Coverage for python/lsst/ap/verify/workspace.py: 45%
91 statements
« prev ^ index » next coverage.py v6.5.0, created at 2023-03-24 04:26 -0700
« prev ^ index » next coverage.py v6.5.0, created at 2023-03-24 04:26 -0700
1#
2# This file is part of ap_verify.
3#
4# Developed for the LSST Data Management System.
5# This product includes software developed by the LSST Project
6# (http://www.lsst.org).
7# See the COPYRIGHT file at the top-level directory of this distribution
8# for details of code ownership.
9#
10# This program is free software: you can redistribute it and/or modify
11# it under the terms of the GNU General Public License as published by
12# the Free Software Foundation, either version 3 of the License, or
13# (at your option) any later version.
14#
15# This program is distributed in the hope that it will be useful,
16# but WITHOUT ANY WARRANTY; without even the implied warranty of
17# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18# GNU General Public License for more details.
19#
20# You should have received a copy of the GNU General Public License
21# along with this program. If not, see <http://www.gnu.org/licenses/>.
22#
24__all__ = ["Workspace", "WorkspaceGen3"]
26import abc
27import os
28import pathlib
29import re
30import stat
32import lsst.daf.butler as dafButler
33import lsst.obs.base as obsBase
36class Workspace(metaclass=abc.ABCMeta):
37 """A directory used by ``ap_verify`` to handle data and outputs.
39 Any object of this class represents a working directory containing
40 (possibly empty) subdirectories for various purposes. Subclasses are
41 typically specialized for particular workflows. Keeping such details in
42 separate classes makes it easier to provide guarantees without forcing
43 awkward directory structures on users.
45 All Workspace classes must guarantee the existence of any subdirectories
46 inside the workspace. Directories corresponding to repositories do not need
47 to be initialized, since creating a valid repository usually requires
48 external information.
50 Parameters
51 ----------
52 location : `str`
53 The location on disk where the workspace will be set up. Will be
54 created if it does not already exist.
56 Raises
57 ------
58 EnvironmentError
59 Raised if ``location`` is not readable or not writeable
60 """
61 def __init__(self, location):
62 # Properties must be `str` for backwards compatibility
63 self._location = str(pathlib.Path(location).resolve())
65 self.mkdir(self._location)
66 self.mkdir(self.configDir)
68 @staticmethod
69 def mkdir(directory):
70 """Create a directory for the workspace.
72 This method is intended to be called only by subclasses, and should
73 not be used by external code.
75 Parameters
76 ----------
77 directory : `str`
78 The directory to create.
79 """
80 mode = stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH # a+r, u+rwx
81 pathlib.Path(directory).mkdir(parents=True, exist_ok=True, mode=mode)
83 def __eq__(self, other):
84 """Test whether two workspaces are of the same type and have the
85 same location.
86 """
87 return type(self) == type(other) and self.workDir == other.workDir
89 def __repr__(self):
90 """A string representation that can be used to reconstruct the Workspace.
91 """
92 return f"{type(self).__name__}({self.workDir!r})"
94 @property
95 def workDir(self):
96 """The absolute location of the workspace as a whole
97 (`str`, read-only).
98 """
99 return self._location
101 @property
102 def configDir(self):
103 """The absolute location of a directory containing custom Task config
104 files for use with the data (`str`, read-only).
105 """
106 return os.path.join(self._location, 'config')
108 @property
109 @abc.abstractmethod
110 def dbLocation(self):
111 """The default absolute location of the source association database to
112 be created or updated by the pipeline (`str`, read-only).
114 Shall be a pathname to a database suitable for the backend of `Apdb`.
115 """
117 @property
118 @abc.abstractmethod
119 def alertLocation(self):
120 """The absolute location of an output directory for persisted
121 alert packets (`str`, read-only).
122 """
124 @property
125 @abc.abstractmethod
126 def workButler(self):
127 """A Butler that can produce pipeline inputs and outputs (read-only).
128 The type is class-dependent.
129 """
131 @property
132 @abc.abstractmethod
133 def analysisButler(self):
134 """A Butler that can read pipeline outputs (read-only).
