Coverage for python/lsst/ap/verify/pipeline_driver.py: 20%
76 statements
« prev ^ index » next coverage.py v6.4.4, created at 2022-08-25 02:04 -0700
« prev ^ index » next coverage.py v6.4.4, created at 2022-08-25 02:04 -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"""Interface between `ap_verify` and `ap_pipe`.
26This module handles calling `ap_pipe` and converting any information
27as needed.
28"""
30__all__ = ["ApPipeParser", "runApPipeGen3"]
32import argparse
33import os
34import re
35import subprocess
36import logging
38import lsst.ctrl.mpexec.execFixupDataId # not part of lsst.ctrl.mpexec
39import lsst.ctrl.mpexec.cli.pipetask
40from lsst.ap.pipe.make_apdb import makeApdb
42_LOG = logging.getLogger(__name__)
45class ApPipeParser(argparse.ArgumentParser):
46 """An argument parser for data needed by ``ap_pipe`` activities.
48 This parser is not complete, and is designed to be passed to another parser
49 using the `parent` parameter.
50 """
52 def __init__(self):
53 # Help and documentation will be handled by main program's parser
54 argparse.ArgumentParser.__init__(self, add_help=False)
55 # namespace.dataIds will always be a list of 0 or more nonempty strings, regardless of inputs.
56 # TODO: in Python 3.8+, action='extend' handles nargs='?' more naturally than 'append'.
57 self.add_argument('-d', '--data-query', dest='dataIds', action='append', default=[],
58 help='An identifier for the data to process.')
59 self.add_argument("-p", "--pipeline", default=None,
60 help="A custom version of the ap_verify pipeline (e.g., with different metrics). "
61 "Defaults to the ApVerify.yaml within --dataset.")
62 self.add_argument("--db", "--db_url", default=None,
63 help="A location for the AP database, formatted as if for ApdbConfig.db_url. "
64 "Defaults to an SQLite file in the --output directory.")
65 self.add_argument("--skip-pipeline", action="store_true",
66 help="Do not run the AP pipeline itself. This argument is useful "
67 "for testing metrics on a fixed data set.")
68 self.add_argument("--clean-run", action="store_true",
69 help="Run the pipeline with a new run collection, "
70 "even if one already exists.")
73def runApPipeGen3(workspace, parsedCmdLine, processes=1):
74 """Run `ap_pipe` on this object's dataset.
76 Parameters
77 ----------
78 workspace : `lsst.ap.verify.workspace.WorkspaceGen3`
79 The abstract location containing input and output repositories.
80 parsedCmdLine : `argparse.Namespace`
81 Command-line arguments, including all arguments supported by `ApPipeParser`.
82 processes : `int`
83 The number of processes with which to call the AP pipeline
85 Returns
86 -------
87 code : `int`
88 An error code that is zero if the pipeline ran without problems, or
89 nonzero if there were errors. The exact meaning of nonzereo values
90 is an implementation detail.
91 """
92 log = _LOG.getChild('runApPipeGen3')
94 makeApdb(_getApdbArguments(workspace, parsedCmdLine))
96 pipelineFile = _getPipelineFile(workspace, parsedCmdLine)
97 pipelineArgs = ["pipetask", "run",
98 "--butler-config", workspace.repo,
99 "--pipeline", pipelineFile,
100 ]
101 # TODO: workaround for inability to generate crosstalk sources in main
102 # processing pipeline (DM-31492).
103 instruments = {id["instrument"] for id in workspace.workButler.registry.queryDataIds("instrument")}
104 if "DECam" in instruments:
105 crosstalkPipeline = "${AP_PIPE_DIR}/pipelines/DarkEnergyCamera/RunIsrForCrosstalkSources.yaml"
106 crosstalkArgs = ["pipetask", "run",
107 "--butler-config", workspace.repo,
108 "--pipeline", crosstalkPipeline,
109 ]
110 crosstalkArgs.extend(_getCollectionArguments(workspace, reuse=(not parsedCmdLine.clean_run)))
111 if parsedCmdLine.dataIds:
112 for singleId in parsedCmdLine.dataIds:
113 crosstalkArgs.extend(["--data-query", singleId])
114 crosstalkArgs.extend(["--processes", str(processes)])
115 crosstalkArgs.extend(["--register-dataset-types"])
116 subprocess.run(crosstalkArgs, capture_output=False, shell=False, check=False)
118 # Force same output run for crosstalk and main processing.
119 pipelineArgs.extend(_getCollectionArguments(workspace, reuse=True))
120 else:
121 # TODO: collections should be determined exclusively by Workspace.workButler,
122 # but I can't find a way to hook that up to the graph builder. So use the CLI
123 # for now and revisit once DM-26239 is done.
124 pipelineArgs.extend(_getCollectionArguments(workspace, reuse=(not parsedCmdLine.clean_run)))
126 pipelineArgs.extend(_getConfigArgumentsGen3(workspace, parsedCmdLine))
127 if parsedCmdLine.dataIds:
128 for singleId in parsedCmdLine.dataIds:
129 pipelineArgs.extend(["--data-query", singleId])
130 pipelineArgs.extend(["--processes", str(processes)])
131 pipelineArgs.extend(["--register-dataset-types"])
132 pipelineArgs.extend(["--graph-fixup", "lsst.ap.verify.pipeline_driver._getExecOrder"])
134 if not parsedCmdLine.skip_pipeline:
135 # subprocess is an unsafe workaround for DM-26239
136 # TODO: generalize this code in DM-26028
137 # TODO: work off of workspace.workButler after DM-26239
138 results = subprocess.run(pipelineArgs, capture_output=False, shell=False, check=False)
139 log.info('Pipeline complete.')
