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 import arvados.logging
  32 from arvados.keep import KeepClient
  33 from arvados.errors import ApiError
  34 import arvados.commands._util as arv_cmd
  35
  36 from .perf import Perf
  37 from ._version import __version__
  38 from .executor import ArvCwlExecutor
  39 from .fsaccess import workflow_uuid_pattern
  40
  41 # These aren't used directly in this file but
  42 # other code expects to import them from here
  43 from .arvcontainer import ArvadosContainer
  44 from .arvtool import ArvadosCommandTool
  45 from .fsaccess import CollectionFsAccess, CollectionCache, CollectionFetcher
  46 from .util import get_current_container
  47 from .executor import RuntimeStatusLoggingHandler, DEFAULT_PRIORITY
  48 from .arvworkflow import ArvadosWorkflow
  49
  50 logger = logging.getLogger('arvados.cwl-runner')
  51 metrics = logging.getLogger('arvados.cwl-runner.metrics')
  52 logger.setLevel(logging.INFO)
  53
  54 arvados.log_handler.setFormatter(logging.Formatter(
  55         '%(asctime)s %(name)s %(levelname)s: %(message)s',
  56         '%Y-%m-%d %H:%M:%S'))
  57
  58 def versionstring():
  59     """Print version string of key packages for provenance and debugging."""
  60
  61     arvcwlpkg = pkg_resources.require("arvados-cwl-runner")
  62     arvpkg = pkg_resources.require("arvados-python-client")
  63     cwlpkg = pkg_resources.require("cwltool")
  64
  65     return "%s %s, %s %s, %s %s" % (sys.argv[0], arvcwlpkg[0].version,
  66                                     "arvados-python-client", arvpkg[0].version,
  67                                     "cwltool", cwlpkg[0].version)
  68
  69
  70 def arg_parser():  # type: () -> argparse.ArgumentParser
  71     parser = argparse.ArgumentParser(
  72         description='Arvados executor for Common Workflow Language',
  73         parents=[arv_cmd.retry_opt],
  74     )
  75
  76     parser.add_argument("--basedir",
  77                         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).")
  78     parser.add_argument("--outdir", default=os.path.abspath('.'),
  79                         help="Output directory, default current directory")
  80
  81     parser.add_argument("--eval-timeout",
  82                         help="Time to wait for a Javascript expression to evaluate before giving an error, default 20s.",
  83                         type=float,
  84                         default=20)
  85
  86     exgroup = parser.add_mutually_exclusive_group()
  87     exgroup.add_argument("--print-dot", action="store_true",
  88                          help="Print workflow visualization in graphviz format and exit")
  89     exgroup.add_argument("--version", action="version", help="Print version and exit", version=versionstring())
  90     exgroup.add_argument("--validate", action="store_true", help="Validate CWL document only.")
  91
  92     exgroup = parser.add_mutually_exclusive_group()
  93     exgroup.add_argument("--verbose", action="store_true", help="Default logging")
  94     exgroup.add_argument("--quiet", action="store_true", help="Only print warnings and errors.")
  95     exgroup.add_argument("--debug", action="store_true", help="Print even more logging")
  96
  97     parser.add_argument("--metrics", action="store_true", help="Print timing metrics")
  98
  99     parser.add_argument("--tool-help", action="store_true", help="Print command line help for tool")
 100
 101     exgroup = parser.add_mutually_exclusive_group()
 102     exgroup.add_argument("--enable-reuse", action="store_true",
 103                         default=True, dest="enable_reuse",
 104                         help="Enable container reuse (default)")
 105     exgroup.add_argument("--disable-reuse", action="store_false",
 106                         default=True, dest="enable_reuse",
 107                         help="Disable container reuse")
 108
 109     parser.add_argument("--project-uuid", metavar="UUID", help="Project that will own the workflow containers, if not provided, will go to home project.")
