2 # Copyright (C) The Arvados Authors. All rights reserved.
4 # SPDX-License-Identifier: Apache-2.0
6 # Implement cwl-runner interface for submitting and running work on Arvados, using
7 # either the Crunch jobs API or Crunch containers API.
14 import pkg_resources # part of setuptools
16 from schema_salad.sourceline import SourceLine
17 import schema_salad.validate as validate
19 import cwltool.workflow
20 import cwltool.process
21 import cwltool.argparser
22 from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
23 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing
27 from arvados.keep import KeepClient
28 from arvados.errors import ApiError
29 import arvados.commands._util as arv_cmd
30 from arvados.api import OrderedJsonModel
32 from .perf import Perf
33 from ._version import __version__
34 from .executor import ArvCwlExecutor
36 # These arn't used directly in this file but
37 # other code expects to import them from here
38 from .arvcontainer import ArvadosContainer
39 from .arvtool import ArvadosCommandTool
40 from .fsaccess import CollectionFsAccess, CollectionCache
41 from .util import get_current_container
42 from .executor import RuntimeStatusLoggingHandler, DEFAULT_PRIORITY
44 logger = logging.getLogger('arvados.cwl-runner')
45 metrics = logging.getLogger('arvados.cwl-runner.metrics')
46 logger.setLevel(logging.INFO)
48 arvados.log_handler.setFormatter(logging.Formatter(
49 '%(asctime)s %(name)s %(levelname)s: %(message)s',
53 """Print version string of key packages for provenance and debugging."""
55 arvcwlpkg = pkg_resources.require("arvados-cwl-runner")
56 arvpkg = pkg_resources.require("arvados-python-client")
57 cwlpkg = pkg_resources.require("cwltool")
59 return "%s %s, %s %s, %s %s" % (sys.argv[0], arvcwlpkg[0].version,
60 "arvados-python-client", arvpkg[0].version,
61 "cwltool", cwlpkg[0].version)
64 def arg_parser(): # type: () -> argparse.ArgumentParser
65 parser = argparse.ArgumentParser(description='Arvados executor for Common Workflow Language')
67 parser.add_argument("--basedir", type=str,
68 help="Base directory used to resolve relative references in the input, default to directory of input object file or current directory (if inputs piped/provided on command line).")
69 parser.add_argument("--outdir", type=str, default=os.path.abspath('.'),
70 help="Output directory, default current directory")
72 parser.add_argument("--eval-timeout",
73 help="Time to wait for a Javascript expression to evaluate before giving an error, default 20s.",
77 exgroup = parser.add_mutually_exclusive_group()
78 exgroup.add_argument("--print-dot", action="store_true",
79 help="Print workflow visualization in graphviz format and exit")
80 exgroup.add_argument("--version", action="version", help="Print version and exit", version=versionstring())
81 exgroup.add_argument("--validate", action="store_true", help="Validate CWL document only.")
83 exgroup = parser.add_mutually_exclusive_group()
84 exgroup.add_argument("--verbose", action="store_true", help="Default logging")
85 exgroup.add_argument("--quiet", action="store_true", help="Only print warnings and errors.")
86 exgroup.add_argument("--debug", action="store_true", help="Print even more logging")
88 parser.add_argument("--metrics", action="store_true", help="Print timing metrics")
90 parser.add_argument("--tool-help", action="store_true", help="Print command line help for tool")
92 exgroup = parser.add_mutually_exclusive_group()
93 exgroup.add_argument("--enable-reuse", action="store_true",
94 default=True, dest="enable_reuse",
95 help="Enable job or container reuse (default)")
96 exgroup.add_argument("--disable-reuse", action="store_false",
97 default=True, dest="enable_reuse",
98 help="Disable job or container reuse")
100 parser.add_argument("--project-uuid", type=str, metavar="UUID", help="Project that will own the workflow jobs, if not provided, will go to home project.")
