because we can't get any temporal information.
391 with self.assertRaises(LookupError):
392 lsst.obs.base.loadCamera(butler, {"exposure": 0}, collections=collection)
394 # Ingest raws in order to get some exposure records.
395 self._ingestRaws(transfer="auto")
397 # Load camera should returned an unversioned camera because there's
398 # nothing in the repo.
399 camera, isVersioned = lsst.obs.base.loadCamera(butler, self.dataIds[0], collections=collection)
400 self.assertFalse(isVersioned)
401 self.assertIsInstance(camera, lsst.afw.cameraGeom.Camera)
403 self._writeCuratedCalibrations()
405 # Make a new butler instance to make sure we don't have any stale
406 # caches (e.g. of DatasetTypes). Note that we didn't give
407 # _writeCuratedCalibrations the butler instance we had, because it's
408 # trying to test the CLI interface anyway.
409 butler = Butler(self.root, writeable=False)
411 for datasetTypeName in self.curatedCalibrationDatasetTypes:
412 with self.subTest(dtype=datasetTypeName):
413 found = list(
414 butler.registry.queryDatasetAssociations(
415 datasetTypeName,
416 collections=collection,
417 )
418 )
419 self.assertGreater(len(found), 0, f"Checking {datasetTypeName}")
421 # Load camera should returned the versioned camera from the repo.
422 camera, isVersioned = lsst.obs.base.loadCamera(butler, self.dataIds[0], collections=collection)
423 self.assertTrue(isVersioned)
424 self.assertIsInstance(camera, lsst.afw.cameraGeom.Camera)
426 def testDefineVisits(self):
427 if self.visits is None:
428 self.skipTest("Expected visits were not defined.")
429 self._ingestRaws(transfer="link")
431 # Calling defineVisits tests the implementation of the butler command
432 # line interface "define-visits" subcommand. Functions in the script
433 # folder are generally considered protected and should not be used
434 # as public api.
435 script.defineVisits(
436 self.root,
437 config_file=None,
438 collections=self.outputRun,
439 instrument=self.instrumentName,
440 raw_name=self.ingestDatasetTypeName,
441 )
443 # Test that we got the visits we expected.
444 butler = Butler(self.root, run=self.outputRun)
445 visits = butler.registry.queryDataIds(["visit"]).expanded().toSet()
446 self.assertCountEqual(visits, self.visits.keys())
447 instr = Instrument.from_string(self.instrumentName, butler.registry)
448 camera = instr.getCamera()
449 for foundVisit, (expectedVisit, expectedExposures) in zip(visits, self.visits.items()):
450 # Test that this visit is associated with the expected exposures.
451 foundExposures = (
452 butler.registry.queryDataIds(["exposure"], dataId=expectedVisit).expanded().toSet()
453 )
454 self.assertCountEqual(foundExposures, expectedExposures)
455 # Test that we have a visit region, and that it contains all of the
456 # detector+visit regions.
457 self.assertIsNotNone(foundVisit.region)
458 detectorVisitDataIds = (
459 butler.registry.queryDataIds(["visit", "detector"], dataId=expectedVisit).expanded().toSet()
460 )
461 self.assertEqual(len(detectorVisitDataIds), len(camera))
462 for dataId in detectorVisitDataIds:
463 self.assertTrue(foundVisit.region.contains(dataId.region))