sdk/cwl/arvados_cwl/__init__.py

   1 #!/usr/bin/env python3
   2 # Copyright (C) The Arvados Authors. All rights reserved.
   3 #
   4 # SPDX-License-Identifier: Apache-2.0
   5
   6 # Implement cwl-runner interface for submitting and running work on Arvados, using
   7 # the Crunch containers API.
   8
   9 from future.utils import viewitems
  10 from builtins import str
  11
  12 import argparse
  13 import logging
  14 import os
  15 import sys
  16 import re
  17 import pkg_resources  # part of setuptools
  18
  19 from schema_salad.sourceline import SourceLine
  20 import schema_salad.validate as validate
  21 import cwltool.main
  22 import cwltool.workflow
  23 import cwltool.process
  24 import cwltool.argparser
  25 from cwltool.errors import WorkflowException
  26 from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
  27 from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing
  28
  29 import arvados
  30 import arvados.config
  31 from arvados.keep import KeepClient
  32 from arvados.errors import ApiError
  33 import arvados.commands._util as arv_cmd
  34 from arvados.api import OrderedJsonModel
  35
  36 from .perf import Perf
  37 from ._version import __version__
  38 from .executor import ArvCwlExecutor
  39
  40 # These aren't used directly in this file but
  41 # other code expects to import them from here
  42 from .arvcontainer import ArvadosContainer
  43 from .arvtool import ArvadosCommandTool
  44 from .fsaccess import CollectionFsAccess, CollectionCache, CollectionFetcher
  45 from .util import get_current_container
  46 from .executor import RuntimeStatusLoggingHandler, DEFAULT_PRIORITY
  47 from .arvworkflow import ArvadosWorkflow
  48
  49 logger = logging.getLogger('arvados.cwl-runner')
  50 metrics = logging.getLogger('arvados.cwl-runner.metrics')
  51 logger.setLevel(logging.INFO)
  52
  53 arvados.log_handler.setFormatter(logging.Formatter(
  54         '%(asctime)s %(name)s %(levelname)s: %(message)s',
  55         '%Y-%m-%d %H:%M:%S'))
  56
  57 def versionstring():
  58     """Print version string of key packages for provenance and debugging."""
  59
  60     arvcwlpkg = pkg_resources.require("arvados-cwl-runner")
  61     arvpkg = pkg_resources.require("arvados-python-client")
  62     cwlpkg = pkg_resources.require("cwltool")
  63
  64     return "%s %s, %s %s, %s %s" % (sys.argv[0], arvcwlpkg[0].version,
  65                                     "arvados-python-client", arvpkg[0].version,
  66                                     "cwltool", cwlpkg[0].version)
  67
  68
  69 def arg_parser():  # type: () -> argparse.ArgumentParser
  70     parser = argparse.ArgumentParser(description='Arvados executor for Common Workflow Language')
  71
  72     parser.add_argument("--basedir",
  73                         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).")
  74     parser.add_argument("--outdir", default=os.path.abspath('.'),
  75                         help="Output directory, default current directory")
  76
  77     parser.add_argument("--eval-timeout",
  78                         help="Time to wait for a Javascript expression to evaluate before giving an error, default 20s.",
  79                         type=float,
  80                         default=20)
  81
  82     exgroup = parser.add_mutually_exclusive_group()
  83     exgroup.add_argument("--print-dot", action="store_true",
  84                          help="Print workflow visualization in graphviz format and exit")
  85     exgroup.add_argument("--version", action="version", help="Print version and exit", version=versionstring())
  86     exgroup.add_argument("--validate", action="store_true", help="Validate CWL document only.")
  87
  88     exgroup = parser.add_mutually_exclusive_group()
  89     exgroup.add_argument("--verbose", action="store_true", help="Default logging")
  90     exgroup.add_argument("--quiet", action="store_true", help="Only print warnings and errors.")