101 parser.add_argument("--output-name", type=str, help="Name to use for collection that stores the final output.", default=None)
102 parser.add_argument("--output-tags", type=str, help="Tags for the final output collection separated by commas, e.g., '--output-tags tag0,tag1,tag2'.", default=None)
103 parser.add_argument("--ignore-docker-for-reuse", action="store_true",
104 help="Ignore Docker image version when deciding whether to reuse past jobs.",
107 exgroup = parser.add_mutually_exclusive_group()
108 exgroup.add_argument("--submit", action="store_true", help="Submit workflow to run on Arvados.",
109 default=True, dest="submit")
110 exgroup.add_argument("--local", action="store_false", help="Run workflow on local host (submits jobs to Arvados).",
111 default=True, dest="submit")
112 exgroup.add_argument("--create-template", action="store_true", help="(Deprecated) synonym for --create-workflow.",
113 dest="create_workflow")
114 exgroup.add_argument("--create-workflow", action="store_true", help="Create an Arvados workflow (if using the 'containers' API) or pipeline template (if using the 'jobs' API). See --api.")
115 exgroup.add_argument("--update-workflow", type=str, metavar="UUID", help="Update an existing Arvados workflow or pipeline template with the given UUID.")
117 exgroup = parser.add_mutually_exclusive_group()
118 exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",
119 default=True, dest="wait")
120 exgroup.add_argument("--no-wait", action="store_false", help="Submit workflow runner job and exit.",
121 default=True, dest="wait")
123 exgroup = parser.add_mutually_exclusive_group()
124 exgroup.add_argument("--log-timestamps", action="store_true", help="Prefix logging lines with timestamp",
125 default=True, dest="log_timestamps")
126 exgroup.add_argument("--no-log-timestamps", action="store_false", help="No timestamp on logging lines",
127 default=True, dest="log_timestamps")
129 parser.add_argument("--api", type=str,
130 default=None, dest="work_api",
131 choices=("jobs", "containers"),
132 help="Select work submission API. Default is 'jobs' if that API is available, otherwise 'containers'.")
134 parser.add_argument("--compute-checksum", action="store_true", default=False,
135 help="Compute checksum of contents while collecting outputs",
136 dest="compute_checksum")
138 parser.add_argument("--submit-runner-ram", type=int,
139 help="RAM (in MiB) required for the workflow runner job (default 1024)",
142 parser.add_argument("--submit-runner-image", type=str,
143 help="Docker image for workflow runner job, default arvados/jobs:%s" % __version__,
146 exgroup = parser.add_mutually_exclusive_group()
147 exgroup.add_argument("--submit-request-uuid", type=str,
149 help="Update and commit to supplied container request instead of creating a new one (containers API only).")
150 exgroup.add_argument("--submit-runner-cluster", type=str,
151 help="Submit toplevel runner to a remote cluster (containers API only)",
154 parser.add_argument("--name", type=str,
155 help="Name to use for workflow execution instance.",
158 parser.add_argument("--on-error", type=str,
159 help="Desired workflow behavior when a step fails. One of 'stop' or 'continue'. "
160 "Default is 'continue'.", default="continue", choices=("stop", "continue"))
162 parser.add_argument("--enable-dev", action="store_true",
163 help="Enable loading and running development versions "
164 "of CWL spec.", default=False)
165 parser.add_argument('--storage-classes', default="default", type=str,
166 help="Specify comma separated list of storage classes to be used when saving workflow output to Keep.")
168 parser.add_argument("--intermediate-output-ttl", type=int, metavar="N",
169 help="If N > 0, intermediate output collections will be trashed N seconds after creation. Default is 0 (don't trash).",
172 parser.add_argument("--priority", type=int,
173 help="Workflow priority (range 1..1000, higher has precedence over lower, containers api only)",
174 default=DEFAULT_PRIORITY)
176 parser.add_argument("--disable-validate", dest="do_validate",
177 action="store_false", default=True,
178 help=argparse.SUPPRESS)
180 parser.add_argument("--disable-js-validation",
181 action="store_true", default=False,
182 help=argparse.SUPPRESS)
184 parser.add_argument("--thread-count", type=int,
185 default=4, help="Number of threads to use for job submit and output collection.")
187 parser.add_argument("--http-timeout", type=int,
188 default=5*60, dest="http_timeout", help="API request timeout in seconds. Default is 300 seconds (5 minutes).")
