Coverage for python/lsst/ap/verify/pipeline_driver.py : 18%

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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"""Interface between `ap_verify` and `ap_pipe`.
26This module handles calling `ap_pipe` and converting any information
27as needed.
28"""
30__all__ = ["ApPipeParser", "runApPipeGen2", "runApPipeGen3"]
32import argparse
33import os
34import re
36import click.testing
38import lsst.log
39from lsst.utils import getPackageDir
40import lsst.pipe.base as pipeBase
41import lsst.obs.base as obsBase
42import lsst.ctrl.mpexec.cli.pipetask
43import lsst.ap.pipe as apPipe
44from lsst.ap.pipe.make_apdb import makeApdb
47class ApPipeParser(argparse.ArgumentParser):
48 """An argument parser for data needed by ``ap_pipe`` activities.
50 This parser is not complete, and is designed to be passed to another parser
51 using the `parent` parameter.
52 """
54 def __init__(self):
55 defaultPipeline = os.path.join(getPackageDir("ap_verify"), "pipelines", "ApVerify.yaml")
57 # Help and documentation will be handled by main program's parser
58 argparse.ArgumentParser.__init__(self, add_help=False)
59 # namespace.dataIds will always be a list of 0 or more nonempty strings, regardless of inputs.
60 # TODO: in Python 3.8+, action='extend' handles nargs='?' more naturally than 'append'.
61 self.add_argument('--id', '-d', '--data-query', dest='dataIds',
62 action=self.AppendOptional, nargs='?', default=[],
63 help='An identifier for the data to process.')
64 self.add_argument("-p", "--pipeline", default=defaultPipeline,
65 help="A custom version of the ap_verify pipeline (e.g., with different metrics).")
66 self.add_argument("--db", "--db_url", default=None,
67 help="A location for the AP database, formatted as if for ApdbConfig.db_url. "
68 "Defaults to an SQLite file in the --output directory.")
69 self.add_argument("--skip-pipeline", action="store_true",
70 help="Do not run the AP pipeline itself. This argument is useful "
71 "for testing metrics on a fixed data set.")
73 class AppendOptional(argparse.Action):
74 """A variant of the built-in "append" action that ignores None values
75 instead of appending them.
76 """
77 # This class can't safely inherit from the built-in "append" action
78 # because there is no public class that implements it.
79 def __call__(self, parser, namespace, values, option_string=None):
80 if values is not None:
81 try:
82 allValues = getattr(namespace, self.dest)
83 allValues.append(values)
84 except AttributeError:
85 setattr(namespace, self.dest, [values])
88def runApPipeGen2(workspace, parsedCmdLine, processes=1):
89 """Run `ap_pipe` on this object's dataset.
91 Parameters
92 ----------
93 workspace : `lsst.ap.verify.workspace.WorkspaceGen2`
94 The abstract location containing input and output repositories.
95 parsedCmdLine : `argparse.Namespace`
96 Command-line arguments, including all arguments supported by `ApPipeParser`.
97 processes : `int`
98 The number of processes with which to call the AP pipeline
100 Returns
101 -------
102 apPipeReturn : `Struct`
103 The `Struct` returned from `~lsst.ap.pipe.ApPipeTask.parseAndRun` with
104 ``doReturnResults=False``. This object is valid even if
105 `~lsst.ap.pipe.ApPipeTask` was never run.
106 """
107 log = lsst.log.Log.getLogger('ap.verify.pipeline_driver.runApPipeGen2')
109 makeApdb(_getApdbArguments(workspace, parsedCmdLine))
111 pipelineArgs = [workspace.dataRepo,
112 "--output", workspace.outputRepo,
113 "--calib", workspace.calibRepo,
114 "--template", workspace.templateRepo]
115 pipelineArgs.extend(_getConfigArguments(workspace, parsedCmdLine))
116 if parsedCmdLine.dataIds:
117 for singleId in parsedCmdLine.dataIds:
118 pipelineArgs.extend(["--id", *singleId.split(" ")])
119 else:
120 pipelineArgs.extend(["--id"])
121 pipelineArgs.extend(["--processes", str(processes)])
122 pipelineArgs.extend(["--noExit"])
124 if not parsedCmdLine.skip_pipeline:
125 results = apPipe.ApPipeTask.parseAndRun(pipelineArgs)
126 log.info('Pipeline complete')
127 else:
128 log.info('Skipping AP pipeline entirely.')