 110     parser.add_argument("--output-name", help="Name to use for collection that stores the final output.", default=None)
 111     parser.add_argument("--output-tags", help="Tags for the final output collection separated by commas, e.g., '--output-tags tag0,tag1,tag2'.", default=None)
 112     parser.add_argument("--ignore-docker-for-reuse", action="store_true",
 113                         help="Ignore Docker image version when deciding whether to reuse past containers.",
 114                         default=False)
 115
 116     exgroup = parser.add_mutually_exclusive_group()
 117     exgroup.add_argument("--submit", action="store_true", help="Submit workflow to run on Arvados.",
 118                         default=True, dest="submit")
 119     exgroup.add_argument("--local", action="store_false", help="Run workflow on local host (submits containers to Arvados).",
 120                         default=True, dest="submit")
 121     exgroup.add_argument("--create-template", action="store_true", help="(Deprecated) synonym for --create-workflow.",
 122                          dest="create_workflow")
 123     exgroup.add_argument("--create-workflow", action="store_true", help="Register an Arvados workflow that can be run from Workbench")
 124     exgroup.add_argument("--update-workflow", metavar="UUID", help="Update an existing Arvados workflow with the given UUID.")
 125
 126     exgroup = parser.add_mutually_exclusive_group()
 127     exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner, wait for completion.",
 128                         default=True, dest="wait")
 129     exgroup.add_argument("--no-wait", action="store_false", help="Submit workflow runner and exit.",
 130                         default=True, dest="wait")
 131
 132     exgroup = parser.add_mutually_exclusive_group()
 133     exgroup.add_argument("--log-timestamps", action="store_true", help="Prefix logging lines with timestamp",
 134                         default=True, dest="log_timestamps")
 135     exgroup.add_argument("--no-log-timestamps", action="store_false", help="No timestamp on logging lines",
 136                         default=True, dest="log_timestamps")
 137
 138     parser.add_argument("--api",
 139                         default=None, dest="work_api",
 140                         choices=("containers",),
 141                         help="Select work submission API.  Only supports 'containers'")
 142
 143     parser.add_argument("--compute-checksum", action="store_true", default=False,
 144                         help="Compute checksum of contents while collecting outputs",
 145                         dest="compute_checksum")
 146
 147     parser.add_argument("--submit-runner-ram", type=int,
 148                         help="RAM (in MiB) required for the workflow runner job (default 1024)",
 149                         default=None)
 150
 151     parser.add_argument("--submit-runner-image",
 152                         help="Docker image for workflow runner job, default arvados/jobs:%s" % __version__,
 153                         default=None)
 154
 155     parser.add_argument("--always-submit-runner", action="store_true",
 156                         help="When invoked with --submit --wait, always submit a runner to manage the workflow, even when only running a single CommandLineTool",
 157                         default=False)
 158
 159     parser.add_argument("--match-submitter-images", action="store_true",
 160                         default=False, dest="match_local_docker",
 161                         help="Where Arvados has more than one Docker image of the same name, use image from the Docker instance on the submitting node.")
 162
 163     exgroup = parser.add_mutually_exclusive_group()
 164     exgroup.add_argument("--submit-request-uuid",
 165                          default=None,
 166                          help="Update and commit to supplied container request instead of creating a new one.",
 167                          metavar="UUID")
 168     exgroup.add_argument("--submit-runner-cluster",
 169                          help="Submit workflow runner to a remote cluster",
 170                          default=None,
 171                          metavar="CLUSTER_ID")
 172
 173     parser.add_argument("--collection-cache-size", type=int,
 174                         default=None,
 175                         help="Collection cache size (in MiB, default 256).")