190 exgroup = parser.add_mutually_exclusive_group()
191 exgroup.add_argument("--trash-intermediate", action="store_true",
192 default=False, dest="trash_intermediate",
193 help="Immediately trash intermediate outputs on workflow success.")
194 exgroup.add_argument("--no-trash-intermediate", action="store_false",
195 default=False, dest="trash_intermediate",
196 help="Do not trash intermediate outputs (default).")
198 parser.add_argument("workflow", type=str, default=None, help="The workflow to execute")
199 parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.")
204 cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
205 cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE
206 res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
207 use_custom_schema("v1.0", "http://arvados.org/cwl", res.read())
209 cwltool.process.supportedProcessRequirements.extend([
210 "http://arvados.org/cwl#RunInSingleContainer",
211 "http://arvados.org/cwl#OutputDirType",
212 "http://arvados.org/cwl#RuntimeConstraints",
213 "http://arvados.org/cwl#PartitionRequirement",
214 "http://arvados.org/cwl#APIRequirement",
215 "http://commonwl.org/cwltool#LoadListingRequirement",
216 "http://arvados.org/cwl#IntermediateOutput",
217 "http://arvados.org/cwl#ReuseRequirement",
218 "http://arvados.org/cwl#ClusterTarget"
221 def exit_signal_handler(sigcode, frame):
222 logger.error("Caught signal {}, exiting.".format(sigcode))
225 def main(args, stdout, stderr, api_client=None, keep_client=None,
226 install_sig_handlers=True):
227 parser = arg_parser()
229 job_order_object = None
230 arvargs = parser.parse_args(args)
232 if len(arvargs.storage_classes.strip().split(',')) > 1:
233 logger.error("Multiple storage classes are not supported currently.")
236 arvargs.use_container = True
237 arvargs.relax_path_checks = True
238 arvargs.print_supported_versions = False
240 if install_sig_handlers:
241 arv_cmd.install_signal_handlers()
243 if arvargs.update_workflow:
244 if arvargs.update_workflow.find('-7fd4e-') == 5:
245 want_api = 'containers'
246 elif arvargs.update_workflow.find('-p5p6p-') == 5:
250 if want_api and arvargs.work_api and want_api != arvargs.work_api:
251 logger.error('--update-workflow arg {!r} uses {!r} API, but --api={!r} specified'.format(
252 arvargs.update_workflow, want_api, arvargs.work_api))
254 arvargs.work_api = want_api
256 if (arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:
257 job_order_object = ({}, "")
261 for key, val in cwltool.argparser.get_default_args().items():
262 if not hasattr(arvargs, key):
263 setattr(arvargs, key, val)
266 if api_client is None:
267 api_client = arvados.safeapi.ThreadSafeApiCache(
268 api_params={"model": OrderedJsonModel(), "timeout": arvargs.http_timeout},
269 keep_params={"num_retries": 4})
270 keep_client = api_client.keep
271 # Make an API object now so errors are reported early.
272 api_client.users().current().execute()
273 if keep_client is None:
274 keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4)
275 executor = ArvCwlExecutor(api_client, arvargs, keep_client=keep_client, num_retries=4)
276 except Exception as e:
281 logger.setLevel(logging.DEBUG)
282 logging.getLogger('arvados').setLevel(logging.DEBUG)
285 logger.setLevel(logging.WARN)
286 logging.getLogger('arvados').setLevel(logging.WARN)
287 logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
290 metrics.setLevel(logging.DEBUG)
291 logging.getLogger("cwltool.metrics").setLevel(logging.DEBUG)
293 if arvargs.log_timestamps:
294 arvados.log_handler.setFormatter(logging.Formatter(
295 '%(asctime)s %(name)s %(levelname)s: %(message)s',
296 '%Y-%m-%d %H:%M:%S'))
298 arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
300 return cwltool.main.main(args=arvargs,
303 executor=executor.arv_executor,
304 versionfunc=versionstring,
305 job_order_object=job_order_object,
306 logger_handler=arvados.log_handler,
307 custom_schema_callback=add_arv_hints,
308 loadingContext=executor.loadingContext,
309 runtimeContext=executor.runtimeContext)