129 apPipeParser = apPipe.ApPipeTask._makeArgumentParser()
130 apPipeParsed = apPipeParser.parse_args(config=apPipe.ApPipeTask.ConfigClass(), args=pipelineArgs)
131 results = pipeBase.Struct(
132 argumentParser=apPipeParser,
133 parsedCmd=apPipeParsed,
134 taskRunner=apPipe.ApPipeTask.RunnerClass(TaskClass=apPipe.ApPipeTask, parsedCmd=apPipeParsed),
135 resultList=[],
136 )
138 return results
141def runApPipeGen3(workspace, parsedCmdLine, processes=1):
142 """Run `ap_pipe` on this object's dataset.
144 Parameters
145 ----------
146 workspace : `lsst.ap.verify.workspace.WorkspaceGen3`
147 The abstract location containing input and output repositories.
148 parsedCmdLine : `argparse.Namespace`
149 Command-line arguments, including all arguments supported by `ApPipeParser`.
150 processes : `int`
151 The number of processes with which to call the AP pipeline
152 """
153 log = lsst.log.Log.getLogger('ap.verify.pipeline_driver.runApPipeGen3')
155 makeApdb(_getApdbArguments(workspace, parsedCmdLine))
157 pipelineArgs = ["run",
158 "--butler-config", workspace.repo,
159 "--pipeline", parsedCmdLine.pipeline,
160 ]
161 # TODO: collections should be determined exclusively by Workspace.workButler,
162 # but I can't find a way to hook that up to the graph builder. So use the CLI
163 # for now and revisit once DM-26239 is done.
164 pipelineArgs.extend(_getCollectionArguments(workspace))
165 pipelineArgs.extend(_getConfigArgumentsGen3(workspace, parsedCmdLine))
166 if parsedCmdLine.dataIds:
167 for singleId in parsedCmdLine.dataIds:
168 pipelineArgs.extend(["--data-query", singleId])
169 pipelineArgs.extend(["--processes", str(processes)])
170 pipelineArgs.extend(["--register-dataset-types"])
172 if not parsedCmdLine.skip_pipeline:
173 # CliRunner is an unsafe workaround for DM-26239
174 runner = click.testing.CliRunner()
175 # TODO: generalize this code in DM-26028
176 # TODO: work off of workspace.workButler after DM-26239
177 results = runner.invoke(lsst.ctrl.mpexec.cli.pipetask.cli, pipelineArgs)
178 if results.exception:
179 raise RuntimeError("Pipeline failed.") from results.exception
181 log.info('Pipeline complete.')
182 return results.exit_code
183 else:
184 log.info('Skipping AP pipeline entirely.')
187def _getApdbArguments(workspace, parsed):
188 """Return the config options for running make_apdb.py on this workspace,
189 as command-line arguments.
191 Parameters
192 ----------
193 workspace : `lsst.ap.verify.workspace.Workspace`
194 A Workspace whose config directory may contain an
195 `~lsst.ap.pipe.ApPipeTask` config.
196 parsed : `argparse.Namespace`
197 Command-line arguments, including all arguments supported by `ApPipeParser`.
199 Returns
200 -------
201 args : `list` of `str`
202 Command-line arguments calling ``--config`` or ``--config-file``,
203 following the conventions of `sys.argv`.
204 """
205 if not parsed.db:
206 parsed.db = "sqlite:///" + workspace.dbLocation
208 args = ["--config", "db_url=" + parsed.db]
209 # Same special-case check as ApdbConfig.validate()
210 if parsed.db.startswith("sqlite"):
211 args.extend(["--config", "isolation_level=READ_UNCOMMITTED"])
213 return args
216def _getConfigArguments(workspace, parsed):
217 """Return the config options for running ApPipeTask on this workspace, as
218 command-line arguments.
