Coverage for python/lsst/daf/butler/tests/utils.py: 38%
104 statements
« prev ^ index » next coverage.py v7.5.0, created at 2024-04-26 02:47 -0700
« prev ^ index » next coverage.py v7.5.0, created at 2024-04-26 02:47 -0700
1# This file is part of daf_butler.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (http://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 software is dual licensed under the GNU General Public License and also
10# under a 3-clause BSD license. Recipients may choose which of these licenses
11# to use; please see the files gpl-3.0.txt and/or bsd_license.txt,
12# respectively. If you choose the GPL option then the following text applies
13# (but note that there is still no warranty even if you opt for BSD instead):
14#
15# This program is free software: you can redistribute it and/or modify
16# it under the terms of the GNU General Public License as published by
17# the Free Software Foundation, either version 3 of the License, or
18# (at your option) any later version.
19#
20# This program is distributed in the hope that it will be useful,
21# but WITHOUT ANY WARRANTY; without even the implied warranty of
22# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23# GNU General Public License for more details.
24#
25# You should have received a copy of the GNU General Public License
26# along with this program. If not, see <http://www.gnu.org/licenses/>.
28from __future__ import annotations
30from unittest.mock import patch
32__all__ = ()
34import os
35import shutil
36import tempfile
37from collections.abc import Callable, Iterator, Sequence
38from contextlib import contextmanager
39from typing import TYPE_CHECKING, Any
41import astropy
42from astropy.table import Table as AstropyTable
44from .. import Butler, Config, DatasetRef, StorageClassFactory, Timespan
45from ..registry import CollectionType
46from ..tests import MetricsExample, addDatasetType
48if TYPE_CHECKING:
49 import unittest
51 from lsst.daf.butler import DatasetType
53 class TestCaseMixin(unittest.TestCase):
54 """Base class for mixin test classes that use TestCase methods."""
56 pass
58else:
60 class TestCaseMixin:
61 """Do-nothing definition of mixin base class for regular execution."""
63 pass
66def makeTestTempDir(default_base: str) -> str:
67 """Create a temporary directory for test usage.
69 The directory will be created within ``DAF_BUTLER_TEST_TMP`` if that
70 environment variable is set, falling back to ``default_base`` if it is
71 not.
73 Parameters
74 ----------
75 default_base : `str`
76 Default parent directory.
78 Returns
79 -------
80 dir : `str`
81 Name of the new temporary directory.
82 """
83 base = os.environ.get("DAF_BUTLER_TEST_TMP", default_base)
84 return tempfile.mkdtemp(dir=base)
87def removeTestTempDir(root: str | None) -> None:
88 """Attempt to remove a temporary test directory, but do not raise if
89 unable to.
91 Unlike `tempfile.TemporaryDirectory`, this passes ``ignore_errors=True``
92 to ``shutil.rmtree`` at close, making it safe to use on NFS.
94 Parameters
95 ----------
96 root : `str`, optional
97 Name of the directory to be removed. If `None`, nothing will be done.
98 """
99 if root is not None and os.path.exists(root):
100 shutil.rmtree(root, ignore_errors=True)
103@contextmanager
104def safeTestTempDir(default_base: str) -> Iterator[str]:
105 """Return a context manager that creates a temporary directory and then
106 attempts to remove it.
108 Parameters
109 ----------
110 default_base : `str`
111 Default parent directory, forwarded to `makeTestTempDir`.
113 Returns
114 -------
115 context : `contextlib.ContextManager`
116 A context manager that returns the new directory name on ``__enter__``
117 and removes the temporary directory (via `removeTestTempDir`) on
118 ``__exit__``.
119 """
120 root = makeTestTempDir(default_base)
121 try:
122 yield root
123 finally:
124 removeTestTempDir(root)
127class ButlerTestHelper:
128 """Mixin with helpers for unit tests."""
130 assertEqual: Callable
131 assertIsInstance: Callable
132 maxDiff: int | None
134 def assertAstropyTablesEqual(
135 self,
136 tables: AstropyTable | Sequence[AstropyTable],
137 expectedTables: AstropyTable | Sequence[AstropyTable],
138 filterColumns: bool = False,
139 unorderedRows: bool = False,
140 ) -> None:
141 """Verify that a list of astropy tables matches a list of expected
142 astropy tables.