135 The type is class-dependent.
137 The Butler should be read-only, if its type supports the restriction.
138 """
141class WorkspaceGen3(Workspace):
142 """A directory used by ``ap_verify`` to handle data.
144 Any object of this class represents a working directory containing
145 subdirectories for a repository and for non-repository files. Constructing
146 a WorkspaceGen3 does not *initialize* its repository, as this requires
147 external information.
149 Parameters
150 ----------
151 location : `str`
152 The location on disk where the workspace will be set up. Will be
153 created if it does not already exist.
155 Raises
156 ------
157 EnvironmentError
158 Raised if ``location`` is not readable or not writeable
159 """
161 def __init__(self, location):
162 super().__init__(location)
164 self.mkdir(self.repo)
165 self.mkdir(self.pipelineDir)
167 # Gen 3 name of the output
168 self.outputName = "ap_verify-output"
170 # Lazy evaluation to optimize butlers
171 self._workButler = None
172 self._analysisButler = None
174 @property
175 def repo(self):
176 """The absolute path/URI to a Butler repo for AP pipeline processing
177 (`str`, read-only).
178 """
179 return os.path.join(self._location, 'repo')
181 @property
182 def pipelineDir(self):
183 """The absolute location of a directory containing custom pipeline
184 files for use with the data (`str`, read-only).
185 """
186 return os.path.join(self._location, 'pipelines')
188 @property
189 def dbLocation(self):
190 return os.path.join(self._location, 'association.db')
192 @property
193 def alertLocation(self):
194 return os.path.join(self._location, 'alerts')
196 def _ensureCollection(self, registry, name, collectionType):
197 """Add a collection to a repository if it does not already exist.
199 Parameters
200 ----------
201 registry : `lsst.daf.butler.Registry`
202 The repository to which to add the collection.
203 name : `str`
204 The name of the collection to test for and add.
205 collectionType : `lsst.daf.butler.CollectionType`
206 The type of collection to add. This field is ignored when
207 testing if a collection exists.
208 """
209 matchingCollections = list(registry.queryCollections(re.compile(name)))
210 if not matchingCollections:
211 registry.registerCollection(name, type=collectionType)
213 @property
214 def workButler(self):
215 """A Butler that can read and write to a Gen 3 repository (`lsst.daf.butler.Butler`, read-only).
217 Notes
218 -----
219 Assumes `repo` has been initialized.
220 """
221 if self._workButler is None:
222 try:
223 # Dataset generation puts all preloaded datasets in <instrument>/defaults.
224 # However, this definition excludes raws, which are not preloaded.
225 queryButler = dafButler.Butler(self.repo, writeable=True) # writeable for _workButler
226 inputs = []
227 for dimension in queryButler.registry.queryDataIds('instrument'):
228 instrument = obsBase.Instrument.fromName(dimension["instrument"], queryButler.registry)
229 defaultName = instrument.makeCollectionName("defaults")
230 inputs.append(defaultName)
231 rawName = instrument.makeDefaultRawIngestRunName()
232 inputs.append(rawName)
233 self._ensureCollection(queryButler.registry, rawName, dafButler.CollectionType.RUN)
235 # Create an output chain here, so that workButler can see it.
236 # Definition does not conflict with what pipetask --output uses.
237 # Regex is workaround for DM-25945.
238 if not list(queryButler.registry.queryCollections(re.compile(self.outputName))):
239 queryButler.registry.registerCollection(self.outputName,
240 dafButler.CollectionType.CHAINED)
241 queryButler.registry.setCollectionChain(self.outputName, inputs)
243 self._workButler = dafButler.Butler(butler=queryButler, collections=self.outputName)
244 except OSError as e:
245 raise RuntimeError(f"{self.repo} is not a Gen 3 repository") from e
246 return self._workButler
248 @property
249 def analysisButler(self):
250 """A Butler that can read from a Gen 3 repository with outputs (`lsst.daf.butler.Butler`, read-only).
252 Notes
253 -----
254 Assumes `repo` has been initialized.
255 """
256 if self._analysisButler is None:
257 try:
258 self._analysisButler = dafButler.Butler(self.repo, collections=self.outputName,
259 writeable=False)
260 except OSError as e:
261 raise RuntimeError(f"{self.repo} is not a Gen 3 repository") from e
262 return self._analysisButler