 176
 177     parser.add_argument("--name",
 178                         help="Name to use for workflow execution instance.",
 179                         default=None)
 180
 181     parser.add_argument("--on-error",
 182                         help="Desired workflow behavior when a step fails.  One of 'stop' (do not submit any more steps) or "
 183                         "'continue' (may submit other steps that are not downstream from the error). Default is 'continue'.",
 184                         default="continue", choices=("stop", "continue"))
 185
 186     parser.add_argument("--enable-dev", action="store_true",
 187                         help="Enable loading and running development versions "
 188                              "of the CWL standards.", default=False)
 189     parser.add_argument('--storage-classes', default="default",
 190                         help="Specify comma separated list of storage classes to be used when saving final workflow output to Keep.")
 191     parser.add_argument('--intermediate-storage-classes', default="default",
 192                         help="Specify comma separated list of storage classes to be used when saving intermediate workflow output to Keep.")
 193
 194     parser.add_argument("--intermediate-output-ttl", type=int, metavar="N",
 195                         help="If N > 0, intermediate output collections will be trashed N seconds after creation.  Default is 0 (don't trash).",
 196                         default=0)
 197
 198     parser.add_argument("--priority", type=int,
 199                         help="Workflow priority (range 1..1000, higher has precedence over lower)",
 200                         default=DEFAULT_PRIORITY)
 201
 202     parser.add_argument("--disable-validate", dest="do_validate",
 203                         action="store_false", default=True,
 204                         help=argparse.SUPPRESS)
 205
 206     parser.add_argument("--disable-git", dest="git_info",
 207                         action="store_false", default=True,
 208                         help=argparse.SUPPRESS)
 209
 210     parser.add_argument("--disable-color", dest="enable_color",
 211                         action="store_false", default=True,
 212                         help=argparse.SUPPRESS)
 213
 214     parser.add_argument("--disable-js-validation",
 215                         action="store_true", default=False,
 216                         help=argparse.SUPPRESS)
 217
 218     parser.add_argument("--fast-parser", dest="fast_parser",
 219                         action="store_true", default=False,
 220                         help=argparse.SUPPRESS)
 221
 222     parser.add_argument("--thread-count", type=int,
 223                         default=0, help="Number of threads to use for job submit and output collection.")
 224
 225     parser.add_argument("--http-timeout", type=int,
 226                         default=5*60, dest="http_timeout", help="API request timeout in seconds. Default is 300 seconds (5 minutes).")
 227
 228     parser.add_argument("--defer-downloads", action="store_true", default=False,
 229                         help="When submitting a workflow, defer downloading HTTP URLs to workflow launch instead of downloading to Keep before submit.")
 230
 231     parser.add_argument("--varying-url-params", type=str, default="",
 232                         help="A comma separated list of URL query parameters that should be ignored when storing HTTP URLs in Keep.")
 233
 234     parser.add_argument("--prefer-cached-downloads", action="store_true", default=False,
 235                         help="If a HTTP URL is found in Keep, skip upstream URL freshness check (will not notice if the upstream has changed, but also not error if upstream is unavailable).")
 236
 237     exgroup = parser.add_mutually_exclusive_group()
 238     exgroup.add_argument("--enable-preemptible", dest="enable_preemptible", default=None, action="store_true", help="Use preemptible instances. Control individual steps with arv:UsePreemptible hint.")
 239     exgroup.add_argument("--disable-preemptible", dest="enable_preemptible", default=None, action="store_false", help="Don't use preemptible instances.")
 240
 241     exgroup = parser.add_mutually_exclusive_group()
 242     exgroup.add_argument("--copy-deps", dest="copy_deps", default=None, action="store_true", help="Copy dependencies into the destination project.")
 243     exgroup.add_argument("--no-copy-deps", dest="copy_deps", default=None, action="store_false", help="Leave dependencies where they are.")
 244
 245     parser.add_argument(
 246         "--skip-schemas",
 247         action="store_true",
 248         help="Skip loading of schemas",
 249         default=False,
 250         dest="skip_schemas",
 251     )
 252
 253     exgroup = parser.add_mutually_exclusive_group()
 254     exgroup.add_argument("--trash-intermediate", action="store_true",
 255                         default=False, dest="trash_intermediate",
 256                          help="Immediately trash intermediate outputs on workflow success.")