144 Parameters
145 ----------
146 tables : `astropy.table.Table` or iterable [`astropy.table.Table`]
147 The table or tables that should match the expected tables.
148 expectedTables : `astropy.table.Table`
149 or iterable [`astropy.table.Table`]
150 The tables with expected values to which the tables under test will
151 be compared.
152 filterColumns : `bool`
153 If `True` then only compare columns that exist in
154 ``expectedTables``.
155 unorderedRows : `bool`, optional
156 If `True` (`False` is default), don't require tables to have their
157 rows in the same order.
158 """
159 # If a single table is passed in for tables or expectedTables, put it
160 # in a list.
161 if isinstance(tables, AstropyTable):
162 tables = [tables]
163 if isinstance(expectedTables, AstropyTable):
164 expectedTables = [expectedTables]
165 self.assertEqual(len(tables), len(expectedTables))
166 for table, expected in zip(tables, expectedTables, strict=True):
167 # Assert that we are testing what we think we are testing:
168 self.assertIsInstance(table, AstropyTable)
169 self.assertIsInstance(expected, AstropyTable)
170 if filterColumns:
171 table = table.copy()
172 table.keep_columns(expected.colnames)
173 if unorderedRows:
174 table = table.copy()
175 table.sort(table.colnames)
176 expected = expected.copy()
177 expected.sort(expected.colnames)
178 # Assert that they match.
179 # Recommendation from Astropy Slack is to format the table into
180 # lines for comparison. We do not compare column data types.
181 table1 = table.pformat_all()
182 expected1 = expected.pformat_all()
183 original_max = self.maxDiff
184 self.maxDiff = None # This is required to get the full diff.
185 try:
186 self.assertEqual(table1, expected1)
187 finally:
188 self.maxDiff = original_max
191def readTable(textTable: str) -> AstropyTable:
192 """Read an astropy table from formatted text.
194 Contains formatting that causes the astropy table to print an empty string
195 instead of "--" for missing/unpopulated values in the text table.
197 Parameters
198 ----------
199 textTable : `str`
200 The text version of the table to read.
202 Returns
203 -------
204 table : `astropy.table.Table`
205 The table as an astropy table.
206 """
207 return AstropyTable.read(
208 textTable,
209 format="ascii",
210 data_start=2, # skip the header row and the header row underlines.
211 fill_values=[("", 0, "")],
212 )
215class MetricTestRepo:
216 """Creates and manage a test repository on disk with datasets that
217 may be queried and modified for unit tests.
219 Parameters
220 ----------
221 root : `str`
222 The location of the repository, to pass to ``Butler.makeRepo``.
223 configFile : `str`
224 The path to the config file, to pass to ``Butler.makeRepo``.
225 forceConfigRoot : `bool`, optional
226 If `False`, any values present in the supplied ``config`` that
227 would normally be reset are not overridden and will appear
228 directly in the output config. Passed to ``Butler.makeRepo``.
229 """
231 METRICS_EXAMPLE_SUMMARY = {"AM1": 5.2, "AM2": 30.6}
232 """The summary data included in ``MetricsExample`` objects stored in the
233 test repo
234 """
236 _DEFAULT_RUN = "ingest/run"
237 _DEFAULT_TAG = "ingest"
239 @staticmethod
240 def _makeExampleMetrics() -> MetricsExample:
241 """Make an object to put into the repository."""
242 return MetricsExample(
243 MetricTestRepo.METRICS_EXAMPLE_SUMMARY,
244 {"a": [1, 2, 3], "b": {"blue": 5, "red": "green"}},
245 [563, 234, 456.7, 752, 8, 9, 27],
246 )
248 def __init__(self, root: str, configFile: str, forceConfigRoot: bool = True) -> None:
249 self.root = root
250 Butler.makeRepo(self.root, config=Config(configFile), forceConfigRoot=forceConfigRoot)
251 butlerConfigFile = os.path.join(self.root, "butler.yaml")
252 butler = Butler.from_config(butlerConfigFile, run=self._DEFAULT_RUN, collections=[self._DEFAULT_TAG])
253 self._do_init(butler, butlerConfigFile)
255 @classmethod
256 def create_from_butler(cls, butler: Butler, butler_config_file: str) -> MetricTestRepo:
257 """Create a MetricTestRepo from an existing Butler instance.