220 Parameters
221 ----------
222 workspace : `lsst.ap.verify.workspace.WorkspaceGen2`
223 A Workspace whose config directory may contain an
224 `~lsst.ap.pipe.ApPipeTask` config.
225 parsed : `argparse.Namespace`
226 Command-line arguments, including all arguments supported by `ApPipeParser`.
228 Returns
229 -------
230 args : `list` of `str`
231 Command-line arguments calling ``--config`` or ``--configfile``,
232 following the conventions of `sys.argv`.
233 """
234 overrideFile = apPipe.ApPipeTask._DefaultName + ".py"
235 overridePath = os.path.join(workspace.configDir, overrideFile)
237 args = ["--configfile", overridePath]
238 # Translate APDB-only arguments to work as a sub-config
239 args.extend([("diaPipe.apdb." + arg if arg != "--config" else arg)
240 for arg in _getApdbArguments(workspace, parsed)])
241 # Put output alerts into the workspace.
242 args.extend(["--config", "diaPipe.alertPackager.alertWriteLocation=" + workspace.alertLocation])
243 args.extend(["--config", "diaPipe.doPackageAlerts=True"])
245 return args
248def _getConfigArgumentsGen3(workspace, parsed):
249 """Return the config options for running the Gen 3 AP Pipeline on this
250 workspace, as command-line arguments.
252 Parameters
253 ----------
254 workspace : `lsst.ap.verify.workspace.WorkspaceGen3`
255 A Workspace whose config directory may contain various configs.
256 parsed : `argparse.Namespace`
257 Command-line arguments, including all arguments supported by `ApPipeParser`.
259 Returns
260 -------
261 args : `list` of `str`
262 Command-line arguments calling ``--config`` or ``--config-file``,
263 following the conventions of `sys.argv`.
264 """
265 # Translate APDB-only arguments to work as a sub-config
266 args = [("diaPipe:apdb." + arg if arg != "--config" else arg)
267 for arg in _getApdbArguments(workspace, parsed)]
268 args.extend([
269 # Put output alerts into the workspace.
270 "--config", "diaPipe:alertPackager.alertWriteLocation=" + workspace.alertLocation,
271 "--config", "diaPipe:doPackageAlerts=True",
272 # TODO: the configs below should not be needed after DM-26140
273 "--config-file", "calibrate:" + os.path.join(workspace.configDir, "calibrate.py"),
274 "--config-file", "imageDifference:" + os.path.join(workspace.configDir, "imageDifference.py"),
275 ])
276 # TODO: reverse-engineering the instrument should not be needed after DM-26140
277 # pipetask will crash if there is more than one instrument
278 for idRecord in workspace.workButler.registry.queryDataIds("instrument").expanded():
279 className = idRecord.records["instrument"].class_name
280 args.extend(["--instrument", className])
282 return args
285def _getCollectionArguments(workspace):
286 """Return the collections for running the Gen 3 AP Pipeline on this
287 workspace, as command-line arguments.
289 Parameters
290 ----------
291 workspace : `lsst.ap.verify.workspace.WorkspaceGen3`
292 A Workspace with a Gen 3 repository.
294 Returns
295 -------
296 args : `list` of `str`
297 Command-line arguments calling ``--input`` or ``--output``,
298 following the conventions of `sys.argv`.
299 """
300 butler = workspace.workButler
301 # Hard-code the collection names because it's hard to infer the inputs from the Butler
302 inputs = {"skymaps", "refcats"}
303 for dimension in butler.registry.queryDataIds('instrument'):
304 instrument = obsBase.Instrument.fromName(dimension["instrument"], butler.registry)
305 inputs.add(instrument.makeDefaultRawIngestRunName())
306 inputs.add(instrument.makeCalibrationCollectionName())
307 inputs.update(butler.registry.queryCollections(re.compile(r"templates/\w+")))
309 return ["--input", ",".join(inputs),
310 "--output-run", workspace.runName,
311 ]