 257     exgroup.add_argument("--no-trash-intermediate", action="store_false",
 258                         default=False, dest="trash_intermediate",
 259                         help="Do not trash intermediate outputs (default).")
 260
 261     parser.add_argument("workflow", default=None, help="The workflow to execute")
 262     parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.")
 263
 264     return parser
 265
 266 def add_arv_hints():
 267     cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
 268     cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE
 269     supported_versions = ["v1.0", "v1.1", "v1.2"]
 270     for s in supported_versions:
 271         res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-%s.yml' % s)
 272         customschema = res.read().decode('utf-8')
 273         use_custom_schema(s, "http://arvados.org/cwl", customschema)
 274         res.close()
 275     cwltool.process.supportedProcessRequirements.extend([
 276         "http://arvados.org/cwl#RunInSingleContainer",
 277         "http://arvados.org/cwl#OutputDirType",
 278         "http://arvados.org/cwl#RuntimeConstraints",
 279         "http://arvados.org/cwl#PartitionRequirement",
 280         "http://arvados.org/cwl#APIRequirement",
 281         "http://commonwl.org/cwltool#LoadListingRequirement",
 282         "http://arvados.org/cwl#IntermediateOutput",
 283         "http://arvados.org/cwl#ReuseRequirement",
 284         "http://arvados.org/cwl#ClusterTarget",
 285         "http://arvados.org/cwl#OutputStorageClass",
 286         "http://arvados.org/cwl#ProcessProperties",
 287         "http://commonwl.org/cwltool#CUDARequirement",
 288         "http://arvados.org/cwl#UsePreemptible",
 289         "http://arvados.org/cwl#OutputCollectionProperties",
 290         "http://arvados.org/cwl#KeepCacheTypeRequirement",
 291         "http://arvados.org/cwl#OutOfMemoryRetry",
 292     ])
 293
 294 def exit_signal_handler(sigcode, frame):
 295     logger.error(str(u"Caught signal {}, exiting.").format(sigcode))
 296     sys.exit(-sigcode)
 297
 298 def main(args=sys.argv[1:],
 299          stdout=sys.stdout,
 300          stderr=sys.stderr,
 301          api_client=None,
 302          keep_client=None,
 303          install_sig_handlers=True):
 304     parser = arg_parser()
 305
 306     job_order_object = None
 307     arvargs = parser.parse_args(args)
 308
 309     arvargs.use_container = True
 310     arvargs.relax_path_checks = True
 311     arvargs.print_supported_versions = False
 312
 313     if install_sig_handlers:
 314         arv_cmd.install_signal_handlers()
 315
 316     if arvargs.update_workflow:
 317         if arvargs.update_workflow.find('-7fd4e-') == 5:
 318             want_api = 'containers'
 319         else:
 320             want_api = None
 321         if want_api and arvargs.work_api and want_api != arvargs.work_api:
 322             logger.error(str(u'--update-workflow arg {!r} uses {!r} API, but --api={!r} specified').format(
 323                 arvargs.update_workflow, want_api, arvargs.work_api))
 324             return 1
 325         arvargs.work_api = want_api
 326
 327     if (arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:
 328         job_order_object = ({}, "")
 329
 330     add_arv_hints()
 331
 332     for key, val in viewitems(cwltool.argparser.get_default_args()):
 333         if not hasattr(arvargs, key):
 334             setattr(arvargs, key, val)
 335
 336     try:
 337         if api_client is None:
 338             api_client = arvados.safeapi.ThreadSafeApiCache(
 339                 api_params={
 340                     'num_retries': arvargs.retries,
 341                     'timeout': arvargs.http_timeout,
 342                 },
 343                 keep_params={
 344                     'num_retries': arvargs.retries,
 345                 },
 346                 version='v1',
 347             )
 348             keep_client = api_client.keep
 349             # Make an API object now so errors are reported early.