259 Parameters
260 ----------
261 butler : `Butler`
262 `Butler` instance used for setting up the repository.
263 butler_config_file : `str`
264 Path to the config file used to set up that Butler instance.
266 Returns
267 -------
268 repo : `MetricTestRepo`
269 New instance of `MetricTestRepo` using the provided `Butler`
270 instance.
271 """
272 self = cls.__new__(cls)
273 butler = butler._clone(run=self._DEFAULT_RUN, collections=[self._DEFAULT_TAG])
274 self._do_init(butler, butler_config_file)
275 return self
277 def _do_init(self, butler: Butler, butlerConfigFile: str) -> None:
278 self.butler = butler
279 self.storageClassFactory = StorageClassFactory()
280 self.storageClassFactory.addFromConfig(butlerConfigFile)
282 # New datasets will be added to run and tag, but we will only look in
283 # tag when looking up datasets.
284 self.butler.registry.registerCollection(self._DEFAULT_TAG, CollectionType.TAGGED)
286 # Create and register a DatasetType
287 self.datasetType = addDatasetType(
288 self.butler, "test_metric_comp", {"instrument", "visit"}, "StructuredCompositeReadComp"
289 )
291 # Add needed Dimensions
292 self.butler.registry.insertDimensionData("instrument", {"name": "DummyCamComp"})
293 self.butler.registry.insertDimensionData(
294 "physical_filter", {"instrument": "DummyCamComp", "name": "d-r", "band": "R"}
295 )
296 self.butler.registry.insertDimensionData("day_obs", {"instrument": "DummyCamComp", "id": 20200101})
297 self.butler.registry.insertDimensionData(
298 "visit_system", {"instrument": "DummyCamComp", "id": 1, "name": "default"}
299 )
300 visitStart = astropy.time.Time("2020-01-01 08:00:00.123456789", scale="tai")
301 visitEnd = astropy.time.Time("2020-01-01 08:00:36.66", scale="tai")
302 self.butler.registry.insertDimensionData(
303 "visit",
304 dict(
305 instrument="DummyCamComp",
306 id=423,
307 name="fourtwentythree",
308 physical_filter="d-r",
309 timespan=Timespan(visitStart, visitEnd),
310 day_obs=20200101,
311 ),
312 )
313 self.butler.registry.insertDimensionData(
314 "visit",
315 dict(
316 instrument="DummyCamComp",
317 id=424,
318 name="fourtwentyfour",
319 physical_filter="d-r",
320 day_obs=20200101,
321 ),
322 )
324 self.addDataset({"instrument": "DummyCamComp", "visit": 423})
325 self.addDataset({"instrument": "DummyCamComp", "visit": 424})
327 def addDataset(
328 self, dataId: dict[str, Any], run: str | None = None, datasetType: DatasetType | None = None
329 ) -> DatasetRef:
330 """Create a new example metric and add it to the named run with the
331 given dataId.
333 Overwrites tags, so this does not try to associate the new dataset with
334 existing tags. (If/when tags are needed this can be added to the
335 arguments of this function.)
337 Parameters
338 ----------
339 dataId : `dict`
340 The dataId for the new metric.
341 run : `str`, optional
342 The name of the run to create and add a dataset to. If `None`, the
343 dataset will be added to the root butler.
344 datasetType : ``DatasetType``, optional
345 The dataset type of the added dataset. If `None`, will use the
346 default dataset type.
348 Returns
349 -------
350 datasetRef : `DatasetRef`
351 A reference to the added dataset.
352 """
353 if run:
354 self.butler.registry.registerCollection(run, type=CollectionType.RUN)
355 else:
356 run = self._DEFAULT_RUN
357 metric = self._makeExampleMetrics()
358 return self.butler.put(
359 metric, self.datasetType if datasetType is None else datasetType, dataId, run=run
360 )
363@contextmanager
364def mock_env(new_environment: dict[str, str]) -> Iterator[None]:
365 """Context manager to clear the process environment variables, replace them
366 with new values, and restore them at the end of the test.
368 Parameters
369 ----------
370 new_environment : `dict`[`str`, `str`]
371 New environment variable values.
372 """
373 with patch.dict(os.environ, new_environment, clear=True):
374 yield