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