  91     exgroup.add_argument("--debug", action="store_true", help="Print even more logging")
  92
  93     parser.add_argument("--metrics", action="store_true", help="Print timing metrics")
  94
  95     parser.add_argument("--tool-help", action="store_true", help="Print command line help for tool")
  96
  97     exgroup = parser.add_mutually_exclusive_group()
  98     exgroup.add_argument("--enable-reuse", action="store_true",
  99                         default=True, dest="enable_reuse",
 100                         help="Enable container reuse (default)")
 101     exgroup.add_argument("--disable-reuse", action="store_false",
 102                         default=True, dest="enable_reuse",
 103                         help="Disable container reuse")
 104
 105     parser.add_argument("--project-uuid", metavar="UUID", help="Project that will own the workflow containers, if not provided, will go to home project.")
 106     parser.add_argument("--output-name", help="Name to use for collection that stores the final output.", default=None)
 107     parser.add_argument("--output-tags", help="Tags for the final output collection separated by commas, e.g., '--output-tags tag0,tag1,tag2'.", default=None)
 108     parser.add_argument("--ignore-docker-for-reuse", action="store_true",
 109                         help="Ignore Docker image version when deciding whether to reuse past containers.",
 110                         default=False)
 111
 112     exgroup = parser.add_mutually_exclusive_group()
 113     exgroup.add_argument("--submit", action="store_true", help="Submit workflow to run on Arvados.",
 114                         default=True, dest="submit")
 115     exgroup.add_argument("--local", action="store_false", help="Run workflow on local host (submits containers to Arvados).",
 116                         default=True, dest="submit")
 117     exgroup.add_argument("--create-template", action="store_true", help="(Deprecated) synonym for --create-workflow.",
 118                          dest="create_workflow")
 119     exgroup.add_argument("--create-workflow", action="store_true", help="Register an Arvados workflow that can be run from Workbench")
 120     exgroup.add_argument("--update-workflow", metavar="UUID", help="Update an existing Arvados workflow with the given UUID.")
 121
 122     exgroup = parser.add_mutually_exclusive_group()
 123     exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner, wait for completion.",
 124                         default=True, dest="wait")
 125     exgroup.add_argument("--no-wait", action="store_false", help="Submit workflow runner and exit.",
 126                         default=True, dest="wait")
 127
 128     exgroup = parser.add_mutually_exclusive_group()
 129     exgroup.add_argument("--log-timestamps", action="store_true", help="Prefix logging lines with timestamp",
 130                         default=True, dest="log_timestamps")
 131     exgroup.add_argument("--no-log-timestamps", action="store_false", help="No timestamp on logging lines",
 132                         default=True, dest="log_timestamps")
 133
 134     parser.add_argument("--api",
 135                         default=None, dest="work_api",
 136                         choices=("containers",),
 137                         help="Select work submission API.  Only supports 'containers'")
 138
 139     parser.add_argument("--compute-checksum", action="store_true", default=False,
 140                         help="Compute checksum of contents while collecting outputs",
 141                         dest="compute_checksum")
 142
 143     parser.add_argument("--submit-runner-ram", type=int,
 144                         help="RAM (in MiB) required for the workflow runner job (default 1024)",
 145                         default=None)
 146
 147     parser.add_argument("--submit-runner-image",
 148                         help="Docker image for workflow runner job, default arvados/jobs:%s" % __version__,
 149                         default=None)
 150
 151     parser.add_argument("--always-submit-runner", action="store_true",
 152                         help="When invoked with --submit --wait, always submit a runner to manage the workflow, even when only running a single CommandLineTool",
 153                         default=False)
 154
 155     exgroup = parser.add_mutually_exclusive_group()
 156     exgroup.add_argument("--submit-request-uuid",
 157                          default=None,
 158                          help="Update and commit to supplied container request instead of creating a new one.",
 159                          metavar="UUID")
 160     exgroup.add_argument("--submit-runner-cluster",
 161                          help="Submit workflow runner to a remote cluster",
 162                          default=None,
 163                          metavar="CLUSTER_ID")
 164
 165     parser.add_argument("--collection-cache-size", type=int,
 166                         default=None,
 167                         help="Collection cache size (in MiB, default 256).")