140 return results.returncode
141 else:
142 log.info('Skipping AP pipeline entirely.')
145def _getExecOrder():
146 """Return any constraints on the Gen 3 execution order.
148 The current constraints are that executions of DiaPipelineTask must be
149 ordered by visit ID, but this is subject to change.
151 Returns
152 -------
153 order : `lsst.ctrl.mpexec.ExecutionGraphFixup`
154 An object encoding the desired execution order as an algorithm for
155 modifying inter-quantum dependencies.
157 Notes
158 -----
159 This function must be importable, but need not be public.
160 """
161 # Source association algorithm is not time-symmetric. Force execution of
162 # association (through DiaPipelineTask) in order of ascending visit number.
163 return lsst.ctrl.mpexec.execFixupDataId.ExecFixupDataId(
164 taskLabel="diaPipe", dimensions=["visit", ], reverse=False)
167def _getPipelineFile(workspace, parsed):
168 """Return the config options for running make_apdb.py on this workspace,
169 as command-line arguments.
171 Parameters
172 ----------
173 workspace : `lsst.ap.verify.workspace.Workspace`
174 A Workspace whose pipeline directory may contain an ApVerify pipeline.
175 parsed : `argparse.Namespace`
176 Command-line arguments, including all arguments supported by `ApPipeParser`.
178 Returns
179 -------
180 pipeline : `str`
181 The location of the pipeline file to use for running ap_verify.
182 """
183 if parsed.pipeline:
184 return parsed.pipeline
185 else:
186 customPipeline = os.path.join(workspace.pipelineDir, "ApVerify.yaml")
187 if os.path.exists(customPipeline):
188 return customPipeline
189 else:
190 return os.path.join("${AP_VERIFY_DIR}", "pipelines", "ApVerify.yaml")
193def _getApdbArguments(workspace, parsed):
194 """Return the config options for running make_apdb.py on this workspace,
195 as command-line arguments.
197 Parameters
198 ----------
199 workspace : `lsst.ap.verify.workspace.Workspace`
200 A Workspace whose config directory may contain an
201 `~lsst.ap.pipe.ApPipeTask` config.
202 parsed : `argparse.Namespace`
203 Command-line arguments, including all arguments supported by `ApPipeParser`.
205 Returns
206 -------
207 args : `list` of `str`
208 Command-line arguments calling ``--config`` or ``--config-file``,
209 following the conventions of `sys.argv`.
210 """
211 if not parsed.db:
212 parsed.db = "sqlite:///" + workspace.dbLocation
214 args = ["--config", "db_url=" + parsed.db]
215 # Same special-case check as ApdbConfig.validate()
216 if parsed.db.startswith("sqlite"):
217 args.extend(["--config", "isolation_level=READ_UNCOMMITTED"])
219 return args
222def _getConfigArgumentsGen3(workspace, parsed):
223 """Return the config options for running the Gen 3 AP Pipeline on this
224 workspace, as command-line arguments.
226 Parameters
227 ----------
228 workspace : `lsst.ap.verify.workspace.WorkspaceGen3`
229 A Workspace whose config directory may contain various configs.
230 parsed : `argparse.Namespace`
231 Command-line arguments, including all arguments supported by `ApPipeParser`.
233 Returns
234 -------
235 args : `list` of `str`
236 Command-line arguments calling ``--config`` or ``--config-file``,
237 following the conventions of `sys.argv`.
238 """
239 # Translate APDB-only arguments to work as a sub-config
240 args = [("diaPipe:apdb." + arg if arg != "--config" else arg)
241 for arg in _getApdbArguments(workspace, parsed)]
242 args.extend([
243 # Put output alerts into the workspace.
244 "--config", "diaPipe:alertPackager.alertWriteLocation=" + workspace.alertLocation,
245 ])
246 return args
249def _getCollectionArguments(workspace, reuse):
250 """Return the collections for running the Gen 3 AP Pipeline on this
251 workspace, as command-line arguments.
253 Parameters
254 ----------
255 workspace : `lsst.ap.verify.workspace.WorkspaceGen3`
256 A Workspace with a Gen 3 repository.
257 reuse : `bool`
258 If true, use the previous run collection if one exists. Otherwise,
259 create a new run.
261 Returns
262 -------
263 args : `list` of `str`
264 Command-line arguments calling ``--input`` or ``--output``,
265 following the conventions of `sys.argv`.
266 """
267 # workspace.outputName is a chained collection containing all inputs
268 args = ["--output", workspace.outputName,
269 "--clobber-outputs",
270 ]
272 registry = workspace.workButler.registry
273 # Should refresh registry to see crosstalk run from DM-31492, but this
274 # currently leads to a bug involving --skip-existing. The only downside of
275 # the cached registry is that, with two runs for DECam datasets, a rerun of
276 # ap_verify will re-run crosstalk sources in the second run. Using
277 # skip-existing-in would work around that, but would lead to a worse bug in
278 # the case that the user is alternating runs with and without --clean-run.
279 # registry.refresh()
280 oldRuns = list(registry.queryCollections(re.compile(workspace.outputName + r"/\d+T\d+Z")))
281 if reuse and oldRuns:
282 args.extend(["--extend-run", "--skip-existing"])
283 return args