 350             api_client.users().current().execute()
 351         if keep_client is None:
 352             block_cache = arvados.keep.KeepBlockCache(disk_cache=True)
 353             keep_client = arvados.keep.KeepClient(
 354                 api_client=api_client,
 355                 block_cache=block_cache,
 356                 num_retries=arvargs.retries,
 357             )
 358         executor = ArvCwlExecutor(
 359             api_client,
 360             arvargs,
 361             keep_client=keep_client,
 362             num_retries=arvargs.retries,
 363             stdout=stdout,
 364         )
 365     except WorkflowException as e:
 366         logger.error(e, exc_info=(sys.exc_info()[1] if arvargs.debug else False))
 367         return 1
 368     except Exception:
 369         logger.exception("Error creating the Arvados CWL Executor")
 370         return 1
 371
 372     # Note that unless in debug mode, some stack traces related to user
 373     # workflow errors may be suppressed.
 374
 375     # Set the logging on most modules INFO (instead of default which is WARNING)
 376     logger.setLevel(logging.INFO)
 377     logging.getLogger('arvados').setLevel(logging.INFO)
 378     logging.getLogger('arvados.keep').setLevel(logging.WARNING)
 379     # API retries are filtered to the INFO level and can be noisy, but as long as
 380     # they succeed we don't need to see warnings about it.
 381     googleapiclient_http_logger = logging.getLogger('googleapiclient.http')
 382     googleapiclient_http_logger.addFilter(arvados.logging.GoogleHTTPClientFilter())
 383     googleapiclient_http_logger.setLevel(logging.WARNING)
 384
 385     if arvargs.debug:
 386         logger.setLevel(logging.DEBUG)
 387         logging.getLogger('arvados').setLevel(logging.DEBUG)
 388         # In debug mode show logs about retries, but we arn't
 389         # debugging the google client so we don't need to see
 390         # everything.
 391         googleapiclient_http_logger.setLevel(logging.NOTSET)
 392         logging.getLogger('googleapiclient').setLevel(logging.INFO)
 393
 394     if arvargs.quiet:
 395         logger.setLevel(logging.WARN)
 396         logging.getLogger('arvados').setLevel(logging.WARN)
 397         logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
 398
 399     if arvargs.metrics:
 400         metrics.setLevel(logging.DEBUG)
 401         logging.getLogger("cwltool.metrics").setLevel(logging.DEBUG)
 402
 403     if arvargs.log_timestamps:
 404         arvados.log_handler.setFormatter(logging.Formatter(
 405             '%(asctime)s %(name)s %(levelname)s: %(message)s',
 406             '%Y-%m-%d %H:%M:%S'))
 407     else:
 408         arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
 409
 410     if stdout is sys.stdout:
 411         # cwltool.main has code to work around encoding issues with
 412         # sys.stdout and unix pipes (they default to ASCII encoding,
 413         # we want utf-8), so when stdout is sys.stdout set it to None
 414         # to take advantage of that.  Don't override it for all cases
 415         # since we still want to be able to capture stdout for the
 416         # unit tests.
 417         stdout = None
 418
 419     if arvargs.workflow.startswith("arvwf:") or workflow_uuid_pattern.match(arvargs.workflow) or arvargs.workflow.startswith("keep:"):
 420         executor.loadingContext.do_validate = False
 421         if arvargs.submit:
 422             executor.fast_submit = True
 423
 424     return cwltool.main.main(args=arvargs,
 425                              stdout=stdout,
 426                              stderr=stderr,
 427                              executor=executor.arv_executor,
 428                              versionfunc=versionstring,
 429                              job_order_object=job_order_object,
 430                              logger_handler=arvados.log_handler,
 431                              custom_schema_callback=add_arv_hints,
 432                              loadingContext=executor.loadingContext,
 433                              runtimeContext=executor.toplevel_runtimeContext,
 434                              input_required=not (arvargs.create_workflow or arvargs.update_workflow))