 168
 169     parser.add_argument("--name",
 170                         help="Name to use for workflow execution instance.",
 171                         default=None)
 172
 173     parser.add_argument("--on-error",
 174                         help="Desired workflow behavior when a step fails.  One of 'stop' (do not submit any more steps) or "
 175                         "'continue' (may submit other steps that are not downstream from the error). Default is 'continue'.",
 176                         default="continue", choices=("stop", "continue"))
 177
 178     parser.add_argument("--enable-dev", action="store_true",
 179                         help="Enable loading and running development versions "
 180                              "of the CWL standards.", default=False)
 181     parser.add_argument('--storage-classes', default="default",
 182                         help="Specify comma separated list of storage classes to be used when saving workflow output to Keep.")
 183
 184     parser.add_argument("--intermediate-output-ttl", type=int, metavar="N",
 185                         help="If N > 0, intermediate output collections will be trashed N seconds after creation.  Default is 0 (don't trash).",
 186                         default=0)
 187
 188     parser.add_argument("--priority", type=int,
 189                         help="Workflow priority (range 1..1000, higher has precedence over lower)",
 190                         default=DEFAULT_PRIORITY)
 191
 192     parser.add_argument("--disable-validate", dest="do_validate",
 193                         action="store_false", default=True,
 194                         help=argparse.SUPPRESS)
 195
 196     parser.add_argument("--disable-color", dest="enable_color",
 197                         action="store_false", default=True,
 198                         help=argparse.SUPPRESS)
 199
 200     parser.add_argument("--disable-js-validation",
 201                         action="store_true", default=False,
 202                         help=argparse.SUPPRESS)
 203
 204     parser.add_argument("--thread-count", type=int,
 205                         default=0, help="Number of threads to use for job submit and output collection.")
 206
 207     parser.add_argument("--http-timeout", type=int,
 208                         default=5*60, dest="http_timeout", help="API request timeout in seconds. Default is 300 seconds (5 minutes).")
 209
 210     parser.add_argument(
 211         "--skip-schemas",
 212         action="store_true",
 213         help="Skip loading of schemas",
 214         default=False,
 215         dest="skip_schemas",
 216     )
 217
 218     exgroup = parser.add_mutually_exclusive_group()
 219     exgroup.add_argument("--trash-intermediate", action="store_true",
 220                         default=False, dest="trash_intermediate",
 221                          help="Immediately trash intermediate outputs on workflow success.")
 222     exgroup.add_argument("--no-trash-intermediate", action="store_false",
 223                         default=False, dest="trash_intermediate",
 224                         help="Do not trash intermediate outputs (default).")
 225
 226     parser.add_argument("workflow", default=None, help="The workflow to execute")
 227     parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.")
 228
 229     return parser
 230
 231 def add_arv_hints():
 232     cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
 233     cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE
 234     supported_versions = ["v1.0", "v1.1", "v1.2"]
 235     for s in supported_versions:
 236         res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-%s.yml' % s)
 237         customschema = res.read().decode('utf-8')
 238         use_custom_schema(s, "http://arvados.org/cwl", customschema)
 239         res.close()
 240     cwltool.process.supportedProcessRequirements.extend([
 241         "http://arvados.org/cwl#RunInSingleContainer",
 242         "http://arvados.org/cwl#OutputDirType",
 243         "http://arvados.org/cwl#RuntimeConstraints",
 244         "http://arvados.org/cwl#PartitionRequirement",
 245         "http://arvados.org/cwl#APIRequirement",
 246         "http://commonwl.org/cwltool#LoadListingRequirement",
 247         "http://arvados.org/cwl#IntermediateOutput",
 248         "http://arvados.org/cwl#ReuseRequirement",
 249         "http://arvados.org/cwl#ClusterTarget"
 250     ])
 251
 252 def exit_signal_handler(sigcode, frame):
 253     logger.error(str(u"Caught signal {}, exiting.").format(sigcode))
 254     sys.exit(-sigcode)
 255
 256 def main(args, stdout, stderr, api_client=None, keep_client=None,
 257          install_sig_handlers=True):
 258     parser = arg_parser()
 259
 260     job_order_object = None
 261     arvargs = parser.parse_args(args)
 262
 263     if len(arvargs.storage_classes.strip().split(',')) > 1:
 264         logger.error(str(u"Multiple storage classes are not supported currently."))
 265         return 1
 266
 267     arvargs.use_container = True
 268     arvargs.relax_path_checks = True
 269     arvargs.print_supported_versions = False
 270
 271     if install_sig_handlers:
 272         arv_cmd.install_signal_handlers()
 273
 274     if arvargs.update_workflow:
 275         if arvargs.update_workflow.find('-7fd4e-') == 5:
 276             want_api = 'containers'
 277         else:
 278             want_api = None
 279         if want_api and arvargs.work_api and want_api != arvargs.work_api:
 280             logger.error(str(u'--update-workflow arg {!r} uses {!r} API, but --api={!r} specified').format(
 281                 arvargs.update_workflow, want_api, arvargs.work_api))
 282             return 1
 283         arvargs.work_api = want_api
 284
 285     if (arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:
 286         job_order_object = ({}, "")
 287
 288     add_arv_hints()
 289
 290     for key, val in viewitems(cwltool.argparser.get_default_args()):
 291         if not hasattr(arvargs, key):
 292             setattr(arvargs, key, val)
 293
 294     try:
 295         if api_client is None:
 296             api_client = arvados.safeapi.ThreadSafeApiCache(
 297                 api_params={"model": OrderedJsonModel(), "timeout": arvargs.http_timeout},
 298                 keep_params={"num_retries": 4})
 299             keep_client = api_client.keep
 300             # Make an API object now so errors are reported early.
 301             api_client.users().current().execute()
 302         if keep_client is None:
 303             keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4)
 304         executor = ArvCwlExecutor(api_client, arvargs, keep_client=keep_client, num_retries=4)
 305     except WorkflowException as e:
 306         logger.error(e, exc_info=(sys.exc_info()[1] if arvargs.debug else False))
 307         return 1
 308     except Exception:
 309         logger.exception("Error creating the Arvados CWL Executor")
 310         return 1
 311
 312     # Note that unless in debug mode, some stack traces related to user
 313     # workflow errors may be suppressed.
 314     if arvargs.debug:
 315         logger.setLevel(logging.DEBUG)
 316         logging.getLogger('arvados').setLevel(logging.DEBUG)
 317
 318     if arvargs.quiet:
 319         logger.setLevel(logging.WARN)
 320         logging.getLogger('arvados').setLevel(logging.WARN)
 321         logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
 322
 323     if arvargs.metrics:
 324         metrics.setLevel(logging.DEBUG)
 325         logging.getLogger("cwltool.metrics").setLevel(logging.DEBUG)
 326
 327     if arvargs.log_timestamps:
 328         arvados.log_handler.setFormatter(logging.Formatter(
 329             '%(asctime)s %(name)s %(levelname)s: %(message)s',
 330             '%Y-%m-%d %H:%M:%S'))
 331     else:
 332         arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
 333
 334     if stdout is sys.stdout:
 335         # cwltool.main has code to work around encoding issues with
 336         # sys.stdout and unix pipes (they default to ASCII encoding,
 337         # we want utf-8), so when stdout is sys.stdout set it to None
 338         # to take advantage of that.  Don't override it for all cases
 339         # since we still want to be able to capture stdout for the
 340         # unit tests.
 341         stdout = None
 342
 343     return cwltool.main.main(args=arvargs,
 344                              stdout=stdout,
 345                              stderr=stderr,
 346                              executor=executor.arv_executor,
 347                              versionfunc=versionstring,
 348                              job_order_object=job_order_object,
 349                              logger_handler=arvados.log_handler,
 350                              custom_schema_callback=add_arv_hints,
 351                              loadingContext=executor.loadingContext,
 352                              runtimeContext=executor.runtimeContext,
 353                              input_required=not (arvargs.create_workflow or arvargs.update_workflow))